WO2024006472A1 - Antibodies that bind to multiple sarbecoviruses - Google Patents

Antibodies that bind to multiple sarbecoviruses Download PDF

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WO2024006472A1
WO2024006472A1 PCT/US2023/026633 US2023026633W WO2024006472A1 WO 2024006472 A1 WO2024006472 A1 WO 2024006472A1 US 2023026633 W US2023026633 W US 2023026633W WO 2024006472 A1 WO2024006472 A1 WO 2024006472A1
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seq
nos
amino acid
antibody
antigen
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PCT/US2023/026633
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French (fr)
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Fabio Benigni
Elisabetta CAMERONI
Chien-Hsun Chen
Davide Corti
Anna De Marco
Dora PINTO
Matteo Samuele PIZZUTO
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Vir Biotechnology, Inc.
Humabs Biomed Sa
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Publication of WO2024006472A1 publication Critical patent/WO2024006472A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/526—CH3 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • SARS-CoV-2 A novel sarbecovirus termed SARS-CoV-2 emerged in Wuhan, China, in late 2019.
  • SARS-CoV-2 and SARS-CoV are members of the sarbecovirus lineage. Sarbecoviruses can be further divided into four clades: la, lb, 2, and 3. SARS-CoV is a member of clade la, while SARS-CoV-2 is a member of clade lb. Therapies for preventing or treating sarbecovirus infections, and diagnostic reagents for diagnosing sarbecovirus infections, are needed.
  • Figure 1 shows a phylogenetic tree of sarbecoviruses, divided into clade la (also referred to as clade 1), clade lb (also referred to as clade 1/2), clade 2, and clade 3.
  • Figure 2 shows differences in receptor binding domain (RBD) amino acid sequences among various sarbecoviruses and the amino acids that are likely significant for wild type S2K146 interaction with viral antigens (boxes).
  • RBD receptor binding domain
  • FIG. 3 illustrates binding certain antibodies on SARS-CoV-2 RBD and their respective binding sites.
  • Figure 4 shows binding by antibodies including S3 A3 and S3 Al 9, as well as comparator antibodies S2X259 and S2K146, to various sarbecoviruses representing Claims la, lb, 2, and 3.
  • Figure 5 summarizes (in the right-hand portion of the table) the binding results from Figure 4 for Clades la, lb, 2, and 3.
  • Figure 5 also shows (in the left-hand portion of the table) neutralization IC50 values obtained in VSV neutralization assays for SARS-CoV-2 and Omicron variants thereof, as well as SARS-Co-V.
  • Figure 6 shows neutralization against SARS-CoV-2 variants by certain antibodies including S3 A3 and S3 Al 9.
  • Figure 7 shows (the results of replicate neutralization tests with antibodies including S3A3 and S3A19.
  • FIG 8 shows the results of biolayer interferometry (BLI) competition studies testing S3 A3 against the indicated antibodies.
  • Figure 9 shows the results of BLI studies testing S3 Al 9 and the indicated antibodies.
  • Figure 10 shows binding (BLI) by S3 A3 and comparator antibody S2X324-v3.1 for SARS-CoV-2 Wuhan-Hu- 1 and the indicated variants.
  • Figure 11 shows binding (BLI) by S3 Al 9 for SARS-CoV-2 Wuhan-Hu- 1 and the indicated variants.
  • Figure 12 shows binding (ELISA) by S3 A3 against various sarbecoviruses.
  • Figure 13 shows binding (ELISA) by S3A19 against various sarbecoviruses.
  • Figure 14 shows ACE-2 binding inhibition to SARS-CoV-2 Wuhan-Hu- 1 RBD by the indicated antibodies.
  • Figure 15 provides neutralization data for S3 A3 and comparator antibody S2X324-v3.1 against SARS-CoV-2 Wuhan-Hu-1 (“WT”) and variants of concern.
  • Figure 16 provides neutralization data for S3 Al 9 against SARS-CoV-2 Wuhan-Hu- 1 (“WT”) and variants.
  • Figure 17 provides neutralization data for S3 A3 and S2X234-v3.1 against SARS-CoV-2 variants that escape S2X324.
  • the indicated variants were generated using a BA.2 backbone.
  • Figure 18 provides synergy and neutralization data for S3 A3 and S3 Al 9 (combined at the indicated concentrations).
  • Figure 19 provides synergy and neutralization data for S3 A3 and sotrovimab (combined at the indicated concentrations).
  • Figure 20 provides synergy and neutralization data S3 A3 and S2K146 (combined at the indicated concentrations).
  • Figure 21 provides synergy and neutralization data for S3A19 and sotrovimab (combined at the indicated concentrations).
  • Figure 22 provides synergy and neutralization data for S3A19 and S2K146 (combined at the indicated concentrations).
  • Figure 23 shows binding by S2V29 to various sarbecoviruses, and neutralization against SARS-CoV-2 variants by S2V29.
  • Figure 24 shows S2V29-vl.2 retains the neutralization profile of the parent antibody (S2V29-vl. l) against a panel of VSV SARS-CoV-2 viruses.
  • Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2V29-vl .2. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV- pp by S2X324. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts.
  • Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2X259v50.
  • VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts.
  • Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3O13. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts.
  • Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3L17. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3I2v2.1. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts.
  • Figure 26 shows binding activity of S2V29 and S2V29-vl.2 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
  • Figure 27 shows binding activity of S2X324 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
  • Figure 28 shows log TCID values for S2X324-v3.1, S3L17 and S3O13, with an isotype control.
  • Figure 29 summarizes neutralizing activity against SARS-CoV-2 Omicron variants for certain variant antibodies.
  • Figure 30 shows neutralization of Wuhan-Hu-1 D614 and G614 mediated by sotrovimab and VIR-7832.
  • Figure 31 illustrates antigenic sites on SARS-CoV-2 RBD recognized by certain variant antibodies of the present disclosure.
  • Figure 32 shows the results of biolayer interferometry (BLI) studies testing S3I2, S3L17, S3O10, and S2V29 against S2K146, S2X259, S2X324, and S309.
  • Figure 33 shows the results of biolayer interferometry (BLI) competition studies testing the indicated antibodies.
  • Figure 34 shows binding results versus a panel of RBDs from sarbecoviruses (ELISA) for S3II, S3L17, S2V29, and S3O13.
  • Figure 35 shows VSV-PV neutralizations against BA.2-escape mutants for S3I2, S3L17, and S2V29.
  • BA.2-G504D is an escape mutant of S2X259.
  • Figure 36 shows additional neutralization results against BA.2-escape mutants, including S2X324 escape mutants, S309 escape mutants, and S2K146 escape mutants, for S3O13. Fold change is relative to BA.2 variant.
  • Figure 37 shows VSV-PV neutralizations against BA.5-escape mutants for S2V29, S3L17, S3I2, and S3O13.
  • Figure 38 summarizes ACE2 binding inhibition to RBDs of SARS-CoV-2 and SARS- CoV.
  • Figure 39 shows SI staining over time, gated on pos cells. SI shedding is shown to be induced by variant antibodies of the present disclosure.
  • Figure 40 shows luminescence results for activation of FcgRIIa and FcgRIIIa.
  • Figure 41 summarizes binding affinity versus a panel of RBDs (BLI), for S3L17 and S3O13.
  • Figure 42 shows binding affinity versus the same panel of RBDs (BLI) for S2V29.
  • Figure 43 shows binding affinity (BLI) versus a panel of RBDs representative of different sarbecovirus clades.
  • Figure 44 illustrates antibody-dependent cellular cytotoxicity (ADCC) and antibodydependent cellular phagocytosis (ADCP).
  • Figure 45 shows binding activity of S3L17 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
  • Figure 46 shows binding activity of S3I2-v2.1 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or B A.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
  • Figure 47 shows binding activity of S3O13 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or B A.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
  • Figure 48 shows binding activity of S2V29 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan-D614 (“Wu- D614”), BA.2, BQ 1.1, XBB. l, and E340 A).
  • Figure 49 shows additional neutralization results against pre-Omicron and Omicron SARS-CoV-2 variants and additional escape mutants, including sotrovimab escape mutants, bebtelovimab escape mutants, S2K146 escape mutants, and S2X259 escape mutants for S3L17- vl.2 (S3L17), S2V29-V1.2 (S2V29), REGEN-COV and Evusheld.
  • Figure 50 shows additional neutralization results against SARS-CoV-2 variants and escape mutants for S3L17 and S2V29.
  • Figure 51 shows additional neutralization results against SARS-CoV and SARS-CoV-2 variants and escape mutants for S2V29-vl.2.
  • Underlines in the variant key indicates mutations associated with low pseudovirus infectivity in either a BQ.1.1 or XBB1.5 background.
  • Figure 52 summarizes escape mutant neutralization and binding data for S2V29 and S3L17.
  • Nt changes number of nucleotide changes required for the mutation to occur.
  • Conservation position identity across sarbecoviruses. *, NT with VSV-pp, IC50 in ng/ml; f, virus with low fitness, IC50s to be confirmed #, L455W found as escapes also with BA.2 DMS; f, FC calculated vs Wu-D614G.
  • Figure 52 also shows putative single-nucleotide mutation intermediates that lead to escape mutants.
  • Figure 53 shows results for two replicates of live virus testing with S2V29-vl.2 (S2V29) and S3L17.
  • Figure 54 shows in vivo viral protection data for S2V29-vl.2 (S2V29) and S3L17.
  • Figure 55 shows binding affinity date for S2V29-vl.2 and S3L17 for the Wuhan, BA.5, and XBB1.5 SARS-Co-V-2 RBDs.
  • Figure 56 shows the results of evolutionary breadth testing for S2V29-vl.2 (S2V29) and S3L17.
  • Figure 57 shows likely epitopes for S3L17 and S2V29 and binding of the antibodies to the SARS-CoV-2 RBD.
  • Figure 58 shows deep mutational scanning (DMS) results for S3L17 and S2V29-vl.2 binding as compared to ACE2 binding for the Wuhan and BA.2 strains.
  • Figure 59 shows binding contacts of S3L17 and S2V29 with the SARS-CoV-2 RBD and overlap with strong Omicron RBD-ACE2 contacts.
  • Figure 60 shows how S2V29 binding competes with RBD-ACE2 binding.
  • Figure 61 shows results of ADCP testing with S3L17 and S2V29-vl.2 (S2V29).
  • Figure 62 shows results of ADCC testing with S3L17-vl.2 and S2V29-vl.2.
  • Figure 63 shows results of FcgR activation testing with S3L17-vl.2 and S2V29-vl.2.
  • Figure 64 shows a comparison of results obtained with authentic virus vs. VSV pseudovirus for S2V29-vl.2.
  • Figure 65 shows binding affinity of S2V29-vl.2 to various BQ1.1 escape mutations as determined by surface plasmon resonance (SPR).
  • Figure 66 shows binding affinity of S2V29-vl.2 to various sarbecoviruses as determined by surface plasmon resonance (SPR).
  • Figure 67 shows pharmacokinetic testing data for S2V29-vl.2.
  • Figure 68 shows additional neutralization data for S2V29-vl.2 against SARS-CoV and SARS-CoV-2 variants.
  • an antibody or antigen-binding fragment is capable of binding to multiple sarbecoviruses (e.g., to a surface glycoprotein, as described herein, of one or more (e.g., one, two, three, four, five, six, or more) different sarbecoviruses, optionally comprised on a virion and/or expressed on the surface of a cell infected by two or more sarbecoviruses).
  • the multiple sarbecoviruses comprise one or more Clade lb sarbecoviruses.
  • presently disclosed antibodies and antigen-binding fragments can neutralize infection by one or more sarbecovirus (e.g., one, two, three, four, or more sarbecoviruses) in an in vitro model of infection and/or in an animal model and/or in a human subject.
  • sarbecovirus e.g., one, two, three, four, or more sarbecoviruses
  • polynucleotides that encode the antibodies and antigen-binding fragments, vectors, host cells, and related compositions, as well as methods of using the antibodies, antigen-binding fragments, polynucleotides, vectors, host cells, and related compositions to treat (e.g., reduce, delay, eliminate, or prevent) infection by two or more sarbecoviruses in a subject and/or in the manufacture of a medicament for treating infection in a subject by one or more sarbecovirus (e.g. one, two, three, four, or more) sarbecoviruses.
  • sarbecovirus e.g. one, two, three, four, or more
  • an “anti-sarbecovirus antibody or antigen-binding fragment” specifically binds at least one sarbecovirus and may, in some embodiments, bind two or more, three or more, four or more, or five or more sarbecoviruses.
  • sarbecovirus refers to any betacoronavirus within lineage B, and includes lineage B viruses in clade la, clade lb, clade 2, and clade 3.
  • clade la sarbecoviruses are SARS-CoV and Bat SARS-like coronavirus WIV1 (WIV1).
  • WIV1 Bat SARS-like coronavirus WIV1
  • clade lb sarbecoviruses are SARS-CoV-2, RatG13, Pangolin-Guanxi-2017 (PANG/GX) and Pangolin-Guangdon-2019 (PANG/GD).
  • Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid), Y453F, S477N, T478K, V483 A, E484A, E484Q, E48
  • Examples of clade 2 sarbecoviruses are Bat ZC45 (ZC45), Bat ZXC21 (ZXC21), YN2013, RmYN02, Anlongl l2, SC2018, SX2011.
  • Examples of clade 3 sarbecoviruses are BtkY72 and BGR2008. Sarbecovirus clades are also illustrated in Figure 1 and differences in RBDs among sarbecoviruses are illustrated in Figure 2.
  • an antibody or antigen-binding fragment thereof is capable of binding to a sarbecovirus of clade lb, such as SARS-CoV-2 (including all variants described herein), RatG13, Pangolin-Guanxi-2017 (PANG/GX), Pangolin-Guangdon-209, or any combination thereof.
  • SARS-CoV-2 including all variants described herein
  • RatG13 RatG13
  • Pangolin-Guanxi-2017 PANG/GX
  • Pangolin-Guangdon-209 or any combination thereof.
  • an antibody or antigen-binding fragment thereof is capable of binding to a SARS-CoV-2 variant; e.g. examples of clade lb also include SARS-CoV- 2 variants, for example variants with any one or more of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where
  • a SARS-Cov-2 variant is an Omicron variant, such as BA.l, BA.2, BA.2.12, BA.3, BA.4, or BA.5.
  • an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng
  • antibody is (or an antigen-binding fragment is from) S3A19, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of in a range between about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to
  • an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng
  • an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100
  • an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100
  • an antibody is (or an antigen-binding fragment is from) S2V29, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100
  • SARS-CoV-2 also originally referred to as "Wuhan coronavirus", “Wuhan seafood market pneumonia virus”, or “Wuhan CoV”, “novel CoV”, or “nCoV”, or “2019 nCoV”, or “Wuhan nCoV”, or a variant thereof, is a betacoronavirus of lineage B (sarbecovirus). SARS-CoV-2 was first identified in Wuhan, Hubei province, China, in late 2019 and spread within China and to other parts of the world by early 2020.
  • SARS CoV-2 infection can result in a disease known as COVID-19; symptoms of COVID-19 include fever or chills, dry cough, dyspnea, fatigue, body aches, headache, new loss of taste or smell, sore throat, congestions or runny nose, nausea or vomiting, diarrhea, persistent pressure or pain in the chest, new confusion, inability to wake or stay awake, and bluish lips or face.
  • SARS-CoV-2 comprises a "spike” or surface (“S") type I transmembrane glycoprotein containing a receptor binding domain (RBD).
  • RBD is believed to mediate entry of the lineage B SARS coronavirus to respiratory epithelial cells by binding to the cell surface receptor angiotensin-converting enzyme 2 (ACE2).
  • ACE2 cell surface receptor angiotensin-converting enzyme 2
  • RBM receptor binding motif
  • the amino acid sequence of the Wuhan-Hu- 1 surface glycoprotein is provided in SEQ ID NO. : 1.
  • the amino acid sequence of the Wuhan-Hu- 1 RBD is provided in SEQ ID NO. :2.
  • Wuhan-Hu- 1 S protein has approximately 73% amino acid sequence identity with SARS-CoV.
  • the amino acid sequence of Wuhan-Hu-1 RBM is provided in SEQ ID NO.:3.
  • SARS-CoV-2 variants which may differ in genomic and amino acid sequences, particularly of the surface glycoprotein or the RBD. Some SARS-CoV-2 variants mutations that increase affinity to the ACE receptor and/or infectiveness of the virus.
  • SARS-CoV-2 include examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except L), Y453F, S477N, T478K, V483 A,
  • a SARS-Cov-2 variant is an Omicron variant such as BA.l, BA.2, BA.2.12, BA.3, BA.4, or BA.5.
  • Omicron variant such as BA.l, BA.2, BA.2.12, BA.3, BA.4, or BA.5.
  • Variants of SARS-CoV-2 circulating in the United States are classified as variants of concern by the U.S. Centers for Disease Control and Prevention (see https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html).
  • an antibody or antigen-binding fragment is provided for treating a sarbecovirus infection.
  • a sarbecovirus infection comprises SARS-CoV- 2 infection. Treating a SARS CoV-2 infection in accordance with the present disclosure includes treating infection by any one or more of the aforementioned SARS-CoV-2 viruses.
  • treating a SARS-CoV-2 infection comprises treating any one or more of: SARS CoV-2 Wuhan-Hu-1;
  • Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except
  • a SARS-CoV-2 variant is an Omicron variant, such as BA.1, BA.2, BA.2.12, BA.3, BA.4, or BA.5.
  • the SARS-CoV-2 variant is BQ.1.1.
  • the SARS-CoV-2 variant is XBB.1
  • any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
  • any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness are to be understood to include any integer within the recited range, unless otherwise indicated.
  • the term “about” means ⁇ 20% of the indicated range, value, or structure, unless otherwise indicated. It should be understood that the terms “a” and “an” as used herein refer to “one or more" of the enumerated components.
  • a protein domain, region, or module e.g., a binding domain
  • a protein "consists essentially of' a particular amino acid sequence when the amino acid sequence of a domain, region, module, or protein includes extensions, deletions, mutations, or a combination thereof (e.g., amino acids at the amino- or carboxyterminus or between domains) that, in combination, contribute to at most 20% (e.g., at most 15%, 10%, 8%, 6%, 5%, 4%, 3%, 2% or 1%) of the length of a domain, region, module, or protein and do not substantially affect (i.e., do not reduce the activity by more than 50%, such as no more than 40%, 30%, 25%, 20%, 15%, 10%, 5%, or 1%) the activity of the domain(s), region(s),
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y- carboxyglutamate, and O-phosphoserine.
  • Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a-carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
  • mutation refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively.
  • a mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s).
  • a “conservative substitution” refers to amino acid substitutions that do not significantly affect or alter binding characteristics of a particular protein. Generally, conservative substitutions are ones in which a substituted amino acid residue is replaced with an amino acid residue having a similar side chain. Conservative substitutions include a substitution found in one of the following groups: Group 1 : Alanine (Ala or A), Glycine (Gly or G), Serine (Ser or S), Threonine (Thr or T); Group 2: Aspartic acid (Asp or D), Glutamic acid (Glu or Z); Group 3: Asparagine (Asn or N), Glutamine (Gin or Q); Group 4: Arginine (Arg or R), Lysine (Lys or K), Histidine (His or H); Group 5: Isoleucine (He or I), Leucine (Leu or L), Methionine (Met or M), Valine (Vai or V); and Group 6: Phenylalanine (Phe or F), Tyrosine (Tyr or
  • amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing).
  • an aliphatic grouping may include, for purposes of substitution, Gly, Ala, Vai, Leu, and He.
  • Other conservative substitutions groups include: sulfur- containing: Met and Cysteine (Cys or C); acidic: Asp, Glu, Asn, and Gin; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gin; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, He, Vai, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information can be found in Creighton (1984) Proteins, W.H. Freeman and Company.
  • protein or “polypeptide” refers to a polymer of amino acid residues. Proteins apply to naturally occurring amino acid polymers, as well as to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, and non-naturally occurring amino acid polymers. Variants of proteins, peptides, and polypeptides of this disclosure are also contemplated.
  • variant proteins, peptides, and polypeptides comprise or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.9% identical to an amino acid sequence of a defined or reference amino acid sequence as described herein.
  • Any polypeptide of this disclosure e.g., VH, VL, Fab, Fd, antibody heavy chain, antibody light chain
  • a polynucleotide sequence can, as encoded by a polynucleotide sequence, comprise a “signal peptide” (also known as a leader sequence, leader peptide, or transit peptide).
  • Signal peptides target newly synthesized polypeptides to their appropriate location inside or outside the cell.
  • a signal peptide may be removed in whole or in part from the polypeptide during or once localization or secretion is completed.
  • Polypeptides that have a(n, e.g., full-length) signal peptide can be referred to as a “pre-protein” and polypeptides having their signal peptide removed - at least in part - can be referred to as “mature” proteins or polypeptides.
  • an antibody or antigen-binding fragment is a mature protein or a pre-protein.
  • Nucleic acid molecule or “polynucleotide” or “polynucleic acid” refers to a polymeric compound including covalently linked nucleotides, which can be made up of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g., morpholine ring).
  • Purine bases include adenine, guanine, hypoxanthine, and xanthine
  • pyrimidine bases include uracil, thymine, and cytosine.
  • Nucleic acid molecules include polyribonucleic acid (RNA), which includes mRNA, microRNA, siRNA, viral genomic RNA, and synthetic RNA, and polydeoxyribonucleic acid (DNA), which includes cDNA, genomic DNA, and synthetic DNA, either of which may be single or double stranded. If single-stranded, the nucleic acid molecule may be the coding strand or non-coding (anti-sense) strand.
  • a nucleic acid molecule encoding an amino acid sequence includes all nucleotide sequences that encode the same amino acid sequence. Some versions of the nucleotide sequences may also include intron(s) to the extent that the intron(s) would be removed through co- or post-transcriptional mechanisms. In other words, different nucleotide sequences may encode the same amino acid sequence as the result of the redundancy or degeneracy of the genetic code, or by splicing.
  • Variants of nucleic acid molecules of this disclosure are also contemplated. Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and are preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical a nucleic acid molecule of a defined or reference polynucleotide as described herein, or that hybridize to a polynucleotide under stringent hybridization conditions of 0.015M sodium chloride, 0.0015M sodium citrate at about 65-68°C or 0.015M sodium chloride, 0.0015M sodium citrate, and 50% formamide at about 42°C. Nucleic acid molecule variants retain the capacity to encode a binding domain thereof having a functionality described herein, such as binding a target molecule.
  • Percent sequence identity refers to a relationship between two or more sequences, as determined by comparing the sequences. Preferred methods to determine sequence identity are designed to give the best match between the sequences being compared. For example, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment). Further, non-homologous sequences may be disregarded for comparison purposes. The percent sequence identity referenced herein is calculated over the length of the reference sequence, unless indicated otherwise. Methods to determine sequence identity and similarity can be found in publicly available computer programs.
  • Sequence alignments and percent identity calculations may be performed using a BLAST program (e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX).
  • BLAST program e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX.
  • the mathematical algorithm used in the BLAST programs can be found in Altschul et al., Nucleic Acids Res. 25:3389-3402, 1997.
  • sequence analysis software is used for analysis, the results of the analysis are based on the "default values" of the program referenced. "Default values" mean any set of values or parameters which originally load with the software when first initialized.
  • Clustal W MAFFT, Clustal Omega
  • AlignMe Praline
  • GAP BESTFIT
  • Needle EMBOSS
  • Stretcher EMBOSS
  • GGEARCH2SEQ Water
  • EMBOSS Matcher
  • LALIGN SSEARCH2SEQ.
  • a global alignment algorithm such as a Needleman and Wunsch algorithm, can be used to align two sequences over their entire length, maximizing the number of matches and minimizes the number of gaps. Default values can be used.
  • scoring matrices can be used that assign positive scores for some non-identical amino acids (e.g., conservative amino acid substitutions, amino acids with similar physio-chemical properties, and/or amino acids that exhibit frequent substitutions in orthologs, homologs, or paralogs).
  • non-identical amino acids e.g., conservative amino acid substitutions, amino acids with similar physio-chemical properties, and/or amino acids that exhibit frequent substitutions in orthologs, homologs, or paralogs.
  • scoring matrices include PAM30, PAM70, PAM250, BLOSUM45, BLOSUM50, BLOUM62, BLOSUM80, and BLOSUM90.
  • isolated means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring).
  • a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated.
  • nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide.
  • gene means the segment of DNA or RNA involved in producing a polypeptide chain; in certain contexts, it includes regions preceding and following the coding region (e.g., 5’ untranslated region (UTR) and 3’ UTR) as well as intervening sequences (introns) between individual coding segments (exons).
  • regions preceding and following the coding region e.g., 5’ untranslated region (UTR) and 3’ UTR
  • intervening sequences introns between individual coding segments (exons).
  • a “functional variant” refers to a polypeptide or polynucleotide that is structurally similar or substantially structurally similar to a parent or reference compound of this disclosure, but differs slightly in composition (e.g., one base, atom or functional group is different, added, or removed), such that the polypeptide or encoded polypeptide is capable of performing at least one function of the parent polypeptide with at least 50% efficiency, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide.
  • a functional variant of a polypeptide or encoded polypeptide of this disclosure has "similar binding,” “similar affinity” or “similar activity” when the functional variant displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide, such as an assay for measuring binding affinity (e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (KD) constant).
  • binding affinity e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (KD) constant.
  • a “functional portion” or “functional fragment” refers to a polypeptide or polynucleotide that comprises only a domain, portion or fragment of a parent or reference compound, and the polypeptide or encoded polypeptide retains at least 50% activity associated with the domain, portion or fragment of the parent or reference compound, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide, or provides a biological benefit e.g., effector function).
  • a “functional portion” or “functional fragment” of a polypeptide or encoded polypeptide of this disclosure has “similar binding” or “similar activity” when the functional portion or fragment displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide (preferably no more than 20% or 10%, or no more than a log difference as compared to the parent or reference with regard to affinity).
  • the term "engineered,” “recombinant,” or “non-natural” refers to an organism, microorganism, cell, nucleic acid molecule, or vector that includes at least one genetic alteration or has been modified by introduction of an exogenous or heterologous nucleic acid molecule, wherein such alterations or modifications are introduced by genetic engineering (i.e., human intervention).
  • Genetic alterations include, for example, modifications introducing expressible nucleic acid molecules encoding functional RNA, proteins, fusion proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of a cell’s genetic material. Additional modifications include, for example, noncoding regulatory regions in which the modifications alter expression of a polynucleotide, gene, or operon.
  • heterologous or non-endogenous or exogenous refers to any gene, protein, compound, nucleic acid molecule, or activity that is not native to a host cell or a subject, or any gene, protein, compound, nucleic acid molecule, or activity native to a host cell or a subject that has been altered.
  • Heterologous, non-endogenous, or exogenous includes genes, proteins, compounds, or nucleic acid molecules that have been mutated or otherwise altered such that the structure, activity, or both is different as between the native and altered genes, proteins, compounds, or nucleic acid molecules.
  • heterologous, non-endogenous, or exogenous genes, proteins, or nucleic acid molecules may not be endogenous to a host cell or a subject, but instead nucleic acids encoding such genes, proteins, or nucleic acid molecules may have been added to a host cell by conjugation, transformation, transfection, electroporation, or the like, wherein the added nucleic acid molecule may integrate into a host cell genome or can exist as extra-chromosomal genetic material (e.g., as a plasmid or other self-replicating vector).
  • homologous or homolog refers to a gene, protein, compound, nucleic acid molecule, or activity found in or derived from a host cell, species, or strain.
  • a heterologous or exogenous polynucleotide or gene encoding a polypeptide may be homologous to a native polynucleotide or gene and encode a homologous polypeptide or activity, but the polynucleotide or polypeptide may have an altered structure, sequence, expression level, or any combination thereof.
  • a non-endogenous polynucleotide or gene, as well as the encoded polypeptide or activity may be from the same species, a different species, or a combination thereof.
  • a nucleic acid molecule or portion thereof native to a host cell will be considered heterologous to the host cell if it has been altered or mutated, or a nucleic acid molecule native to a host cell may be considered heterologous if it has been altered with a heterologous expression control sequence or has been altered with an endogenous expression control sequence not normally associated with the nucleic acid molecule native to a host cell.
  • heterologous can refer to a biological activity that is different, altered, or not endogenous to a host cell.
  • heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a fusion protein, or any combination thereof.
  • endogenous or “native” refers to a polynucleotide, gene, protein, compound, molecule, or activity that is normally present in a host cell or a subject.
  • expression refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene.
  • the process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post-translational modification, or any combination thereof.
  • An expressed nucleic acid molecule is typically operably linked to an expression control sequence (e.g., a promoter).
  • operably linked refers to the association of two or more nucleic acid molecules on a single nucleic acid fragment so that the function of one is affected by the other.
  • a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter).
  • "Unlinked" means that the associated genetic elements are not closely associated with one another and the function of one does not affect the other.
  • more than one heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a protein (e.g, a heavy chain of an antibody), or any combination thereof.
  • a protein e.g, a heavy chain of an antibody
  • two or more heterologous nucleic acid molecules can be introduced as a single nucleic acid molecule (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof.
  • the number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of separate nucleic acid molecules introduced into a host cell.
  • construct refers to any polynucleotide that contains a recombinant nucleic acid molecule (or, when the context clearly indicates, a fusion protein of the present disclosure).
  • a (polynucleotide) construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome.
  • a "vector” is a nucleic acid molecule that is capable of transporting another nucleic acid molecule. Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules.
  • Vectors of the present disclosure also include transposon systems (e.g., Sleeping Beauty, see, e.g., Geurts et al., Mol. Ther. 5:108, 2003: Mates et al., Nat. Genet. 41.753, 2009).
  • Exemplary vectors are those capable of autonomous replication (episomal vector), capable of delivering a polynucleotide to a cell genome (e.g., viral vector), or capable of expressing nucleic acid molecules to which they are linked (expression vectors).
  • expression vector refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host.
  • control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation.
  • the vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert.
  • the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself or deliver the polynucleotide contained in the vector into the genome without the vector sequence.
  • plasmid "expression plasmid,” “virus,” and “vector” are often used interchangeably.
  • the term "introduced” in the context of inserting a nucleic acid molecule into a cell means “transfection", “transformation,” or “transduction” and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
  • a cell e.g., chromosome, plasmid, plastid, or mitochondrial DNA
  • transiently expressed e.g., transfected mRNA
  • polynucleotides of the present disclosure may be operatively linked to certain elements of a vector.
  • polynucleotide sequences that are needed to effect the expression and processing of coding sequences to which they are ligated may be operatively linked.
  • Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion.
  • Expression control sequences may be operatively linked if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
  • the vector comprises a plasmid vector or a viral vector (e.g., a lentiviral vector or a y-retroviral vector).
  • Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox, and canarypox).
  • herpesvirus e.g
  • viruses include, for example, Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus.
  • retroviruses include avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
  • “Retroviruses” are viruses having an RNA genome, which is reverse-transcribed into DNA using a reverse transcriptase enzyme, the reverse-transcribed DNA is then incorporated into the host cell genome.
  • “Gammaretrovirus” refers to a genus of the retroviridae family. Examples of gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses.
  • Lentiviral vectors include HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope, and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells.
  • the viral vector can be a gammaretrovirus, e.g., Moloney murine leukemia virus (MLV)-derived vectors.
  • the viral vector can be a more complex retrovirus-derived vector, e.g., a lentivirus-derived vector. HIV-l-derived vectors belong to this category.
  • Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus).
  • Retroviral and lentiviral vector constructs and expression systems are also commercially available.
  • Other viral vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defective HSV and attenuated HSV (Krisky et al., Gene Ther. 5: 1517, 1998).
  • HSVs herpes simplex viruses
  • the viral vector may also comprise additional sequences between the two (or more) transcripts allowing for bicistronic or multi ci stronic expression.
  • additional sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide, or any combination thereof.
  • Plasmid vectors including DNA-based antibody or antigen-binding fragment-encoding plasmid vectors for direct administration to a subject, are described further herein.
  • the term "host” refers to a cell or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest (e.g., an antibody of the present disclosure).
  • a host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids or express proteins. The term also encompasses progeny of the host cell, whether genetically or phenotypically the same or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate the vector or other material by use of a viral vector, transformation via calcium phosphate precipitation, DEAE-dextran, electroporation, microinjection, or other methods. See, for example, Sambrook el al., Molecular Cloning: A Laboratory Manual 2d ed. (Cold Spring Harbor Laboratory, 1989).
  • a "host” refers to a cell or a subject infected with a sarbecovirus.
  • Antigen refers to an immunogenic molecule that provokes an immune response. This immune response may involve antibody production, activation of specific immunologically-competent cells, activation of complement, antibody dependent cytotoxicity, or any combination thereof.
  • An antigen immunogenic molecule
  • An antigen may be, for example, a peptide, glycopeptide, polypeptide, glycopolypeptide, polynucleotide, polysaccharide, lipid, or the like. It is readily apparent that an antigen can be synthesized, produced recombinantly, or derived from a biological sample. Exemplary biological samples that can contain one or more antigens include tissue samples, stool samples, cells, biological fluids, or combinations thereof.
  • Antigens can be produced by cells that have been modified or genetically engineered to express an antigen. Antigens can also be present in a sarbecovirus (e.g., a surface glycoprotein or portion thereof), such as present in a virion, or expressed or presented on the surface of a cell infected by a sarbecovirus.
  • a sarbecovirus e.g., a surface glycoprotein or portion thereof
  • epitope includes any molecule, structure, amino acid sequence, or protein determinant that is recognized and specifically bound by a cognate binding molecule, such as an immunoglobulin, or other binding molecule, domain, or protein.
  • Epitopic determinants generally contain chemically active surface groupings of molecules, such as amino acids or sugar side chains, and can have specific three-dimensional structural characteristics, as well as specific charge characteristics.
  • the epitope can be comprised of consecutive amino acids (e.g., a linear epitope), or can be comprised of amino acids from different parts or regions of the protein that are brought into proximity by protein folding (e.g., a discontinuous or conformational epitope), or non-contiguous amino acids that are in close proximity irrespective of protein folding.
  • the present disclosure provides an isolated antibody, or an antigen-binding fragment thereof, that is capable of binding to a surface glycoprotein of a sarbecoviruses (e.g. of a SARS-CoV-2).
  • a sarbecoviruses e.g. of a SARS-CoV-2
  • the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of two or more sarbecoviruses, three or more sarbecoviruses, four or more sarbecoviruses, or five or more sarbecoviruses.
  • the antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • the two or more, three or more, four or more, or five or more sarbecoviruses comprise or one or more, or are selected from, clade lb sarbecoviruses or naturally occurring variants thereof, and any combination thereof.
  • the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of two or more, three or more, four or more, or five or more sarbecoviruses; e.g. capable of binding when a sarbecovirus surface glycoprotein is expressed on a cell surface of a host cell and/or on a sarbecovirus virion.
  • the two or more, three or more, four or more, or five or more sarbecoviruses are selected from SARS-CoV-2, PANG/GD, PANG/GX, RatG13, and naturally occurring variants thereof.
  • the two or more, three or more, four or more, or five or more sarbecoviruses include one or more of SARS-CoV-2 variants.
  • an antibody or antigen-binding fragment thereof is capable of binding to one or more SARS-CoV-2 variant.
  • Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except L), Y453F, S477N, T478K, V483 A, E484A, E484Q,
  • the two or more, three or more, four or more, or five or more sarbecoviruses include one or more SARS-CoV-2 variants having S protein mutations D614G, Q493R, G496S, Q498R, N501 Y, Y453F, N439K, K417V, E484K, or any combination thereof.
  • two or more sarbecoviruses include one or more SARS-CoV-2 variants having S protein mutations K417N, Q493K, G496S, or any combination thereof.
  • an antibody or antigen-binding fragment of the present disclosure associates with or unites with a sarbecovirus surface glycoprotein epitope or antigen comprising the epitope, while not significantly associating or uniting with any other molecules or components in a sample.
  • the epitope is comprised in a SI subunit of a S protein.
  • the epitope is comprised in a RBD of a S protein.
  • the epitope is a conformational epitope or a linear epitope.
  • an antibody or antigen-binding fragment of the present disclosure associates with or unites (e.g., binds) to a first sarbecovirus surface glycoprotein epitope, and can also associate with or unite with an epitope from another sarbecovirus present in the sample, but not significantly associating or uniting with any other molecules or components in the sample.
  • an antibody or antigen-binding fragment of the present disclosure is cross-reactive against and specifically binds to two or more sarbecoviruses (e.g., against SARS-CoV-2 Wuhan-Hu-1 and one or more variants thereof).
  • an antibody or antigen-binding fragment of the present disclosure specifically binds to a sarbecovirus surface glycoprotein.
  • “specifically binds” refers to an association or union of an antibody or antigen-binding fragment to an antigen with an affinity or K a (i.e., an equilibrium association constant of a particular binding interaction with units of 1/M) equal to or greater than 10 5 M' 1 (which equals the ratio of the on-rate [K on ] to the off rate [K O ff] for this association reaction), while not significantly associating or uniting with any other molecules or components in a sample.
  • K a i.e., an equilibrium association constant of a particular binding interaction with units of 1/M
  • affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (c.g, 10' 5 M to 10' 13 M).
  • Antibodies may be classified as “high-affinity” antibodies or as “low- affinity” antibodies.
  • “High-affinity” antibodies refer to those antibodies having a K a of at least 10 7 M -1 , at least 10 8 M’ 1 , at least 10 9 M’ 1 , at least IO 10 M’ 1 , at least IO 11 M’ 1 , at least 10 12 M -1 , or at least IO 13 M' 1 .
  • “Low-affinity” antibodies refer to those antibodies having a K a of up to 10 7 M -1 , up to 10 6 M’ 1 , up to 10 5 M' 1 .
  • affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (e.g., 10' 5 M to 10' 13 M).
  • assays for identifying antibodies of the present disclosure that bind a particular target, as well as determining binding domain or binding protein affinities, such as Western blot, ELISA (e.g., direct, indirect, or sandwich), analytical ultracentrifugation, spectroscopy, and surface plasmon resonance (Biacore®) analysis (see, e.g., Scatchard et al., Ann. N.Y. Acad. Sci. 57:660, 1949; Wilson, Science 295:2103, 2002; Wolff et al., Cancer Res. 55:2560, 1993; and U.S. Patent Nos. 5,283,173, 5,468,614, or the equivalent). Assays for assessing affinity or apparent affinity or relative affinity are also known.
  • an antibody or antigen-binding fragment of the present disclosure binds one or more, or two or more, sarbecoviruses of Clade lb with an EC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL,
  • the antibody or antigen-binding fragment is capable of binding to a first and a second sarbecovirus each independently selected from Clade lb, wherein the antibody or antigen-binding fragment and is capable of binding to the first sarbecovirus with an EC50 of about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng
  • an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x IO' 09 M and about 1.0 x IO' 08 M, about 1.2 x IO' 09 M and about 1.0 x IO' 08 M, about 1.5 x IO' 09 M and about 1.0 x IO' 08 M, about 2.0 x IO' 09 M and about 1.0 x IO' 08 M, about 2.25 x IO' 09 M and about 1.0 x IO' 08 M, about 2.5 x IO' 09 M and about 1.0 x
  • an antibody is (or an antigen-binding fragment is from) S3 Al 9, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10' 12 M and about 5.0 x IO' 08 M, about 1.5 x 10' 12 M and about 5.0 x IO' 08 M, about 2.0 x 10' 12 M and about 5.0 x IO' 08 M, about 2.25 x 10' 12 M and about 5.0 x IO' 08 M, about 2.5 x 10' 12 M and about 5.0 x IO' 08 M, about 1.0 x 10' 11 M and about 5.0 x IO' 08 M,
  • an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10' 12 M and about 5.0 x IO' 08 M.
  • an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10' 12 M and about 5.0 x IO' 08 M.
  • an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10' 12 M and about 5.0 x IO' 08 M.
  • binding can be determined by recombinantly expressing a sarbecovirus antigen in a host cell (e.g., by transfection) and immunostaining the (e.g., fixed, or fixed and permeabilized) host cell with antibody and analyzing binding by flow cytometry (e.g., using a ZE5 Cell Analyzer (BioRad®) and FlowJo software (TreeStar).
  • positive binding can be defined by differential staining by antibody of sarbecovirus-expressing cells versus control (e.g., mock) cells.
  • an antibody or antigen-binding fragment of the present disclosure binds to a sarbecovirus spike protein (/. ⁇ ., from two or more, three or more, four or more, or five or more sarbecoviruses) expressed on the surface of a host cell (e.g., an Expi-CHO cell), as determined by flow cytometry.
  • a sarbecovirus spike protein /. ⁇ ., from two or more, three or more, four or more, or five or more sarbecoviruses
  • a host cell e.g., an Expi-CHO cell
  • an antibody or antigen-binding fragment of the present disclosure binds to a sarbecovirus S protein, as measured using biolayer interferometry.
  • an antibody of the present disclosure is capable of neutralizing infection by one or more, or by two or more, sarbecoviruses.
  • a “neutralizing antibody” is one that can neutralize, z.e., prevent, inhibit, reduce, impede, or interfere with, the ability of a pathogen to initiate and/or perpetuate an infection in a host.
  • neutralizing antibody and “an antibody that neutralizes” or “antibodies that neutralize” are used interchangeably herein.
  • the antibody or antigenbinding fragment is capable of preventing and/or neutralizing infection by one or more, or by two or more, sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
  • an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng
  • an antibody is (or an antigen-binding fragment is from) S3 Al 9, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 1
  • a pseudovirus system
  • an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
  • a pseudovirus system e.g., MLV-pp-based or VSV-pp-based
  • an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
  • a pseudovirus system e.g., MLV-pp-based or VSV-pp-based
  • an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
  • a pseudovirus system e.g., MLV-pp-based or VSV-pp-based
  • an antibody is (or an antigen-binding fragment is from) S2V29, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29 or a variant disclosed herein.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
  • a pseudovirus system e.g., MLV-pp-based or VSV-pp-based
  • the antibody or antigen-binding fragment (i) recognizes an epitope in the Spike protein of two or more sarbecoviruses; (ii) is capable of blocking an interaction between the Spike protein of one or more sarbecoviruses and a cell surface receptor;
  • (iv) is cross-reactive against two or more sarbecoviruses; or (v) any combination of (i)-(iv).
  • antibody refers to an intact antibody comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as any antigen-binding portion or fragment of an intact antibody that has or retains the ability to bind to the antigen target molecule recognized by the intact antibody, such as an scFv, Fab, or Fab'2 fragment.
  • antibody herein is used in the broadest sense and includes polyclonal and monoclonal antibodies, including intact antibodies and functional (antigen-binding) antibody fragments thereof, including fragment antigen-binding (Fab) fragments, F(ab')2 fragments, Fab' fragments, Fv fragments, recombinant IgG (rlgG) fragments, single chain antibody fragments, including single chain variable fragments (scFv), and single domain antibodies (e.g., sdAb, sdFv, nanobody) fragments.
  • Fab fragment antigen-binding
  • rlgG fragment antigen-binding
  • rlgG fragment antigen-binding
  • single chain antibody fragments including single chain variable fragments (scFv), and single domain antibodies (e.g., sdAb, sdFv, nanobody) fragments.
  • the term encompasses genetically engineered and/or otherwise modified forms of immunoglobulins, such as intrabodies, peptibodies, chimeric antibodies, fully human antibodies, humanized antibodies, and heteroconjugate antibodies, multispecific, e.g., bispecific antibodies, diabodies, triabodies, tetrabodies, tandem di-scFv, and tandem tri-scFv.
  • antibody should be understood to encompass functional antibody fragments thereof.
  • the term also encompasses intact or full-length antibodies, including antibodies of any class or sub-class, including IgG and sub-classes thereof (IgGl, IgG2, IgG3, IgG4), IgM, IgE, IgA, and IgD.
  • VL or “VL” and “ VH” or “VH” refer to the variable binding region from an antibody light chain and an antibody heavy chain, respectively.
  • a VL is a kappa (K) class (also “VK” herein).
  • a VL is a lambda ( ) class.
  • the variable binding regions comprise discrete, well-defined sub-regions known as “complementarity determining regions” (CDRs) and “framework regions” (FRs).
  • CDR complementarity determining region
  • HVR hypervariable region
  • CDR1 and CDR2, CDR2 and CDR3 are synonymous with “hypervariable region” or “HVR,” and refer to sequences of amino acids within antibody variable regions, which, in general, together confer the antigen specificity and/or binding affinity of the antibody, wherein consecutive CDRs (/. ⁇ ., CDR1 and CDR2, CDR2 and CDR3) are separated from one another in primary structure by a framework region.
  • CDRs There are three CDRs in each variable region (HCDR1, HCDR2, HCDR3; LCDR1, LCDR2, LCDR3; also referred to as CDRHs and CDRLs, respectively).
  • an antibody VH comprises four FRs and three CDRs as follows: FR1-HCDR1- FR2-HCDR2-FR3-HCDR3-FR4, and an antibody VL comprises four FRs and three CDRs as follows: FR1-LCDR1-FR2-LCDR2-FR3-LCDR3-FR4.
  • the VH and the VL together form the antigen-binding site through their respective CDRs.
  • the antibody or antigen-binding fragment is capable of preventing and/or neutralizing infection by one or more, or by two or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
  • the antibody or antigen-binding fragment comprises a VH and a VL that comprise or consist of the amino acid sequences according to: 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87
  • an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 23 and 27, respectively.
  • an antibody is (or an antigen-binding fragment is from) S3 Al 9, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to any one of SEQ ID NOs: 31 and 37, respectively; 35 and 37, respectively; 36 and 37, respectively; and 43 and 37, respectively.
  • an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 83 and 87, respectively.
  • an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 93 and 97, respectively.
  • an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 102 and 105, respectively.
  • an antibody is (or an antigen-binding fragment is from) S2V29a, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29a.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29a to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 111 and 115, respectively.
  • an antibody is (or an antigen-binding fragment is from) S2V29b, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29b.
  • an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29b to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 111 and 121, respectively.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) that comprises or consists of the amino acid sequence according to any one of SEQ ID NOs: 23, 31, 35, 36, 43, 83, 93, 102, 111, 125, 128, 131, 137, 141, 145, 149, 453, 179, 181, 183, 185, 188, 190, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, 222, 235, 238, 241, 243, 245, 247, 249, 251, 264, 266, or 269.
  • VH heavy chain variable domain
  • an antibody or an antigen-binding fragment comprises a light chain variable domain (VL) that comprises or consists of the amino acid sequence according to any one of SEQ ID NOs: 27, 37, 87, 97, 105, 115, 121, 157, 193, 225, 228, 231, 254, 257, 260, 272, 277, 279, 282, 286, 290.
  • VL light chain variable domain
  • a "variant" of a CDR refers to a functional variant of a CDR sequence having up to 1-3 amino acid substitutions (e.g., conservative or non-conservative substitutions), deletions, or combinations thereof.
  • Numbering of CDR and framework regions may be according to any known method or scheme, such as the Kabat, Chothia, EU, IMGT, Contact, North, Martin, AbM, and AHo numbering schemes (see, e.g., Kabat et al., "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5th ed.; Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)); Lefranc et al., Dev. Comp. Immunol. 27:55, 2003; Honegger and Pluckthun, J. Mol. Bio. 309:657-670 (2001); North et al. J Mol Biol.
  • an antibody or antigen-binding fragment comprises one or more CDRs of a VH sequence according to any one of SEQ ID NOs: 23, 31, 35, 36, 43, 83, 93, 102, 111, 125, 128, 131, 137, 141, 145, 149, 453, 179, 181, 183, 185, 188, 190, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, 222, 235, 238, 241, 243, 245, 247, 249, 251, 264, 266, or 269, and/or of a VL sequence according to any one of SEQ ID NOs: 27, 37, 87, 97, 105, 115, 121, 157, 193, 225, 228, 231, 254, 257, 260, 272, 277, 279, 282, 286, 290, in accordance with any known CDR numbering method, including the Kabat, Chothia,
  • CDRs are according to the IMGT numbering method (optionally using junction definitions for CDR3 amino acid sequences).
  • CDRs are according to the antibody numbering method developed by the Chemical Computing Group (CCG); e.g., using Molecular Operating Environment (MOE) software (chemcomp.com).
  • CDRs are in accordance with the IMGT numbering method.
  • an antibody or antigen-binding fragment comprises a VH sequence according to SEQ ID NO.: 23 and a VL sequence according to SEQ ID NO.: 27.
  • amino acid sequence variation relative to SEQ ID NO.:23 or SEQ ID NO.:27 is limited to variation relative to one or more framework regions (FRs) of SEQ ID NO.:23 or SEQ ID NO.:27, respectively.
  • FRs framework regions
  • Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these).
  • the CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
  • an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in SEQ ID NO.:23, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in SEQ ID NO.:27.
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO.:27.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in SEQ ID NO.:27.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in SEQ ID NO.:27.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in SEQ ID NO.:27.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises CDRs identified in a VH sequence according to SEQ ID NOs.: 23, and in a VL sequence according to SEQ ID NOs.: 27, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 24 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 25, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 24-26 and 28-30, respectively.
  • an antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 31, 35, 36, and 43 and a VL sequence according to SEQ ID NO.: 37.
  • amino acid sequence variation relative to any one of SEQ ID NOs.: 31, 35, 36, and 43 or SEQ ID NO.:37 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 31, 35, 36, and 43 or SEQ ID NO.:37, respectively.
  • FRs framework regions
  • Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these).
  • the CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
  • an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43, and a VL comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in SEQ ID NO.:37.
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO.:37.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in SEQ ID NO.:37.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in SEQ ID NO.:37.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in SEQ ID NO.:37.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • the S3 Al 9 antibodies may be as described in Table 3.
  • an antibody or antigen-binding fragment comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs.: 31, 35, 36, and 43 and in a VL sequence according to SEQ ID NO.: 37, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 32 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 33, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID
  • the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 32-34 and 38-40, respectively.
  • an antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 and a VL sequence according to any one of SEQ ID NOs.: 87 or 193.
  • amino acid sequence variation relative to any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 or any one of SEQ ID NOs.: 87 or 193 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 or any one of SEQ ID NOs.: 87 or 193, respectively.
  • FRs framework regions
  • Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these).
  • the CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
  • an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190, and a VL comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises CDRs identified in a VH sequence according to and one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 and in a VL sequence according to and one of SEQ ID NOs.: 87 or 193, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 84 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 84-86 or 84, 85 and 186 and 88-90 or 194, 89, and 90, respectively.
  • an antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence according to any one of SEQ ID NOs.: 97, 225, 228, or 231.
  • amino acid sequence variation relative to any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 or any one of SEQ ID NOs.: 97, 225, 228, or 231 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 or any one of SEQ ID NOs.: 97, 225, 228, or 231, respectively.
  • FRs framework regions
  • Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these).
  • the CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
  • an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs. : 97, 225, 228, or 231.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs .: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and in a VL sequence according to any one of SEQ ID NOs.: 97, 225, 228, or 231, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 94, 198, or 208 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 95, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii
  • the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 94-96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232, respectively.
  • an antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260.
  • amino acid sequence variation relative to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 or any one of SEQ ID NOs.: 105, 254, 257, or 260 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 or any one of SEQ ID NOs.: 105, 254, 257, or 260, respectively.
  • FRs framework regions
  • Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these).
  • the CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
  • an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and in a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 103, 85, and 104; 103, 85, and 236; or 103, 85, and 239, and 106-108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, respectively.
  • an antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences of S3 A3, S3A19 VH. l, S3A19 VH.2, S3A19 VH.3, S3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as set forth in Table 3.
  • an antibody or antigen-binding fragment comprises VH and VL amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising the VH and VL amino acid sequences (respectively) of S3 A3, S3A19 VH. l, S3A19 VH.2, S3A19 VH.3, o3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as set forth in Table 3.
  • an antibody or antigen-binding fragment comprises the VH and VL amino acid sequences (respectively) of S3 A3, S3A19 VH.l, S3A19 VH.2, S3A19 VH.3, S3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as set forth in Table 3.
  • an antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
  • amino acid sequence variation relative to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 or any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 or any one of SEQ ID NOs. : 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively.
  • FRs framework regions
  • Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these).
  • the CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
  • an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.:
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs. : 115, 121, 157, 272, 277, 279, 282, 286, or 290.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 1 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
  • VH heavy chain variable domain
  • VL light chain variable domain
  • an antibody or antigen-binding fragment comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and in a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
  • an antibody or an antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 112 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112-114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112,
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112-114 and 116-118, respectively (S2V29a), 112-114 and 116, 117, and 122, respectively (S2V29b).
  • the antibody or antigen-binding fragment comprises a VH or VL comprising or consisting of SEQ ID NOs: 111 and 157, respectively, or at having at least 85%, 90%, or 95% identity to these sequences, particularly with framework region mutations as disclosed herein.
  • the antibody or antigen-binding fragment comprises CDRS as set forth in the VH and VL of SEQ ID NOs: 111 and 157, according to any numbering scheme as described herein.
  • the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112-114 and 116-117, and 158, respectively.
  • any of these antibodies may include an Fc modification as described herein, or may have an unmodified human IgGl constant region.
  • the antibody may have a VH according to SEQ ID NO: 111, a CH according to SEQ ID NOs: 44-80, a VL according to SEQ ID NO: 157 and a CL according to SEQ ID NO: 292.
  • the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 293 and the light chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 294.
  • the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence of SEQ ID NO: 293 and the light chain comprises or consists of a sequence of SEQ ID NO: 294.
  • the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 295 and the light chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 296.
  • the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence of SEQ ID NO: 295 and the light chain comprises or consists of a sequence of SEQ ID NO: 296.
  • CL refers to an "immunoglobulin light chain constant region” or a "light chain constant region,” /. ⁇ ., a constant region from an antibody light chain.
  • CH refers to an "immunoglobulin heavy chain constant region” or a "heavy chain constant region,” which is further divisible, depending on the antibody isotype, into CHI, CH2, and CH3 (IgA, IgD, IgG), or CHI, CH2, CH3, and CH4 domains (IgE, IgM).
  • CHI unimmunoglobulin heavy chain constant region
  • an antibody or antigenbinding fragment of the present disclosure comprises any one or more of CL, a CHI, a CH2, and a CH3.
  • an antibody or antigen-binding fragment of the present disclosure may comprise any one or more of CL, a CHI, a CH2, and a CH3.
  • a CL comprises an amino acid sequence having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the amino acid sequence of SEQ ID NO.:292.
  • a CL comprises an amino acid sequence having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to a human lambda light chain constant domain.
  • CH refers to an "immunoglobulin heavy chain constant region" or a "heavy chain constant region,” which is further divisible, depending on the antibody isotype into CHI, CH2, and CH3 (IgA, IgD, IgG), or CHI, CH2, CH3, and CH4 domains (IgE, IgM).
  • the Fc region of an antibody heavy chain is described further herein.
  • an antibody or antigen-binding fragment of the present disclosure comprises any one or more of CL, a CHI, a CH2, and a CH3.
  • an antibody or antigen-binding fragment comprises an (e.g. human) IgG (e.g., IgGl, IgG2, IgG3, or IgG4), IgA, IgD, IgE, or IgM isotype, or comprises amino acid sequences from two or more of these isotypes.
  • an antibody or antigen-binding fragment comprises an IgGl isotype; it will be understood that such an antibody or antigen-binding fragment may comprise one or more amino acid substitutions in a heavy chain constant domain and still be considered an “IgGl” isotype.
  • an IgGl comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in SEQ ID NOs: 44-80.
  • production in a mammalian cell line can remove one or more C-terminal lysine of an antibody heavy chain (see, e.g., Liu et al. mAbs 6(5): 1145- 1154 (2014)).
  • an antibody or antigen-binding fragment of the present disclosure can comprise a heavy chain, a CH1-CH3, a CH3, or an Fc polypeptide wherein a C-terminal lysine residue or a C-terminal glycine-lysine is present or is absent; in other words, encompassed are embodiments where the C-terminal residue of a heavy chain, a CH1-CH3, or an Fc polypeptide is not a lysine, and embodiments where a lysine is the C-terminal residue.
  • a composition comprises a plurality of an antibody and/or an antigen-binding fragment of the present disclosure, wherein one or more antibody or antigen-binding fragment does not comprise a lysine residue or a C-terminal glycine-lysine at the C-terminal end of the heavy chain, CH1- CH3, or Fc polypeptide, and wherein one or more antibody or antigen-binding fragment comprises a lysine residue at the C-terminal end of the heavy chain, CH1-CH3, or Fc polypeptide.
  • a “Fab” fragment antigen-binding is the part of an antibody that binds to antigens and includes the variable region and CHI of the heavy chain linked to the light chain via an interchain disulfide bond. Each Fab fragment is monovalent with respect to antigen-binding, z.e., it has a single antigen-binding site. Pepsin treatment of an antibody yields a single large F(ab')2 fragment that roughly corresponds to two disulfide linked Fab fragments having divalent antigenbinding activity and is still capable of cross-linking antigen.
  • Both the Fab and F(ab’)2 are examples of "antigen-binding fragments.”
  • Fab' fragments differ from Fab fragments by having additional few residues at the carboxy terminus of the CHI domain including one or more cysteines from the antibody hinge region.
  • Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • Fab fragments may be joined, e.g., by a peptide linker, to form a single chain Fab, also referred to herein as "scFab.”
  • a single chain Fab also referred to herein as "scFab.”
  • an inter-chain disulfide bond that is present in a native Fab may not be present, and the linker serves in full or in part to link or connect the Fab fragments in a single polypeptide chain.
  • a heavy chain-derived Fab fragment e.g., comprising, consisting of, or consisting essentially of VH + CHI, or "Fd
  • a light chain- derived Fab fragment e.g., comprising, consisting of, or consisting essentially of VL + CL
  • a scFab may be arranged, in N- terminal to C-terminal direction, according to (heavy chain Fab fragment - linker - light chain Fab fragment) or (light chain Fab fragment - linker - heavy chain Fab fragment).
  • Peptide linkers and exemplary linker sequences for use in scFabs are discussed in further detail herein.
  • Fv is a small antibody fragment that contains a complete antigen-recognition and antigen-binding site. This fragment generally consists of a dimer of one heavy- and one lightchain variable region domain in tight, non-covalent association. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although typically at a lower affinity than the entire binding site.
  • Single-chain Fv also abbreviated as “sFv” or “scFv”
  • sFv single-chain Fv
  • the scFv polypeptide comprises a polypeptide linker disposed between and linking the VH and VL domains that enables the scFv to retain or form the desired structure for antigenbinding.
  • a peptide linker can be incorporated into a fusion polypeptide using standard techniques well known in the art.
  • the antibody or antigenbinding fragment comprises a scFv comprising a VH domain, a VL domain, and a peptide linker linking the VH domain to the VL domain.
  • a scFv comprises a VH domain linked to a VL domain by a peptide linker, which can be in a VH-linker-VL orientation or in a VL-linker-VH orientation.
  • Any scFv of the present disclosure may be engineered so that the C-terminal end of the VL domain is linked by a short peptide sequence to the N-terminal end of the VH domain, or vice versa (i.e., (N)VL(C)-linker-(N)VH(C) or (N)VH(C)-linker- (N)VL(C).
  • a linker may be linked to an N-terminal portion or end of the VH domain, the VL domain, or both.
  • Peptide linker sequences may be chosen, for example, based on: (1) their ability to adopt a flexible extended conformation; (2) their inability or lack of ability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides and/or on a target molecule; and/or (3) the lack or relative lack of hydrophobic or charged residues that might react with the polypeptides and/or target molecule.
  • linker design e.g., length
  • linker design can include the conformation or range of conformations in which the VH and VL can form a functional antigen-binding site.
  • peptide linker sequences contain, for example, Gly, Asn and Ser residues.
  • linker sequence may also be included in a linker sequence.
  • Other amino acid sequences which may be usefully employed as linker include those disclosed in Maratea et al., Gene 40:39 46 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258 8262 (1986); U.S. Pat. No. 4,935,233, and U.S. Pat. No. 4,751,180.
  • linkers may include, for example, Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys-Val-Asp (SEQ ID NO: 19) (Chaudhary et al., Proc. Natl. Acad. Sci.
  • Any suitable linker may be used, and in general can be about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100 amino acids in length, or less than about 200 amino acids in length, and will preferably comprise a flexible structure (can provide flexibility and room for conformational movement between two regions, domains, motifs, fragments, or modules connected by the linker), and will preferably be biologically inert and/or have a low risk of immunogenicity in a human.
  • Exemplary linkers include those comprising or consisting of the amino acid sequence set forth in any one or more of SEQ ID NOs: 4-13 and Linker SEQs A and B.
  • the linker comprises or consists of an amino acid sequence having at least 75% (i.e., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in any one of SEQ ID NOs: 4-13 and Linker SEQs A and B.
  • scFv can be constructed using any combination of the VH and VL sequences or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein.
  • linker sequences are not required; for example, when the first and second polypeptides have non-essential N-terminal (or C-terminal) amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • DNA in the germline variable (V), joining (J), and diversity (D) gene loci may be rearranged and insertions and/or deletions of nucleotides in the coding sequence may occur. Somatic mutations may be encoded by the resultant sequence, and can be identified by reference to a corresponding known germline sequence.
  • somatic mutations that are not critical to a desired property of the antibody e.g., binding to a SARS-CoV-2 antigen
  • that confer an undesirable property upon the antibody e.g., an increased risk of immunogenicity in a subject administered the antibody
  • the antibody or antigenbinding fragment of the present disclosure comprises at least one more germline-encoded amino acid in a variable region as compared to a parent antibody or antigen-binding fragment, provided that the parent antibody or antigen-binding fragment comprises one or more somatic mutations.
  • Variable region and CDR amino acid sequences of exemplary anti-sarbecovirus antibodies of the present disclosure are provided in Table 1, and Table 3 herein.
  • an antibody or antigen-binding fragment comprises an amino acid modification (e.g., a substitution mutation) to remove an undesired risk of oxidation, deamination, and/or isomerization.
  • an amino acid modification e.g., a substitution mutation
  • variant antibodies that comprise one or more amino acid alterations in a variable region (e.g., VH, VL, framework or CDR) as compared to the presently disclosed S3 A3, S3A19, S3I2, S3O13, S3L17, or S2V29 (“parent") antibodies, wherein the variant antibody is capable of binding to a SARS-CoV-2 antigen.
  • the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to SEQ ID NO.: 23, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to SEQ ID NO.: 27, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid.
  • the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 31, 35, 36, and 43, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to SEQ ID NO.: 37, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germ
  • the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, and 190, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 87 and 193, wherein the variation is optionally
  • the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, and 222, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline- encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs
  • the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, and 251, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 105, 254, 257, and
  • the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, and 269, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline- encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of
  • the antibody or antigen-binding fragment is an IgG (e.g., IgGl, IgG2, IgG3, or IgG4), IgA, IgM, IgE, or IgD isotype, or comprises amino acid sequences from two or more of these.
  • the antibody or antigen-binding fragment is human, humanized, or chimeric.
  • An antibody or antigen-binding fragment may be of any allotype or combination of allotypes.
  • Allotype refers to the allelic variation found among the IgG subclasses.
  • an allotype may comprise Glml (or Glm(a)), Glm2 (or Glm(x)), Glm3 (or Glm(f)), Glml7 (or Gm(z))m), Glm27, and/or Glm28 (Glm27 and Glm28 have been described as “alloallotypes”).
  • the Glm3 and Glml7 allotypes are located at the same position in the CHI domain (position 214 according to EU numbering).
  • Glm3 comprises R214 (EU)
  • Glml7 comprises K214 (EU).
  • the Glml allotype is located in the CH3 domain (at positions 356 and 358 (EU)) and refers to the replacements E356D and M358L.
  • the Glm2 allotype refers to a replacement of the alanine in position 431 (EU) by a glycine.
  • Glm allotypes, alloallotypes, and features thereof are known in the art and described at, for example, www.imgt.org/IMGTrepertoire/Proteins/allotypes/human/IGH/IGHC/Glm_allotypes.html and Lefranc, M.-P. and Lefranc, G. Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism In: B. Tait, F. Christiansen (Eds.), Immunogenetics, chap. 34, Humana Press, Springer, New York, USA. Methods Mol. Biol. 2012; 882, 635-680. PMID: 22665258, LIGM: 406, the contents and allotypes and allotype information of which are incorporated herein by reference.
  • the Glml allotype may be combined, for example, with the Glm3, Glm 17, Glm27, Glm2, and/or Glm28 allotype.
  • an allotype is Glm3 with no Glml (Glm3,-1).
  • an allotype is Glml7,l allotype.
  • an allotype is Glm3,l.
  • an allotype is Glml7 with no Glml (Glml7,-1).
  • these allotypes may be combined (or not combined) with the Glm2, Glm27 or Glm28 allotype.
  • an allotype may be Glml7,l,2.
  • an antibody or antigen-binding fragment of the present disclosure comprises a Glm3 allotype or a Glm3,l allotype. In some embodiments, an antibody or antigenbinding fragment of the present disclosure comprises a Glm3 allotype and comprises M428L and N434S or M428L and N434A mutations or any other mutation(s) that enhance binding to a human FcRn, such as those described herein.
  • an antibody or antigenbinding fragment of the present disclosure comprises a Glm3,l allotype and comprises M428L and N434S or M428L and N434A mutations or any other mutation(s) that enhance binding to a human FcRn, such as those described herein.
  • an antibody or antigenbinding fragment of the present disclosure comprises a Glml7, 1 allotype.
  • an antibody or antigen-binding fragment of the present disclosure comprises a Glml7, 1 allotype and comprises M428L and N434S or M428L and N434A mutations or any other mutation(s) that enhance binding to a human FcRn, as described further herein.
  • the antibody, or the antigen-binding fragment comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab.
  • an antibody or antigen-binding fragment of the present disclosure is monospecific (e.g., binds to a single epitope) or is multispecific (e.g., binds to multiple epitopes and/or target molecules).
  • Antibodies and antigen-binding fragments may be constructed in various formats. Exemplary antibody formats disclosed in Spiess et al., Mol. Immunol.
  • FIT-Ig e.g., PCT Publication No.
  • the antibody or antigen-binding fragment comprises two or more of VH domains, two or more VL domains, or both (i.e., two or more VH domains and two or more VL domains).
  • an antigen-binding fragment comprises the format (N-terminal to C-terminal direction) VH-linker-VL-linker-VH-linker-VL, wherein the two VH sequences can be the same or different and the two VL sequences can be the same or different.
  • Such linked scFvs can include any combination of VH and VL domains arranged to bind to a given target, and in formats comprising two or more VH and/or two or more VL, one, two, or more different epitopes or antigens may be bound. It will be appreciated that formats incorporating multiple antigen-binding domains may include VH and/or VL sequences in any combination or orientation.
  • the antigen-binding fragment can comprise the format VL-linker-VH-linker-VL-linker-VH, VH-linker-VL-linker-VL-linker-VH, or VL-linker-VH- linker-VH-linker-VL.
  • Monospecific or multispecific antibodies or antigen-binding fragments of the present disclosure constructed comprise any combination of the VH and VL sequences and/or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein.
  • a bispecific or multispecific antibody or antigen-binding fragment may, in some embodiments, comprise one, two, or more antigen-binding domains (e.g., a VH and a VL) of the instant disclosure.
  • Two or more binding domains may be present that bind to the same or a different SARS-CoV-2 epitope, and a bispecific or multispecific antibody or antigen-binding fragment as provided herein can, in some embodiments, comprise a further SARS-CoV-2 binding domain, and/or can comprise a binding domain that binds to a different antigen or pathogen altogether.
  • the antibody or antigen-binding fragment can be multispecific; e.g., bispecific, trispecific, or the like.
  • the antibody or antigen-binding fragment comprises: (i) a first VH and a first VL; and (ii) a second VH and a second VL, wherein the first VH and the second VH are different.
  • the first VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%
  • the antibody or antigen-binding fragment may further comprise a Fc polypeptide or fragment thereof that comprises or consists of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the amino acid sequences set forth in SEQ ID NOs: 44-80.
  • the antibody or antigen-binding fragment comprises a Fc polypeptide, or a fragment thereof.
  • the "Fc" fragment or Fc polypeptide comprises the carboxyterminal portions (i.e., the CH2 and CH3 domains of IgG) of both antibody H chains held together by disulfides.
  • An Fc may comprise a dimer comprised of two Fc polypeptides (i.e., two CH2-CH3 polypeptides).
  • Antibody "effector functions" refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype.
  • antibody effector functions include: Clq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.
  • modifications e.g., amino acid substitutions
  • Fc domain in order to modify (e.g., improve, reduce, or ablate) one or more functionality of an Fc-containing polypeptide (e.g., an antibody of the present disclosure).
  • Such functions include, for example, Fc receptor (FcR) binding, antibody half-life modulation (e.g., by binding to FcRn), ADCC function, protein A binding, protein G binding, and complement binding.
  • Amino acid modifications that modify (e.g., improve, reduce, or ablate) Fc functionalities include, for example, the T250Q/M428L, M252Y/S254T/T256E, H433K/N434F, M428L/N434S, M428L/N434A, E233P/L234V/L235A/G236 + A327G/A330S/P331S, E333A, S239D/A330L/I332E, P257VQ311, K326W/E333S, S239D/I332E/G236A, N297Q, K322A, S228P, L235E + E318A/K320A/K322A, L234A/L235A (also referred to herein as "LALA"), and L234A/L235A/P329G mutations, which mutations are summarized and annotated in "Engineered Fc Regions",
  • the Clq protein complex can bind to at least two molecules of IgGl or one molecule of IgM when the immunoglobulin molecule(s) is attached to the antigenic target (Ward, E. S., and Ghetie, V., Ther. Immunol. 2 (1995) 77-94).
  • Burton, D. R. described (Mol. Immunol. 22 (1985) 161-206) that the heavy chain region comprising amino acid residues 318 to 337 is involved in complement fixation.
  • FcR binding can be mediated by the interaction of the Fc moiety (of an antibody) with Fc receptors (FcRs), which are specialized cell surface receptors on cells including hematopoietic cells.
  • Fc receptors belong to the immunoglobulin superfamily, and shown to mediate both the removal of antibody-coated pathogens by phagocytosis of immune complexes, and the lysis of erythrocytes and various other cellular targets (e.g. tumor cells) coated with the corresponding antibody, via antibody dependent cell mediated cytotoxicity (ADCC; Van de Winkel, J. G., and Anderson, C. L., J. Leukoc. Biol. 49 (1991) 511-524).
  • ADCC antibody dependent cell mediated cytotoxicity
  • FcRs are defined by their specificity for immunoglobulin classes; Fc receptors for IgG antibodies are referred to as FcyR, for IgE as FcsR, for IgA as FcaR and so on and neonatal Fc receptors are referred to as FcRn.
  • Fc receptor binding is described for example in Ravetch, J. V., and Kinet, J. P., Annu. Rev. Immunol. 9 (1991) 457-492; Capel, P. J., et al., Immunomethods 4 (1994) 25-34; de Haas, M., et al., J Lab. Clin. Med. 126 (1995) 330-341; and Gessner, J. E., et al., Ann. Hematol. 76 (1998) 231-248.
  • FcyR Fc domain of native IgG antibodies
  • FcyR In humans, three classes of FcyR have been characterized to-date, which are: (i) FcyRI (CD64), which binds monomeric IgG with high affinity and is expressed on macrophages, monocytes, neutrophils and eosinophils; (ii) FcyRII (CD32), which binds complexed IgG with medium to low affinity, is widely expressed, in particular on leukocytes, is believed to be a central player in antibody-mediated immunity, and which can be divided into FcyRIIA, FcyRIIB and FcyRIIC, which perform different functions in the immune system, but bind with similar low affinity to the IgG-Fc, and the ectodomains of these receptors are highly homologous; and (iii) FcyRIII (CD 16), which binds IgG with medium to low affinity and has been found in two forms: FcyRIIIA, which has been found on NK cells, macrophages,
  • FcyRIIA is found on many cells involved in killing (e.g. macrophages, monocytes, neutrophils) and seems able to activate the killing process.
  • FcyRIIB seems to play a role in inhibitory processes and is found on B-cells, macrophages and on mast cells and eosinophils. Importantly, it has been shown that 75% of all FcyRIIB is found in the liver (Ganesan, L. P. et al., 2012: “FcyRIIb on liver sinusoidal endothelium clears small immune complexes," Journal of Immunology 189: 4981-4988).
  • FcyRIIB is abundantly expressed on Liver Sinusoidal Endothelium, called LSEC, and in Kupffer cells in the liver and LSEC are the major site of small immune complexes clearance (Ganesan, L. P. et al., 2012: FcyRIIb on liver sinusoidal endothelium clears small immune complexes. Journal of Immunology 189: 4981-4988).
  • the antibodies disclosed herein and the antigen-binding fragments thereof comprise an Fc polypeptide or fragment thereof for binding to FcyRIIb, in particular an Fc region, such as, for example IgG-type antibodies.
  • FcyRIIb an Fc region
  • it is possible to engineer the Fc moiety to enhance FcyRIIB binding by introducing the mutations S267E and L328F as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies.
  • Molecular Immunology 45, 3926-3933 are examples of the FcyRIIb.
  • the antibodies of the present disclosure, or the antigen-binding fragments thereof comprise an engineered Fc moiety with the mutations S267E and L328F, in particular as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies.
  • FcyRIIB may function to suppress further immunoglobulin production and isotype switching to, for example, the IgE class.
  • FcyRIIB On macrophages, FcyRIIB is thought to inhibit phagocytosis as mediated through FcyRIIA.
  • the B form On eosinophils and mast cells, the B form may help to suppress activation of these cells through IgE binding to its separate receptor.
  • modification in native IgG of at least one of E233-G236, P238, D265, N297, A327 and P329 reduces binding to FcyRI.
  • IgG2 residues at positions 233-236, substituted into corresponding positions IgGl and IgG4, reduces binding of IgGl and IgG4 to FcyRI by 103-fold and eliminated the human monocyte response to antibody-sensitized red blood cells (Armour, K. L., et al. Eur. J. Immunol. 29 (1999) 2613-2624).
  • FcyRIIA reduced binding for FcyRIIA is found, e.g., for IgG mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, R292 and K414.
  • FcyRIII binding reduced binding to FcyRIIIA is found, e.g., for mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, S239, E269, E293, Y296, V303, A327, K338 and D376. Mapping of the binding sites on human IgGl for Fc receptors, the above-mentioned mutation sites, and methods for measuring binding to FcyRI and FcyRIIA, are described in Shields, R. L., et al., J. Biol. Chem. 276 (2001) 6591-6604.
  • FcyRIIIA Two allelic forms of human FcyRIIIA are the "Fl 58" variant, which binds to IgGl Fc with lower affinity, and the "VI 58" variant, which binds to IgGl Fc with higher affinity. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009).
  • two regions of native IgG Fc appear to be involved in interactions between FcyRIIs and IgGs, namely (i) the lower hinge site of IgG Fc, in particular amino acid residues L, L, G, G (234 - 237, EU numbering), and (ii) the adjacent region of the CH2 domain of IgG Fc, in particular a loop and strands in the upper CH2 domain adjacent to the lower hinge region, e.g. in a region of P331 (Wines, B.D., et al., J. Immunol. 2000; 164: 5313 - 5318).
  • FcyRI appears to bind to the same site on IgG Fc
  • FcRn and Protein A bind to a different site on IgG Fc, which appears to be at the CH2-CH3 interface
  • mutations that increase binding affinity of an Fc polypeptide or fragment thereof of the present disclosure to a (i.e., one or more) Fey receptor (e.g., as compared to a reference Fc polypeptide or fragment thereof or containing the same that does not comprise the mutation(s)). See, e.g., Delillo and Ravetch, Cell 161(5): 1035-1045 (2015) and Ahmed et al., J. Struc. Biol. 194(1):78 (2016), the Fc mutations and techniques of which are incorporated herein by reference.
  • an antibody or antigen-binding fragment can comprise a Fc polypeptide or fragment thereof comprising a mutation selected from G236A; S239D; A330L; and I332E; or a combination comprising any two or more of the same; e.g., S239D/I332E; S239D/A330L/I332E; G236A/S239D/I332E; G236A/A330L/I332E (also referred to herein as "GAALIE"); or G236A/S239D/A330L/I332E.
  • the Fc polypeptide or fragment thereof does not comprise S239D.
  • the Fc polypeptide or fragment thereof comprises S at position 239 (EU numbering).
  • the Fc polypeptide or fragment thereof comprises the amino acid sequences set forth in SEQ ID NOs: 52-58.
  • the Fc polypeptide or fragment thereof may comprise or consist of at least a portion of an Fc polypeptide or fragment thereof that is involved in FcRn binding.
  • the Fc polypeptide or fragment thereof comprises one or more amino acid modifications that improve binding affinity for (e.g., enhance binding to) FcRn (e.g., at a pH of about 6.0) and, in some embodiments, thereby extend in vivo half-life of a molecule comprising the Fc polypeptide or fragment thereof (e.g., as compared to a reference Fc polypeptide or fragment thereof or antibody that is otherwise the same but does not comprise the modification(s)).
  • the Fc polypeptide or fragment thereof comprises or is derived from a IgG Fc and a half-life-extending mutation comprises any one or more of: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I Q311I; D376V; T307A; E380A (EU numbering).
  • a half-life-extending mutation comprises M428L/N434S (also referred to herein as "MLNS”, "LS”, “_LS”, and "-LS").
  • the half-life extending mutation is in a Fc polypeptide or fragment thereof comprising or consisting of the amino acid sequences set forth in SEQ ID NOs: 59-64.
  • a half-life-extending mutation comprises M252Y/S254T/T256E.
  • a half-life-extending mutation comprises T250Q/M428L.
  • a half-life-extending mutation comprises P257I/Q31 II.
  • a half-life- extending mutation comprises P257I/N434H.
  • a half-life-extending mutation comprises D376V/N434H.
  • a half-life-extending mutation comprises T307A/E380A/N434A.
  • a half-life-extending mutation comprises M428L/N434A (also referred to herein as “MLNA”, “LA”, _LA”, and “-LA”).
  • the half-life extending mutation is in a Fc polypeptide or fragment thereof comprising or consisting of the amino acid sequences set forth in SEQ ID NOs: 65-70.
  • an antibody or antigen-binding fragment includes a Fc moiety that comprises the substitution mutations M428L/N434S or M428L/N434A. In some embodiments, an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mutations G236A/A330L/I332E. In certain embodiments, an antibody or antigen-binding fragment includes a (e.g., IgG) Fc moiety that comprises a G236A mutation, an A330L mutation, and a I332E mutation (GAALIE), and does not comprise a S239D mutation (e.g., comprises a native S at position 239).
  • a S239D mutation e.g., comprises a native S at position 239
  • an antibody or antigenbinding fragment includes an Fc polypeptide or fragment thereof that comprises the substitution mutation: M428L/N434S and G236A/A330L/I332E, (and may comprises or consist of the amino acid sequences set forth in SEQ ID NOs: 71-75) and, optionally does not comprise S239D (e.g., comprises S at 239).
  • an antibody or antigen-binding fragment includes an Fc polypeptide or fragment thereof that comprises the substitution mutation: M428L/N434A and G236A/A330L/I332E, (and may comprises or consist of the amino acid sequences set forth in SEQ ID NOs: 76-80) and, optionally does not comprise S239D (e.g., comprises S at 239).
  • an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mutations: M428L/N434S (or M428L/N434A) and G236A/S239D/A330L/I332E.
  • an antibody or antigen-binding fragment (described further herein) that comprises, in a(n e.g. human) IgGl heavy chain, the amino acid mutation(s) set forth in any one of (i)-(xviii): (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A
  • the antibody or antigen-binding fragment is afucosylated.
  • the antibody or antigen-binding fragment further comprises one or more mutation that enhances binding to a human FcRn, such as M428L and N434S mutations or M428L and N434A mutations (EU numbering) or any other mutation(s) that enhance binding to a human FcRn, such as those described herein.
  • the antibody or antigenbinding fragment is afucosylated.
  • the antibody or antigen-binding fragment comprises I) a VH and a VL having the amino acid sequences set forth in any one of SEQ ID NOs: 23 and 27, respectively; 31 and 37, respectively; 35 and 37, respectively; and 36 and 37, respectively; II) a CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 as set forth in a VH and a VL having the amino acid sequences set forth in any one of 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ
  • the antibody or antigen-binding fragment comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or the antibody or antigen-binding fragment is partially or fully aglycosylated and/or is partially or fully afucosylated.
  • Host cell lines and methods of making partially or fully aglycosylated or partially or fully afucosylated antibodies and antigen-binding fragments are known (see, e.g., PCT Publication No. WO 2016/181357; Suzuki et al. Clin. Cancer Res. 13(6): 1875-82 (2007); Huang et al. MAbs 6: 1-12 (2018)).
  • An antibody or antigen-binding fragment of the present disclosure can be fucosylated (e.g., comprising one or more fucosyl moiety, and typically comprising a native (wild-type) fucosylation pattern or a fucosylation pattern that includes one or more additional, or fewer, fucosyl moieties as compared to native), or can be afucosylated.
  • native IgGl antibodies carry a glycan site at N297, and this is typically the only site where a core fucose moiety may be found in the antibody, though some glycan sites may arise through mutation (e.g. in the variable domains) during antibody development.
  • Fucosylation of an Fc polypeptide or fragment thereof, or of an antibody can be effected by introducing amino acid mutations to introduce or disrupt a fucosylation site (e.g. a mutation at N297, such as N297Q or N297A, to disrupt formation of a glycan that can include a core fucose moiety), though typically it is preferred to maintain N297 and the glycan thereof, such as by expressing the polypeptide in a host cell which has been genetically engineered to lack the ability (or have an inhibited or compromised ability) to fucosylate the polypeptide; by expressing the polypeptide under conditions in which a host cell is impaired in its ability to fucosylate the polypeptide (e.g., in the presence of 2-fluoro-L-fucose (2FF)), or the like.
  • a fucosylation site e.g. a mutation at N297, such as N297Q or N297A, to disrupt formation of a glycan that can
  • An afucosylated polypeptide can comprise no fucose moieties, or substantially no fucose moieties, and/or can be expressed by a host cell that is genetically engineered to lack the ability (or have an inhibited or compromised ability) to fucosylate the polypeptide and/or can be expressed under conditions in which a host cell is impaired in its ability to fucosylate the polypeptide (e.g., in the presence of 2-fluoro-L-fucose (2FF)).
  • a polypeptide does not comprise a core fucose moiety at Asn297.
  • afucosylated polypeptides have increased binding to FcyRIIIA.
  • a plurality of antibodies may be described as “afucosylated” when the plurality was produced in the presence of 2FF or like reagent.
  • a plurality of polypeptides or antibodies may be described as, for example, afucosylated, meaning that about 85% or more of the single polypeptide or antibody molecules of the plurality do not comprise a fucose moiety.
  • an afucosylated antibody or polypeptide or a population or a plurality thereof comprises an asparagine (N) at EU position 297.
  • compositions that comprise a plurality of any one or more of the presently disclosed polypeptides, wherein the composition comprises afucosylated polypeptides.
  • the antibody or antigen-binding fragment is capable of eliciting continued protection in vivo in a subject even once no detectable levels of the antibody or antigen-binding fragment can be found in the subject (i.e., when the antibody or antigen-binding fragment has been cleared from the subject following administration). Such protection is referred to herein as a vaccinal effect. Without wishing to be bound by theory, it is believed that dendritic cells can internalize complexes of antibody and antigen and thereafter induce or contribute to an endogenous immune response against antigen.
  • an antibody or antigenbinding fragment comprises one or more modifications, such as, for example, mutations in the Fc comprising G236A, A330L, and I332E, that are capable of activating dendritic cells that may induce, e.g., T cell immunity to the antigen.
  • an antibody or antigen-binding fragment fo the present disclosure comprises an Fc variant selected from the Fc variants summarized in Table 1 (see also PCT Publication No. WO 2022/251119).
  • the Fc variant, or the antibody or antigen-binding fragment is fucosylated.
  • the Fc variant, or the antibody or antigen-binding fragment is afucosylated. Table 1. Fc Variants (fucosylated unless otherwise indicated) and Properties Thereof
  • an anti-parvovirus antibody or antigen-binding fragment comprises, in a(n e.g. human) IgGl heavy chain, the amino acid mutation(s) set forth in any one of (i)-(xviii): (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A and R
  • the antibody or antigen-binding fragment is afucosylated.
  • the antibody or antigen-binding fragment further comprises one or more mutation that enhances binding to a human FcRn, such as M428L and N434S mutations or M428L and N434A mutations (EU numbering) or any other mutation(s) that enhance binding to a human FcRn, such as those described herein.
  • the antibody or antigen- binding fragment is afucosylated.
  • the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof, including a CH2 (or a fragment thereof, a CH3 (or a fragment thereof), or a CH2 and a CH3, wherein the CH2, the CH3, or both can be of any isotype and may contain amino acid substitutions or other modifications as compared to a corresponding wild-type CH2 or CH3, respectively.
  • a Fc of the present disclosure comprises two CH2-CH3 polypeptides that associate to form a dimer.
  • the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof, including a CH2 (or a fragment thereof, a CH3 (or a fragment thereof), or a CH2 and a CH3, wherein the CH2, the CH3, or both can be of any isotype and may contain amino acid substitutions or other modifications as compared to a corresponding wild-type CH2 or CH3, respectively.
  • a Fc of the present disclosure comprises two CH2-CH3 polypeptides that associate to form a dimer.
  • the antibody or antigen-binding fragment can be monoclonal.
  • the term "monoclonal antibody” (mAb) as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, /. ⁇ ., individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present, in some cases in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations that include different antibodies directed against different epitopes, each monoclonal antibody is directed against a single epitope of the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies.
  • monoclonal antibodies useful in the present invention may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256 :495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal, or plant cells (see, e.g., U.S. Pat. No. 4,816,567).
  • Monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example.
  • Monoclonal antibodies may also be obtained using methods disclosed in PCT Publication No. WO 2004/076677A2.
  • Antibodies and antigen-binding fragments of the present disclosure include "chimeric antibodies" in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see, U.S. Pat. Nos. 4,816,567; 5,530,101 and 7,498,415; and Morrison et al., Proc. Natl. Acad. Sci. USA, 57:6851-6855 (1984)).
  • chimeric antibodies may comprise human and non-human residues.
  • chimeric antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. For further details, see Jones et al., Nature 321 :522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). Chimeric antibodies also include primatized and humanized antibodies.
  • a “humanized antibody” is generally considered to be a human antibody that has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are typically taken from a variable domain. Humanization may be performed following the method of Winter and co-workers (Jones et al., Nature, 321 :522-525 (1986); Reichmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239: 1534- 1536 (1988)), by substituting non-human variable sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized” antibodies are chimeric antibodies (U.S. Pat. Nos.
  • a “humanized” antibody is one which is produced by a non-human cell or animal and comprises human sequences, e.g., He domains.
  • human antibody is an antibody containing only sequences that are present in an antibody that is produced by a human.
  • human antibodies may comprise residues or modifications not found in a naturally occurring human antibody (e.g., an antibody that is isolated from a human), including those modifications and variant sequences described herein. These are typically made to further refine or enhance antibody performance.
  • human antibodies are produced by transgenic animals. For example, see U.S. Pat. Nos. 5,770,429; 6,596,541 and 7,049,426.
  • an antibody or antigen-binding fragment of the present disclosure is chimeric, humanized, or human.
  • the present disclosure provides isolated polynucleotides that encode any of the presently disclosed antibodies or an antigen-binding fragment thereof, or a portion thereof (e.g., a CDR, a VH, a VL, a heavy chain, or a light chain).
  • the polynucleotide is codon-optimized for expression in a host cell. Once a coding sequence is known or identified, codon optimization can be performed using known techniques and tools, e.g., using the GenScript® OptimiumGeneTM tool; see also Scholten et al., Clin. Immunol. 119: 135, 2006). Codon-optimized sequences include sequences that are partially codon- optimized (i.e., one or more codon is optimized for expression in the host cell) and those that are fully codon-optimized.
  • polynucleotides encoding antibodies and antigen-binding fragments of the present disclosure may possess different nucleotide sequences while still encoding a same antibody or antigen-binding fragment due to, for example, the degeneracy of the genetic code, splicing, and the like.
  • the polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 82, 91, 92, 100, 101, 109, 110, 119, 120, 123, 127, 130, 133, 136, 140, 144, 148, 152, 156, 159, 180, 182, 184, 187, 189, 191, 192, 195, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246,248, 250, 252, 253, 256, 259, 261, 262, 26
  • single polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 91, 100, 109, 119, 123, 127, 130, 133, 136, 140, 144, 152, 180, 182, 184, 187, 189, 191, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 262, 263, 265, and 268 and one or more of SEQ ID NOs: 82, 92, 101, 110, 120, 159, 192, 195, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246, 248, 250,
  • the first polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 91, 100, 109, 119, 123, 127, 130, 133, 136, 140, 144, 152, 180, 182, 184, 187, 189, 191, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 262, 263, 265, and 268, particularly SEQ ID NO: 123
  • the second polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%,
  • a single polynucleotide or combination of polynucleotides comprise or consist of combinations of two nucleic acid sequences, both having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to any one of SEQ ID NOs: i) 81 and 82; ii) 91, 180, 182, 184, 187, 189, or 191 and 92, 192, or 195; iii) 100, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, or 223 and 101, 224, 227, 230, or 233; iv) 109 and 110, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, or 261; or
  • the polynucleotide can comprise deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
  • the RNA comprises messenger RNA (mRNA).
  • Vectors are also provided, wherein the vectors comprise or contain a polynucleotide as disclosed herein (e.g., a polynucleotide that encodes an antibody or antigen-binding fragment that binds to two or more sarbecoviruses).
  • a vector can comprise any one or more of the vectors disclosed herein.
  • a vector is provided that comprises a DNA plasmid construct encoding the antibody or antigen-binding fragment, or a portion thereof (e.g., so-called "DMAb” ; sss, Muthumani st al., J Inf ct Dis.
  • a DNA plasmid construct comprises a single open reading frame encoding a heavy chain and a light chain (or a VH and a VL) of the antibody or antigen-binding fragment, wherein the sequence encoding the heavy chain and the sequence encoding the light chain are optionally separated by polynucleotide encoding a protease cleavage site and/or by a polynucleotide encoding a self-cleaving peptide.
  • the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in a single plasmid.
  • the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in two or more plasmids (e.g., a first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL).
  • a single plasmid comprises a polynucleotide encoding a heavy chain and/or a light chain from two or more antibodies or antigen-binding fragments of the present disclosure.
  • An exemplary expression vector is pVaxl, available from Invitrogen®.
  • a DNA plasmid of the present disclosure can be delivered to a subject by, for example, electroporation (e.g., intramuscular electroporation), or with an appropriate formulation (e.g., hyaluronidase).
  • the present disclosure also provides a host cell expressing an antibody or antigen-binding fragment according to the present disclosure; or comprising or containing a vector or polynucleotide according the present disclosure.
  • the cells include but are not limited to, eukaryotic cells, e.g., yeast cells, animal cells, insect cells, plant cells; and prokaryotic cells, including E. coli.
  • the cells are mammalian cells.
  • the cells are a mammalian cell line such as CHO cells (e.g., DHFR- CHO cells (Urlaub et al., PNAS 77:4216 (1980)), human embryonic kidney cells (e.g., HEK293T cells), PER.C6 cells, Y0 cells, Sp2/0 cells.
  • CHO cells e.g., DHFR- CHO cells (Urlaub et al., PNAS 77:4216 (1980)
  • human embryonic kidney cells e.g., HEK293T cells
  • PER.C6 cells Y0 cells
  • Sp2/0 cells e.g. NSO cells
  • human liver cells e.g. Hepa RG cells, myeloma cells
  • mammalian host cell lines include mouse sertoli cells (e.g, TM4 cells); monkey kidney CV1 line transformed by SV40 (COS-7); baby hamster kidney cells (BHK); African green monkey kidney cells (VERO-76); monkey kidney cells (CV1); human cervical carcinoma cells (HELA); human lung cells (W138); human liver cells (Hep G2); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3 A); mouse mammary tumor (MMT 060562); TRI cells; MRC 5 cells; and FS4 cells.
  • Mammalian host cell lines suitable for antibody production also include those described in, for example, Yazaki and Wu, Methods in Molecular Biology, Vol. 248 (B. K. C. Lo, ed., Humana Press, Totowa, N.J.), pp. 255-268 (2003).
  • a host cell is a prokaryotic cell, such as an E. coli.
  • a prokaryotic cell such as an E. coli.
  • the expression of peptides in prokaryotic cells such as E. coli is well established (see, e.g., Pluckthun, A. Bio/Technology 9:545-551 (1991).
  • antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed.
  • For expression of antibody fragments and polypeptides in bacteria see, e.g., U.S. Pat. Nos. 5,648,237; 5,789,199; and 5,840,523.
  • the cell may be transfected with a vector according to the present description with an expression vector.
  • transfection refers to the introduction of nucleic acid molecules, such as DNA or RNA (e.g. mRNA) molecules, into cells, such as into eukaryotic cells.
  • RNA e.g. mRNA
  • transfection encompasses any method known to the skilled person for introducing nucleic acid molecules into cells, such as into eukaryotic cells, including into mammalian cells.
  • Such methods encompass, for example, electroporation, lipofection, e.g., based on cationic lipids and/or liposomes, calcium phosphate precipitation, nanoparticle based transfection, virus based transfection, or transfection based on cationic polymers, such as DEAE-dextran or polyethylenimine, etc.
  • the introduction is non-viral.
  • host cells of the present disclosure may be transfected stably or transiently with a vector according to the present disclosure, e.g. for expressing an antibody, or an antigenbinding fragment thereof, according to the present disclosure.
  • the cells may be stably transfected with the vector as described herein.
  • cells may be transiently transfected with a vector according to the present disclosure encoding an antibody or antigen-binding fragment as disclosed herein.
  • a polynucleotide may be heterologous to the host cell.
  • the present disclosure also provides recombinant host cells that heterologously express an antibody or antigen-binding fragment of the present disclosure.
  • the cell may be of a species that is different to the species from which the antibody was fully or partially obtained (e.g., CHO cells expressing a human antibody or an engineered human antibody).
  • the cell type of the host cell does not express the antibody or antigen-binding fragment in nature.
  • the host cell may impart a post-translational modification (PTM; e.g., glycosylation or fucosylation) on the antibody or antigen-binding fragment that is not present in a native state of the antibody or antigen-binding fragment (or in a native state of a parent antibody from which the antibody or antigen-binding fragment was engineered or derived).
  • PTM post-translational modification
  • Such a PTM may result in a functional difference (e.g., reduced immunogenicity).
  • an antibody or antigen-binding fragment of the present disclosure that is produced by a host cell as disclosed herein may include one or more post- translational modification that is distinct from the antibody (or parent antibody) in its native state (e.g., a human antibody produced by a CHO cell can comprise a more post-translational modification that is distinct from the antibody when isolated from the human and/or produced by the native human B cell or plasma cell).
  • a post- translational modification that is distinct from the antibody (or parent antibody) in its native state
  • a human antibody produced by a CHO cell can comprise a more post-translational modification that is distinct from the antibody when isolated from the human and/or produced by the native human B cell or plasma cell.
  • Insect cells useful expressing a binding protein of the present disclosure are known in the art and include, for example, Spodoptera frugipera Sf9 cells, Trichoplusia in BTI-TN5B1-4 cells, and Spodoptera frugipera SfSWTOl “MimicTM” cells. See, e.g., Palmberger et a!., J. Biotechnol. 752(3-4): 160-166 (2011). Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells.
  • Eukaryotic microbes such as filamentous fungi or yeast are also suitable hosts for cloning or expressing protein-encoding vectors, and include fungi and yeast strains with "humanized” glycosylation pathways, resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gemgross, Nat. Biotech. 22: 1409-1414 (2004); Li et al., Nat. Biotech. 24:210-215 (2006).
  • Plant cells can also be utilized as hosts for expressing a binding protein of the present disclosure.
  • PLANTIBODIESTM technology (described in, for example, U.S. Pat. Nos. 5,959,177; 6,040,498; 6,420,548; 7,125,978; and 6,417,429) employs transgenic plants to produce antibodies.
  • the host cell comprises a mammalian cell.
  • the host cell is a CHO cell, a HEK293 cell, a PER.C6 cell, a Y0 cell, a Sp2/0 cell, a NSO cell, a human liver cell, a myeloma cell, or a hybridoma cell.
  • the present disclosure provides methods for producing an antibody, or antigen-binding fragment, wherein the methods comprise culturing a host cell of the present disclosure under conditions and for a time sufficient to produce the antibody, or the antigenbinding fragment.
  • Methods useful for isolating and purifying recombinantly produced antibodies may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant antibody into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin.
  • One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide. These purification methods may also be employed when isolating an immunogen from its natural environment. Methods for large scale production of one or more of the isolated/recombinant antibody described herein include batch cell culture, which is monitored and controlled to maintain appropriate culture conditions. Purification of soluble antibodies may be performed according to methods described herein and known in the art and that comport with laws and guidelines of domestic and foreign regulatory agencies.
  • compositions that comprise any one or more of the presently disclosed antibodies, antigen-binding fragments, polynucleotides, vectors, or host cells, singly or in any combination, and can further comprise a pharmaceutically acceptable carrier, excipient, or diluent. Carriers, excipients, and diluents are discussed in further detail herein.
  • a composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure.
  • antibodies or antigen-binding fragments to be used in a combination each independently have one or more of the following characteristics: neutralize one, two, three, four, five, or more naturally occurring sarbecovirus variants; do not compete with one another for Spike protein binding; bind distinct sarbecovirus Spike protein epitopes; have a reduced formation of resistance to sarbecovirus; when in a combination, have a reduced formation of resistance to sarbecovirus; potently neutralize one, two, three, four, five or more live sarbecoviruses; exhibit additive or synergistic effects on neutralization of one, two, three, four, five or more or more live sarbecoviruses when used in combination; exhibit effector functions; are protective in relevant animal model(s) of infection; are capable of being produced in sufficient quantities for large- scale production.
  • a composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure.
  • the first antibody or antigen-binding fragment and the second antibody or antigen-binding fragment may A) both be an antibody or antigen-binding fragment that are S3 A3, an antibody with sufficient CDR, VH, and/or VH identity to S3 A3 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to SEQ ID NO.: 23 and a VL sequence according to SEQ ID NO.: 27, ii) CDRs as set forth in SEQ ID NOs: 23 and 27, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 24-26 (H1-H3) and 28-30 (L1-L3); B) both be an antibody or antigen-binding fragment that are S3A19, an antibody with sufficient CDR, VH, and/or VH identity to S3 Al 9 to confer similar
  • a composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure.
  • the first antibody or antigen-binding fragment may be A) an antibody or antigen-binding fragment that are S3 A3, an antibody with sufficient CDR, VH, and/or VH identity to S3 A3 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to SEQ ID NO.: 23 and a VL sequence according to SEQ ID NO.: 27, ii) CDRs as set forth in SEQ ID NOs: 23 and 27, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 24-26 (H1-H3) and 28-30 (L1-L3); B) an antibody or antigen-binding fragment that are S3 Al 9, an antibody with sufficient CDR, VH, and/or VH identity to S3 Al 9 to confer similar specific binding, or a fragment thereof, such as those comprising
  • the composition may comprise or may comprise antibodies or antigen-binding fragment comprising or consisting of A) a first antibody or antigen-binding fragment which may be an antibody or antigen-binding fragment that are S3L17, an antibody with sufficient CDR, VH, and/or VH identity to S3L17 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, ii) CDRs as set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of SEQ ID NOs.: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) C
  • a composition comprises a first antibody or antigen-binding fragment and a second antibody or antigen-binding fragment; a multispecific (e.g. bispecific) antibody or antigen-binding fragment is provided; or a combination therapy comprises a first antibody or antigen-binding fragment and a second antibody or antigen-binding fragment, wherein the first antibody or antigen-binding fragment and second antibody or antigen-binding fragment, respectively, or the multispecific antibody or antigen-binding fragment, comprise(s) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, according to (i) any S3 A3 antibody and any S3 Al 9 antibody; (ii) any S3 A3 antibody and sotrovimab; (iii) any S3A3 antibody and S2K146; (iv) any S3 A3 antibody and S2X259; (v) any S3A3 antibody and any S2X324 antibody; (vi) any S3A
  • a composition comprises a first vector comprising a first plasmid, and a second vector comprising a second plasmid, wherein the first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL of the antibody or antigenbinding fragment thereof.
  • a composition comprises a polynucleotide (e.g., mRNA) coupled to a suitable delivery vehicle or carrier.
  • Exemplary vehicles or carriers for administration to a human subject include a lipid or lipid-derived delivery vehicle, such as a liposome, solid lipid nanoparticle, oily suspension, submicron lipid emulsion, lipid microbubble, inverse lipid micelle, cochlear liposome, lipid microtubule, lipid microcylinder, or lipid nanoparticle (LNP) or a nanoscale platform (see, e.g., Li et al. Wilery Interdiscip Rev. Nanomed Nanobiotechnol. 77(2):el530 (2019)). Principles, reagents, and techniques for designing appropriate mRNA and formulating mRNA-LNP and delivering the same are described in, for example, Pardi et al.
  • lipid nanoparticles e.g., ionizable cationic lipid/phosphatidylcholine/cholesterol/PEG-lipid; ionizable lipid:distearoyl
  • PC cholesterol: polyethylene glycol lipid
  • subcutaneous, intramuscular, intradermal, intravenous, intraperitoneal, and intratracheal administration of the same, are incorporated herein by reference.
  • Methods of diagnosis may include contacting an antibody, antibody fragment (e.g., antigen-binding fragment) with a sample.
  • samples may be isolated from a subject, for example an isolated tissue sample taken from, for example, nasal passages, sinus cavities, salivary glands, lung, liver, pancreas, kidney, ear, eye, placenta, alimentary tract, heart, ovaries, pituitary, adrenals, thyroid, brain, skin or blood.
  • the methods of diagnosis may also include the detection of an antigen/antibody complex, in particular following the contacting of an antibody or antibody fragment with a sample. Such a detection step can be performed at the bench, i.e. without any contact to the human or animal body. Examples of detection methods are well-known to the person skilled in the art and include, e.g, ELISA (enzyme-linked immunosorbent assay), including direct, indirect, and sandwich ELISA.
  • Treatment refers to medical management of a disease, disorder, or condition of a subject (e.g, a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat).
  • an appropriate dose or treatment regimen comprising an antibody or composition of the present disclosure is administered in an amount sufficient to elicit a therapeutic or prophylactic benefit.
  • Therapeutic or prophylactic/preventive benefit includes improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay or prevention of disease progression; remission; survival; prolonged survival; or any combination thereof.
  • therapeutic or prophylactic/preventive benefit includes reduction or prevention of hospitalization for treatment of a sarbecovirus infection (i.e., in a statistically significant manner).
  • therapeutic or prophylactic/preventive benefit includes a reduced duration of hospitalization for treatment of a sarbecovirus infection (i.e., in a statistically significant manner).
  • therapeutic or prophylactic/preventive benefit includes a reduced or abrogated need for respiratory intervention, such as intubation and/or the use of a respirator device.
  • therapeutic or prophylactic/preventive benefit includes reversing a late-stage disease pathology and/or reducing mortality.
  • a “therapeutically effective amount” or “effective amount” of an antibody, antigenbinding fragment, polynucleotide, vector, host cell, or composition of this disclosure refers to an amount of the composition or molecule sufficient to result in a therapeutic effect, including improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay of disease progression; remission; survival; or prolonged survival in a statistically significant manner.
  • a therapeutically effective amount refers to the effects of that ingredient or cell expressing that ingredient alone.
  • a therapeutically effective amount refers to the combined amounts of active ingredients or combined adjunctive active ingredient with a cell expressing an active ingredient that results in a therapeutic effect, whether administered serially, sequentially, or simultaneously.
  • a combination may comprise, for example, two different antibodies that specifically bind sarbecovirus antigens, which in certain embodiments, may be the same or different sarbecovirus antigens, and/or can comprise the same or different epitopes.
  • methods for treating a sarbecovirus infection in a subject, wherein the methods comprise administering to the subject an effective amount of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition as disclosed herein.
  • Subjects that can be treated by the present disclosure are, in general, human and other primate subjects, such as monkeys and apes for veterinary medicine purposes. Other model organisms, such as mice and rats, may also be treated according to the present disclosure.
  • the subject may be a human subject.
  • the subjects can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects.
  • a subject treated according to the present disclosure comprises one or more risk factors.
  • a human subject treated according to the present disclosure is an infant, a child, a young adult, an adult of middle age, or an elderly person. In certain embodiments, a human subject treated according to the present disclosure is less than 1 year old, or is 1 to 5 years old, or is between 5 and 125 years old (e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 125 years old, including any and all ages therein or therebetween).
  • a human subject treated according to the present disclosure is 0-19 years old, 20-44 years old, 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older. Persons of middle, and especially of elderly age are believed to be at particular risk.
  • the human subject is 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older.
  • the human subject is male.
  • the human subject is female.
  • a human subject treated according to the present disclosure is a resident of a nursing home or a long-term care facility, is a hospice care worker, is a healthcare provider or healthcare worker, is a first responder, is a family member or other close contact of a subject diagnosed with or suspected of having a sarbecovirus infection, is overweight or clinically obese, is or has been a smoker, has or had chronic obstructive pulmonary disease (COPD), is asthmatic (e.g, having moderate to severe asthma), has an autoimmune disease or condition (e.g, diabetes), and/or has a compromised or depleted immune system (e.g., due to AIDS/HIV infection, a cancer such as a blood cancer, a lymphodepleting therapy such as a chemotherapy, a bone marrow or organ transplantation, or a genetic immune condition), has chronic liver disease, has cardiovascular disease, has a pulmonary or heart defect, works or otherwise spends time in close proximity with others, such as in a factory, shipping center, hospital
  • COPD
  • a subject treated according to the present disclosure has received a vaccine for a sarbecovirus and the vaccine is determined to be ineffective, e.g, by post-vaccine infection or symptoms in the subject, by clinical diagnosis or scientific or regulatory criteria.
  • treatment is administered as peri-exposure prophylaxis.
  • treatment is administered to a subject with mild-to-moderate disease, which may be in an outpatient setting.
  • treatment is administered to a subject with moderate-to-severe disease, such as requiring hospitalization.
  • Typical routes of administering the presently disclosed compositions thus include, without limitation, oral, topical, transdermal, inhalation, parenteral, sublingual, buccal, rectal, vaginal, and intranasal.
  • parenteral includes subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques.
  • administering comprises administering by a route that is selected from oral, intravenous, parenteral, intragastric, intrapleural, intrapulmonary, intrarectal, intradermal, intraperitoneal, intratumoral, subcutaneous, topical, transdermal, intracisternal, intrathecal, intranasal, and intramuscular.
  • a method comprises orally administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition to the subject.
  • compositions according to certain embodiments of the present invention are formulated so as to allow the active ingredients contained therein to be bioavailable upon administration of the composition to a patient.
  • Compositions that will be administered to a subject or patient may take the form of one or more dosage units, where for example, a tablet may be a single dosage unit, and a container of a herein described an antibody or antigen-binding in aerosol form may hold a plurality of dosage units.
  • Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art; for example, see Remington: The Science and Practice of Pharmacy, 20th Edition (Philadelphia College of Pharmacy and Science, 2000).
  • composition to be administered will, in any event, contain an effective amount of an antibody or antigen-binding fragment, polynucleotide, vector, host cell, , or composition of the present disclosure, for treatment of a disease or condition of interest in accordance with teachings herein.
  • a composition may be in the form of a solid or liquid.
  • the carrier(s) are particulate, so that the compositions are, for example, in tablet or powder form.
  • the carrier(s) may be liquid, with the compositions being, for example, an oral oil, injectable liquid or an aerosol, which is useful in, for example, inhalatory administration.
  • the pharmaceutical composition is preferably in either solid or liquid form, where semi solid, semi liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid.
  • the pharmaceutical composition may be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like.
  • a solid composition will typically contain one or more inert diluents or edible carriers.
  • binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, gum tragacanth or gelatin; excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, com starch and the like; lubricants such as magnesium stearate or Sterotex; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; a flavoring agent such as peppermint, methyl salicylate or orange flavoring; and a coloring agent.
  • excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, com starch and the like
  • lubricants such as magnesium stearate or Sterotex
  • glidants such as colloidal silicon dioxide
  • sweetening agents such as sucrose or saccharin
  • a flavoring agent such as peppermint,
  • compositions When the composition is in the form of a capsule, for example, a gelatin capsule, it may contain, in addition to materials of the above type, a liquid carrier such as polyethylene glycol or oil.
  • a liquid carrier such as polyethylene glycol or oil.
  • the composition may be in the form of a liquid, for example, an elixir, syrup, solution, emulsion or suspension.
  • the liquid may be for oral administration or for delivery by injection, as two examples.
  • preferred compositions contain, in addition to the present compounds, one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer.
  • a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent may be included.
  • Liquid pharmaceutical compositions may include one or more of the following adjuvants: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer’s solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose.
  • the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • Physiological saline is a preferred adjuvant.
  • a liquid composition intended for either parenteral or oral administration should contain an amount of an antibody or antigen-binding fragment as herein disclosed such that a suitable dosage will be obtained. Typically, this amount is at least 0.01% of the antibody or antigenbinding fragment in the composition. When intended for oral administration, this amount may be varied to be between 0.1 and about 70% of the weight of the composition. Certain oral pharmaceutical compositions contain between about 4% and about 75% of the antibody or antigen-binding fragment. In certain embodiments, pharmaceutical compositions and preparations according to the present invention are prepared so that a parenteral dosage unit contains between 0.01 to 10% by weight of antibody or antigen-binding fragment prior to dilution.
  • the composition may be intended for topical administration, in which case the carrier may suitably comprise a solution, emulsion, ointment or gel base.
  • the base may comprise one or more of the following: petrolatum, lanolin, polyethylene glycols, bee wax, mineral oil, diluents such as water and alcohol, and emulsifiers and stabilizers. Thickening agents may be present in a composition for topical administration. If intended for transdermal administration, the composition may include a transdermal patch or iontophoresis device.
  • the pharmaceutical composition may be intended for rectal administration, in the form, for example, of a suppository, which will melt in the rectum and release the drug.
  • the composition for rectal administration may contain an oleaginous base as a suitable nonirritating excipient.
  • bases include, without limitation, lanolin, cocoa butter and polyethylene glycol.
  • a composition may include various materials which modify the physical form of a solid or liquid dosage unit.
  • the composition may include materials that form a coating shell around the active ingredients.
  • the materials that form the coating shell are typically inert, and may be selected from, for example, sugar, shellac, and other enteric coating agents.
  • the active ingredients may be encased in a gelatin capsule.
  • the composition in solid or liquid form may include an agent that binds to the antibody or antigen-binding fragment of the disclosure and thereby assists in the delivery of the compound. Suitable agents that may act in this capacity include monoclonal or polyclonal antibodies, one or more proteins or a liposome.
  • the composition may consist essentially of dosage units that can be administered as an aerosol.
  • aerosol is used to denote a variety of systems ranging from those of colloidal nature to systems consisting of pressurized packages. Delivery may be by a liquefied or compressed gas or by a suitable pump system that dispenses the active ingredients. Aerosols may be delivered in single phase, bi phasic, or tri phasic systems in order to deliver the active ingredient(s). Delivery of the aerosol includes the necessary container, activators, valves, subcontainers, and the like, which together may form a kit. One of ordinary skill in the art, without undue experimentation, may determine preferred aerosols.
  • compositions of the present disclosure also encompass carrier molecules for polynucleotides, as described herein (e.g., lipid nanoparticles, nanoscale delivery platforms, and the like).
  • compositions may be prepared by methodology well known in the pharmaceutical art.
  • a composition intended to be administered by injection can be prepared by combining a composition that comprises an antibody, antigen-binding fragment thereof, or antibody conjugate as described herein and optionally, one or more of salts, buffers and/or stabilizers, with sterile, distilled water so as to form a solution.
  • a surfactant may be added to facilitate the formation of a homogeneous solution or suspension.
  • Surfactants are compounds that non-covalently interact with the peptide composition so as to facilitate dissolution or homogeneous suspension of the antibody or antigen-binding fragment thereof in the aqueous delivery system.
  • an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome (e.g., a decrease in frequency, duration, or severity of diarrhea or associated dehydration, or inflammation, or longer disease-free and/or overall survival, or a lessening of symptom severity).
  • a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder.
  • Prophylactic benefit of the compositions administered according to the methods described herein can be determined by performing pre-clinical (including in vitro and in vivo animal studies) and clinical studies and analyzing data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques, all of which can readily be practiced by a person skilled in the art.
  • compositions are administered in an effective amount (e.g., to treat a sarbecovirus infection), which will vary depending upon a variety of factors including the activity of the specific compound employed; the metabolic stability and length of action of the compound; the age, body weight, general health, sex, and diet of the subject; the mode and time of administration; the rate of excretion; the drug combination; the severity of the particular disorder or condition; and the subject undergoing therapy.
  • an effective amount e.g., to treat a sarbecovirus infection
  • test subjects will exhibit about a 10% up to about a 99% reduction in one or more symptoms associated with the disease or disorder being treated as compared to placebo-treated or other suitable control subjects.
  • a therapeutically effective daily dose of an antibody or antigen-binding fragment is (for a 70 kg mammal) from about 0.001 mg/kg (z.e., 0.07 mg) to about 100 mg/kg (z.e., 7.0 g); preferably a therapeutically effective dose is (for a 70 kg mammal) from about 0.01 mg/kg (z.e., 0.7 mg) to about 50 mg/kg (z.e., 3.5 g); more preferably a therapeutically effective dose is (for a 70 kg mammal) from about 1 mg/kg (z.e., 70 mg) to about 25 mg/kg (z.e., 1.75 g).
  • a therapeutically effective dose may be different than for an antibody or antigen-binding fragment.
  • a single intramuscular (IM) injection of an age and/or weight appropriate dose of an S2V29-vl.2 antibody or fragment thereof, particularly a S2V29-vl.2-IgGlml7_Lamda or S2V29-vl.2-IgGlml7,l-LS antibody as described herein may be sufficient to treat a SARS- CoV-2 infection or to have a prophylactic effect for between three and six months or up to six months.
  • a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition to the subject at 2, 3, 4, 5, 6, 7, 8, 9, 10 times, or more.
  • a method comprises administering the antibody, antigen-binding fragment, or composition to the subject a plurality of times, wherein a second or successive administration is performed at about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 24, about 48, about 74, about 96 hours, or more, following a first or prior administration, respectively.
  • a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition at least one time prior to the subject being infected by a sarbecovirus.
  • compositions comprising an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition of the present disclosure may also be administered simultaneously with, prior to, or after administration of one or more other therapeutic agents.
  • combination therapy may include administration of a single pharmaceutical dosage formulation which contains a compound of the invention and one or more additional active agents, as well as administration of compositions comprising an antibody or antigen-binding fragment of the disclosure and each active agent in its own separate dosage formulation.
  • an antibody or antigen-binding fragment thereof as described herein and the other active agent can be administered to the patient together in a single oral dosage composition such as a tablet or capsule, or each agent administered in separate oral dosage formulations.
  • an antibody or antigen-binding fragment as described herein and the other active agent can be administered to the subject together in a single parenteral dosage composition such as in a saline solution or other physiologically acceptable solution, or each agent administered in separate parenteral dosage formulations.
  • a single parenteral dosage composition such as in a saline solution or other physiologically acceptable solution, or each agent administered in separate parenteral dosage formulations.
  • the compositions comprising an antibody or antigen-binding fragment and one or more additional active agents can be administered at essentially the same time, ie., concurrently, or at separately staggered times, /. ⁇ ., sequentially and in any order; combination therapy is understood to include all these regimens.
  • a combination therapy comprises one or more anti-sarbecovirus antibody (or one or more nucleic acid, host cell, vector, or composition) of the present disclosure and one or more anti-inflammatory agent and/or one or more anti-viral agent.
  • the one or more anti-inflammatory agent comprises a corticosteroid such as, for example, dexamethasone, prednisone, or the like.
  • the one or more anti-inflammatory agents comprise a cytokine antagonist such as, for example, an antibody that binds to IL6 (such as siltuximab), or to IL-6R (such as tocilizumab), or to IL-ip, IL-7, IL-8, IL-9, IL-10, FGF, G-CSF, GM-CSF, IFN-y, IP-10, MCP-1, MIP-1A, MIP1-B, PDGR, TNF-a, or VEGF.
  • a cytokine antagonist such as, for example, an antibody that binds to IL6 (such as siltuximab), or to IL-6R (such as tocilizumab), or to IL-ip, IL-7, IL-8, IL-9, IL-10, FGF, G-CSF, GM-CSF, IFN-y, IP-10, MCP-1, MIP-1A, MIP1-B, PDGR, TNF-a,
  • the one or more anti-viral agents comprise nucleotide analogs or nucleotide analog prodrugs such as, for example, remdesivir, sofosbuvir, acyclovir, and zidovudine.
  • an anti-viral agent comprises lopinavir, ritonavir, favipiravir, or any combination thereof.
  • Other anti-inflammatory agents for use in a combination therapy of the present disclosure include non-steroidal anti-inflammatory drugs (NSAIDS).
  • the one or more antibody or one or more nucleic acid, host cell, vector, or composition
  • the one or more anti-inflammatory agent and/or one or the more antiviral agent can be administered in any order and any sequence, or together.
  • an antibody (or one or more nucleic acid, host cell, vector, or composition) is administered to a subject who has previously received one or more antiinflammatory agent and/or one or more antiviral agent.
  • one or more antiinflammatory agent and/or one or more antiviral agent is administered to a subject who has previously received an antibody (or one or more nucleic acid, host cell, vector, or composition).
  • a combination therapy comprises two or more anti-sarbecovirus antibodies of the present disclosure.
  • a method can comprise administering a first antibody to a subject who has received a second antibody, or can comprise administering two or more antibodies together.
  • a method is provided that comprises administering to the subject (a) a first antibody or antigen-binding fragment, when the subject has received a second antibody or antigen-binding fragment; (b) the second antibody or antigen-binding fragment, when the subject has received the first antibody or antigen-binding fragment; or (c) the first antibody or antigen-binding fragment, and the second antibody or antigen-binding fragment.
  • the present disclosure further provides a kit comprising one or more of any antibodies, antigen-binding fragments, polynucleotides, nucleic acids, vectors, or other compositions disclosed herein.
  • the kit may further include one or more of a container, such as a tube, vial, or syringe, an activator, a valve, a subcontainer, or instructions for use, such as for administering to a subject.
  • an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition is provided for use in a method of treating a sarbecovirus infection in a subject.
  • an antibody, antigen-binding fragment, or composition is provided for use in a method of manufacturing or preparing a medicament for treating a sarbecovirus infection in a subject.
  • Embodiment 1 An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (A) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO: 24, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO: 25, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists
  • the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 84 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid
  • the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid
  • the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 86 or 186, or
  • the CDRH1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 94, 198, or 208 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid
  • the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 95, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid
  • the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.
  • Embodiment 2 An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, having amino acid sequences according to (A) SEQ ID NOs.: 24-26 and 28-30, respectively; (B) SEQ ID NOs.: 32- 34 and 38-40, respectively; (C) SEQ ID NOs.: 84-86 or 84, 85 and 186 and 88-90 or 194, 89, and 90, respectively; (D) SEQ ID NOs.: 94-96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202
  • Embodiment 3 The antibody or antigen-binding fragment of Embodiment lor 2, wherein the sarbecovirus is a Clade lb sarbecovirus.
  • Embodiment 4 The antibody or antigen-binding fragment of Embodiment 3, wherein the sarbecovirus is SARS-CoV-2 WT, SARS-CoV-2 BA.l, RATG13, PANG/GD, or PAND/GX.
  • Embodiment 5 The antibody or antigen-binding fragment of any one of Embodiments 1-4, wherein the antibody or antigen-binding fragment is capable of binding to the surface glycoprotein when the surface glycoprotein is expressed on a cell surface of a host cell and/or is comprised on a virion.
  • Embodiment 6 The antibody or antigen-binding fragment of any one of Embodiments 1-5 which is capable of binding to a surface glycoprotein from two or more (e.g., two, three, four, five, or more) sarbecoviruses.
  • Embodiment 7 The antibody or antigen-binding fragment of any one of Embodiments 1-6, which is capable of neutralizing an infection by one or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
  • Embodiment 8 The antibody or antigen-binding fragment of any one of claims 1-7, which is capable of neutralizing an infection by two or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
  • Embodiment 9 The antibody or antigen-binding fragment of any one of Embodiments 1-8, wherein the VH and the VL comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in: (I) 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs:
  • Embodiment 10 The antibody or antigen-binding fragment of any one of
  • Embodiments 1-9 wherein the VH and the VL comprise or consist of amino acid sequences set forth in 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18) SEQ ID NOs: 183 and 19
  • Embodiment 11 The antibody or antigen-binding fragment of any one of Embodiments 1-10, wherein i) the VH and the VL comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in SEQ ID NOs: 111 and 157, respectively; ii) the VH and the VL comprise or consist of amino acid sequences set forth in SEQ ID NOs: 111 and 157, respectively; iii) the VH of i) or ii) comprises a CDRH1, a CDRH2, and a CDRH3, and the VL of i) or ii) comprises a CDRL1, a CDRL2, and a CD
  • Embodiment 12 The antibody or antigen-binding fragment of any one of Embodiment 1-11, which: (i) recognizes an epitope in the Spike protein of two or more, three or more, four or more, or five or more sarbecoviruses; (ii) is capable of blocking an interaction between the Spike protein of two or more, three or more, four or more, or five or more sarbecoviruses and their respective cell surface receptor(s), wherein, optionally, a cell surface receptor comprises a human ACE2; (iii) recognizes an epitope that is conserved in the Spike protein of two or more, , three or more, four or more, or five or more sarbecoviruses; (iv) is cross-reactive against two or more, three or more, four or more, or five or more sarbecoviruses, optionally comprising one or more clade lb sarbecoviruses; or (v) any combination of (i)-(iv
  • Embodiment 13 The antibody or antigen-binding fragment of any one of Embodiments 1-12, which is an IgG, IgA, IgM, IgE, or IgD isotype.
  • Embodiment 14 The antibody or antigen-binding fragment of Embodiment 13, which is an IgG isotype selected from IgGl, IgG2, IgG3, and IgG4, and is preferably an IgGl isotype.
  • Embodiment 15 The antibody or antigen-binding fragment of any one of Embodiments 1-14, which is human, humanized, or chimeric.
  • Embodiment 16 The antibody or antigen-binding fragment of any one of Embodiments 1-15, wherein the antibody, or the antigen-binding fragment, comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab.
  • Embodiment 17 The antibody or antigen-binding fragment of Embodiment 16, wherein the scFv comprises more than one VH domain and more than one VL domain.
  • Embodiment 18 The antibody or antigen-binding fragment of any one of Embodiments 1-17, wherein the antibody or antigen-binding fragment is a multi-specific antibody or antigen-binding fragment.
  • Embodiment 19 The antibody or antigen-binding fragment of Embodiment 18, wherein the antibody or antigen-binding fragment is a bispecific antibody or antigen-binding fragment.
  • Embodiment 20 The antibody or antigen-binding fragment of Embodiment 19, comprising: a first VH and a first VL; and a second VH and a second VL, wherein the first VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.
  • Embodiment 21 The antibody or antigen-binding fragment of any one of Embodiments 1-20, wherein the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof.
  • Embodiment 22 The antibody or antigen-binding fragment of Embodiment 21, wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to a FcRn as compared to a reference Fc polypeptide that does not comprise the mutation; (ii) a mutation that enhances binding to a FcyR as compared to a reference Fc polypeptide that does not comprise the mutation; (iii) a mutation that enhances binding to human FcyRIIa and/or decreases binding to a human FcyRIIb as compared to a reference Fc polypeptide that does not comprise the mutation; and/or (iv) a mutation that enhances binding to a human Clq compared to a reference Fc polypeptide that does not comprise the mutation.
  • Embodiment 23 The antibody or antigen-binding fragment of Embodiment 22, wherein the Fc polypeptide comprises the substitution mutations M428L/N434S, M428L/N434A, G236A/A330L/I332E/M428L/N434S, or G236A/A330L/I332E/M428L/N434A, wherein, optionally, the antibody or antigen-binding fragment is an IgGl isotype, and comprises or consists of a Fc polypeptide or fragment thereof that comprises or consists of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NOs: 44-80, optionally other than naturally occurring variants thereof, or that comprises or
  • Embodiment 24 An isolated polynucleotide encoding the antibody or antigenbinding fragment of any one of Embodiments 1-23.
  • Embodiment 25 The polynucleotide of Embodiment 24, wherein the polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (/. ⁇ ., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 82, 91, 92, 100, 101, 109, 110, 119, 120, 123, 127, 130, 133,
  • Embodiment 26 The polynucleotide of Embodiment 24 or Embodiment 25, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA).
  • DNA deoxyribonucleic acid
  • RNA ribonucleic acid
  • mRNA messenger RNA
  • Embodiment 27 The polynucleotide of any one of Embodiments 24-26, which is codon-optimized for expression in a host cell.
  • Embodiment 28 A recombinant vector comprising the polynucleotide of any one of Embodiments 24-27.
  • Embodiment 29 A host cell comprising the polynucleotide of any one of Embodiments 24-27 and/or the vector of Embodiment 28, wherein the polynucleotide is heterologous to the host cell.
  • Embodiment 30 A human B cell comprising the polynucleotide of any one of Embodiments 24-27 and/or the vector of Embodiment 28, wherein polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized.
  • Embodiment 31 A composition comprising: (i) the antibody or antigen-binding fragment of any one of Embodiments 1-23; (ii) the polynucleotide of any one of Embodiments 24-27; (iii) the recombinant vector of Embodiment 28; (iv) the host cell of Embodiment 29; and/or (v)the human B cell of Embodiment 30, and a pharmaceutically acceptable excipient, carrier, or diluent.
  • Embodiment 32 The composition of Embodiment 31, comprising two or more antibodies or antigen-binding fragments, wherein the first antibody or antigen-binding fragment and second antibody or antigen-binding fragment, respectively, or the multispecific antibody or antigen-binding fragment, comprise(s) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, according to (i) any S3A3 antibody and any S3A19 antibody; (ii) any S3A3 antibody and sotrovimab; (iii) any S3 A3 antibody and S2K146; (iv) any S3 A3 antibody and S2X259; (v) any S3 A3 antibody and any S2X324 antibody; (vi) any S3 A3 antibody and S309; (vi) any S3A19 antibody and sotrovimab; (vii) any S3A19 antibody and S2K146; (viii) any S3A19 antibody and S2X259; (
  • Embodiment 33 The composition of Embodiment 31, where the first antibody or antigen-binding fragment comprises a S3L17 antibody or antigen-binding fragment and the second antibody or antigen-binding fragment comprises a S2V29 antibody.
  • Embodiment 34 A composition of Embodiment 33, wherein the first antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 103, 85, and, 104; 103, 85, and 236; or 103, 85, and 239, and 106-108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, respectively, and the second antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112- 114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154
  • Embodiment 35 The composition of Embodiment 33, wherein the first antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more
  • the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
  • the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 116, 273, or 283, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is
  • the CDRL2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 117, 274, or 287, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid.
  • Embodiment 36 The composition of Embodiment 33, wherein the first antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, and wherein the second antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
  • the first antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243
  • Embodiment 37 A composition comprising the polynucleotide of any one of Embodiments 24-27 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform.
  • a lipid-derived delivery vehicle such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform
  • Embodiment 38 A method of treating a sarbecovirus infection (e.g. infection by a SARS-CoV-2) in a subject, the method comprising administering to the subject an effective amount of (i) the antibody or antigen-binding fragment of any one of Embodiments 1-23; (ii) the polynucleotide of any one of Embodiments 24-27; (iii) the recombinant vector of Embodiment 28; (iv) the host cell of Embodiment 29; and/or (v) the human B cell of Embodiment 30, and/or
  • Embodiment 39 The antibody or antigen-binding fragment of any one of Embodiments 1-23, the polynucleotide of any one of Embodiments 24-27, the recombinant vector of Embodiment 28, the host cell of Embodiment 29, the human B cell of Embodiment 30, and/or the composition of any one of Embodiments 31-37 for use in a method of treating a sarbecovirus infection (e.g. infection by a SARS-CoV-2) in a subject.
  • a sarbecovirus infection e.g. infection by a SARS-CoV-2
  • Embodiment 40 The antibody or antigen-binding fragment of any one of Embodiments 1-23, the polynucleotide of any one of Embodiments 24-27, the recombinant vector of Embodiment 28, the host cell of Embodiment 29, the human B cell of Embodiment 30, and/or the composition of any one of Embodiments 31-37 for use in the preparation of a medicament for the treatment of a sarbecovirus infection (e.g. infection by a SARS-CoV-2) in a subject.
  • a sarbecovirus infection e.g. infection by a SARS-CoV-2
  • Embodiment 41 The antibody or antigen-binding fragment of any one of Embodiments 1-23 or 39-40 wherein the antibody or antigen-binding fragment binds to two or more sarbecovirus S proteins, as measured using biolayer interferometry.
  • Embodiment 42 A kit comprising a liquid composition comprising and antibody or antigen-binding fragment of any one of Embodiments 1-23 or 39-40 and instructions for use thereof in treating a SARS-CoV-2 infection in a subject.
  • Embodiment 43 The kit of Embodiment 42, wherein the instructions for use are for the method of Embodiment 38 or the use according to any one of Embodiments 39-40.
  • Embodiment 44 A method for in vitro diagnosis of a sarbecovirus infection (e.g. infection by a SARS-CoV-2), the method comprising: (i) contacting a sample from a subject with an antibody or antigen-binding fragment of any one of Embodiments 1-23; and (ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigenbinding fragment.
  • a sarbecovirus infection e.g. infection by a SARS-CoV-2
  • Embodiment 45 A method for producing an antibody or antigen-binding fragment of any one of Embodiments 1-23 or 39-40, wherein the method comprises culturing a host cell expressing the antibody or antigen-binding fragment under conditions and for a time sufficient to produce the antibody, or the antigen-binding fragment.
  • Embodiment 46 The method for producing an antibody or antigen-binding fragment of Embodiment 45, wherein the host cell comprises a recombinant vector of Embodiment 28.
  • Embodiment 47 The method for producing an antibody or antigen-binding fragment of Embodiment 46, wherein the host cell is a mammalian cell. Table 2. Sequences
  • Table 2 indicates CDRH1, CDRH2 and CDRH3d (IMGT definition), in that order, in bold in each corresponding VH sequence; and CDRL1, CDRL2, CDRL3, in that order, in bold in each corresponding VL sequence.
  • Table 3 S3A3, S3A19 and Variants, S3I2, S3O13, and S3L17, and S2V29 and Variants
  • Example 1 The following materials and methods were used in Example 1 and, unless otherwise noted, in Example 2 and Example 3.
  • Example 1 Cell lines used in Example 1 were obtained from ATCC (HEK293T, Vero and Vero-E6), ThermoFisher Scientific (Expi293FTM cells).
  • Antigen specific IgG + memory B cells were isolated and cloned from PBMC of convalescent individuals who were previously vaccinated for or infected with SARS-CoV-2, then later were infected with a SARS-CoV-2 Omicron variant. Briefly, CD19 + B cells were enriched by staining with CD 19 PE-Cy7 and anti -PE microbeads (Milteniy), followed by positive selection using LS columns. Enriched B cells were stained with anti-IgD, anti-IgM, anti-IgA, anti-CD14, all PE labelled and prefusion SARS-CoV-2 S-Avi tag conjugated with streptavidin Alexa-Fluor 647 (Life Technologies).
  • SARS-CoV-2-specific IgG + memory B cells were sorted and seeded on MSC (mesenchymal stromal cells) at 0.5 cell/well in the presence of CpG2006, IL-2, IL6, IL- 10 and IL-21 using known methods. After 7 days, B cell supernatants were screened by ELISA for binding to a panel of RBDs representative of different sarbecovirus clades as well as by neutralization using high-throughput VSV SARS-CoV-2 S-based microneutralization.
  • MSC meenchymal stromal cells
  • Abs VH and VL sequences were obtained by reverse transcription PCR (RT-PCR) and mAbs were expressed as recombinant human IgGl, carrying the half-life extending M428L/N434S (“LS”, or “MLNS”) mutation in the Fc region fragment.
  • ExpiCHO cells were transiently transfected with heavy and light chain expression vectors using known methods.
  • IMGT the VH and VL gene family and the number of somatic mutations were determined by analyzing the homology of the VH and VL sequences to known human V, D and J genes.
  • UCA sequences of heavy and light variable regions were constructed using IMGT/V-QUEST.
  • MAbs affinity purification was performed on AKTA Xpress FPLC (Cytiva) operated by UNICORN software version 5.11 (Build 407) using HiTrap Protein A columns (Cytiva) for full length human and hamster mAbs and CaptureSelect CH1-XL MiniChrom columns (ThermoFisher Scientific) for Fab fragments, using PBS as mobile phase. Buffer exchange to the appropriate formulation buffer was performed with a HiTrap Fast desalting column (Cytiva). The final products were sterilized by filtration through 0.22 pm filters and stored at 4°C.
  • S2X259 is described in Tortorici, M.A., et al. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature 597, 103-108 (2021). https://doi.org/10.1038/s41586-021-03817-4.
  • S2K146 is described in Park, Y-J., et al. Science https://doi.org/10.1126/science.abm8143 (2022).
  • S2X324 is described in WO2021/226560.
  • S309 is described in Pinto, D., et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody.
  • Sotrovimab (VIR-7831) was developed from S309 and is described in Cathcart, A., et al. The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2; bioRxiv 2021.03.09.434607; doi: https://doi.org/10.1101/2021.03.09.434607. Sotrovimab, in addition to having the VH and VL sequences noted in Table 4, is an IgGl antibody with MLNS F mutations.

Abstract

The instant disclosure provides antibodies and antigen-binding fragments thereof that can bind to S proteins of sarbecoviruses (including, in some embodiments, multiple sarbecoviruses) and, in certain embodiments, are capable of neutralizing infection by multiple sarbecoviruses.

Description

ANTIBODIES THAT BIND TO MULTIPLE SARBECOVIRUSES
BACKGROUND
A novel sarbecovirus termed SARS-CoV-2 emerged in Wuhan, China, in late 2019.
SARS-CoV-2 and SARS-CoV are members of the sarbecovirus lineage. Sarbecoviruses can be further divided into four clades: la, lb, 2, and 3. SARS-CoV is a member of clade la, while SARS-CoV-2 is a member of clade lb. Therapies for preventing or treating sarbecovirus infections, and diagnostic reagents for diagnosing sarbecovirus infections, are needed.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Figure 1 shows a phylogenetic tree of sarbecoviruses, divided into clade la (also referred to as clade 1), clade lb (also referred to as clade 1/2), clade 2, and clade 3.
Figure 2 shows differences in receptor binding domain (RBD) amino acid sequences among various sarbecoviruses and the amino acids that are likely significant for wild type S2K146 interaction with viral antigens (boxes).
Figure 3 illustrates binding certain antibodies on SARS-CoV-2 RBD and their respective binding sites.
Figure 4 shows binding by antibodies including S3 A3 and S3 Al 9, as well as comparator antibodies S2X259 and S2K146, to various sarbecoviruses representing Claims la, lb, 2, and 3.
Figure 5 summarizes (in the right-hand portion of the table) the binding results from Figure 4 for Clades la, lb, 2, and 3. Figure 5 also shows (in the left-hand portion of the table) neutralization IC50 values obtained in VSV neutralization assays for SARS-CoV-2 and Omicron variants thereof, as well as SARS-Co-V.
Figure 6 shows neutralization against SARS-CoV-2 variants by certain antibodies including S3 A3 and S3 Al 9.
Figure 7 shows (the results of replicate neutralization tests with antibodies including S3A3 and S3A19.
Figure 8 shows the results of biolayer interferometry (BLI) competition studies testing S3 A3 against the indicated antibodies.
Figure 9 shows the results of BLI studies testing S3 Al 9 and the indicated antibodies.
Figure 10 shows binding (BLI) by S3 A3 and comparator antibody S2X324-v3.1 for SARS-CoV-2 Wuhan-Hu- 1 and the indicated variants. Figure 11 shows binding (BLI) by S3 Al 9 for SARS-CoV-2 Wuhan-Hu- 1 and the indicated variants.
Figure 12 shows binding (ELISA) by S3 A3 against various sarbecoviruses.
Figure 13 shows binding (ELISA) by S3A19 against various sarbecoviruses.
Figure 14 shows ACE-2 binding inhibition to SARS-CoV-2 Wuhan-Hu- 1 RBD by the indicated antibodies.
Figure 15 provides neutralization data for S3 A3 and comparator antibody S2X324-v3.1 against SARS-CoV-2 Wuhan-Hu-1 (“WT”) and variants of concern.
Figure 16 provides neutralization data for S3 Al 9 against SARS-CoV-2 Wuhan-Hu- 1 (“WT”) and variants.
Figure 17 provides neutralization data for S3 A3 and S2X234-v3.1 against SARS-CoV-2 variants that escape S2X324. The indicated variants were generated using a BA.2 backbone.
Figure 18 provides synergy and neutralization data for S3 A3 and S3 Al 9 (combined at the indicated concentrations).
Figure 19 provides synergy and neutralization data for S3 A3 and sotrovimab (combined at the indicated concentrations).
Figure 20 provides synergy and neutralization data S3 A3 and S2K146 (combined at the indicated concentrations).
Figure 21 provides synergy and neutralization data for S3A19 and sotrovimab (combined at the indicated concentrations).
Figure 22 provides synergy and neutralization data for S3A19 and S2K146 (combined at the indicated concentrations).
Figure 23 shows binding by S2V29 to various sarbecoviruses, and neutralization against SARS-CoV-2 variants by S2V29.
Figure 24 shows S2V29-vl.2 retains the neutralization profile of the parent antibody (S2V29-vl. l) against a panel of VSV SARS-CoV-2 viruses.
Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2V29-vl .2. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV- pp by S2X324. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2X259v50. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3O13. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3L17. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3I2v2.1. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts.
Figure 26 shows binding activity of S2V29 and S2V29-vl.2 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
Figure 27 shows binding activity of S2X324 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
Figure 28 shows log TCID values for S2X324-v3.1, S3L17 and S3O13, with an isotype control.
Figure 29 summarizes neutralizing activity against SARS-CoV-2 Omicron variants for certain variant antibodies.
Figure 30 shows neutralization of Wuhan-Hu-1 D614 and G614 mediated by sotrovimab and VIR-7832.
Figure 31 illustrates antigenic sites on SARS-CoV-2 RBD recognized by certain variant antibodies of the present disclosure.
Figure 32 shows the results of biolayer interferometry (BLI) studies testing S3I2, S3L17, S3O10, and S2V29 against S2K146, S2X259, S2X324, and S309.
Figure 33 shows the results of biolayer interferometry (BLI) competition studies testing the indicated antibodies.
Figure 34 shows binding results versus a panel of RBDs from sarbecoviruses (ELISA) for S3II, S3L17, S2V29, and S3O13.
Figure 35 shows VSV-PV neutralizations against BA.2-escape mutants for S3I2, S3L17, and S2V29. BA.2-G504D is an escape mutant of S2X259.
Figure 36 shows additional neutralization results against BA.2-escape mutants, including S2X324 escape mutants, S309 escape mutants, and S2K146 escape mutants, for S3O13. Fold change is relative to BA.2 variant. Figure 37 shows VSV-PV neutralizations against BA.5-escape mutants for S2V29, S3L17, S3I2, and S3O13.
Figure 38 summarizes ACE2 binding inhibition to RBDs of SARS-CoV-2 and SARS- CoV.
Figure 39 shows SI staining over time, gated on pos cells. SI shedding is shown to be induced by variant antibodies of the present disclosure.
Figure 40 shows luminescence results for activation of FcgRIIa and FcgRIIIa.
Figure 41 summarizes binding affinity versus a panel of RBDs (BLI), for S3L17 and S3O13.
Figure 42 shows binding affinity versus the same panel of RBDs (BLI) for S2V29.
Figure 43 shows binding affinity (BLI) versus a panel of RBDs representative of different sarbecovirus clades.
Figure 44 illustrates antibody-dependent cellular cytotoxicity (ADCC) and antibodydependent cellular phagocytosis (ADCP).
Figure 45 shows binding activity of S3L17 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
Figure 46 shows binding activity of S3I2-v2.1 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or B A.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
Figure 47 shows binding activity of S3O13 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or B A.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647.
Figure 48 shows binding activity of S2V29 tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan-D614 (“Wu- D614”), BA.2, BQ 1.1, XBB. l, and E340 A).
Figure 49 shows additional neutralization results against pre-Omicron and Omicron SARS-CoV-2 variants and additional escape mutants, including sotrovimab escape mutants, bebtelovimab escape mutants, S2K146 escape mutants, and S2X259 escape mutants for S3L17- vl.2 (S3L17), S2V29-V1.2 (S2V29), REGEN-COV and Evusheld.
Figure 50 shows additional neutralization results against SARS-CoV-2 variants and escape mutants for S3L17 and S2V29. Figure 51 shows additional neutralization results against SARS-CoV and SARS-CoV-2 variants and escape mutants for S2V29-vl.2. Underlines in the variant key indicates mutations associated with low pseudovirus infectivity in either a BQ.1.1 or XBB1.5 background.
Figure 52 summarizes escape mutant neutralization and binding data for S2V29 and S3L17. Nt changes: number of nucleotide changes required for the mutation to occur. Conservation: position identity across sarbecoviruses. *, NT with VSV-pp, IC50 in ng/ml; f, virus with low fitness, IC50s to be confirmed #, L455W found as escapes also with BA.2 DMS; f, FC calculated vs Wu-D614G. Figure 52 also shows putative single-nucleotide mutation intermediates that lead to escape mutants.
Figure 53 shows results for two replicates of live virus testing with S2V29-vl.2 (S2V29) and S3L17.
Figure 54 shows in vivo viral protection data for S2V29-vl.2 (S2V29) and S3L17.
Figure 55 shows binding affinity date for S2V29-vl.2 and S3L17 for the Wuhan, BA.5, and XBB1.5 SARS-Co-V-2 RBDs.
Figure 56 shows the results of evolutionary breadth testing for S2V29-vl.2 (S2V29) and S3L17.
Figure 57 shows likely epitopes for S3L17 and S2V29 and binding of the antibodies to the SARS-CoV-2 RBD.
Figure 58 shows deep mutational scanning (DMS) results for S3L17 and S2V29-vl.2 binding as compared to ACE2 binding for the Wuhan and BA.2 strains.
Figure 59 shows binding contacts of S3L17 and S2V29 with the SARS-CoV-2 RBD and overlap with strong Omicron RBD-ACE2 contacts.
Figure 60 shows how S2V29 binding competes with RBD-ACE2 binding.
Figure 61 shows results of ADCP testing with S3L17 and S2V29-vl.2 (S2V29).
Figure 62 shows results of ADCC testing with S3L17-vl.2 and S2V29-vl.2.
Figure 63 shows results of FcgR activation testing with S3L17-vl.2 and S2V29-vl.2.
Figure 64 shows a comparison of results obtained with authentic virus vs. VSV pseudovirus for S2V29-vl.2.
Figure 65 shows binding affinity of S2V29-vl.2 to various BQ1.1 escape mutations as determined by surface plasmon resonance (SPR).
Figure 66 shows binding affinity of S2V29-vl.2 to various sarbecoviruses as determined by surface plasmon resonance (SPR).
Figure 67 shows pharmacokinetic testing data for S2V29-vl.2.
Figure 68 shows additional neutralization data for S2V29-vl.2 against SARS-CoV and SARS-CoV-2 variants. DETAILED DESCRIPTION
Provided herein are antibodies and antigen-binding fragments that are capable of binding to a sarbecovirus (e.g., SARS-CoV-2). In some embodiments, an antibody or antigen-binding fragment is capable of binding to multiple sarbecoviruses (e.g., to a surface glycoprotein, as described herein, of one or more (e.g., one, two, three, four, five, six, or more) different sarbecoviruses, optionally comprised on a virion and/or expressed on the surface of a cell infected by two or more sarbecoviruses). In certain embodiments, the multiple sarbecoviruses comprise one or more Clade lb sarbecoviruses. In certain embodiments, presently disclosed antibodies and antigen-binding fragments can neutralize infection by one or more sarbecovirus (e.g., one, two, three, four, or more sarbecoviruses) in an in vitro model of infection and/or in an animal model and/or in a human subject. Also provided are polynucleotides that encode the antibodies and antigen-binding fragments, vectors, host cells, and related compositions, as well as methods of using the antibodies, antigen-binding fragments, polynucleotides, vectors, host cells, and related compositions to treat (e.g., reduce, delay, eliminate, or prevent) infection by two or more sarbecoviruses in a subject and/or in the manufacture of a medicament for treating infection in a subject by one or more sarbecovirus (e.g. one, two, three, four, or more) sarbecoviruses. Combinations of two or more antibodies or antigen-binding fragments, e.g. for use in therapy and/or prophylaxis, are also provided.
Prior to setting forth this disclosure in more detail, it may be helpful to an understanding thereof to provide definitions of certain terms to be used herein. Additional definitions are set forth throughout this disclosure.
As used herein, an “anti-sarbecovirus antibody or antigen-binding fragment” specifically binds at least one sarbecovirus and may, in some embodiments, bind two or more, three or more, four or more, or five or more sarbecoviruses.
As used herein, “sarbecovirus” refers to any betacoronavirus within lineage B, and includes lineage B viruses in clade la, clade lb, clade 2, and clade 3. Examples of clade la sarbecoviruses are SARS-CoV and Bat SARS-like coronavirus WIV1 (WIV1). Examples of clade lb sarbecoviruses are SARS-CoV-2, RatG13, Pangolin-Guanxi-2017 (PANG/GX) and Pangolin-Guangdon-2019 (PANG/GD). Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid), Y453F, S477N, T478K, V483 A, E484A, E484Q, E484K, E484X (where X is any amino acid), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, or the variants in B.E E7 and Q lineages and descendant lineages (Alpha);
B.1.351 and descendant lineages (Beta); B.1.429 and B.1.427 and descendant lineages (Epsilon); P.l and descendant lineages (Gamma); B.1.1.222; C.37; B.1.617.2; AY.1, AY.2, other AY lineages, and descendant lineages (Delta); B.1.525 and descendant lineages (Eta); B.1.526 and descendant lineages (Iota); B.1.617.1 and descendant lineages (Kappa); 1.617.3; B.1.621 and B.1.621.1 and descendant lineages (Mu); P.2 (Zeta); and B.1.1.529.1, BA.l, BA.2, BA.2.12, BA.3, BA.4, BA.5 and descendant lineages (Omicron). Examples of clade 2 sarbecoviruses are Bat ZC45 (ZC45), Bat ZXC21 (ZXC21), YN2013, RmYN02, Anlongl l2, SC2018, SX2011. Examples of clade 3 sarbecoviruses are BtkY72 and BGR2008. Sarbecovirus clades are also illustrated in Figure 1 and differences in RBDs among sarbecoviruses are illustrated in Figure 2.
In some embodiments, an antibody or antigen-binding fragment thereof is capable of binding to a sarbecovirus of clade lb, such as SARS-CoV-2 (including all variants described herein), RatG13, Pangolin-Guanxi-2017 (PANG/GX), Pangolin-Guangdon-209, or any combination thereof.
In certain further embodiments, an antibody or antigen-binding fragment thereof is capable of binding to a SARS-CoV-2 variant; e.g. examples of clade lb also include SARS-CoV- 2 variants, for example variants with any one or more of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except L), Y453F, S477N, T478K, V483 A, E484A, E484Q, E484K, E484X (where X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, or the variants in B.1.1.7 and Q lineages and descendant lineages (Alpha); B.1.351 and descendant lineages (Beta); B.1.429 and B.1.427 and descendant lineages (Epsilon); P. l and descendant lineages (Gamma); B.1.1.222; C.37;
B.1.617.2; AY.l, AY.2, other AY lineages, and descendant lineages (Delta); B.1.525 and descendant lineages (Eta); B.1.526 and descendant lineages (Iota); B.1.617.1 and descendant lineages (Kappa); 1.617.3; B.1.621 and B.1.621.1 and descendant lineages (Mu); P.2 (Zeta); and B.1.1.529.1, BA.l, BA.2, BA.2.12, BA.3, BA.4, BA.5 and descendant lineages (Omicron), or any combination thereof. In some embodiments, a SARS-Cov-2 variant is an Omicron variant, such as BA.l, BA.2, BA.2.12, BA.3, BA.4, or BA.5.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, antibody is (or an antigen-binding fragment is from) S3A19, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 of in a range between about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL. “S2V29” as used herein includes any of the VH and VL variants disclosed herein.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S2V29, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of inhibiting a binding interaction between human ACE2 and a sarbecovirus (e.g., SARS-CoV-2) receptor binding domain (RBD) with an IC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
As used herein, "SARS-CoV-2", also originally referred to as "Wuhan coronavirus", "Wuhan seafood market pneumonia virus", or "Wuhan CoV", "novel CoV", or "nCoV", or "2019 nCoV", or "Wuhan nCoV", or a variant thereof, is a betacoronavirus of lineage B (sarbecovirus). SARS-CoV-2 was first identified in Wuhan, Hubei province, China, in late 2019 and spread within China and to other parts of the world by early 2020. SARS CoV-2 infection can result in a disease known as COVID-19; symptoms of COVID-19 include fever or chills, dry cough, dyspnea, fatigue, body aches, headache, new loss of taste or smell, sore throat, congestions or runny nose, nausea or vomiting, diarrhea, persistent pressure or pain in the chest, new confusion, inability to wake or stay awake, and bluish lips or face.
The genomic sequence of SARS-CoV-2 isolate Wuhan-Hu-1 is provided at GenBank MN908947.3, January 23, 2020, and the amino acid translation of the genome is at GenBank QHD43416.1, January 23, 2020. These GenBank sequences and GenBank sequences for all SARS-CoV-2 variants are incorporated by reference herein as describing a sarbecovirus or a SARS-CoV-2 that an antibody or antigen-binding fragment thereof according to the present disclosure specifically binds. Like other coronaviruses (e.g., SARS-CoV), SARS-CoV-2 comprises a "spike" or surface ("S") type I transmembrane glycoprotein containing a receptor binding domain (RBD). RBD is believed to mediate entry of the lineage B SARS coronavirus to respiratory epithelial cells by binding to the cell surface receptor angiotensin-converting enzyme 2 (ACE2). In particular, a receptor binding motif (RBM) in the virus RBD is believed to interact with ACE2.
The amino acid sequence of the Wuhan-Hu- 1 surface glycoprotein is provided in SEQ ID NO. : 1. The amino acid sequence of the Wuhan-Hu- 1 RBD is provided in SEQ ID NO. :2. Wuhan-Hu- 1 S protein has approximately 73% amino acid sequence identity with SARS-CoV. The amino acid sequence of Wuhan-Hu-1 RBM is provided in SEQ ID NO.:3.
There have been a number of emerging SARS-CoV-2 variants, which may differ in genomic and amino acid sequences, particularly of the surface glycoprotein or the RBD. Some SARS-CoV-2 variants mutations that increase affinity to the ACE receptor and/or infectiveness of the virus. Significant variants of SARS-CoV-2 include Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except L), Y453F, S477N, T478K, V483 A, E484A, E484Q, E484K, E484X (where X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, or the variants in B.1.1.7 and Q lineages and descendant lineages (Alpha); B.1.351 and descendant lineages (Beta); B.1.429 and B.1.427 and descendant lineages (Epsilon); P. l and descendant lineages (Gamma); B.1.1.222; C.37;
B.1.617.2; AY.l, AY.2, other AY lineages, and descendant lineages (Delta); B.1.525 and descendant lineages (Eta); B.1.526 and descendant lineages (Iota); B.1.617.1 and descendant lineages (Kappa); 1.617.3; B.1.621 and B.1.621.1 and descendant lineages (Mu); P.2 (Zeta); and B.1.1.529.1, BA.l, BA.2, BA.2.12, BA.3, BA.4, BA.5 and descendant lineages (Omicron), or any combination thereof. In some embodiments, a SARS-Cov-2 variant is an Omicron variant such as BA.l, BA.2, BA.2.12, BA.3, BA.4, or BA.5. Variants of SARS-CoV-2 circulating in the United States are classified as variants of concern by the U.S. Centers for Disease Control and Prevention (see https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html).
In some embodiments, an antibody or antigen-binding fragment is provided for treating a sarbecovirus infection. In certain embodiments, a sarbecovirus infection comprises SARS-CoV- 2 infection. Treating a SARS CoV-2 infection in accordance with the present disclosure includes treating infection by any one or more of the aforementioned SARS-CoV-2 viruses. In certain embodiments, treating a SARS-CoV-2 infection comprises treating any one or more of: SARS CoV-2 Wuhan-Hu-1; Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except L), Y453F, S477N, T478K, V483 A, E484A, E484Q, E484K, E484X (where X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, D614, E340A, or the variants in B.1.1.7 and Q lineages and descendant lineages (Alpha); B.1.351 and descendant lineages (Beta); B.1.429 and B.1.427 and descendant lineages (Epsilon); P. l and descendant lineages (Gamma); B.1.1.222; C.37; B.1.617.2; AY.l, AY.2, other AY lineages, and descendant lineages (Delta); B.1.525 and descendant lineages (Eta); B.1.526 and descendant lineages (Iota); B.1.617.1 and descendant lineages (Kappa); 1.617.3; B.1.621 and B.1.621.1 and descendant lineages (Mu); P.2 (Zeta); and B.1.1.529.1, BA.l, BA.2, BA.2.12, BA.3, BA.4, BA.5 and descendant lineages (Omicron), BQ.1.1, XBB.l or any combination thereof. In some embodiments, a SARS-CoV-2 variant is an Omicron variant, such as BA.1, BA.2, BA.2.12, BA.3, BA.4, or BA.5. In some embodiments, the SARS-CoV-2 variant is BQ.1.1. In some embodiments, the SARS-CoV-2 variant is XBB.1
In the present description, any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated. Also, any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness, are to be understood to include any integer within the recited range, unless otherwise indicated. As used herein, the term "about" means ± 20% of the indicated range, value, or structure, unless otherwise indicated. It should be understood that the terms "a" and "an" as used herein refer to "one or more" of the enumerated components. The use of the alternative (e.g., "or") should be understood to mean either one, both, or any combination thereof of the alternatives. As used herein, the terms "include," "have," and "comprise" are used synonymously, which terms and variants thereof are intended to be construed as non-limiting.
"Optional" or "optionally" means that the subsequently described element, component, event, or circumstance may or may not occur, and that the description includes instances in which the element, component, event, or circumstance occurs and instances in which they do not.
In addition, it should be understood that the individual constructs, or groups of constructs, derived from the various combinations of the structures and subunits described herein, are disclosed by the present application to the same extent as if each construct or group of constructs was set forth individually. Thus, selection of particular structures or particular subunits is within the scope of the present disclosure.
The term "consisting essentially of is not equivalent to "comprising" and refers to the specified materials or steps of a claim, or to those that do not materially affect the basic characteristics of a claimed subject matter. For example, a protein domain, region, or module (e.g., a binding domain) or a protein "consists essentially of' a particular amino acid sequence when the amino acid sequence of a domain, region, module, or protein includes extensions, deletions, mutations, or a combination thereof (e.g., amino acids at the amino- or carboxyterminus or between domains) that, in combination, contribute to at most 20% (e.g., at most 15%, 10%, 8%, 6%, 5%, 4%, 3%, 2% or 1%) of the length of a domain, region, module, or protein and do not substantially affect (i.e., do not reduce the activity by more than 50%, such as no more than 40%, 30%, 25%, 20%, 15%, 10%, 5%, or 1%) the activity of the domain(s), region(s), module(s), or protein (e.g., the target binding affinity of a binding protein).
As used herein, "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y- carboxyglutamate, and O-phosphoserine. Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a-carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
As used herein, "mutation" refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively. A mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s).
A "conservative substitution" refers to amino acid substitutions that do not significantly affect or alter binding characteristics of a particular protein. Generally, conservative substitutions are ones in which a substituted amino acid residue is replaced with an amino acid residue having a similar side chain. Conservative substitutions include a substitution found in one of the following groups: Group 1 : Alanine (Ala or A), Glycine (Gly or G), Serine (Ser or S), Threonine (Thr or T); Group 2: Aspartic acid (Asp or D), Glutamic acid (Glu or Z); Group 3: Asparagine (Asn or N), Glutamine (Gin or Q); Group 4: Arginine (Arg or R), Lysine (Lys or K), Histidine (His or H); Group 5: Isoleucine (He or I), Leucine (Leu or L), Methionine (Met or M), Valine (Vai or V); and Group 6: Phenylalanine (Phe or F), Tyrosine (Tyr or Y), Tryptophan (Trp or W). Additionally or alternatively, amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing). For example, an aliphatic grouping may include, for purposes of substitution, Gly, Ala, Vai, Leu, and He. Other conservative substitutions groups include: sulfur- containing: Met and Cysteine (Cys or C); acidic: Asp, Glu, Asn, and Gin; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gin; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, He, Vai, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information can be found in Creighton (1984) Proteins, W.H. Freeman and Company.
As used herein, "protein" or "polypeptide" refers to a polymer of amino acid residues. Proteins apply to naturally occurring amino acid polymers, as well as to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, and non-naturally occurring amino acid polymers. Variants of proteins, peptides, and polypeptides of this disclosure are also contemplated. In certain embodiments, variant proteins, peptides, and polypeptides comprise or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.9% identical to an amino acid sequence of a defined or reference amino acid sequence as described herein. Any polypeptide of this disclosure (e.g., VH, VL, Fab, Fd, antibody heavy chain, antibody light chain) can, as encoded by a polynucleotide sequence, comprise a “signal peptide” (also known as a leader sequence, leader peptide, or transit peptide). Signal peptides target newly synthesized polypeptides to their appropriate location inside or outside the cell. A signal peptide may be removed in whole or in part from the polypeptide during or once localization or secretion is completed. Polypeptides that have a(n, e.g., full-length) signal peptide can be referred to as a “pre-protein” and polypeptides having their signal peptide removed - at least in part - can be referred to as “mature” proteins or polypeptides. In certain embodiments, an antibody or antigen-binding fragment is a mature protein or a pre-protein.
"Nucleic acid molecule" or "polynucleotide" or "polynucleic acid" refers to a polymeric compound including covalently linked nucleotides, which can be made up of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g., morpholine ring). Purine bases include adenine, guanine, hypoxanthine, and xanthine, and pyrimidine bases include uracil, thymine, and cytosine. Nucleic acid molecules include polyribonucleic acid (RNA), which includes mRNA, microRNA, siRNA, viral genomic RNA, and synthetic RNA, and polydeoxyribonucleic acid (DNA), which includes cDNA, genomic DNA, and synthetic DNA, either of which may be single or double stranded. If single-stranded, the nucleic acid molecule may be the coding strand or non-coding (anti-sense) strand. A nucleic acid molecule encoding an amino acid sequence includes all nucleotide sequences that encode the same amino acid sequence. Some versions of the nucleotide sequences may also include intron(s) to the extent that the intron(s) would be removed through co- or post-transcriptional mechanisms. In other words, different nucleotide sequences may encode the same amino acid sequence as the result of the redundancy or degeneracy of the genetic code, or by splicing.
Variants of nucleic acid molecules of this disclosure are also contemplated. Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and are preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical a nucleic acid molecule of a defined or reference polynucleotide as described herein, or that hybridize to a polynucleotide under stringent hybridization conditions of 0.015M sodium chloride, 0.0015M sodium citrate at about 65-68°C or 0.015M sodium chloride, 0.0015M sodium citrate, and 50% formamide at about 42°C. Nucleic acid molecule variants retain the capacity to encode a binding domain thereof having a functionality described herein, such as binding a target molecule.
"Percent sequence identity" refers to a relationship between two or more sequences, as determined by comparing the sequences. Preferred methods to determine sequence identity are designed to give the best match between the sequences being compared. For example, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment). Further, non-homologous sequences may be disregarded for comparison purposes. The percent sequence identity referenced herein is calculated over the length of the reference sequence, unless indicated otherwise. Methods to determine sequence identity and similarity can be found in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using a BLAST program (e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX). The mathematical algorithm used in the BLAST programs can be found in Altschul et al., Nucleic Acids Res. 25:3389-3402, 1997. Within the context of this disclosure, it will be understood that where sequence analysis software is used for analysis, the results of the analysis are based on the "default values" of the program referenced. "Default values" mean any set of values or parameters which originally load with the software when first initialized.
Other examples include Clustal W, MAFFT, Clustal Omega, AlignMe, Praline, GAP, BESTFIT, Needle (EMBOSS), Stretcher (EMBOSS), GGEARCH2SEQ, Water (EMBOSS), Matcher (EMBOSS), LALIGN, and SSEARCH2SEQ. A global alignment algorithm, such as a Needleman and Wunsch algorithm, can be used to align two sequences over their entire length, maximizing the number of matches and minimizes the number of gaps. Default values can be used.
To generate similarity scores for two amino acid sequences, scoring matrices can be used that assign positive scores for some non-identical amino acids (e.g., conservative amino acid substitutions, amino acids with similar physio-chemical properties, and/or amino acids that exhibit frequent substitutions in orthologs, homologs, or paralogs). Non-limiting examples of scoring matrices include PAM30, PAM70, PAM250, BLOSUM45, BLOSUM50, BLOUM62, BLOSUM80, and BLOSUM90.
The term "isolated" means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated. Such nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide.
The term "gene" means the segment of DNA or RNA involved in producing a polypeptide chain; in certain contexts, it includes regions preceding and following the coding region (e.g., 5’ untranslated region (UTR) and 3’ UTR) as well as intervening sequences (introns) between individual coding segments (exons).
A "functional variant" refers to a polypeptide or polynucleotide that is structurally similar or substantially structurally similar to a parent or reference compound of this disclosure, but differs slightly in composition (e.g., one base, atom or functional group is different, added, or removed), such that the polypeptide or encoded polypeptide is capable of performing at least one function of the parent polypeptide with at least 50% efficiency, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide. In other words, a functional variant of a polypeptide or encoded polypeptide of this disclosure has "similar binding," "similar affinity" or "similar activity" when the functional variant displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide, such as an assay for measuring binding affinity (e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (KD) constant).
As used herein, a "functional portion" or "functional fragment" refers to a polypeptide or polynucleotide that comprises only a domain, portion or fragment of a parent or reference compound, and the polypeptide or encoded polypeptide retains at least 50% activity associated with the domain, portion or fragment of the parent or reference compound, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide, or provides a biological benefit e.g., effector function). A "functional portion" or "functional fragment" of a polypeptide or encoded polypeptide of this disclosure has "similar binding" or "similar activity" when the functional portion or fragment displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide (preferably no more than 20% or 10%, or no more than a log difference as compared to the parent or reference with regard to affinity).
As used herein, the term "engineered," "recombinant," or "non-natural" refers to an organism, microorganism, cell, nucleic acid molecule, or vector that includes at least one genetic alteration or has been modified by introduction of an exogenous or heterologous nucleic acid molecule, wherein such alterations or modifications are introduced by genetic engineering (i.e., human intervention). Genetic alterations include, for example, modifications introducing expressible nucleic acid molecules encoding functional RNA, proteins, fusion proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of a cell’s genetic material. Additional modifications include, for example, noncoding regulatory regions in which the modifications alter expression of a polynucleotide, gene, or operon.
As used herein, "heterologous" or "non-endogenous" or "exogenous" refers to any gene, protein, compound, nucleic acid molecule, or activity that is not native to a host cell or a subject, or any gene, protein, compound, nucleic acid molecule, or activity native to a host cell or a subject that has been altered. Heterologous, non-endogenous, or exogenous includes genes, proteins, compounds, or nucleic acid molecules that have been mutated or otherwise altered such that the structure, activity, or both is different as between the native and altered genes, proteins, compounds, or nucleic acid molecules. In certain embodiments, heterologous, non-endogenous, or exogenous genes, proteins, or nucleic acid molecules (e.g., receptors, ligands, etc.) may not be endogenous to a host cell or a subject, but instead nucleic acids encoding such genes, proteins, or nucleic acid molecules may have been added to a host cell by conjugation, transformation, transfection, electroporation, or the like, wherein the added nucleic acid molecule may integrate into a host cell genome or can exist as extra-chromosomal genetic material (e.g., as a plasmid or other self-replicating vector). The term "homologous" or "homolog" refers to a gene, protein, compound, nucleic acid molecule, or activity found in or derived from a host cell, species, or strain. For example, a heterologous or exogenous polynucleotide or gene encoding a polypeptide may be homologous to a native polynucleotide or gene and encode a homologous polypeptide or activity, but the polynucleotide or polypeptide may have an altered structure, sequence, expression level, or any combination thereof. A non-endogenous polynucleotide or gene, as well as the encoded polypeptide or activity, may be from the same species, a different species, or a combination thereof.
In certain embodiments, a nucleic acid molecule or portion thereof native to a host cell will be considered heterologous to the host cell if it has been altered or mutated, or a nucleic acid molecule native to a host cell may be considered heterologous if it has been altered with a heterologous expression control sequence or has been altered with an endogenous expression control sequence not normally associated with the nucleic acid molecule native to a host cell. In addition, the term "heterologous" can refer to a biological activity that is different, altered, or not endogenous to a host cell. As described herein, more than one heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a fusion protein, or any combination thereof.
As used herein, the term "endogenous" or "native" refers to a polynucleotide, gene, protein, compound, molecule, or activity that is normally present in a host cell or a subject.
The term "expression", as used herein, refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene. The process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post-translational modification, or any combination thereof. An expressed nucleic acid molecule is typically operably linked to an expression control sequence (e.g., a promoter). The term "operably linked" refers to the association of two or more nucleic acid molecules on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter). "Unlinked" means that the associated genetic elements are not closely associated with one another and the function of one does not affect the other.
As described herein, more than one heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a protein (e.g, a heavy chain of an antibody), or any combination thereof. When two or more heterologous nucleic acid molecules are introduced into a host cell, it is understood that the two or more heterologous nucleic acid molecules can be introduced as a single nucleic acid molecule (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof. The number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of separate nucleic acid molecules introduced into a host cell.
The term "construct" refers to any polynucleotide that contains a recombinant nucleic acid molecule (or, when the context clearly indicates, a fusion protein of the present disclosure). A (polynucleotide) construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome. A "vector" is a nucleic acid molecule that is capable of transporting another nucleic acid molecule. Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules. Vectors of the present disclosure also include transposon systems (e.g., Sleeping Beauty, see, e.g., Geurts et al., Mol. Ther. 5:108, 2003: Mates et al., Nat. Genet. 41.753, 2009). Exemplary vectors are those capable of autonomous replication (episomal vector), capable of delivering a polynucleotide to a cell genome (e.g., viral vector), or capable of expressing nucleic acid molecules to which they are linked (expression vectors).
As used herein, "expression vector" or "vector" refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host. Such control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation. The vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself or deliver the polynucleotide contained in the vector into the genome without the vector sequence. In the present specification, "plasmid," "expression plasmid," "virus," and "vector" are often used interchangeably.
The term "introduced" in the context of inserting a nucleic acid molecule into a cell, means "transfection", "transformation," or "transduction" and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
In certain embodiments, polynucleotides of the present disclosure may be operatively linked to certain elements of a vector. For example, polynucleotide sequences that are needed to effect the expression and processing of coding sequences to which they are ligated may be operatively linked. Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion. Expression control sequences may be operatively linked if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
In certain embodiments, the vector comprises a plasmid vector or a viral vector (e.g., a lentiviral vector or a y-retroviral vector). Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox, and canarypox). Other viruses include, for example, Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus. Examples of retroviruses include avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
"Retroviruses" are viruses having an RNA genome, which is reverse-transcribed into DNA using a reverse transcriptase enzyme, the reverse-transcribed DNA is then incorporated into the host cell genome. "Gammaretrovirus" refers to a genus of the retroviridae family. Examples of gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses.
"Lentiviral vectors" include HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope, and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells.
In certain embodiments, the viral vector can be a gammaretrovirus, e.g., Moloney murine leukemia virus (MLV)-derived vectors. In other embodiments, the viral vector can be a more complex retrovirus-derived vector, e.g., a lentivirus-derived vector. HIV-l-derived vectors belong to this category. Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus). Methods of using retroviral and lentiviral viral vectors and packaging cells for transducing mammalian host cells with viral particles containing transgenes are known in the art and have been previous described, for example, in: U.S. Patent 8,119,772; Walchli et al., PLoS One 6 327939, 2011; Zhao et al., J. Immunol. 174'AM5, 2005; Engels et al., Hum. Gene Ther. 14'.1155, 2003; Frecha et al., Mol. Ther. 18A74 , 2010; and Verhoeyen et al., Methods Mol. Biol. 506:97, 2009. Retroviral and lentiviral vector constructs and expression systems are also commercially available. Other viral vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defective HSV and attenuated HSV (Krisky et al., Gene Ther. 5: 1517, 1998).
Other vectors that can be used with the compositions and methods of this disclosure include those derived from baculoviruses and a-viruses. (Jolly, D J. 1999. Emerging Viral Vectors, pp 209-40 in Friedmann T. ed. The Development of Human Gene Therapy. New York: Cold Spring Harbor Lab), or plasmid vectors (such as sleeping beauty or other transposon vectors).
When a viral vector genome comprises a plurality of polynucleotides to be expressed in a host cell as separate transcripts, the viral vector may also comprise additional sequences between the two (or more) transcripts allowing for bicistronic or multi ci stronic expression. Examples of such sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide, or any combination thereof.
Plasmid vectors, including DNA-based antibody or antigen-binding fragment-encoding plasmid vectors for direct administration to a subject, are described further herein.
As used herein, the term "host" refers to a cell or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest (e.g., an antibody of the present disclosure).
A host cell may include any individual cell or cell culture which may receive a vector or the incorporation of nucleic acids or express proteins. The term also encompasses progeny of the host cell, whether genetically or phenotypically the same or different. Suitable host cells may depend on the vector and may include mammalian cells, animal cells, human cells, simian cells, insect cells, yeast cells, and bacterial cells. These cells may be induced to incorporate the vector or other material by use of a viral vector, transformation via calcium phosphate precipitation, DEAE-dextran, electroporation, microinjection, or other methods. See, for example, Sambrook el al., Molecular Cloning: A Laboratory Manual 2d ed. (Cold Spring Harbor Laboratory, 1989).
In the context of a sarbecovirus infection, a "host" refers to a cell or a subject infected with a sarbecovirus.
"Antigen" or "Ag", as used herein, refers to an immunogenic molecule that provokes an immune response. This immune response may involve antibody production, activation of specific immunologically-competent cells, activation of complement, antibody dependent cytotoxicity, or any combination thereof. An antigen (immunogenic molecule) may be, for example, a peptide, glycopeptide, polypeptide, glycopolypeptide, polynucleotide, polysaccharide, lipid, or the like. It is readily apparent that an antigen can be synthesized, produced recombinantly, or derived from a biological sample. Exemplary biological samples that can contain one or more antigens include tissue samples, stool samples, cells, biological fluids, or combinations thereof. Antigens can be produced by cells that have been modified or genetically engineered to express an antigen. Antigens can also be present in a sarbecovirus (e.g., a surface glycoprotein or portion thereof), such as present in a virion, or expressed or presented on the surface of a cell infected by a sarbecovirus.
The term "epitope" or "antigenic epitope" includes any molecule, structure, amino acid sequence, or protein determinant that is recognized and specifically bound by a cognate binding molecule, such as an immunoglobulin, or other binding molecule, domain, or protein. Epitopic determinants generally contain chemically active surface groupings of molecules, such as amino acids or sugar side chains, and can have specific three-dimensional structural characteristics, as well as specific charge characteristics. Where an antigen is or comprises a peptide or protein, the epitope can be comprised of consecutive amino acids (e.g., a linear epitope), or can be comprised of amino acids from different parts or regions of the protein that are brought into proximity by protein folding (e.g., a discontinuous or conformational epitope), or non-contiguous amino acids that are in close proximity irrespective of protein folding.
Antibodies, Antigen-Binding Fragments, and Compositions
In one aspect, the present disclosure provides an isolated antibody, or an antigen-binding fragment thereof, that is capable of binding to a surface glycoprotein of a sarbecoviruses (e.g. of a SARS-CoV-2). In some embodiments, the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of two or more sarbecoviruses, three or more sarbecoviruses, four or more sarbecoviruses, or five or more sarbecoviruses. In some embodiments, the antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3.
In some embodiments, the two or more, three or more, four or more, or five or more sarbecoviruses comprise or one or more, or are selected from, clade lb sarbecoviruses or naturally occurring variants thereof, and any combination thereof. In certain embodiments, the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of two or more, three or more, four or more, or five or more sarbecoviruses; e.g. capable of binding when a sarbecovirus surface glycoprotein is expressed on a cell surface of a host cell and/or on a sarbecovirus virion. In certain embodiments, the two or more, three or more, four or more, or five or more sarbecoviruses are selected from SARS-CoV-2, PANG/GD, PANG/GX, RatG13, and naturally occurring variants thereof. In some embodiments, the two or more, three or more, four or more, or five or more sarbecoviruses include one or more of SARS-CoV-2 variants. In certain further embodiments, an antibody or antigen-binding fragment thereof is capable of binding to one or more SARS-CoV-2 variant. Examples of clade lb also include SARS-CoV-2 variants, for example variants with any of the mutations: A67V, A69-70, T95I, G142D, 137-145de, 143-145de, Y145H, N211I, A212, V213G, ins214TDR, ins215EPE, A222V, G339D, R346K, R346S, V367F, S371L, S373P, S375F, T376A, P384L, N394S, D405N, R408S, Q414K, K417N, K417V, K417T, N439K, N440K, G446S, Y449H, Y449N, L452R, L452Q, L452X (where X is any amino acid except L), Y453F, S477N, T478K, V483 A, E484A, E484Q, E484K, E484X (where X is any amino acid except E), F490R, F486V, F490S, R493Q, Q493R, S494P, G496S, Q498R, N501Y, N501T, Y505H, E516Q, T547K, Q613H, D614G, A653V, H655Y, G669S, Q677H, N679K, ins679GIAL, P681H, P681R, A701V, N764K, D796Y, N856K, Q954H, N969K, L981F, D614, E340A, or the variants in B. l.1.7 and Q lineages and descendant lineages (Alpha); B.1.351 and descendant lineages (Beta); B.1.429 and B.1.427 and descendant lineages (Epsilon); P. l and descendant lineages (Gamma); B.1.1.222; C.37;
B.1.617.2; AY.l, AY.2, other AY lineages, and descendant lineages (Delta); B.1.525 and descendant lineages (Eta); B.1.526 and descendant lineages (Iota); B.1.617.1 and descendant lineages (Kappa); 1.617.3; B.1.621 and B.1.621.1 and descendant lineages (Mu); P.2 (Zeta);
B.1.1.529.1, BA.l, BA.2, BA.2.12, BA.3, BA.4, BA.5 and descendant lineages (Omicron); BQ.1.1; and XBB. l .
In some embodiments, the two or more, three or more, four or more, or five or more sarbecoviruses include one or more SARS-CoV-2 variants having S protein mutations D614G, Q493R, G496S, Q498R, N501 Y, Y453F, N439K, K417V, E484K, or any combination thereof. In certain embodiments, two or more sarbecoviruses include one or more SARS-CoV-2 variants having S protein mutations K417N, Q493K, G496S, or any combination thereof.
In certain embodiments, an antibody or antigen-binding fragment of the present disclosure associates with or unites with a sarbecovirus surface glycoprotein epitope or antigen comprising the epitope, while not significantly associating or uniting with any other molecules or components in a sample. In some embodiments, the epitope is comprised in a SI subunit of a S protein. In further embodiments, the epitope is comprised in a RBD of a S protein. In some embodiments, the epitope is a conformational epitope or a linear epitope.
In certain embodiments, an antibody or antigen-binding fragment of the present disclosure associates with or unites (e.g., binds) to a first sarbecovirus surface glycoprotein epitope, and can also associate with or unite with an epitope from another sarbecovirus present in the sample, but not significantly associating or uniting with any other molecules or components in the sample. In other words, in certain embodiments, an antibody or antigen-binding fragment of the present disclosure is cross-reactive against and specifically binds to two or more sarbecoviruses (e.g., against SARS-CoV-2 Wuhan-Hu-1 and one or more variants thereof).
In certain embodiments, an antibody or antigen-binding fragment of the present disclosure specifically binds to a sarbecovirus surface glycoprotein. As used herein, "specifically binds" refers to an association or union of an antibody or antigen-binding fragment to an antigen with an affinity or Ka (i.e., an equilibrium association constant of a particular binding interaction with units of 1/M) equal to or greater than 105 M'1 (which equals the ratio of the on-rate [Kon] to the off rate [KOff] for this association reaction), while not significantly associating or uniting with any other molecules or components in a sample. Alternatively, affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (c.g, 10'5 M to 10'13 M). Antibodies may be classified as "high-affinity" antibodies or as "low- affinity" antibodies. "High-affinity" antibodies refer to those antibodies having a Ka of at least 107M-1, at least 108 M’1, at least 109 M’1, at least IO10 M’1, at least IO11 M’1, at least 1012M-1, or at least IO13 M'1. "Low-affinity" antibodies refer to those antibodies having a Ka of up to 107M-1, up to 106 M’1, up to 105 M'1. Alternatively, affinity may be defined as an equilibrium dissociation constant (Kd) of a particular binding interaction with units of M (e.g., 10'5 M to 10'13 M).
A variety of assays are known for identifying antibodies of the present disclosure that bind a particular target, as well as determining binding domain or binding protein affinities, such as Western blot, ELISA (e.g., direct, indirect, or sandwich), analytical ultracentrifugation, spectroscopy, and surface plasmon resonance (Biacore®) analysis (see, e.g., Scatchard et al., Ann. N.Y. Acad. Sci. 57:660, 1949; Wilson, Science 295:2103, 2002; Wolff et al., Cancer Res. 55:2560, 1993; and U.S. Patent Nos. 5,283,173, 5,468,614, or the equivalent). Assays for assessing affinity or apparent affinity or relative affinity are also known.
In certain embodiments, an antibody or antigen-binding fragment of the present disclosure binds one or more, or two or more, sarbecoviruses of Clade lb with an EC50 in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, which may be as determined by ELISA. In some embodiments, the antibody or antigen-binding fragment binds to a spike (S) protein RBD from one, two, three, four, or five sarbecoviruses.
In some embodiments, the antibody or antigen-binding fragment is capable of binding to a first and a second sarbecovirus each independently selected from Clade lb, wherein the antibody or antigen-binding fragment and is capable of binding to the first sarbecovirus with an EC50 of about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, and is capable of binding to the second sarbecovirus with an EC50 of about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x IO'09 M and about 1.0 x IO'08 M, about 1.2 x IO'09 M and about 1.0 x IO'08 M, about 1.5 x IO'09 M and about 1.0 x IO'08 M, about 2.0 x IO'09 M and about 1.0 x IO'08 M, about 2.25 x IO'09 M and about 1.0 x IO'08 M, about 2.5 x IO'09 M and about 1.0 x IO'08 M, about 3.0 x IO'09 M and about 1.0 x IO'08 M, about 3.5 x IO'09 M and about 1.0 x IO'08 M, about 4.0 x IO'09 M and about 1.0 x IO'08 M, about 4.5 x IO'09 M and about 1.0 x IO'08 M, or about 5.0 x IO'09 M and about 1.0 x IO'08 M, about 1.0 x IO'09 M, or about 1.2 x IO'09 M, about 1.5 x IO'09 M, about 2.0 x 1 O'09 M, about 2.25 x 1 O'09 M, about 2.5 x IO'09 M, about 3.0 x 1 O'09 M, about 4.0 x IO'09 M, about 4.5 x IO'09 M, or about 5.0 x IO'09 M, or no greater than about 1.0 x IO'09 M, or about 1.2 x IO'09 M, about 1.5 x IO'09 M, about 2.0 x IO'09 M, about 2.25 x IO'09 M, about 2.5 x IO'09 M, about 3.0 x IO'09 M, about 4.0 x IO'09 M, about 4.5 x IO'09 M, or about 5.0 x IO'09 M, as may be determined by biolayer interferometry (e.g., using Octet).
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 Al 9, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10'12 M and about 5.0 x IO'08 M, about 1.5 x 10'12 M and about 5.0 x IO'08 M, about 2.0 x 10'12 M and about 5.0 x IO'08 M, about 2.25 x 10'12 M and about 5.0 x IO'08 M, about 2.5 x 10'12 M and about 5.0 x IO'08 M, about 1.0 x 10'11 M and about 5.0 x IO'08 M, about 1.0 x 10'10 M and about 5.0 x IO'08 M, about 1.0 x IO'09 M and about 5.0 x IO'08 M, about 1.0 x IO'08 M and about 5.0 x IO'08 M, about 1.0 x 10'12 M, or about 1.5 x 10'12 M, about 2.0 x 10'12 M, about 2.25 X 1 O'12 M, about 2.5 X 10'12 M, about 1.0 X 10'11 M, about 1.0 X 1 O'10 M, about 1.0 x IO'09 M, or no greater than about 1.0 x 10'12 M, or about 1.5 x 10'12 M, about 2.0 x 10'12 M, about 2.25 X 1 O'12 M, about 2.5 X 10'12 M, about 1.0 X 10'11 M, about 1.0 X 1 O'10 M, about 1.0 x IO'09 M, as may be determined by biolayer interferometry (e.g., using Octet).
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10'12 M and about 5.0 x IO'08 M.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10'12 M and about 5.0 x IO'08 M.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of binding to a SARS-CoV-2 RBD with a KD in a range between about 1.0 x 10'12 M and about 5.0 x IO'08 M.
In certain examples, binding can be determined by recombinantly expressing a sarbecovirus antigen in a host cell (e.g., by transfection) and immunostaining the (e.g., fixed, or fixed and permeabilized) host cell with antibody and analyzing binding by flow cytometry (e.g., using a ZE5 Cell Analyzer (BioRad®) and FlowJo software (TreeStar). In some embodiments, positive binding can be defined by differential staining by antibody of sarbecovirus-expressing cells versus control (e.g., mock) cells.
In some embodiments, an antibody or antigen-binding fragment of the present disclosure binds to a sarbecovirus spike protein (/.< ., from two or more, three or more, four or more, or five or more sarbecoviruses) expressed on the surface of a host cell (e.g., an Expi-CHO cell), as determined by flow cytometry.
In some embodiments an antibody or antigen-binding fragment of the present disclosure binds to a sarbecovirus S protein, as measured using biolayer interferometry.
In certain embodiments, an antibody of the present disclosure is capable of neutralizing infection by one or more, or by two or more, sarbecoviruses. As used herein, a "neutralizing antibody" is one that can neutralize, z.e., prevent, inhibit, reduce, impede, or interfere with, the ability of a pathogen to initiate and/or perpetuate an infection in a host. The terms "neutralizing antibody" and "an antibody that neutralizes" or "antibodies that neutralize" are used interchangeably herein. In any of the presently disclosed embodiments, the antibody or antigenbinding fragment is capable of preventing and/or neutralizing infection by one or more, or by two or more, sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL, about 1 ng/mL to about 100 ng/mL, about 2.0 ng/mL to about 100 ng/mL, about 2.5 ng/mL to about 100 ng/mL, about 5.0 ng/mL to about 100 ng/mL, about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 1 ng/mL to about 50 ng/mL, about 2.0 ng/mL to about 50 ng/mL, about 2.5 ng/mL to about 50 ng/mL, about 5.0 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 Al 9, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 7.5 ng/mL to about 100 ng/mL, about 8.0 ng/mL to about 100 ng/mL, about 9.0 ng/mL to about 100 ng/mL, about 10.0 ng/mL to about 100 ng/mL, about 12.5 ng/mL to about 100 ng/mL, about 15.0 ng/mL to about 100 ng/mL, about 17.5 ng/mL to about 100 ng/mL, about 20 ng/mL to about 100 ng/mL, about 25.0 ng/mL to about 100 ng/mL, about 27.5 ng/mL to about 100 ng/mL, about 30 ng/mL to about 100 ng/mL, about 0.5 ng/mL to about 50 ng/mL, about 7.5 ng/mL to about 50 ng/mL, about 8.0 ng/mL to about 50 ng/mL, about 9.0 ng/mL to about 50 ng/mL, about 10.0 ng/mL to about 50 ng/mL, about 12.5 ng/mL to about 50 ng/mL, about 15.0 ng/mL to about 50 ng/mL, about 17.5 ng/mL to about 50 ng/mL, about 20 ng/mL to about 50 ng/mL, about 25.0 ng/mL to about 50 ng/mL, about 27.5 ng/mL to 50 ng/mL, or about 30 ng/mL to about 50 ng/mL, about 0.5 ng/mL, about 0.9 ng/mL, about 1.0 ng/mL, about 1.25 ng/mL, about 1.5 ng/mL, about 1.75 ng/mL, about 2.0 ng/mL, about 2.25 ng/mL, about 2.5 ng/mL, about 3.0 ng/mL, about 4.0 ng/mL, about 5.0 ng/mL, about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL, or at least about 7.5 ng/mL, about 8.0 ng/mL, about 9.0 ng/mL, about 10.0 ng/mL, about 12.5 ng/mL, about 15.0 ng/mL, about 17.5 ng/mL, about 20.0 ng/mL, about 22.5 ng/mL, about 25.0 ng/mL, about 27.5 ng/mL, or about 30 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S2V29, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29 or a variant disclosed herein. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29 or a variant disclosed herein to confer similar specific binding, or a fragment thereof, and is capable of neutralizing infection by SARS-CoV-2 in a pseudovirus system (e.g., MLV-pp-based or VSV-pp-based) in a range between about 0.5 ng/mL to about 100 ng/mL.
In certain embodiments, the antibody or antigen-binding fragment (i) recognizes an epitope in the Spike protein of two or more sarbecoviruses; (ii) is capable of blocking an interaction between the Spike protein of one or more sarbecoviruses and a cell surface receptor;
(iii) recognizes an epitope that is conserved in the Spike protein of two or more sarbecoviruses;
(iv) is cross-reactive against two or more sarbecoviruses; or (v) any combination of (i)-(iv).
Terms understood by those in the art of antibody technology are each given the meaning acquired in the art, unless expressly defined differently herein. For example, the term "antibody" refers to an intact antibody comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as any antigen-binding portion or fragment of an intact antibody that has or retains the ability to bind to the antigen target molecule recognized by the intact antibody, such as an scFv, Fab, or Fab'2 fragment. Thus, the term "antibody" herein is used in the broadest sense and includes polyclonal and monoclonal antibodies, including intact antibodies and functional (antigen-binding) antibody fragments thereof, including fragment antigen-binding (Fab) fragments, F(ab')2 fragments, Fab' fragments, Fv fragments, recombinant IgG (rlgG) fragments, single chain antibody fragments, including single chain variable fragments (scFv), and single domain antibodies (e.g., sdAb, sdFv, nanobody) fragments. The term encompasses genetically engineered and/or otherwise modified forms of immunoglobulins, such as intrabodies, peptibodies, chimeric antibodies, fully human antibodies, humanized antibodies, and heteroconjugate antibodies, multispecific, e.g., bispecific antibodies, diabodies, triabodies, tetrabodies, tandem di-scFv, and tandem tri-scFv. Unless otherwise stated, the term "antibody" should be understood to encompass functional antibody fragments thereof. The term also encompasses intact or full-length antibodies, including antibodies of any class or sub-class, including IgG and sub-classes thereof (IgGl, IgG2, IgG3, IgG4), IgM, IgE, IgA, and IgD.
The terms "VL" or "VL" and " VH" or "VH" refer to the variable binding region from an antibody light chain and an antibody heavy chain, respectively. In certain embodiments, a VL is a kappa (K) class (also "VK" herein). In certain embodiments, a VL is a lambda ( ) class. The variable binding regions comprise discrete, well-defined sub-regions known as "complementarity determining regions" (CDRs) and "framework regions" (FRs). The terms "complementarity determining region," and "CDR," are synonymous with "hypervariable region" or "HVR," and refer to sequences of amino acids within antibody variable regions, which, in general, together confer the antigen specificity and/or binding affinity of the antibody, wherein consecutive CDRs (/.< ., CDR1 and CDR2, CDR2 and CDR3) are separated from one another in primary structure by a framework region. There are three CDRs in each variable region (HCDR1, HCDR2, HCDR3; LCDR1, LCDR2, LCDR3; also referred to as CDRHs and CDRLs, respectively). In certain embodiments, an antibody VH comprises four FRs and three CDRs as follows: FR1-HCDR1- FR2-HCDR2-FR3-HCDR3-FR4, and an antibody VL comprises four FRs and three CDRs as follows: FR1-LCDR1-FR2-LCDR2-FR3-LCDR3-FR4. In general, the VH and the VL together form the antigen-binding site through their respective CDRs.
In any of the presently disclosed embodiments, the antibody or antigen-binding fragment is capable of preventing and/or neutralizing infection by one or more, or by two or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
In certain embodiments, the antibody or antigen-binding fragment is provided that comprises a VH and a VL that comprise or consist of the amino acid sequences according to: 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18) SEQ ID NOs: 183 and 193; 18) SEQ ID NOs: 185 and 87; 19) SEQ ID NOs: 185 and 193; 20) SEQ ID NOs: 188 and 87; 21) SEQ ID NOs: 188 and 193; 22) SEQ ID NOs: 190 and 87; 23) SEQ ID NOs: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 204 and 228; 39) SEQ ID NOs: 204 and 231; 40) SEQ ID NOs: 207 and 97; 41) SEQ ID NOs: 207 and 225; 42) SEQ ID NOs: 207 and 228; 43) SEQ ID NOs: 207 and 231; 44) SEQ ID NOs: 210 and 97; 45) SEQ ID NOs: 210 and 225; 46) SEQ ID NOs: 210 and 228; 47) SEQ ID NOs: 210 and 231; 48) SEQ ID NOs: 212 and 97; 49) SEQ ID NOs: 212 and 225; 50) SEQ ID NOs: 212 and 228; 51) SEQ ID NOs: 212 and 231; 52) SEQ ID NOs: 214 and 97; 53) SEQ ID NOs: 214 and 225; 54) SEQ ID NOs: 214 and 228; 55) SEQ ID NOs: 214 and 231; 56) SEQ ID NOs: 216 and 97; 57) SEQ ID NOs: 216 and 225; 58) SEQ ID NOs: 216 and 228; 59) SEQ ID NOs: 216 and 231; 60) SEQ ID NOs: 218 and 97; 61) SEQ ID NOs: 218 and 225; 62) SEQ ID NOs: 218 and 228; 63) SEQ ID NOs: 218 and 231; 64) SEQ ID NOs: 220 and 97; 65) SEQ ID NOs: 220 and 225; 66) SEQ ID NOs: 220 and 228; 67) SEQ ID NOs: 220 and 231; 68) SEQ ID NOs: 222 and 97; 69) SEQ ID NOs: 222 and 225; 70) SEQ ID NOs: 222 and 228; 71) SEQ ID NOs: 222 and 231; 72) SEQ ID NOs: 102 and 105; 73) SEQ ID
NOs: 102 and 254; 74) SEQ ID NOs: 102 and 257; 75) SEQ ID NOs: 102 and 260; 76) SEQ ID
NOs: 235 and 105; 77) SEQ ID NOs: 235 and 254; 78) SEQ ID NOs: 235 and 257; 79) SEQ ID
NOs: 235 and 260; 80) SEQ ID NOs: 238 and 105; 81) SEQ ID NOs: 238 and 254; 82) SEQ ID
NOs: 238 and 257; 83) SEQ ID NOs: 238 and 260; 84) SEQ ID NOs: 241 and 105; 85) SEQ ID
NOs: 241 and 254; 86) SEQ ID NOs: 241 and 257; 87) SEQ ID NOs: 241 and 260; 88) SEQ ID
NOs: 243 and 105; 89) SEQ ID NOs: 243 and 254; 90) SEQ ID NOs: 243 and 257; 91) SEQ ID
NOs: 243 and 260; 92) SEQ ID NOs: 245 and 105; 93) SEQ ID NOs: 245 and 254; 94) SEQ ID
NOs: 245 and 257; 95) SEQ ID NOs: 245 and 260; 96) SEQ ID NOs: 247 and 105; 97) SEQ ID
NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100) SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: l l l and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NOs: 111 and 272; 112) SEQ ID NOs: 111 and 277; 113) SEQ ID NOs: 111 and 279; 114) SEQ ID NOs: 111 and 282; 115) SEQ ID NOs: 111 and 286; 116) SEQ ID NOs: 111 and 290; 117) SEQ ID NOs: 125 and 115; 118) SEQ ID NOs: 125 and 121; 119) SEQ ID NOs: 125 and 157; 120) SEQ ID NOs: 125 and 272; 121) SEQ ID NOs: 125 and 277; 122) SEQ ID NOs: 125 and 279; 123) SEQ ID NOs: 125 and 282; 124) SEQ ID NOs: 125 and 286; 125) SEQ ID NOs: 125 and 290; 126) SEQ ID NOs: 128 and 115; 127) SEQ ID NOs: 128 and 121; 128) SEQ ID NOs: 128 and 157; 129) SEQ ID NOs: 128 and 272; 129) SEQ ID NOs: 128 and 279; 130) SEQ ID NOs: 128 and 282; 131) SEQ ID NOs: 128 and 286; 132) SEQ ID NOs: 128 and 290; 133) SEQ ID NOs: 131 and 115; 134) SEQ ID NOs: 131 and 121; 135) SEQ ID NOs: 131 and 157; 136) SEQ ID NOs: 131 and 272; 137) SEQ ID NOs: 131 and 277; 138) SEQ ID NOs: 131 and 279; 139) SEQ ID NOs: 131 and 282; 140) SEQ ID NOs: 131 and 286; 141) SEQ ID NOs: 131 and 290; 142) SEQ ID NOs: 134 and 115; 143) SEQ ID NOs: 134 and 121; 144) SEQ ID NOs: 134 and 157; 145) SEQ ID NOs: 134 and 272; 146) SEQ ID NOs: 134 and 277; 147) SEQ ID NOs: 134 and 279; 148) SEQ ID NOs: 134 and 282; 149) SEQ ID NOs: 134 and 286; 150) SEQ ID NOs: 134 and 290; 151) SEQ ID NOs: 137 and 115; 152) SEQ ID NOs: 137 and 121; 153) SEQ ID NOs: 137 and 157; 154) SEQ ID NOs: 137 and 272; 155) SEQ ID NOs: 137 and 277; 156) SEQ ID NOs: 137 and 279; 157) SEQ ID NOs: 137 and 282; 158) SEQ ID NOs: 137 and 286; 159) SEQ ID NOs: 137 and 290; 160) SEQ ID NOs: 141 and 115; 161) SEQ ID NOs: 141 and 121; 162) SEQ ID NOs: 141 and 157; 162) SEQ ID NOs: 141 and 272; 162) SEQ ID NOs: 141 and 277; 163) SEQ ID NOs: 141 and 279; 164) SEQ ID NOs: 141 and 282; 165) SEQ ID NOs: 141 and 286; 166) SEQ ID NOs: 141 290; 167) SEQ ID NOs: 145 and 115; 168) SEQ ID NOs: 145 and 121; 169) SEQ ID NOs: 145 and 157; 170) SEQ ID NOs: 145 and 272; 171) SEQ ID NOs: 145 and 277; 172) SEQ ID NOs: 145 and 279; 173) SEQ ID NOs: 145 and 282; 174) SEQ ID NOs: 145 and 282; 175) SEQ ID NOs: 145 and 286; 176) SEQ ID NOs: 145 and 290; 177) SEQ ID NOs: 149 and 115; 178) SEQ ID NOs: 149 and 121; 179) SEQ ID NOs: 149 and 157; 180) SEQ ID NOs: 149 and 272; 181) SEQ ID NOs: 149 and 277; 182) SEQ ID NOs: 149 and 279; and 183) SEQ ID NOs: 149 and 282; 184) SEQ ID NOs: 149 and 286; 185) SEQ ID NOs: 149 and 290; 186) SEQ ID NOs: 153 and 115; 187) SEQ ID NOs: 153 and 121; 188) SEQ ID NOs: 153 and 157; 189) SEQ ID NOs: 153 and 272; 190) SEQ ID NOs: 153 and 277; 191) SEQ ID NOs: 153 and 279; 192) SEQ ID NOs: 153 and 282; 193) SEQ ID NOs: 153 and 286; 194) SEQ ID NOs: 153 and 290; 195) SEQ ID NOs: 264 and 115; 196) SEQ ID NOs: 264 and 121; 197) SEQ ID NOs: 264 and 157; 198) SEQ ID NOs: 264 and 272; 199) SEQ ID NOs: 264 and 277; 200) SEQ ID NOs: 264 and 279; 201) SEQ ID NOs: 264 and 282; 202) SEQ ID NOs: 264 and 286; 203) SEQ ID NOs: 264 and 290; 204) SEQ ID NOs: 266 and 115; 205) SEQ ID NOs: 266 and 121; 206) SEQ ID NOs: 266 and 157; 207) SEQ ID NOs: 266 and 272; 208) SEQ ID NOs: 266 and 277; 209) SEQ ID NOs: 266 and 279; 210) SEQ ID NOs: 266 and 282; 211) SEQ ID NOs: 266 and 286; 212) SEQ ID NOs: 266 and 290; 213) SEQ ID NOs: 269 and 115; 214) SEQ ID NOs: 269 and 121; 215) SEQ ID NOs: 269 and 157; 216) SEQ ID NOs: 269 and 157; 217) SEQ ID NOs: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 A3, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 A3. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 A3 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 23 and 27, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3 Al 9, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3 Al 9. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3 Al 9 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to any one of SEQ ID NOs: 31 and 37, respectively; 35 and 37, respectively; 36 and 37, respectively; and 43 and 37, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3I2, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3I2. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3I2 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 83 and 87, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3O13, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3O13. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3O13 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 93 and 97, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S3L17, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S3L17. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S3L17 to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 102 and 105, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S2V29a, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29a. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29a to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 111 and 115, respectively.
In some embodiments, an antibody is (or an antigen-binding fragment is from) S2V29b, or an antibody or antigen-binding fragment comprises the CDRs and optionally the VH and VL of S2V29b. In some embodiments, an antibody comprises sufficient CDR, VH, and/or VL identity to S2V29b to confer similar specific binding, or a fragment thereof, and the VH and VL comprise or consist of the amino acid sequences according to SEQ ID NOs: 111 and 121, respectively.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) that comprises or consists of the amino acid sequence according to any one of SEQ ID NOs: 23, 31, 35, 36, 43, 83, 93, 102, 111, 125, 128, 131, 137, 141, 145, 149, 453, 179, 181, 183, 185, 188, 190, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, 222, 235, 238, 241, 243, 245, 247, 249, 251, 264, 266, or 269.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a light chain variable domain (VL) that comprises or consists of the amino acid sequence according to any one of SEQ ID NOs: 27, 37, 87, 97, 105, 115, 121, 157, 193, 225, 228, 231, 254, 257, 260, 272, 277, 279, 282, 286, 290.
As used herein, a "variant" of a CDR refers to a functional variant of a CDR sequence having up to 1-3 amino acid substitutions (e.g., conservative or non-conservative substitutions), deletions, or combinations thereof.
Numbering of CDR and framework regions may be according to any known method or scheme, such as the Kabat, Chothia, EU, IMGT, Contact, North, Martin, AbM, and AHo numbering schemes (see, e.g., Kabat et al., "Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, Public Health Service National Institutes of Health, 1991, 5th ed.; Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987)); Lefranc et al., Dev. Comp. Immunol. 27:55, 2003; Honegger and Pluckthun, J. Mol. Bio. 309:657-670 (2001); North et al. J Mol Biol. (2011) 406:228-56; doi: 10.1016/j.jmb.2010.10.030; Abhinandan and Martin, Mol Immunol. (2008) 45:3832-9. 10.1016/j.molimm.2008.05.022). The antibody and CDR numbering systems of these references are incorporated herein by reference. Equivalent residue positions can be annotated and for different molecules to be compared using Antigen receptor Numbering And Receptor Classification (ANARCI) software tool (2016, Bioinformatics 15:298-300). Accordingly, identification of CDRs of an exemplary variable domain (VH or VL) sequence as provided herein according to one numbering scheme is not exclusive of an antibody comprising CDRs of the same variable domain as determined using a different numbering scheme. In certain embodiments, an antibody or antigen-binding fragment is provided that comprises one or more CDRs of a VH sequence according to any one of SEQ ID NOs: 23, 31, 35, 36, 43, 83, 93, 102, 111, 125, 128, 131, 137, 141, 145, 149, 453, 179, 181, 183, 185, 188, 190, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, 222, 235, 238, 241, 243, 245, 247, 249, 251, 264, 266, or 269, and/or of a VL sequence according to any one of SEQ ID NOs: 27, 37, 87, 97, 105, 115, 121, 157, 193, 225, 228, 231, 254, 257, 260, 272, 277, 279, 282, 286, 290, in accordance with any known CDR numbering method, including the Kabat, Chothia, North, EU, IMGT, Martin (Enhanced Chothia), Contact, AbM, and AHo numbering methods, or in accordance with a combination of two or more of these methods (e.g., including those residues falling within a CDR as defined by either or all of the numbering methods). In certain embodiments, CDRs are according to the IMGT numbering method (optionally using junction definitions for CDR3 amino acid sequences). In certain embodiments, CDRs are according to the antibody numbering method developed by the Chemical Computing Group (CCG); e.g., using Molecular Operating Environment (MOE) software (chemcomp.com). In some embodiments, CDRs are in accordance with the IMGT numbering method.
S3A3 Antibodies, Antigen-binding Fragments, and Variants
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises a VH sequence according to SEQ ID NO.: 23 and a VL sequence according to SEQ ID NO.: 27.
In some embodiments, amino acid sequence variation relative to SEQ ID NO.:23 or SEQ ID NO.:27 is limited to variation relative to one or more framework regions (FRs) of SEQ ID NO.:23 or SEQ ID NO.:27, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these). The CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in SEQ ID NO.:23, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in SEQ ID NO.:27. In some embodiments, the FRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO.:27.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in SEQ ID NO.:27.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in SEQ ID NO.:27.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in SEQ ID NO.:23; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in SEQ ID NO.:27.
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises CDRs identified in a VH sequence according to SEQ ID NOs.: 23, and in a VL sequence according to SEQ ID NOs.: 27, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 24 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 25, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID NO.: 26, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 28, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 29, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs.: 30, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 24-26 and 28-30, respectively.
S3 A 19 Antibodies, Antigen-binding Fragments, and Variants
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises a VH sequence according to any one of SEQ ID NOs.: 31, 35, 36, and 43 and a VL sequence according to SEQ ID NO.: 37.
In some embodiments, amino acid sequence variation relative to any one of SEQ ID NOs.: 31, 35, 36, and 43 or SEQ ID NO.:37 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 31, 35, 36, and 43 or SEQ ID NO.:37, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these). The CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43, and a VL comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in SEQ ID NO.:37. In some embodiments, the FRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO.:37.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in SEQ ID NO.:37.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in SEQ ID NO.:37.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, and 43; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in SEQ ID NO.:37.
The S3 Al 9 antibodies may be as described in Table 3.
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs.: 31, 35, 36, and 43 and in a VL sequence according to SEQ ID NO.: 37, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof..
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 32 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 33, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID NO.: 34, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 38, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 39, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs. : 40, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
In any of the presently disclosed embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 32-34 and 38-40, respectively.
83/ 2 Antibodies, Antigen-binding Fragments, and Variants
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises a VH sequence according to any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 and a VL sequence according to any one of SEQ ID NOs.: 87 or 193.
In some embodiments, amino acid sequence variation relative to any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 or any one of SEQ ID NOs.: 87 or 193 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 or any one of SEQ ID NOs.: 87 or 193, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these). The CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190, and a VL comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193. In some embodiments, the FRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 87 or 193.
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises CDRs identified in a VH sequence according to and one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, 190 and in a VL sequence according to and one of SEQ ID NOs.: 87 or 193, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 84 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 86 or 186, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 88 or 194, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 89, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs.: 90, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 84-86 or 84, 85 and 186 and 88-90 or 194, 89, and 90, respectively.
S3O13 Antibodies, Antigen-binding Fragments, and Variants
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises a VH sequence according to any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence according to any one of SEQ ID NOs.: 97, 225, 228, or 231.
In some embodiments, amino acid sequence variation relative to any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 or any one of SEQ ID NOs.: 97, 225, 228, or 231 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 or any one of SEQ ID NOs.: 97, 225, 228, or 231, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these). The CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231. In some embodiments, the FRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs. : 97, 225, 228, or 231.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 97, 225, 228, or 231.
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs .: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and in a VL sequence according to any one of SEQ ID NOs.: 97, 225, 228, or 231, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 94, 198, or 208 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 95, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 96, 199, 202, or 205, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 98, 226, 229, 232, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 39, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs. : 99, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 94-96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232, respectively.
S3L17 Antibodies, Antigen-binding Fragments, and Variants
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260.
In some embodiments, amino acid sequence variation relative to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 or any one of SEQ ID NOs.: 105, 254, 257, or 260 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 or any one of SEQ ID NOs.: 105, 254, 257, or 260, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these). The CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260. In some embodiments, the FRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 105, 254, 257, or 260.
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and in a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 104, 236, or 239, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 106 or 255, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 107, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 108 or 258, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 103, 85, and 104; 103, 85, and 236; or 103, 85, and 239, and 106-108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, respectively.
In some embodiments, an antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences of S3 A3, S3A19 VH. l, S3A19 VH.2, S3A19 VH.3, S3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as set forth in Table 3. In certain embodiments, an antibody or antigen-binding fragment comprises VH and VL amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising the VH and VL amino acid sequences (respectively) of S3 A3, S3A19 VH. l, S3A19 VH.2, S3A19 VH.3, o3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as set forth in Table 3. In certain embodiments, an antibody or antigen-binding fragment comprises the VH and VL amino acid sequences (respectively) of S3 A3, S3A19 VH.l, S3A19 VH.2, S3A19 VH.3, S3A19 VH.1-VH.3 consensus antibody, S3I2, S3O13, or S3L17 as set forth in Table 3. S2V29 Antibodies, Antigen-binding Fragments, and Variants
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
In some embodiments, amino acid sequence variation relative to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 or any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290 is limited to variation relative to one or more framework regions (FRs) of any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 or any one of SEQ ID NOs. : 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively.
Framework regions can be identified according to a numbering scheme (e.g., IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo, or a combination of two or more of these). The CDRs may be identified within a variable domain or within a heavy or light chain according to a numbering scheme or a combination of numbering schemes, and, preferably, the FRs may be identified using the same numbering scheme or combination of numbering schemes.
In certain embodiments, an antibody or antigen-binding fragment comprises a VH comprising a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VH amino acid sequence set forth in any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269, and a VL comprising a a FR1, a FR2, a FR3, and/or a FR4 (or a variant of the FR1, FR2, FR3, and/or FR4 comprising one, two, three, four, or five amino acid substitutions, insertions, and/or deletions) of the VL amino acid sequence set forth in any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290. In some embodiments, the FRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs. : 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) comprising, consisting essentially of, or consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) comprising the amino acid sequence set forth in any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) consisting essentially of the amino acid sequence set forth in any one of SEQ ID NOs. : 115, 121, 157, 272, 277, 279, 282, 286, or 290.
In some embodiments, an antibody or antigen-binding fragment comprises: (i) a heavy chain variable domain (VH) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 1 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269; and (ii) a light chain variable domain (VL) consisting of the amino acid sequence set forth in any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
In certain embodiments, an antibody or antigen-binding fragment is provided that comprises CDRs identified in a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and in a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290, wherein the CDRs are defined in accordance with the IMGT, Kabat, Chothia, North, EU, Martin (Enhanced Chothia), Contact, AbM, CCG, or AHo numbering system, or in accordance with any combination thereof.
In certain embodiments, an antibody or an antigen-binding fragment is provided that comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 112 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 116, 273, or 283, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 117, 274, or 287, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid, wherein the antibody or antigen-binding fragment is capable of binding to a surface glycoprotein of one or more or two or more sarbecoviruses expressed on a cell surface of a host cell.
In certain embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112-114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112,
267, and 114; 112, 270, and 114; 112, 113, and 139; 112, 126, and 139; 112, 129 and 139; 112,
132, and 139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112,
150, and 139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112,
126, and 143; 112, 129 and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129 and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112,
154, and 147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112,
129 and 151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112,
113, and 155; 112, 126, and 155; 112, 129 and 155; 112, 132, and 155; 112, 135, and 155; 112,
138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116-118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116,
287, and 275; 116, 117, and 280; 116, 274, and 280; 116, 287, and 280; 116, 117, and 284; 116,
274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116,
117, and 291; 116, 274, and 291; 116, 287, and 291; 273, 117, and 118; 273, 274, and 118; 273,
287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273,
117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273,
287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 283, 117, 118; 283, 274, and 118; 283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 280; 283, 287, and 280; 283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291, respectively.
In certain embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112-114 and 116-118, respectively (S2V29a), 112-114 and 116, 117, and 122, respectively (S2V29b).
In certain embodiments, the antibody or antigen-binding fragment comprises a VH or VL comprising or consisting of SEQ ID NOs: 111 and 157, respectively, or at having at least 85%, 90%, or 95% identity to these sequences, particularly with framework region mutations as disclosed herein. In still further embodiments, the antibody or antigen-binding fragment comprises CDRS as set forth in the VH and VL of SEQ ID NOs: 111 and 157, according to any numbering scheme as described herein. In some embodiments, the antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112-114 and 116-117, and 158, respectively. Any of these antibodies may include an Fc modification as described herein, or may have an unmodified human IgGl constant region. Specifically, the antibody may have a VH according to SEQ ID NO: 111, a CH according to SEQ ID NOs: 44-80, a VL according to SEQ ID NO: 157 and a CL according to SEQ ID NO: 292.
In a specific embodiment, the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 293 and the light chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 294. In some embodiments, the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence of SEQ ID NO: 293 and the light chain comprises or consists of a sequence of SEQ ID NO: 294.
In a specific embodiment, the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 295 and the light chain comprises or consists of a sequence having at least 85%, 90%, 95%, or 99% identify to SEQ ID NO: 296. In some embodiments, the antibody or antigen-binding fragment heavy chain comprises or consists of a sequence of SEQ ID NO: 295 and the light chain comprises or consists of a sequence of SEQ ID NO: 296.
The term "CL" refers to an "immunoglobulin light chain constant region" or a "light chain constant region," /.< ., a constant region from an antibody light chain. The term "CH" refers to an "immunoglobulin heavy chain constant region" or a "heavy chain constant region," which is further divisible, depending on the antibody isotype, into CHI, CH2, and CH3 (IgA, IgD, IgG), or CHI, CH2, CH3, and CH4 domains (IgE, IgM). The Fc region of an antibody heavy chain is described further herein. In any of the presently disclosed embodiments, an antibody or antigenbinding fragment of the present disclosure comprises any one or more of CL, a CHI, a CH2, and a CH3. In any of the presently disclosed embodiments, an antibody or antigen-binding fragment of the present disclosure may comprise any one or more of CL, a CHI, a CH2, and a CH3. In certain embodiments, a CL comprises an amino acid sequence having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to the amino acid sequence of SEQ ID NO.:292. In certain embodiments, a CL comprises an amino acid sequence having at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity to a human lambda light chain constant domain.
The term "CH" refers to an "immunoglobulin heavy chain constant region" or a "heavy chain constant region," which is further divisible, depending on the antibody isotype into CHI, CH2, and CH3 (IgA, IgD, IgG), or CHI, CH2, CH3, and CH4 domains (IgE, IgM). The Fc region of an antibody heavy chain is described further herein. In any of the presently disclosed embodiments, an antibody or antigen-binding fragment of the present disclosure comprises any one or more of CL, a CHI, a CH2, and a CH3.
In some embodiments, an antibody or antigen-binding fragment comprises an (e.g. human) IgG (e.g., IgGl, IgG2, IgG3, or IgG4), IgA, IgD, IgE, or IgM isotype, or comprises amino acid sequences from two or more of these isotypes. In some embodiments, an antibody or antigen-binding fragment comprises an IgGl isotype; it will be understood that such an antibody or antigen-binding fragment may comprise one or more amino acid substitutions in a heavy chain constant domain and still be considered an “IgGl” isotype. In some embodiments, an IgGl comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in SEQ ID NOs: 44-80.
It will be understood that, for example, production in a mammalian cell line can remove one or more C-terminal lysine of an antibody heavy chain (see, e.g., Liu et al. mAbs 6(5): 1145- 1154 (2014)). Accordingly, an antibody or antigen-binding fragment of the present disclosure can comprise a heavy chain, a CH1-CH3, a CH3, or an Fc polypeptide wherein a C-terminal lysine residue or a C-terminal glycine-lysine is present or is absent; in other words, encompassed are embodiments where the C-terminal residue of a heavy chain, a CH1-CH3, or an Fc polypeptide is not a lysine, and embodiments where a lysine is the C-terminal residue. In certain embodiments, a composition comprises a plurality of an antibody and/or an antigen-binding fragment of the present disclosure, wherein one or more antibody or antigen-binding fragment does not comprise a lysine residue or a C-terminal glycine-lysine at the C-terminal end of the heavy chain, CH1- CH3, or Fc polypeptide, and wherein one or more antibody or antigen-binding fragment comprises a lysine residue at the C-terminal end of the heavy chain, CH1-CH3, or Fc polypeptide.
A "Fab" (fragment antigen-binding) is the part of an antibody that binds to antigens and includes the variable region and CHI of the heavy chain linked to the light chain via an interchain disulfide bond. Each Fab fragment is monovalent with respect to antigen-binding, z.e., it has a single antigen-binding site. Pepsin treatment of an antibody yields a single large F(ab')2 fragment that roughly corresponds to two disulfide linked Fab fragments having divalent antigenbinding activity and is still capable of cross-linking antigen. Both the Fab and F(ab’)2 are examples of "antigen-binding fragments." Fab' fragments differ from Fab fragments by having additional few residues at the carboxy terminus of the CHI domain including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
Fab fragments may be joined, e.g., by a peptide linker, to form a single chain Fab, also referred to herein as "scFab." In these embodiments, an inter-chain disulfide bond that is present in a native Fab may not be present, and the linker serves in full or in part to link or connect the Fab fragments in a single polypeptide chain. A heavy chain-derived Fab fragment (e.g., comprising, consisting of, or consisting essentially of VH + CHI, or "Fd") and a light chain- derived Fab fragment (e.g., comprising, consisting of, or consisting essentially of VL + CL) may be linked in any arrangement to form a scFab. For example, a scFab may be arranged, in N- terminal to C-terminal direction, according to (heavy chain Fab fragment - linker - light chain Fab fragment) or (light chain Fab fragment - linker - heavy chain Fab fragment). Peptide linkers and exemplary linker sequences for use in scFabs are discussed in further detail herein.
"Fv" is a small antibody fragment that contains a complete antigen-recognition and antigen-binding site. This fragment generally consists of a dimer of one heavy- and one lightchain variable region domain in tight, non-covalent association. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although typically at a lower affinity than the entire binding site.
"Single-chain Fv" also abbreviated as "sFv" or "scFv", are antibody fragments that comprise the VH and VL antibody domains connected into a single polypeptide chain. In some embodiments, the scFv polypeptide comprises a polypeptide linker disposed between and linking the VH and VL domains that enables the scFv to retain or form the desired structure for antigenbinding. Such a peptide linker can be incorporated into a fusion polypeptide using standard techniques well known in the art. For a review of scFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994); Borrebaeck 1995, infra. In certain embodiments, the antibody or antigenbinding fragment comprises a scFv comprising a VH domain, a VL domain, and a peptide linker linking the VH domain to the VL domain. In particular embodiments, a scFv comprises a VH domain linked to a VL domain by a peptide linker, which can be in a VH-linker-VL orientation or in a VL-linker-VH orientation. Any scFv of the present disclosure may be engineered so that the C-terminal end of the VL domain is linked by a short peptide sequence to the N-terminal end of the VH domain, or vice versa (i.e., (N)VL(C)-linker-(N)VH(C) or (N)VH(C)-linker- (N)VL(C). Alternatively, in some embodiments, a linker may be linked to an N-terminal portion or end of the VH domain, the VL domain, or both.
Peptide linker sequences may be chosen, for example, based on: (1) their ability to adopt a flexible extended conformation; (2) their inability or lack of ability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides and/or on a target molecule; and/or (3) the lack or relative lack of hydrophobic or charged residues that might react with the polypeptides and/or target molecule. Other considerations regarding linker design (e.g., length) can include the conformation or range of conformations in which the VH and VL can form a functional antigen-binding site. In certain embodiments, peptide linker sequences contain, for example, Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala, may also be included in a linker sequence. Other amino acid sequences which may be usefully employed as linker include those disclosed in Maratea et al., Gene 40:39 46 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258 8262 (1986); U.S. Pat. No. 4,935,233, and U.S. Pat. No. 4,751,180. Other illustrative and non-limiting examples of linkers may include, for example, Glu-Gly-Lys-Ser-Ser-Gly-Ser-Gly-Ser-Glu-Ser-Lys-Val-Asp (SEQ ID NO: 19) (Chaudhary et al., Proc. Natl. Acad. Sci. USA 87: 1066-1070 (1990)) and Lys-Glu-Ser-Gly- Ser-Val-Ser-Ser-Glu-Gln-Leu-Ala-Gln-Phe-Arg-Ser-Leu-Asp (SEQ ID NO: 20) (Bird et al., Science 242:423-426 (1988)) and the pentamer Gly-Gly-Gly-Gly-Ser (SEQ ID NO: 21) when present in a single iteration or repeated 1 to 5 or more times, or more. Any suitable linker may be used, and in general can be about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100 amino acids in length, or less than about 200 amino acids in length, and will preferably comprise a flexible structure (can provide flexibility and room for conformational movement between two regions, domains, motifs, fragments, or modules connected by the linker), and will preferably be biologically inert and/or have a low risk of immunogenicity in a human. Exemplary linkers include those comprising or consisting of the amino acid sequence set forth in any one or more of SEQ ID NOs: 4-13 and Linker SEQs A and B. In certain embodiments, the linker comprises or consists of an amino acid sequence having at least 75% (i.e., at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in any one of SEQ ID NOs: 4-13 and Linker SEQs A and B. scFv can be constructed using any combination of the VH and VL sequences or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein.
In some embodiments, linker sequences are not required; for example, when the first and second polypeptides have non-essential N-terminal (or C-terminal) amino acid regions that can be used to separate the functional domains and prevent steric interference.
During antibody development, DNA in the germline variable (V), joining (J), and diversity (D) gene loci may be rearranged and insertions and/or deletions of nucleotides in the coding sequence may occur. Somatic mutations may be encoded by the resultant sequence, and can be identified by reference to a corresponding known germline sequence. In some contexts, somatic mutations that are not critical to a desired property of the antibody (e.g., binding to a SARS-CoV-2 antigen), or that confer an undesirable property upon the antibody (e.g., an increased risk of immunogenicity in a subject administered the antibody), or both, may be replaced by the corresponding germline-encoded amino acid, or by a different amino acid, so that a desirable property of the antibody is improved or maintained and the undesirable property of the antibody is reduced or abrogated. Thus, in some embodiments, the antibody or antigenbinding fragment of the present disclosure comprises at least one more germline-encoded amino acid in a variable region as compared to a parent antibody or antigen-binding fragment, provided that the parent antibody or antigen-binding fragment comprises one or more somatic mutations. Variable region and CDR amino acid sequences of exemplary anti-sarbecovirus antibodies of the present disclosure are provided in Table 1, and Table 3 herein.
In certain embodiments, an antibody or antigen-binding fragment comprises an amino acid modification (e.g., a substitution mutation) to remove an undesired risk of oxidation, deamination, and/or isomerization. Provided herein are variant antibodies that comprise one or more amino acid alterations in a variable region (e.g., VH, VL, framework or CDR) as compared to the presently disclosed S3 A3, S3A19, S3I2, S3O13, S3L17, or S2V29 ("parent") antibodies, wherein the variant antibody is capable of binding to a SARS-CoV-2 antigen.
In certain embodiments, the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to SEQ ID NO.: 23, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to SEQ ID NO.: 27, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid.
In certain embodiments, the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 31, 35, 36, and 43, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to SEQ ID NO.: 37, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid.
In certain embodiments, the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, and 190, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 87 and 193, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline- encoded amino acid.
In certain embodiments, the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, and 222, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline- encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 97, 225, 228, and 231, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid.
In certain embodiments, the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, and 251, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 105, 254, 257, and 260, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid.
In certain embodiments, the VH comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, and 269, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline- encoded amino acid; and/or (ii) the VL comprises or consists of an amino acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the amino acid sequence according to one or more of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, and 290, wherein the variation is optionally limited to one or more framework regions and/or the variation comprises one or more substitution to a germline-encoded amino acid.
In some embodiments, the antibody or antigen-binding fragment is an IgG (e.g., IgGl, IgG2, IgG3, or IgG4), IgA, IgM, IgE, or IgD isotype, or comprises amino acid sequences from two or more of these. In some embodiments, the antibody or antigen-binding fragment is human, humanized, or chimeric.
An antibody or antigen-binding fragment, may be of any allotype or combination of allotypes. “Allotype” refers to the allelic variation found among the IgG subclasses. For example, an allotype may comprise Glml (or Glm(a)), Glm2 (or Glm(x)), Glm3 (or Glm(f)), Glml7 (or Gm(z))m), Glm27, and/or Glm28 (Glm27 and Glm28 have been described as “alloallotypes”).
The Glm3 and Glml7 allotypes are located at the same position in the CHI domain (position 214 according to EU numbering). Glm3 comprises R214 (EU), while Glml7 comprises K214 (EU). The Glml allotype is located in the CH3 domain (at positions 356 and 358 (EU)) and refers to the replacements E356D and M358L. The Glm2 allotype refers to a replacement of the alanine in position 431 (EU) by a glycine. Glm allotypes, alloallotypes, and features thereof are known in the art and described at, for example, www.imgt.org/IMGTrepertoire/Proteins/allotypes/human/IGH/IGHC/Glm_allotypes.html and Lefranc, M.-P. and Lefranc, G. Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism In: B. Tait, F. Christiansen (Eds.), Immunogenetics, chap. 34, Humana Press, Springer, New York, USA. Methods Mol. Biol. 2012; 882, 635-680. PMID: 22665258, LIGM: 406, the contents and allotypes and allotype information of which are incorporated herein by reference.
The Glml allotype may be combined, for example, with the Glm3, Glm 17, Glm27, Glm2, and/or Glm28 allotype. In some embodiments, an allotype is Glm3 with no Glml (Glm3,-1). In some embodiments, an allotype is Glml7,l allotype. In some embodiments, an allotype is Glm3,l. In some embodiments, an allotype is Glml7 with no Glml (Glml7,-1). Optionally, these allotypes may be combined (or not combined) with the Glm2, Glm27 or Glm28 allotype. For example, an allotype may be Glml7,l,2.
In some embodiments, an antibody or antigen-binding fragment of the present disclosure comprises a Glm3 allotype or a Glm3,l allotype. In some embodiments, an antibody or antigenbinding fragment of the present disclosure comprises a Glm3 allotype and comprises M428L and N434S or M428L and N434A mutations or any other mutation(s) that enhance binding to a human FcRn, such as those described herein. In some embodiments, an antibody or antigenbinding fragment of the present disclosure comprises a Glm3,l allotype and comprises M428L and N434S or M428L and N434A mutations or any other mutation(s) that enhance binding to a human FcRn, such as those described herein. In some embodiments, an antibody or antigenbinding fragment of the present disclosure comprises a Glml7, 1 allotype. In some embodiments, an antibody or antigen-binding fragment of the present disclosure comprises a Glml7, 1 allotype and comprises M428L and N434S or M428L and N434A mutations or any other mutation(s) that enhance binding to a human FcRn, as described further herein.
In some embodiments, the antibody, or the antigen-binding fragment, comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab. In certain embodiments, an antibody or antigen-binding fragment of the present disclosure is monospecific (e.g., binds to a single epitope) or is multispecific (e.g., binds to multiple epitopes and/or target molecules). Antibodies and antigen-binding fragments may be constructed in various formats. Exemplary antibody formats disclosed in Spiess et al., Mol. Immunol. 67(2):95 (2015), and in Brinkmann and Kontermann, mAbs 9(2): 182-212 (2017), which formats and methods of making the same are incorporated herein by reference and include, for example, Bispecific T cell Engagers (BiTEs), DARTs, Knobs-Into-Holes (KIH) assemblies, scFv-CH3-KIH assemblies, KIH Common Light-Chain antibodies, TandAbs, Triple Bodies, TriBi Minibodies, Fab-scFv, scFv-CH-CL-scFv, F(ab')2-scFv2, tetraval ent HCabs, Intrabodies, CrossMabs, Dual Action Fabs (DAFs) (two-in-one or four-in-one), DutaMabs, DT-IgG, Charge Pairs, Fab-arm Exchange, SEEDbodies, Triomabs, LUZ-Y assemblies, Fcabs, Kk-bodies, orthogonal Fabs, DVD-Igs (e.g., US Patent No. 8,258,268, which formats are incorporated herein by reference in their entirety), IgG(H)-scFv, scFv-(H)IgG, IgG(L)-scFv, scFv-(L)IgG, IgG(L,H)- Fv, IgG(H)-V, V(H)-IgG, IgG(L)-V, V(L)-IgG, KIH IgG-scFab, 2scFv-IgG, IgG-2scFv, scFv4- Ig, Zybody, and DVLIgG (four-in-one), as well as so-called FIT-Ig (e.g., PCT Publication No. WO 2015/103072, which formats are incorporated herein by reference in their entirety), so-called WuxiBody formats (e.g., PCT Publication No. WO 2019/057122, which formats are incorporated herein by reference in their entirety), and so-called In-Elbow-Insert Ig formats (lELIg; e.g., PCT Publication Nos. WO 2019/024979 and WO 2019/025391, which formats are incorporated herein by reference in their entirety).
In certain embodiments, the antibody or antigen-binding fragment comprises two or more of VH domains, two or more VL domains, or both (i.e., two or more VH domains and two or more VL domains). In particular embodiments, an antigen-binding fragment comprises the format (N-terminal to C-terminal direction) VH-linker-VL-linker-VH-linker-VL, wherein the two VH sequences can be the same or different and the two VL sequences can be the same or different. Such linked scFvs can include any combination of VH and VL domains arranged to bind to a given target, and in formats comprising two or more VH and/or two or more VL, one, two, or more different epitopes or antigens may be bound. It will be appreciated that formats incorporating multiple antigen-binding domains may include VH and/or VL sequences in any combination or orientation. For example, the antigen-binding fragment can comprise the format VL-linker-VH-linker-VL-linker-VH, VH-linker-VL-linker-VL-linker-VH, or VL-linker-VH- linker-VH-linker-VL.
Monospecific or multispecific antibodies or antigen-binding fragments of the present disclosure constructed comprise any combination of the VH and VL sequences and/or any combination of the CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 sequences disclosed herein. A bispecific or multispecific antibody or antigen-binding fragment may, in some embodiments, comprise one, two, or more antigen-binding domains (e.g., a VH and a VL) of the instant disclosure. Two or more binding domains may be present that bind to the same or a different SARS-CoV-2 epitope, and a bispecific or multispecific antibody or antigen-binding fragment as provided herein can, in some embodiments, comprise a further SARS-CoV-2 binding domain, and/or can comprise a binding domain that binds to a different antigen or pathogen altogether.
In any of the presently disclosed embodiments, the antibody or antigen-binding fragment can be multispecific; e.g., bispecific, trispecific, or the like.
In certain embodiments, the antibody or antigen-binding fragment comprises: (i) a first VH and a first VL; and (ii) a second VH and a second VL, wherein the first VH and the second VH are different.
In some embodiments, the first VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and 87 or 193, respectively; iv) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and 97, 225, 228, or 231, respectively; v) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and 105, 254, 257, or 260, respectively; or vi) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NO.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; and wherein the second VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and 87 or 193, respectively; iv) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and 97, 225, 228, or 231, respectively; v) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and 105, 254, 257, or 260, respectively; or vi) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NO.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; wherein the first VH and the second VL are different from the second VH and VL, and wherein the first VH and the first VL together form a first antigen-binding site, and wherein the second VH and the second VL together form a second antigen-binding site. In some embodiments, the antibody or antigen-binding fragment may further comprise a Fc polypeptide or fragment thereof that comprises or consists of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprises or consists of, the amino acid sequences set forth in SEQ ID NOs: 44-80.
In certain embodiments, the antibody or antigen-binding fragment comprises a Fc polypeptide, or a fragment thereof. The "Fc" fragment or Fc polypeptide comprises the carboxyterminal portions (i.e., the CH2 and CH3 domains of IgG) of both antibody H chains held together by disulfides. An Fc may comprise a dimer comprised of two Fc polypeptides (i.e., two CH2-CH3 polypeptides). Antibody "effector functions" refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: Clq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation. As discussed herein, modifications (e.g., amino acid substitutions) may be made to an Fc domain in order to modify (e.g., improve, reduce, or ablate) one or more functionality of an Fc-containing polypeptide (e.g., an antibody of the present disclosure). Such functions include, for example, Fc receptor (FcR) binding, antibody half-life modulation (e.g., by binding to FcRn), ADCC function, protein A binding, protein G binding, and complement binding. Amino acid modifications that modify (e.g., improve, reduce, or ablate) Fc functionalities include, for example, the T250Q/M428L, M252Y/S254T/T256E, H433K/N434F, M428L/N434S, M428L/N434A, E233P/L234V/L235A/G236 + A327G/A330S/P331S, E333A, S239D/A330L/I332E, P257VQ311, K326W/E333S, S239D/I332E/G236A, N297Q, K322A, S228P, L235E + E318A/K320A/K322A, L234A/L235A (also referred to herein as "LALA"), and L234A/L235A/P329G mutations, which mutations are summarized and annotated in "Engineered Fc Regions", published by InvivoGen (2011) and available online at invivogen.com/PDF/review/review-Engineered-Fc-Regions- invivogen.pdf?utm_source=review&utm_medium=pdf&utm_ campaign=review&utm_content=Engineered-Fc-Regions, and are incorporated herein by reference.
For example, to activate the complement cascade, the Clq protein complex can bind to at least two molecules of IgGl or one molecule of IgM when the immunoglobulin molecule(s) is attached to the antigenic target (Ward, E. S., and Ghetie, V., Ther. Immunol. 2 (1995) 77-94). Burton, D. R., described (Mol. Immunol. 22 (1985) 161-206) that the heavy chain region comprising amino acid residues 318 to 337 is involved in complement fixation. Duncan, A. R., and Winter, G. (Nature 332 (1988) 738-740), using site directed mutagenesis, reported that Glu318, Lys320 and Lys322 form the binding site to Clq. The role of Glu318, Lys320 and Lys 322 residues in the binding of Clq was confirmed by the ability of a short synthetic peptide containing these residues to inhibit complement mediated lysis.
For example, FcR binding can be mediated by the interaction of the Fc moiety (of an antibody) with Fc receptors (FcRs), which are specialized cell surface receptors on cells including hematopoietic cells. Fc receptors belong to the immunoglobulin superfamily, and shown to mediate both the removal of antibody-coated pathogens by phagocytosis of immune complexes, and the lysis of erythrocytes and various other cellular targets (e.g. tumor cells) coated with the corresponding antibody, via antibody dependent cell mediated cytotoxicity (ADCC; Van de Winkel, J. G., and Anderson, C. L., J. Leukoc. Biol. 49 (1991) 511-524). FcRs are defined by their specificity for immunoglobulin classes; Fc receptors for IgG antibodies are referred to as FcyR, for IgE as FcsR, for IgA as FcaR and so on and neonatal Fc receptors are referred to as FcRn. Fc receptor binding is described for example in Ravetch, J. V., and Kinet, J. P., Annu. Rev. Immunol. 9 (1991) 457-492; Capel, P. J., et al., Immunomethods 4 (1994) 25-34; de Haas, M., et al., J Lab. Clin. Med. 126 (1995) 330-341; and Gessner, J. E., et al., Ann. Hematol. 76 (1998) 231-248.
Cross-linking of receptors by the Fc domain of native IgG antibodies (FcyR) triggers a wide variety of effector functions including phagocytosis, antibody-dependent cellular cytotoxicity, and release of inflammatory mediators, as well as immune complex clearance and regulation of antibody production. Fc moieties providing cross-linking of receptors (e.g., FcyR) are contemplated herein. In humans, three classes of FcyR have been characterized to-date, which are: (i) FcyRI (CD64), which binds monomeric IgG with high affinity and is expressed on macrophages, monocytes, neutrophils and eosinophils; (ii) FcyRII (CD32), which binds complexed IgG with medium to low affinity, is widely expressed, in particular on leukocytes, is believed to be a central player in antibody-mediated immunity, and which can be divided into FcyRIIA, FcyRIIB and FcyRIIC, which perform different functions in the immune system, but bind with similar low affinity to the IgG-Fc, and the ectodomains of these receptors are highly homologous; and (iii) FcyRIII (CD 16), which binds IgG with medium to low affinity and has been found in two forms: FcyRIIIA, which has been found on NK cells, macrophages, eosinophils, and some monocytes and T cells, and is believed to mediate ADCC; and FcyRIIIB, which is highly expressed on neutrophils.
FcyRIIA is found on many cells involved in killing (e.g. macrophages, monocytes, neutrophils) and seems able to activate the killing process. FcyRIIB seems to play a role in inhibitory processes and is found on B-cells, macrophages and on mast cells and eosinophils. Importantly, it has been shown that 75% of all FcyRIIB is found in the liver (Ganesan, L. P. et al., 2012: "FcyRIIb on liver sinusoidal endothelium clears small immune complexes," Journal of Immunology 189: 4981-4988). FcyRIIB is abundantly expressed on Liver Sinusoidal Endothelium, called LSEC, and in Kupffer cells in the liver and LSEC are the major site of small immune complexes clearance (Ganesan, L. P. et al., 2012: FcyRIIb on liver sinusoidal endothelium clears small immune complexes. Journal of Immunology 189: 4981-4988).
In some embodiments, the antibodies disclosed herein and the antigen-binding fragments thereof comprise an Fc polypeptide or fragment thereof for binding to FcyRIIb, in particular an Fc region, such as, for example IgG-type antibodies. Moreover, it is possible to engineer the Fc moiety to enhance FcyRIIB binding by introducing the mutations S267E and L328F as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926-3933. Thereby, the clearance of immune complexes can be enhanced (Chu, S., et al., 2014: Accelerated Clearance of IgE In Chimpanzees Is Mediated By Xmab7195, An Fc-Engineered Antibody With Enhanced Affinity For Inhibitory Receptor FcyRIIb. Am J Respir Crit, American Thoracic Society International Conference Abstracts). In some embodiments, the antibodies of the present disclosure, or the antigen-binding fragments thereof, comprise an engineered Fc moiety with the mutations S267E and L328F, in particular as described by Chu, S. Y. et al., 2008: Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies. Molecular Immunology 45, 3926-3933.
On B cells, FcyRIIB may function to suppress further immunoglobulin production and isotype switching to, for example, the IgE class. On macrophages, FcyRIIB is thought to inhibit phagocytosis as mediated through FcyRIIA. On eosinophils and mast cells, the B form may help to suppress activation of these cells through IgE binding to its separate receptor.
Regarding FcyRI binding, modification in native IgG of at least one of E233-G236, P238, D265, N297, A327 and P329 reduces binding to FcyRI. IgG2 residues at positions 233-236, substituted into corresponding positions IgGl and IgG4, reduces binding of IgGl and IgG4 to FcyRI by 103-fold and eliminated the human monocyte response to antibody-sensitized red blood cells (Armour, K. L., et al. Eur. J. Immunol. 29 (1999) 2613-2624).
Regarding FcyRII binding, reduced binding for FcyRIIA is found, e.g., for IgG mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, R292 and K414.
Two allelic forms of human FcyRIIA are the "H131" variant, which binds to IgGl Fc with higher affinity, and the "R131 " variant, which binds to IgGl Fc with low affinity er. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009).
Regarding FcyRIII binding, reduced binding to FcyRIIIA is found, e.g., for mutation of at least one of E233-G236, P238, D265, N297, A327, P329, D270, Q295, A327, S239, E269, E293, Y296, V303, A327, K338 and D376. Mapping of the binding sites on human IgGl for Fc receptors, the above-mentioned mutation sites, and methods for measuring binding to FcyRI and FcyRIIA, are described in Shields, R. L., et al., J. Biol. Chem. 276 (2001) 6591-6604.
Two allelic forms of human FcyRIIIA are the "Fl 58" variant, which binds to IgGl Fc with lower affinity, and the "VI 58" variant, which binds to IgGl Fc with higher affinity. See, e.g., Bruhns et al., Blood 113:3716-3725 (2009).
Regarding binding to FcyRII, two regions of native IgG Fc appear to be involved in interactions between FcyRIIs and IgGs, namely (i) the lower hinge site of IgG Fc, in particular amino acid residues L, L, G, G (234 - 237, EU numbering), and (ii) the adjacent region of the CH2 domain of IgG Fc, in particular a loop and strands in the upper CH2 domain adjacent to the lower hinge region, e.g. in a region of P331 (Wines, B.D., et al., J. Immunol. 2000; 164: 5313 - 5318). Moreover, FcyRI appears to bind to the same site on IgG Fc, whereas FcRn and Protein A bind to a different site on IgG Fc, which appears to be at the CH2-CH3 interface (Wines, B.D., et al., J. Immunol. 2000; 164: 5313 - 5318).
Also contemplated are mutations that increase binding affinity of an Fc polypeptide or fragment thereof of the present disclosure to a (i.e., one or more) Fey receptor (e.g., as compared to a reference Fc polypeptide or fragment thereof or containing the same that does not comprise the mutation(s)). See, e.g., Delillo and Ravetch, Cell 161(5): 1035-1045 (2015) and Ahmed et al., J. Struc. Biol. 194(1):78 (2016), the Fc mutations and techniques of which are incorporated herein by reference.
In any of the herein disclosed embodiments, an antibody or antigen-binding fragment can comprise a Fc polypeptide or fragment thereof comprising a mutation selected from G236A; S239D; A330L; and I332E; or a combination comprising any two or more of the same; e.g., S239D/I332E; S239D/A330L/I332E; G236A/S239D/I332E; G236A/A330L/I332E (also referred to herein as "GAALIE"); or G236A/S239D/A330L/I332E. In some embodiments, the Fc polypeptide or fragment thereof does not comprise S239D. In some embodiments, the Fc polypeptide or fragment thereof comprises S at position 239 (EU numbering). In some embodiments, the Fc polypeptide or fragment thereof comprises the amino acid sequences set forth in SEQ ID NOs: 52-58.
In certain embodiments, the Fc polypeptide or fragment thereof may comprise or consist of at least a portion of an Fc polypeptide or fragment thereof that is involved in FcRn binding. In certain embodiments, the Fc polypeptide or fragment thereof comprises one or more amino acid modifications that improve binding affinity for (e.g., enhance binding to) FcRn (e.g., at a pH of about 6.0) and, in some embodiments, thereby extend in vivo half-life of a molecule comprising the Fc polypeptide or fragment thereof (e.g., as compared to a reference Fc polypeptide or fragment thereof or antibody that is otherwise the same but does not comprise the modification(s)). In certain embodiments, the Fc polypeptide or fragment thereof comprises or is derived from a IgG Fc and a half-life-extending mutation comprises any one or more of: M428L; N434S; N434H; N434A; N434S; M252Y; S254T; T256E; T250Q; P257I Q311I; D376V; T307A; E380A (EU numbering). In certain embodiments, a half-life-extending mutation comprises M428L/N434S (also referred to herein as "MLNS", "LS", "_LS", and "-LS"). In certain embodiments, the half-life extending mutation is in a Fc polypeptide or fragment thereof comprising or consisting of the amino acid sequences set forth in SEQ ID NOs: 59-64. In certain embodiments, a half-life-extending mutation comprises M252Y/S254T/T256E. In certain embodiments, a half-life-extending mutation comprises T250Q/M428L. In certain embodiments, a half-life-extending mutation comprises P257I/Q31 II. In certain embodiments, a half-life- extending mutation comprises P257I/N434H. In certain embodiments, a half-life-extending mutation comprises D376V/N434H. In certain embodiments, a half-life-extending mutation comprises T307A/E380A/N434A. In certain embodiments, a half-life-extending mutation comprises M428L/N434A (also referred to herein as “MLNA”, “LA”, _LA”, and “-LA”). In certain embodiments, the half-life extending mutation is in a Fc polypeptide or fragment thereof comprising or consisting of the amino acid sequences set forth in SEQ ID NOs: 65-70.
In some embodiments, an antibody or antigen-binding fragment includes a Fc moiety that comprises the substitution mutations M428L/N434S or M428L/N434A. In some embodiments, an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mutations G236A/A330L/I332E. In certain embodiments, an antibody or antigen-binding fragment includes a (e.g., IgG) Fc moiety that comprises a G236A mutation, an A330L mutation, and a I332E mutation (GAALIE), and does not comprise a S239D mutation (e.g., comprises a native S at position 239). In particular embodiments, an antibody or antigenbinding fragment includes an Fc polypeptide or fragment thereof that comprises the substitution mutation: M428L/N434S and G236A/A330L/I332E, (and may comprises or consist of the amino acid sequences set forth in SEQ ID NOs: 71-75) and, optionally does not comprise S239D (e.g., comprises S at 239). In particular embodiments, an antibody or antigen-binding fragment includes an Fc polypeptide or fragment thereof that comprises the substitution mutation: M428L/N434A and G236A/A330L/I332E, (and may comprises or consist of the amino acid sequences set forth in SEQ ID NOs: 76-80) and, optionally does not comprise S239D (e.g., comprises S at 239). In certain embodiments, an antibody or antigen-binding fragment includes a Fc polypeptide or fragment thereof that comprises the substitution mutations: M428L/N434S (or M428L/N434A) and G236A/S239D/A330L/I332E.
In some embodiments, an antibody or antigen-binding fragment (described further herein) is provided that comprises, in a(n e.g. human) IgGl heavy chain, the amino acid mutation(s) set forth in any one of (i)-(xviii): (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A and R292P; (xii) Y300L; (xiii) E345K, G236S, L235Y, and S267E; (xiv) E272R, L309T, S219Y, and S267E; (xv) G236Y; (xvi) G236W; (xvii) F243L, G446E, P396L, and S267E; (xviii) G236A, S239D, and H268E, wherein the numbering of amino acid residues is according to the EU index as set forth in Kabat. In certain embodiments, the antibody or antigen-binding fragment is afucosylated. In some embodiments, the antibody or antigen-binding fragment further comprises one or more mutation that enhances binding to a human FcRn, such as M428L and N434S mutations or M428L and N434A mutations (EU numbering) or any other mutation(s) that enhance binding to a human FcRn, such as those described herein. In certain embodiments, the antibody or antigenbinding fragment is afucosylated.
In specific embodiments, the antibody or antigen-binding fragment comprises I) a VH and a VL having the amino acid sequences set forth in any one of SEQ ID NOs: 23 and 27, respectively; 31 and 37, respectively; 35 and 37, respectively; and 36 and 37, respectively; II) a CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 as set forth in a VH and a VL having the amino acid sequences set forth in any one of 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18) SEQ ID NOs: 183 and 193; 18) SEQ ID NOs: 185 and 87; 19) SEQ ID NOs: 185 and 193; 20) SEQ ID NOs: 188 and 87; 21) SEQ ID NOs: 188 and 193; 22) SEQ ID NOs: 190 and 87; 23) SEQ ID NOs: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 204 and 228; 39) SEQ ID NOs: 204 and 231; 40) SEQ ID NOs: 207 and 97; 41) SEQ ID NOs: 207 and 225; 42) SEQ ID NOs: 207 and 228; 43) SEQ ID NOs: 207 and 231; 44) SEQ ID NOs: 210 and 97; 45) SEQ ID NOs: 210 and 225; 46) SEQ ID NOs: 210 and 228; 47) SEQ ID NOs: 210 and 231; 48) SEQ ID NOs: 212 and 97; 49) SEQ ID NOs: 212 and 225; 50) SEQ ID NOs: 212 and 228; 51) SEQ ID NOs: 212 and 231; 52) SEQ ID NOs: 214 and 97; 53) SEQ ID NOs: 214 and 225; 54) SEQ ID NOs: 214 and 228; 55) SEQ ID NOs: 214 and 231; 56) SEQ ID NOs: 216 and 97; 57) SEQ ID NOs: 216 and 225; 58) SEQ ID NOs: 216 and 228; 59) SEQ ID NOs: 216 and 231; 60) SEQ ID NOs: 218 and 97; 61) SEQ ID NOs: 218 and 225; 62) SEQ ID NOs: 218 and 228; 63) SEQ ID NOs: 218 and 231; 64) SEQ ID NOs: 220 and 97; 65) SEQ ID NOs: 220 and 225; 66) SEQ ID NOs: 220 and 228; 67) SEQ ID NOs: 220 and 231; 68) SEQ ID NOs: 222 and 97; 69) SEQ ID NOs: 222 and 225; 70) SEQ ID NOs: 222 and 228; 71) SEQ ID NOs: 222 and 231; 72)
SEQ ID NOs: 102 and 105; 73) SEQ ID NOs: 102 and 254; 74) SEQ ID NOs: 102 and 257; 75)
SEQ ID NOs: 102 and 260; 76) SEQ ID NOs: 235 and 105; 77) SEQ ID NOs: 235 and 254; 78)
SEQ ID NOs: 235 and 257; 79) SEQ ID NOs: 235 and 260; 80) SEQ ID NOs: 238 and 105; 81) SEQ ID NOs: 238 and 254; 82) SEQ ID NOs: 238 and 257; 83) SEQ ID NOs: 238 and 260; 84) SEQ ID NOs: 241 and 105; 85) SEQ ID NOs: 241 and 254; 86) SEQ ID NOs: 241 and 257; 87) SEQ ID NOs: 241 and 260; 88) SEQ ID NOs: 243 and 105; 89) SEQ ID NOs: 243 and 254; 90) SEQ ID NOs: 243 and 257; 91) SEQ ID NOs: 243 and 260; 92) SEQ ID NOs: 245 and 105; 93) SEQ ID NOs: 245 and 254; 94) SEQ ID NOs: 245 and 257; 95) SEQ ID NOs: 245 and 260; 96) SEQ ID NOs: 247 and 105; 97) SEQ ID NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100) SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: l l l and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NOs: 111 and 272; 112) SEQ ID NOs: 111 and 277; 113) SEQ ID NOs: 111 and 279; 114) SEQ ID NOs: 111 and 282; 115) SEQ ID NOs: 111 and 286; 116) SEQ ID NOs: 111 and 290; 117) SEQ ID NOs: 125 and 115; 118) SEQ ID NOs: 125 and 121; 119) SEQ ID NOs: 125 and 157; 120) SEQ ID NOs: 125 and 272; 121) SEQ ID NOs: 125 and 277; 122) SEQ ID NOs: 125 and 279; 123) SEQ ID NOs: 125 and 282; 124) SEQ ID NOs: 125 and 286; 125) SEQ ID NOs: 125 and 290; 126) SEQ ID NOs: 128 and 115; 127) SEQ ID NOs: 128 and 121; 128) SEQ ID NOs: 128 and 157; 129) SEQ ID NOs: 128 and 272; 129) SEQ ID NOs: 128 and 279; 130) SEQ ID NOs: 128 and 282; 131) SEQ ID NOs: 128 and 286; 132) SEQ ID NOs: 128 and 290; 133) SEQ ID NOs: 131 and 115; 134) SEQ ID NOs: 131 and 121; 135) SEQ ID NOs: 131 and 157; 136) SEQ ID NOs: 131 and 272; 137) SEQ ID NOs: 131 and 277; 138) SEQ ID NOs: 131 and 279; 139) SEQ ID NOs: 131 and 282; 140) SEQ ID NOs: 131 and 286; 141) SEQ ID NOs: 131 and 290; 142) SEQ ID NOs: 134 and 115; 143) SEQ ID NOs: 134 and 121; 144) SEQ ID NOs: 134 and 157; 145) SEQ ID NOs: 134 and 272; 146) SEQ ID NOs: 134 and 277; 147) SEQ ID NOs: 134 and 279; 148) SEQ ID NOs: 134 and 282; 149) SEQ ID NOs: 134 and 286; 150) SEQ ID NOs: 134 and 290; 151) SEQ ID NOs: 137 and 115; 152) SEQ ID NOs: 137 and 121; 153) SEQ ID NOs: 137 and 157; 154) SEQ ID NOs: 137 and 272; 155) SEQ ID NOs: 137 and 277; 156) SEQ ID NOs: 137 and 279; 157) SEQ ID NOs: 137 and 282; 158) SEQ ID NOs: 137 and 286; 159) SEQ ID NOs: 137 and 290; 160) SEQ ID NOs: 141 and 115; 161) SEQ ID NOs: 141 and 121; 162) SEQ ID NOs: 141 and 157; 162) SEQ ID NOs: 141 and 272; 162) SEQ ID NOs: 141 and 277; 163) SEQ ID NOs: 141 and 279; 164) SEQ ID NOs: 141 and 282; 165) SEQ ID NOs: 141 and 286; 166) SEQ ID NOs: 141 290; 167) SEQ ID NOs: 145 and 115; 168) SEQ ID NOs: 145 and 121; 169) SEQ ID NOs: 145 and 157; 170) SEQ ID NOs: 145 and 272; 171) SEQ ID NOs: 145 and 277; 172) SEQ ID NOs: 145 and 279; 173) SEQ ID NOs: 145 and 282; 174) SEQ ID NOs: 145 and 282; 175) SEQ ID NOs: 145 and 286; 176) SEQ ID NOs: 145 and 290; 177) SEQ ID NOs: 149 and 115; 178) SEQ ID NOs: 149 and 121; 179) SEQ ID NOs: 149 and 157; 180) SEQ ID NOs: 149 and 272; 181) SEQ ID NOs: 149 and 277; 182) SEQ ID NOs: 149 and 279; and 183) SEQ ID NOs: 149 and 282; 184) SEQ ID NOs: 149 and 286; 185) SEQ ID NOs: 149 and 290; 186) SEQ ID NOs: 153 and 115; 187) SEQ ID NOs: 153 and 121; 188) SEQ ID NOs: 153 and 157; 189) SEQ ID NOs: 153 and 272; 190) SEQ ID NOs: 153 and 277; 191) SEQ ID NOs: 153 and 279; 192) SEQ ID NOs: 153 and 282; 193) SEQ ID NOs: 153 and 286; 194) SEQ ID NOs: 153 and 290; 195) SEQ ID NOs: 264 and 115; 196) SEQ ID NOs: 264 and 121; 197) SEQ ID NOs: 264 and 157; 198) SEQ ID NOs: 264 and 272; 199) SEQ ID NOs: 264 and 277; 200) SEQ ID NOs: 264 and 279; 201) SEQ ID NOs: 264 and 282; 202) SEQ ID NOs: 264 and 286; 203) SEQ ID NOs: 264 and 290; 204) SEQ ID NOs: 266 and 115; 205) SEQ ID NOs: 266 and 121; 206) SEQ ID NOs: 266 and 157; 207) SEQ ID NOs: 266 and 272; 208) SEQ ID NOs: 266 and 277; 209) SEQ ID NOs: 266 and 279; 210) SEQ ID NOs: 266 and 282; 211) SEQ ID NOs: 266 and 286; 212) SEQ ID NOs: 266 and 290; 213) SEQ ID NOs: 269 and 115; 214) SEQ ID NOs: 269 and 121; 215) SEQ ID NOs: 269 and 157; 216) SEQ ID NOs: 269 and 157; 217) SEQ ID NOs: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290, respectively, as determined by any CDL determination scheme disclosed herein; or (III) a CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 having the amino acid sequences according to wherein (i) SEQ ID NOs.: 24-26 or 32-34 and 28- 30 or 38-40, respectively; (ii) SEQ ID NOs.: 32-34 and 38-40, respectively; (iii) SEQ ID NOs.: 84-86 or 84, 85 and 186 and 88-90 or 194, 89, and 90, respectively; (iv) SEQ ID NOs.: 94-96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232, respectively; (v) *SEQ ID NOs.: 112-114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and 114; 112, 270, and 114; 112, 113, and 139; 112, 126, and 139; 112, 129 and 139; 112, 132, and 139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and 139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 126, and 143; 112, 129 and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129 and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and 147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and 151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and 155; 112, 126, and 155; 112, 129 and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116-118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275; 116, 117, and 280; 116, 274, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and 291; 116, 274, and 291; 116, 287, and 291; 273, 117, and 118; 273, 274, and 118; 273, 287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 283, 117, 118; 283, 274, and 118; 283, 287, and
118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283, 274, and
275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 280; 283, 287, and 280; 283, 117, and
284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and
288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291, respectively; and (A) a Fc moiety that comprises the substitution mutations: (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A and R292P; (xii) Y300L; (xiii) E345K, G236S, L235Y, and S267E; (xiv) E272R, L309T, S219Y, and S267E; (xv) G236Y; (xvi) G236W; (xvii) F243L, G446E, P396L, and S267E; (xviii) G236A, S239D, and H268E; (xix) M428L/N434S; (xx) M428L/N434A; (xxi) G236A/A330L/I332E/M428L/N434S; (xxii) G236A/A330L/I332E/M428L/N434A; or (xxiii) any two or more of (i)-(xxii); or (B) an Fc moiety that comprises or consists of a Fc polypeptide or fragment thereof that comprises or consists of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NOs: 44-80, optionally other than naturally occurring variants thereof, or that comprises or consists of, the amino acid sequences set forth in SEQ ID NOs: 52-80.
In certain embodiments, the antibody or antigen-binding fragment comprises a mutation that alters glycosylation, wherein the mutation that alters glycosylation comprises N297A, N297Q, or N297G, and/or the antibody or antigen-binding fragment is partially or fully aglycosylated and/or is partially or fully afucosylated. Host cell lines and methods of making partially or fully aglycosylated or partially or fully afucosylated antibodies and antigen-binding fragments are known (see, e.g., PCT Publication No. WO 2016/181357; Suzuki et al. Clin. Cancer Res. 13(6): 1875-82 (2007); Huang et al. MAbs 6: 1-12 (2018)).
An antibody or antigen-binding fragment of the present disclosure can be fucosylated (e.g., comprising one or more fucosyl moiety, and typically comprising a native (wild-type) fucosylation pattern or a fucosylation pattern that includes one or more additional, or fewer, fucosyl moieties as compared to native), or can be afucosylated. In particular, native IgGl antibodies carry a glycan site at N297, and this is typically the only site where a core fucose moiety may be found in the antibody, though some glycan sites may arise through mutation (e.g. in the variable domains) during antibody development. Fucosylation of an Fc polypeptide or fragment thereof, or of an antibody, can be effected by introducing amino acid mutations to introduce or disrupt a fucosylation site (e.g. a mutation at N297, such as N297Q or N297A, to disrupt formation of a glycan that can include a core fucose moiety), though typically it is preferred to maintain N297 and the glycan thereof, such as by expressing the polypeptide in a host cell which has been genetically engineered to lack the ability (or have an inhibited or compromised ability) to fucosylate the polypeptide; by expressing the polypeptide under conditions in which a host cell is impaired in its ability to fucosylate the polypeptide (e.g., in the presence of 2-fluoro-L-fucose (2FF)), or the like. An afucosylated polypeptide can comprise no fucose moieties, or substantially no fucose moieties, and/or can be expressed by a host cell that is genetically engineered to lack the ability (or have an inhibited or compromised ability) to fucosylate the polypeptide and/or can be expressed under conditions in which a host cell is impaired in its ability to fucosylate the polypeptide (e.g., in the presence of 2-fluoro-L-fucose (2FF)). In some embodiments, a polypeptide does not comprise a core fucose moiety at Asn297. In some embodiments, afucosylated polypeptides have increased binding to FcyRIIIA. In some contexts, addition of 2FF to a culture media comprising host cells expressing an antibody results in about 85% or more of the antibodies not carrying a fucose moiety. Accordingly, a plurality of antibodies may be described as “afucosylated” when the plurality was produced in the presence of 2FF or like reagent. In some contexts, a plurality of polypeptides or antibodies may be described as, for example, afucosylated, meaning that about 85% or more of the single polypeptide or antibody molecules of the plurality do not comprise a fucose moiety. In certain preferred embodiments, an afucosylated antibody or polypeptide or a population or a plurality thereof comprises an asparagine (N) at EU position 297. Fucosylation or lack thereof can be assessed using, for example, mass spectrometry (e.g. Electrospray mass spectrometry (ESLMS)). In some embodiments, compositions are provided that comprise a plurality of any one or more of the presently disclosed polypeptides, wherein the composition comprises afucosylated polypeptides.
In certain embodiments, the antibody or antigen-binding fragment is capable of eliciting continued protection in vivo in a subject even once no detectable levels of the antibody or antigen-binding fragment can be found in the subject (i.e., when the antibody or antigen-binding fragment has been cleared from the subject following administration). Such protection is referred to herein as a vaccinal effect. Without wishing to be bound by theory, it is believed that dendritic cells can internalize complexes of antibody and antigen and thereafter induce or contribute to an endogenous immune response against antigen. In certain embodiments, an antibody or antigenbinding fragment comprises one or more modifications, such as, for example, mutations in the Fc comprising G236A, A330L, and I332E, that are capable of activating dendritic cells that may induce, e.g., T cell immunity to the antigen. In certain embodiments, an antibody or antigen-binding fragment fo the present disclosure comprises an Fc variant selected from the Fc variants summarized in Table 1 (see also PCT Publication No. WO 2022/251119). In certain embodiments, the Fc variant, or the antibody or antigen-binding fragment, is fucosylated. In other embodiments, the Fc variant, or the antibody or antigen-binding fragment, is afucosylated. Table 1. Fc Variants (fucosylated unless otherwise indicated) and Properties Thereof
Figure imgf000076_0001
Figure imgf000077_0001
In some embodiments, an anti-parvovirus antibody or antigen-binding fragment is provided that comprises, in a(n e.g. human) IgGl heavy chain, the amino acid mutation(s) set forth in any one of (i)-(xviii): (i) G236A, L328V, and Q295E; (ii) G236A, P230A, and Q295E; (iii) G236A, R292P, and I377N; (iv) G236A, K334A, and Q295E; (v) G236S, R292P, and Y300L; (vi) G236A and Y300L; (vii) G236A, R292P, and Y300L; (viii) G236S, G420V, G446E, and L309T; (ix) G236A and R292P; (x) R292P and Y300L; (xi) G236A and R292P; (xii) Y300L; (xiii) E345K, G236S, L235Y, and S267E; (xiv) E272R, L309T, S219Y, and S267E; (xv) G236Y; (xvi) G236W; (xvii) F243L, G446E, P396L, and S267E; (xviii) G236A, S239D, and H268E, wherein the numbering of amino acid residues is according to the EU index as set forth in Kabat. In certain embodiments, the antibody or antigen-binding fragment is afucosylated. In some embodiments, the antibody or antigen-binding fragment further comprises one or more mutation that enhances binding to a human FcRn, such as M428L and N434S mutations or M428L and N434A mutations (EU numbering) or any other mutation(s) that enhance binding to a human FcRn, such as those described herein. In certain embodiments, the antibody or antigen- binding fragment is afucosylated.
In any of the presently disclosed embodiments, the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof, including a CH2 (or a fragment thereof, a CH3 (or a fragment thereof), or a CH2 and a CH3, wherein the CH2, the CH3, or both can be of any isotype and may contain amino acid substitutions or other modifications as compared to a corresponding wild-type CH2 or CH3, respectively. In certain embodiments, a Fc of the present disclosure comprises two CH2-CH3 polypeptides that associate to form a dimer.
In any of the presently disclosed embodiments, the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof, including a CH2 (or a fragment thereof, a CH3 (or a fragment thereof), or a CH2 and a CH3, wherein the CH2, the CH3, or both can be of any isotype and may contain amino acid substitutions or other modifications as compared to a corresponding wild-type CH2 or CH3, respectively. In certain embodiments, a Fc of the present disclosure comprises two CH2-CH3 polypeptides that associate to form a dimer.
In any of the presently disclosed embodiments, the antibody or antigen-binding fragment can be monoclonal. The term "monoclonal antibody" (mAb) as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, /.< ., individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present, in some cases in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations that include different antibodies directed against different epitopes, each monoclonal antibody is directed against a single epitope of the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies. The term "monoclonal" is not to be construed as requiring production of the antibody by any particular method. For example, monoclonal antibodies useful in the present invention may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256 :495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal, or plant cells (see, e.g., U.S. Pat. No. 4,816,567). Monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991), for example. Monoclonal antibodies may also be obtained using methods disclosed in PCT Publication No. WO 2004/076677A2.
Antibodies and antigen-binding fragments of the present disclosure include "chimeric antibodies" in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see, U.S. Pat. Nos. 4,816,567; 5,530,101 and 7,498,415; and Morrison et al., Proc. Natl. Acad. Sci. USA, 57:6851-6855 (1984)). For example, chimeric antibodies may comprise human and non-human residues. Furthermore, chimeric antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. For further details, see Jones et al., Nature 321 :522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). Chimeric antibodies also include primatized and humanized antibodies.
A "humanized antibody" is generally considered to be a human antibody that has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are typically taken from a variable domain. Humanization may be performed following the method of Winter and co-workers (Jones et al., Nature, 321 :522-525 (1986); Reichmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239: 1534- 1536 (1988)), by substituting non-human variable sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Pat. Nos. 4,816,567; 5,530,101 and 7,498,415) wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In some instances, a “humanized” antibody is one which is produced by a non-human cell or animal and comprises human sequences, e.g., He domains.
A "human antibody" is an antibody containing only sequences that are present in an antibody that is produced by a human. However, as used herein, human antibodies may comprise residues or modifications not found in a naturally occurring human antibody (e.g., an antibody that is isolated from a human), including those modifications and variant sequences described herein. These are typically made to further refine or enhance antibody performance. In some instances, human antibodies are produced by transgenic animals. For example, see U.S. Pat. Nos. 5,770,429; 6,596,541 and 7,049,426.
In certain embodiments, an antibody or antigen-binding fragment of the present disclosure is chimeric, humanized, or human.
Polynucleotides, Vectors, and Host Cells
In another aspect, the present disclosure provides isolated polynucleotides that encode any of the presently disclosed antibodies or an antigen-binding fragment thereof, or a portion thereof (e.g., a CDR, a VH, a VL, a heavy chain, or a light chain). In certain embodiments, the polynucleotide is codon-optimized for expression in a host cell. Once a coding sequence is known or identified, codon optimization can be performed using known techniques and tools, e.g., using the GenScript® OptimiumGene™ tool; see also Scholten et al., Clin. Immunol. 119: 135, 2006). Codon-optimized sequences include sequences that are partially codon- optimized (i.e., one or more codon is optimized for expression in the host cell) and those that are fully codon-optimized.
It will also be appreciated that polynucleotides encoding antibodies and antigen-binding fragments of the present disclosure may possess different nucleotide sequences while still encoding a same antibody or antigen-binding fragment due to, for example, the degeneracy of the genetic code, splicing, and the like.
In some embodiments, the polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 82, 91, 92, 100, 101, 109, 110, 119, 120, 123, 127, 130, 133, 136, 140, 144, 148, 152, 156, 159, 180, 182, 184, 187, 189, 191, 192, 195, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246,248, 250, 252, 253, 256, 259, 261, 262, 263, 265, 268, 271, 276, 278, 281, 285, and 289, particularly SEQ ID NOs: 123 and 159. In more specific embodiments, single polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 91, 100, 109, 119, 123, 127, 130, 133, 136, 140, 144, 152, 180, 182, 184, 187, 189, 191, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 262, 263, 265, and 268 and one or more of SEQ ID NOs: 82, 92, 101, 110, 120, 159, 192, 195, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, 261, 271, 276, 278, 281, 285, and 289, particularly SEQ ID NOs: 123 and 159. In other more specific embodiments, at least two polynucleotides are provided, in which the first polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 91, 100, 109, 119, 123, 127, 130, 133, 136, 140, 144, 152, 180, 182, 184, 187, 189, 191, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, 223, 262, 263, 265, and 268, particularly SEQ ID NO: 123, and the second polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 82, 92, 101, 110, 120, 159, 192, 195, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, 261, 271, 276, 278, 281, 285, and 289, particularly SEQ ID NO: 159.
In some embodiments, a single polynucleotide or combination of polynucleotides comprise or consist of combinations of two nucleic acid sequences, both having at least 85% (i.e., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to any one of SEQ ID NOs: i) 81 and 82; ii) 91, 180, 182, 184, 187, 189, or 191 and 92, 192, or 195; iii) 100, 196, 200, 203, 206, 209, 211, 213, 215, 217, 219, 221, or 223 and 101, 224, 227, 230, or 233; iv) 109 and 110, 234, 237, 240, 242, 244, 246, 248, 250, 252, 253, 256, 259, or 261; or v) 119, 123, 127, 130, 133, 136, 140, 144, 148, 152, 156, 262, 263, 265, or 268 and 120, 159, 271, 276, 178, 281, 285, or 289, particularly 123 and 159.
In any of the presently disclosed embodiments, the polynucleotide can comprise deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). In some embodiments, the RNA comprises messenger RNA (mRNA).
Vectors are also provided, wherein the vectors comprise or contain a polynucleotide as disclosed herein (e.g., a polynucleotide that encodes an antibody or antigen-binding fragment that binds to two or more sarbecoviruses). A vector can comprise any one or more of the vectors disclosed herein. In particular embodiments, a vector is provided that comprises a DNA plasmid construct encoding the antibody or antigen-binding fragment, or a portion thereof (e.g., so-called "DMAb" ; sss,
Figure imgf000081_0001
Muthumani st al., J Inf ct Dis. 274(3):369-378 (2016); Muthumani st al., Hum Vaccin Immunothsr 9 253-2262 (2013)); Flingai st al., Sci Rsp. 5: 12616 (2015); and Elliott st al., NPJ Vaccinss 18 (2017), which antibody-coding DNA constructs and related methods of use, including administration of the same, are incorporated herein by reference). In certain embodiments, a DNA plasmid construct comprises a single open reading frame encoding a heavy chain and a light chain (or a VH and a VL) of the antibody or antigen-binding fragment, wherein the sequence encoding the heavy chain and the sequence encoding the light chain are optionally separated by polynucleotide encoding a protease cleavage site and/or by a polynucleotide encoding a self-cleaving peptide. In some embodiments, the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in a single plasmid. In other embodiments, the substituent components of the antibody or antigen-binding fragment are encoded by a polynucleotide comprised in two or more plasmids (e.g., a first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL). In certain embodiments, a single plasmid comprises a polynucleotide encoding a heavy chain and/or a light chain from two or more antibodies or antigen-binding fragments of the present disclosure. An exemplary expression vector is pVaxl, available from Invitrogen®. A DNA plasmid of the present disclosure can be delivered to a subject by, for example, electroporation (e.g., intramuscular electroporation), or with an appropriate formulation (e.g., hyaluronidase).
In a further aspect, the present disclosure also provides a host cell expressing an antibody or antigen-binding fragment according to the present disclosure; or comprising or containing a vector or polynucleotide according the present disclosure.
Examples of such cells include but are not limited to, eukaryotic cells, e.g., yeast cells, animal cells, insect cells, plant cells; and prokaryotic cells, including E. coli. In some embodiments, the cells are mammalian cells. In certain such embodiments, the cells are a mammalian cell line such as CHO cells (e.g., DHFR- CHO cells (Urlaub et al., PNAS 77:4216 (1980)), human embryonic kidney cells (e.g., HEK293T cells), PER.C6 cells, Y0 cells, Sp2/0 cells. NSO cells, human liver cells, e.g. Hepa RG cells, myeloma cells or hybridoma cells. Other examples of mammalian host cell lines include mouse sertoli cells (e.g, TM4 cells); monkey kidney CV1 line transformed by SV40 (COS-7); baby hamster kidney cells (BHK); African green monkey kidney cells (VERO-76); monkey kidney cells (CV1); human cervical carcinoma cells (HELA); human lung cells (W138); human liver cells (Hep G2); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3 A); mouse mammary tumor (MMT 060562); TRI cells; MRC 5 cells; and FS4 cells. Mammalian host cell lines suitable for antibody production also include those described in, for example, Yazaki and Wu, Methods in Molecular Biology, Vol. 248 (B. K. C. Lo, ed., Humana Press, Totowa, N.J.), pp. 255-268 (2003).
In certain embodiments, a host cell is a prokaryotic cell, such as an E. coli. The expression of peptides in prokaryotic cells such as E. coli is well established (see, e.g., Pluckthun, A. Bio/Technology 9:545-551 (1991). For example, antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237; 5,789,199; and 5,840,523.
In particular embodiments, the cell may be transfected with a vector according to the present description with an expression vector. The term "transfection" refers to the introduction of nucleic acid molecules, such as DNA or RNA (e.g. mRNA) molecules, into cells, such as into eukaryotic cells. In the context of the present description, the term "transfection" encompasses any method known to the skilled person for introducing nucleic acid molecules into cells, such as into eukaryotic cells, including into mammalian cells. Such methods encompass, for example, electroporation, lipofection, e.g., based on cationic lipids and/or liposomes, calcium phosphate precipitation, nanoparticle based transfection, virus based transfection, or transfection based on cationic polymers, such as DEAE-dextran or polyethylenimine, etc. In certain embodiments, the introduction is non-viral.
Moreover, host cells of the present disclosure may be transfected stably or transiently with a vector according to the present disclosure, e.g. for expressing an antibody, or an antigenbinding fragment thereof, according to the present disclosure. In such embodiments, the cells may be stably transfected with the vector as described herein. Alternatively, cells may be transiently transfected with a vector according to the present disclosure encoding an antibody or antigen-binding fragment as disclosed herein. In any of the presently disclosed embodiments, a polynucleotide may be heterologous to the host cell.
Accordingly, the present disclosure also provides recombinant host cells that heterologously express an antibody or antigen-binding fragment of the present disclosure. For example, the cell may be of a species that is different to the species from which the antibody was fully or partially obtained (e.g., CHO cells expressing a human antibody or an engineered human antibody). In some embodiments, the cell type of the host cell does not express the antibody or antigen-binding fragment in nature. Moreover, the host cell may impart a post-translational modification (PTM; e.g., glycosylation or fucosylation) on the antibody or antigen-binding fragment that is not present in a native state of the antibody or antigen-binding fragment (or in a native state of a parent antibody from which the antibody or antigen-binding fragment was engineered or derived). Such a PTM may result in a functional difference (e.g., reduced immunogenicity). Accordingly, an antibody or antigen-binding fragment of the present disclosure that is produced by a host cell as disclosed herein may include one or more post- translational modification that is distinct from the antibody (or parent antibody) in its native state (e.g., a human antibody produced by a CHO cell can comprise a more post-translational modification that is distinct from the antibody when isolated from the human and/or produced by the native human B cell or plasma cell).
Insect cells useful expressing a binding protein of the present disclosure are known in the art and include, for example, Spodoptera frugipera Sf9 cells, Trichoplusia in BTI-TN5B1-4 cells, and Spodoptera frugipera SfSWTOl “Mimic™” cells. See, e.g., Palmberger et a!., J. Biotechnol. 752(3-4): 160-166 (2011). Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells.
Eukaryotic microbes such as filamentous fungi or yeast are also suitable hosts for cloning or expressing protein-encoding vectors, and include fungi and yeast strains with "humanized" glycosylation pathways, resulting in the production of an antibody with a partially or fully human glycosylation pattern. See Gemgross, Nat. Biotech. 22: 1409-1414 (2004); Li et al., Nat. Biotech. 24:210-215 (2006).
Plant cells can also be utilized as hosts for expressing a binding protein of the present disclosure. For example, PLANTIBODIES™ technology (described in, for example, U.S. Pat. Nos. 5,959,177; 6,040,498; 6,420,548; 7,125,978; and 6,417,429) employs transgenic plants to produce antibodies.
In certain embodiments, the host cell comprises a mammalian cell. In particular embodiments, the host cell is a CHO cell, a HEK293 cell, a PER.C6 cell, a Y0 cell, a Sp2/0 cell, a NSO cell, a human liver cell, a myeloma cell, or a hybridoma cell.
In a related aspect, the present disclosure provides methods for producing an antibody, or antigen-binding fragment, wherein the methods comprise culturing a host cell of the present disclosure under conditions and for a time sufficient to produce the antibody, or the antigenbinding fragment. Methods useful for isolating and purifying recombinantly produced antibodies, by way of example, may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant antibody into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin. One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide. These purification methods may also be employed when isolating an immunogen from its natural environment. Methods for large scale production of one or more of the isolated/recombinant antibody described herein include batch cell culture, which is monitored and controlled to maintain appropriate culture conditions. Purification of soluble antibodies may be performed according to methods described herein and known in the art and that comport with laws and guidelines of domestic and foreign regulatory agencies.
Compositions
Also provided herein are compositions that comprise any one or more of the presently disclosed antibodies, antigen-binding fragments, polynucleotides, vectors, or host cells, singly or in any combination, and can further comprise a pharmaceutically acceptable carrier, excipient, or diluent. Carriers, excipients, and diluents are discussed in further detail herein.
In certain embodiments, a composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure. In certain embodiments, antibodies or antigen-binding fragments to be used in a combination each independently have one or more of the following characteristics: neutralize one, two, three, four, five, or more naturally occurring sarbecovirus variants; do not compete with one another for Spike protein binding; bind distinct sarbecovirus Spike protein epitopes; have a reduced formation of resistance to sarbecovirus; when in a combination, have a reduced formation of resistance to sarbecovirus; potently neutralize one, two, three, four, five or more live sarbecoviruses; exhibit additive or synergistic effects on neutralization of one, two, three, four, five or more or more live sarbecoviruses when used in combination; exhibit effector functions; are protective in relevant animal model(s) of infection; are capable of being produced in sufficient quantities for large- scale production.
In certain embodiments, a composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure. In certain embodiments, the first antibody or antigen-binding fragment and the second antibody or antigen-binding fragment may A) both be an antibody or antigen-binding fragment that are S3 A3, an antibody with sufficient CDR, VH, and/or VH identity to S3 A3 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to SEQ ID NO.: 23 and a VL sequence according to SEQ ID NO.: 27, ii) CDRs as set forth in SEQ ID NOs: 23 and 27, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 24-26 (H1-H3) and 28-30 (L1-L3); B) both be an antibody or antigen-binding fragment that are S3A19, an antibody with sufficient CDR, VH, and/or VH identity to S3 Al 9 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 31, 35, 36 or 43, and a VL sequence according to SEQ ID NO.: 37, iii) CDRs as set forth in any one of SEQ ID NOs: 31, 35, 36, or 43 and SEQ ID NO: 37, according to any numbering system disclosed herein, or CDRs as set forth in SEQ ID NOs: 32-34 (H1-H3) and 37-40 (LILS); C) both be an antibody or antigen-binding fragment that are S3I2, an antibody with sufficient CDR, VH, and/or VH identity to S3I2 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and a VL sequence according to any one of SEQ ID NOs.: 87 or 194, ii) CDRs as set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190, and any one of SEQ ID NOs.: 87 or 193, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 84 (Hl), 85 (H2), and 86 or 186 (H3) and 88 or 194 (LI), 89 (L2), and 90 (L3); D) both be an antibody or antigen-binding fragment that are S3O13, an antibody with sufficient CDR, VH, and/or VH identity to S3O13 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NO.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence according to any one of SEQ ID NO.: 97, 225, 228, or 231, ii) CDRs as set forth in any one of SEQ ID NO.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of SEQ ID NO.: 97, 225, 228, or 231, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 94, 198, or 208 (Hl), 95 (H2), and 96, 199, 202, or 205 (H3), and 98, 226, 229, or 232 (LI), 39 (L2), and 99 (L3); E) both be an antibody or antigen-binding fragment that are S3L17, an antibody with sufficient CDR, VH, and/or VH identity to S3L17 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, ii) CDRs as set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of SEQ ID NOs.: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 103 (Hl), 85, (H2), and 104, 236, or 239 (H3), and 106 or 255 (LI), 107 (L2), and 108 or 258 (H3); F) both be an antibody or antigen-binding fragment that are S2V29 (or both S2V29a or S2V29b), an antibody with sufficient CDR, VH, and/or VH identity to S2V29 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290, ii) CDRs as set forth in any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 112 (Hl), 113 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270 (H2), and 114, 139, 143, 147, 151, or 155 (H3) and 116, 273, or 283 (LI), 117, 274, or 287 (L2), and 118, 122, 158, 275, 280, 284, 288, or 192 (L3); G) be an antibody or antigenbinding fragment according to A), B), C), D), E), or F) and an different antibody or antigenbinding fragment according to A), B), C), D), E), or F).
In certain embodiments, a composition comprises two or more different antibodies or antigen-binding fragments according to the present disclosure. In certain embodiments, the first antibody or antigen-binding fragment may be A) an antibody or antigen-binding fragment that are S3 A3, an antibody with sufficient CDR, VH, and/or VH identity to S3 A3 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to SEQ ID NO.: 23 and a VL sequence according to SEQ ID NO.: 27, ii) CDRs as set forth in SEQ ID NOs: 23 and 27, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 24-26 (H1-H3) and 28-30 (L1-L3); B) an antibody or antigen-binding fragment that are S3 Al 9, an antibody with sufficient CDR, VH, and/or VH identity to S3 Al 9 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs. : 31, 35, 36 or 43, and a VL sequence according to SEQ ID NO.: 37, iii) CDRs as set forth in any one of SEQ ID NOs: 31, 35, 36, or 43 and SEQ ID NO: 37, according to any numbering system disclosed herein, or CDRs as set forth in SEQ ID NOs: 32-34 (H1-H3) and 37-40 (L1-L3); C) an antibody or antigen-binding fragment that are S3I2, an antibody with sufficient CDR, VH, and/or VH identity to S3I2 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and a VL sequence according to any one of SEQ ID NOs.: 87 or 194, ii) CDRs as set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190, and any one of SEQ ID NOs.: 87 or 193, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 84 (Hl), 85 (H2), and 86 or 186 (H3) and 88 or 194 (LI), 89 (L2), and 90 (L3); D) an antibody or antigen-binding fragment that are S3O13, an antibody with sufficient CDR, VH, and/or VH identity to S3O13 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NO.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and a VL sequence according to any one of SEQ ID NO.: 97, 225, 228, or 231, ii) CDRs as set forth in any one of SEQ ID NO.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and any one of SEQ ID NO.: 97, 225, 228, or 231, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 94, 198, or 208 (Hl), 95 (H2), and 96, 199, 202, or 205 (H3), and 98, 226, 229, or 232 (LI), 39 (L2), and 99 (L3); E) an antibody or antigen-binding fragment that are S3L17, an antibody with sufficient CDR, VH, and/or VH identity to S3L17 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, ii) CDRs as set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of SEQ ID NOs.: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 103 (Hl), 85, (H2), and 104, 236, or 239 (H3), and 106 or 255 (LI), 107 (L2), and 108 or 258 (H3); F) an antibody or antigen-binding fragment that are S2V29 (or both S2V29a or S2V29b), an antibody with sufficient CDR, VH, and/or VH identity to S2V29 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290, ii) CDRs as set forth in any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 112 (Hl), 113 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270 (H2), and 114, 139, 143, 147, 151, or 155 (H3) and 116, 273, or 283 (LI), 117, 274, or 287 (L2), and 118, 122, 158, 275, 280, 284, 288, or 192 (L3); and the second antibody or antigen-binding fragment may be sotrovimab, S2K146, S2X259, S2X324, S2X324-v3.1, or S309 or an antigenbinding fragment thereof, particularly an antibody or antigen-binding fragment having a VH with an amino acid sequence of SEQ ID NO: 14 and a VL with an amino acid sequence of SEQ ID NO: 15, an antibody or antigen-binding fragment having a VH with an amino acid sequence of SEQ ID NO: 16 and a VL with an amino acid sequence of SEQ ID NO: 17, an antibody or antigen-binding fragment having a VH with an amino acid sequence of SEQ ID NO: 18 and a VL with an amino acid sequence of SEQ ID NO: 19, an antibody or antigen-binding fragment having a VH with an amino acid sequence of SEQ ID NO: 20 and a VL with an amino acid sequence of SEQ ID NO: 22, an antibody or antigen-binding fragment having a VH with an amino acid sequence of SEQ ID NO: 21 and a VL with an amino acid sequence of SEQ ID NO: 22, or an antibody or antigen-binding fragment having a VH with an amino acid sequence of SEQ ID NO: 41 and a VL with an amino acid sequence of SEQ ID NO: 42, or an antibody or antigen-binding fragment having CDRs as found in any of the preceding VH and VL combinations according to any numbering system disclosed herein. In particular embodiments, the second antibody or antigen-binding fragment may be sotrovimab or S2K146.
In some embodiments, the composition may comprise or may comprise antibodies or antigen-binding fragment comprising or consisting of A) a first antibody or antigen-binding fragment which may be an antibody or antigen-binding fragment that are S3L17, an antibody with sufficient CDR, VH, and/or VH identity to S3L17 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, ii) CDRs as set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and any one of SEQ ID NOs.: 105, 254, 257, or 260, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 103 (Hl), 85, (H2), and 104, 236, or 239 (H3), and 106 or 255 (LI), 107 (L2), and 108 or 258 (H3); and B) a second antibody or antigen-binding fragment which may be an antibody or antigen-binding fragment that are S2V29 (or both S2V29a or S2V29b), an antibody with sufficient CDR, VH, and/or VH identity to S2V29 to confer similar specific binding, or a fragment thereof, such as those comprising i) a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290, ii) CDRs as set forth in any one of SEQ ID NOs: 111, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and any one of SEQ ID NOs: 115, 121, 157, 272, 277, 279, 282, 286, or 290, according to any numbering system disclosed herein, or iii) CDRs as set forth in SEQ ID NOs: 112 (Hl), 113 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270 (H2), and 114, 139, 143, 147, 151, or 155 (H3) and 116, 273, or 283 (LI), 117, 274, or 287 (L2), and 118, 122, 158, 275, 280, 284, 288, or 192 (L3).
In some embodiments: a composition comprises a first antibody or antigen-binding fragment and a second antibody or antigen-binding fragment; a multispecific (e.g. bispecific) antibody or antigen-binding fragment is provided; or a combination therapy comprises a first antibody or antigen-binding fragment and a second antibody or antigen-binding fragment, wherein the first antibody or antigen-binding fragment and second antibody or antigen-binding fragment, respectively, or the multispecific antibody or antigen-binding fragment, comprise(s) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, according to (i) any S3 A3 antibody and any S3 Al 9 antibody; (ii) any S3 A3 antibody and sotrovimab; (iii) any S3A3 antibody and S2K146; (iv) any S3 A3 antibody and S2X259; (v) any S3A3 antibody and any S2X324 antibody; (vi) any S3A3 antibody and S309; (vi) any S3A19 antibody and sotrovimab; (vii) any S3A19 antibody and S2K146; (viii) any S3A19 antibody and S2X259; (ix) any S3A19 antibody and any S2X324 antibody; (x) any S3A19 antibody and S309; (xi) any S3I2 antibody and any S3 A3 antibody; (xii) any S3I2 antibody and any S3 Al 9 antibody; (xiii) any S3I2 antibody and sotrovimab; (xiv) any S3I2 antibody and S2K146; (xv) any S3I2 antibody and S2X259; (xvi) any S3I2 antibody and any S2X324 antibody; (xvii) any S3I2 antibody and S309; (xviii) any S3I2 antibody and any S3O13 antibody; (xix) any S3I2 antibody and any S3L17 antibody; (xx) any S3O13 antibody and any S3 A3 antibody; (xxi) any S3O13 antibody and any S3A19 antibody; (xxii) any S3O13 antibody and sotrovimab; (xxiii) any S3O13 antibody and S2K146; (xxiv) any S3O13 antibody and S2X259; (xxv) any S3O13 antibody and any S2X324 antibody; (xxvi) any S3O13 antibody and S309; (xxvii) any S3O13 antibody and any S3L17 antibody; (xxviii) any S3L17 antibody and any S3 A3 antibody; (xxix) any S3L17 antibody and any S3A19 antibody; (xxx) any S3L17 antibody and sotrovimab; (xxxi) any S3L17 antibody and S2K146; (xxxii) any S3L17 antibody and S2X259; (xxxiii) any S3L17 antibody and any S2X324 antibody; (xxxiv) any S3L17 antibody and S309; (xxxv) any S2V29 antibody and any S3 A3 antibody; (xxxvi) any S2V29 antibody and any S3 Al 9 antibody; (xxxvii) any S2V29 antibody and sotrovimab; (xxxviii) any S2V29 antibody and S2K146; (xxxix) any S2V29 antibody and S2X259; (xl) any S2V29 antibody and any S2X324 antibody; (xli) any S2V29 antibody and S309; (Ixlii) any S2V29 antibody and any S3L17 antibody; and (xliii) any S2V29 antibody and any S3O13 antibody.
In certain embodiments, a composition comprises a first vector comprising a first plasmid, and a second vector comprising a second plasmid, wherein the first plasmid comprises a polynucleotide encoding a heavy chain, VH, or VH+CH, and a second plasmid comprises a polynucleotide encoding the cognate light chain, VL, or VL+CL of the antibody or antigenbinding fragment thereof. In certain embodiments, a composition comprises a polynucleotide (e.g., mRNA) coupled to a suitable delivery vehicle or carrier. Exemplary vehicles or carriers for administration to a human subject include a lipid or lipid-derived delivery vehicle, such as a liposome, solid lipid nanoparticle, oily suspension, submicron lipid emulsion, lipid microbubble, inverse lipid micelle, cochlear liposome, lipid microtubule, lipid microcylinder, or lipid nanoparticle (LNP) or a nanoscale platform (see, e.g., Li et al. Wilery Interdiscip Rev. Nanomed Nanobiotechnol. 77(2):el530 (2019)). Principles, reagents, and techniques for designing appropriate mRNA and formulating mRNA-LNP and delivering the same are described in, for example, Pardi et al. (J Control Release 277345-351 (2015)); Thess et al. (Mol Ther 23: 1456- 1464 (2015)); Thran et al. EMBO MolMed 9(10): 1434-1448 (2017); Kose et al. (Sci. Immunol. 4 eaaw6647 (2019); and Sabnis et al. (Mol. Ther. 26: 1509-1519 (2018)), which techniques, include capping, codon optimization, nucleoside modification, purification of mRNA, incorporation of the mRNA into stable lipid nanoparticles (e.g., ionizable cationic lipid/phosphatidylcholine/cholesterol/PEG-lipid; ionizable lipid:distearoyl
PC: cholesterol: polyethylene glycol lipid), and subcutaneous, intramuscular, intradermal, intravenous, intraperitoneal, and intratracheal administration of the same, are incorporated herein by reference.
Methods and Uses
Also provided herein are methods for use of an antibody or antigen-binding fragment, nucleic acid, vector, cell, or composition of the present disclosure in the diagnosis of a sarbecovirus infection (e.g., in a human subject, or in a sample obtained from a human subject).
Methods of diagnosis (e.g., in vitro, ex vivo) may include contacting an antibody, antibody fragment (e.g., antigen-binding fragment) with a sample. Such samples may be isolated from a subject, for example an isolated tissue sample taken from, for example, nasal passages, sinus cavities, salivary glands, lung, liver, pancreas, kidney, ear, eye, placenta, alimentary tract, heart, ovaries, pituitary, adrenals, thyroid, brain, skin or blood. The methods of diagnosis may also include the detection of an antigen/antibody complex, in particular following the contacting of an antibody or antibody fragment with a sample. Such a detection step can be performed at the bench, i.e. without any contact to the human or animal body. Examples of detection methods are well-known to the person skilled in the art and include, e.g, ELISA (enzyme-linked immunosorbent assay), including direct, indirect, and sandwich ELISA.
Also provided herein are methods of treating a subject using an antibody or antigenbinding fragment of the present disclosure, or a composition comprising the same, wherein the subject has, is believed to have, or is at risk for having an infection by a sarbecovirus. "Treat," "treatment," or "ameliorate" refers to medical management of a disease, disorder, or condition of a subject (e.g, a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat). In general, an appropriate dose or treatment regimen comprising an antibody or composition of the present disclosure is administered in an amount sufficient to elicit a therapeutic or prophylactic benefit. Therapeutic or prophylactic/preventive benefit includes improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay or prevention of disease progression; remission; survival; prolonged survival; or any combination thereof. In certain embodiments, therapeutic or prophylactic/preventive benefit includes reduction or prevention of hospitalization for treatment of a sarbecovirus infection (i.e., in a statistically significant manner). In certain embodiments, therapeutic or prophylactic/preventive benefit includes a reduced duration of hospitalization for treatment of a sarbecovirus infection (i.e., in a statistically significant manner). In certain embodiments, therapeutic or prophylactic/preventive benefit includes a reduced or abrogated need for respiratory intervention, such as intubation and/or the use of a respirator device. In certain embodiments, therapeutic or prophylactic/preventive benefit includes reversing a late-stage disease pathology and/or reducing mortality.
A "therapeutically effective amount" or "effective amount" of an antibody, antigenbinding fragment, polynucleotide, vector, host cell, or composition of this disclosure refers to an amount of the composition or molecule sufficient to result in a therapeutic effect, including improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay of disease progression; remission; survival; or prolonged survival in a statistically significant manner. When referring to an individual active ingredient, administered alone, a therapeutically effective amount refers to the effects of that ingredient or cell expressing that ingredient alone. When referring to a combination, a therapeutically effective amount refers to the combined amounts of active ingredients or combined adjunctive active ingredient with a cell expressing an active ingredient that results in a therapeutic effect, whether administered serially, sequentially, or simultaneously. A combination may comprise, for example, two different antibodies that specifically bind sarbecovirus antigens, which in certain embodiments, may be the same or different sarbecovirus antigens, and/or can comprise the same or different epitopes.
Accordingly, in certain embodiments, methods are provided for treating a sarbecovirus infection in a subject, wherein the methods comprise administering to the subject an effective amount of an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition as disclosed herein.
Subjects that can be treated by the present disclosure are, in general, human and other primate subjects, such as monkeys and apes for veterinary medicine purposes. Other model organisms, such as mice and rats, may also be treated according to the present disclosure. In any of the aforementioned embodiments, the subject may be a human subject. The subjects can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects.
A number of criteria are believed to contribute to high risk for severe symptoms or death associated with a sarbecovirus infection. These include, but are not limited to, age, occupation, general health, pre-existing health conditions, and lifestyle habits. In some embodiments, a subject treated according to the present disclosure comprises one or more risk factors.
In certain embodiments, a human subject treated according to the present disclosure is an infant, a child, a young adult, an adult of middle age, or an elderly person. In certain embodiments, a human subject treated according to the present disclosure is less than 1 year old, or is 1 to 5 years old, or is between 5 and 125 years old (e.g., 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, or 125 years old, including any and all ages therein or therebetween). In certain embodiments, a human subject treated according to the present disclosure is 0-19 years old, 20-44 years old, 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older. Persons of middle, and especially of elderly age are believed to be at particular risk. In particular embodiments, the human subject is 45-54 years old, 55-64 years old, 65-74 years old, 75-84 years old, or 85 years old, or older. In some embodiments, the human subject is male. In some embodiments, the human subject is female.
In certain embodiments, a human subject treated according to the present disclosure is a resident of a nursing home or a long-term care facility, is a hospice care worker, is a healthcare provider or healthcare worker, is a first responder, is a family member or other close contact of a subject diagnosed with or suspected of having a sarbecovirus infection, is overweight or clinically obese, is or has been a smoker, has or had chronic obstructive pulmonary disease (COPD), is asthmatic (e.g, having moderate to severe asthma), has an autoimmune disease or condition (e.g, diabetes), and/or has a compromised or depleted immune system (e.g., due to AIDS/HIV infection, a cancer such as a blood cancer, a lymphodepleting therapy such as a chemotherapy, a bone marrow or organ transplantation, or a genetic immune condition), has chronic liver disease, has cardiovascular disease, has a pulmonary or heart defect, works or otherwise spends time in close proximity with others, such as in a factory, shipping center, hospital setting, or the like.
In certain embodiments, a subject treated according to the present disclosure has received a vaccine for a sarbecovirus and the vaccine is determined to be ineffective, e.g, by post-vaccine infection or symptoms in the subject, by clinical diagnosis or scientific or regulatory criteria.
In certain embodiments, treatment is administered as peri-exposure prophylaxis. In certain embodiments, treatment is administered to a subject with mild-to-moderate disease, which may be in an outpatient setting. In certain embodiments, treatment is administered to a subject with moderate-to-severe disease, such as requiring hospitalization.
Typical routes of administering the presently disclosed compositions thus include, without limitation, oral, topical, transdermal, inhalation, parenteral, sublingual, buccal, rectal, vaginal, and intranasal. The term "parenteral", as used herein, includes subcutaneous injections, intravenous, intramuscular, intrasternal injection or infusion techniques. In certain embodiments, administering comprises administering by a route that is selected from oral, intravenous, parenteral, intragastric, intrapleural, intrapulmonary, intrarectal, intradermal, intraperitoneal, intratumoral, subcutaneous, topical, transdermal, intracisternal, intrathecal, intranasal, and intramuscular. In particular embodiments, a method comprises orally administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition to the subject.
Pharmaceutical compositions according to certain embodiments of the present invention are formulated so as to allow the active ingredients contained therein to be bioavailable upon administration of the composition to a patient. Compositions that will be administered to a subject or patient may take the form of one or more dosage units, where for example, a tablet may be a single dosage unit, and a container of a herein described an antibody or antigen-binding in aerosol form may hold a plurality of dosage units. Actual methods of preparing such dosage forms are known, or will be apparent, to those skilled in this art; for example, see Remington: The Science and Practice of Pharmacy, 20th Edition (Philadelphia College of Pharmacy and Science, 2000). The composition to be administered will, in any event, contain an effective amount of an antibody or antigen-binding fragment, polynucleotide, vector, host cell, , or composition of the present disclosure, for treatment of a disease or condition of interest in accordance with teachings herein.
A composition may be in the form of a solid or liquid. In some embodiments, the carrier(s) are particulate, so that the compositions are, for example, in tablet or powder form. The carrier(s) may be liquid, with the compositions being, for example, an oral oil, injectable liquid or an aerosol, which is useful in, for example, inhalatory administration. When intended for oral administration, the pharmaceutical composition is preferably in either solid or liquid form, where semi solid, semi liquid, suspension and gel forms are included within the forms considered herein as either solid or liquid.
As a solid composition for oral administration, the pharmaceutical composition may be formulated into a powder, granule, compressed tablet, pill, capsule, chewing gum, wafer or the like. Such a solid composition will typically contain one or more inert diluents or edible carriers. In addition, one or more of the following may be present: binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, gum tragacanth or gelatin; excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, com starch and the like; lubricants such as magnesium stearate or Sterotex; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; a flavoring agent such as peppermint, methyl salicylate or orange flavoring; and a coloring agent. When the composition is in the form of a capsule, for example, a gelatin capsule, it may contain, in addition to materials of the above type, a liquid carrier such as polyethylene glycol or oil. The composition may be in the form of a liquid, for example, an elixir, syrup, solution, emulsion or suspension. The liquid may be for oral administration or for delivery by injection, as two examples. When intended for oral administration, preferred compositions contain, in addition to the present compounds, one or more of a sweetening agent, preservatives, dye/colorant and flavor enhancer. In a composition intended to be administered by injection, one or more of a surfactant, preservative, wetting agent, dispersing agent, suspending agent, buffer, stabilizer and isotonic agent may be included.
Liquid pharmaceutical compositions, whether they be solutions, suspensions or other like form, may include one or more of the following adjuvants: sterile diluents such as water for injection, saline solution, preferably physiological saline, Ringer’s solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides which may serve as the solvent or suspending medium, polyethylene glycols, glycerin, propylene glycol or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. Physiological saline is a preferred adjuvant. An injectable pharmaceutical composition is preferably sterile.
A liquid composition intended for either parenteral or oral administration should contain an amount of an antibody or antigen-binding fragment as herein disclosed such that a suitable dosage will be obtained. Typically, this amount is at least 0.01% of the antibody or antigenbinding fragment in the composition. When intended for oral administration, this amount may be varied to be between 0.1 and about 70% of the weight of the composition. Certain oral pharmaceutical compositions contain between about 4% and about 75% of the antibody or antigen-binding fragment. In certain embodiments, pharmaceutical compositions and preparations according to the present invention are prepared so that a parenteral dosage unit contains between 0.01 to 10% by weight of antibody or antigen-binding fragment prior to dilution.
The composition may be intended for topical administration, in which case the carrier may suitably comprise a solution, emulsion, ointment or gel base. The base, for example, may comprise one or more of the following: petrolatum, lanolin, polyethylene glycols, bee wax, mineral oil, diluents such as water and alcohol, and emulsifiers and stabilizers. Thickening agents may be present in a composition for topical administration. If intended for transdermal administration, the composition may include a transdermal patch or iontophoresis device. The pharmaceutical composition may be intended for rectal administration, in the form, for example, of a suppository, which will melt in the rectum and release the drug. The composition for rectal administration may contain an oleaginous base as a suitable nonirritating excipient. Such bases include, without limitation, lanolin, cocoa butter and polyethylene glycol.
A composition may include various materials which modify the physical form of a solid or liquid dosage unit. For example, the composition may include materials that form a coating shell around the active ingredients. The materials that form the coating shell are typically inert, and may be selected from, for example, sugar, shellac, and other enteric coating agents. Alternatively, the active ingredients may be encased in a gelatin capsule. The composition in solid or liquid form may include an agent that binds to the antibody or antigen-binding fragment of the disclosure and thereby assists in the delivery of the compound. Suitable agents that may act in this capacity include monoclonal or polyclonal antibodies, one or more proteins or a liposome. The composition may consist essentially of dosage units that can be administered as an aerosol. The term aerosol is used to denote a variety of systems ranging from those of colloidal nature to systems consisting of pressurized packages. Delivery may be by a liquefied or compressed gas or by a suitable pump system that dispenses the active ingredients. Aerosols may be delivered in single phase, bi phasic, or tri phasic systems in order to deliver the active ingredient(s). Delivery of the aerosol includes the necessary container, activators, valves, subcontainers, and the like, which together may form a kit. One of ordinary skill in the art, without undue experimentation, may determine preferred aerosols.
It will be understood that compositions of the present disclosure also encompass carrier molecules for polynucleotides, as described herein (e.g., lipid nanoparticles, nanoscale delivery platforms, and the like).
The pharmaceutical compositions may be prepared by methodology well known in the pharmaceutical art. For example, a composition intended to be administered by injection can be prepared by combining a composition that comprises an antibody, antigen-binding fragment thereof, or antibody conjugate as described herein and optionally, one or more of salts, buffers and/or stabilizers, with sterile, distilled water so as to form a solution. A surfactant may be added to facilitate the formation of a homogeneous solution or suspension. Surfactants are compounds that non-covalently interact with the peptide composition so as to facilitate dissolution or homogeneous suspension of the antibody or antigen-binding fragment thereof in the aqueous delivery system.
In general, an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome (e.g., a decrease in frequency, duration, or severity of diarrhea or associated dehydration, or inflammation, or longer disease-free and/or overall survival, or a lessening of symptom severity). For prophylactic use, a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder. Prophylactic benefit of the compositions administered according to the methods described herein can be determined by performing pre-clinical (including in vitro and in vivo animal studies) and clinical studies and analyzing data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques, all of which can readily be practiced by a person skilled in the art.
Compositions are administered in an effective amount (e.g., to treat a sarbecovirus infection), which will vary depending upon a variety of factors including the activity of the specific compound employed; the metabolic stability and length of action of the compound; the age, body weight, general health, sex, and diet of the subject; the mode and time of administration; the rate of excretion; the drug combination; the severity of the particular disorder or condition; and the subject undergoing therapy. In certain embodiments, following administration of therapies according to the formulations and methods of this disclosure, test subjects will exhibit about a 10% up to about a 99% reduction in one or more symptoms associated with the disease or disorder being treated as compared to placebo-treated or other suitable control subjects.
Generally, a therapeutically effective daily dose of an antibody or antigen-binding fragment is (for a 70 kg mammal) from about 0.001 mg/kg (z.e., 0.07 mg) to about 100 mg/kg (z.e., 7.0 g); preferably a therapeutically effective dose is (for a 70 kg mammal) from about 0.01 mg/kg (z.e., 0.7 mg) to about 50 mg/kg (z.e., 3.5 g); more preferably a therapeutically effective dose is (for a 70 kg mammal) from about 1 mg/kg (z.e., 70 mg) to about 25 mg/kg (z.e., 1.75 g). For polynucleotides, vectors, host cells, and related compositions of the present disclosure, a therapeutically effective dose may be different than for an antibody or antigen-binding fragment.
A single intramuscular (IM) injection of an age and/or weight appropriate dose of an S2V29-vl.2 antibody or fragment thereof, particularly a S2V29-vl.2-IgGlml7_Lamda or S2V29-vl.2-IgGlml7,l-LS antibody as described herein may be sufficient to treat a SARS- CoV-2 infection or to have a prophylactic effect for between three and six months or up to six months.
In certain embodiments, a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition to the subject at 2, 3, 4, 5, 6, 7, 8, 9, 10 times, or more.
In certain embodiments, a method comprises administering the antibody, antigen-binding fragment, or composition to the subject a plurality of times, wherein a second or successive administration is performed at about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 24, about 48, about 74, about 96 hours, or more, following a first or prior administration, respectively.
In certain embodiments, a method comprises administering the antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition at least one time prior to the subject being infected by a sarbecovirus.
Compositions comprising an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition of the present disclosure may also be administered simultaneously with, prior to, or after administration of one or more other therapeutic agents. Such combination therapy may include administration of a single pharmaceutical dosage formulation which contains a compound of the invention and one or more additional active agents, as well as administration of compositions comprising an antibody or antigen-binding fragment of the disclosure and each active agent in its own separate dosage formulation. For example, an antibody or antigen-binding fragment thereof as described herein and the other active agent can be administered to the patient together in a single oral dosage composition such as a tablet or capsule, or each agent administered in separate oral dosage formulations. Similarly, an antibody or antigen-binding fragment as described herein and the other active agent can be administered to the subject together in a single parenteral dosage composition such as in a saline solution or other physiologically acceptable solution, or each agent administered in separate parenteral dosage formulations. Where separate dosage formulations are used, the compositions comprising an antibody or antigen-binding fragment and one or more additional active agents can be administered at essentially the same time, ie., concurrently, or at separately staggered times, /.< ., sequentially and in any order; combination therapy is understood to include all these regimens.
In certain embodiments, a combination therapy is provided that comprises one or more anti-sarbecovirus antibody (or one or more nucleic acid, host cell, vector, or composition) of the present disclosure and one or more anti-inflammatory agent and/or one or more anti-viral agent. In particular embodiments, the one or more anti-inflammatory agent comprises a corticosteroid such as, for example, dexamethasone, prednisone, or the like. In some embodiments, the one or more anti-inflammatory agents comprise a cytokine antagonist such as, for example, an antibody that binds to IL6 (such as siltuximab), or to IL-6R (such as tocilizumab), or to IL-ip, IL-7, IL-8, IL-9, IL-10, FGF, G-CSF, GM-CSF, IFN-y, IP-10, MCP-1, MIP-1A, MIP1-B, PDGR, TNF-a, or VEGF. In some embodiments, anti-inflammatory agents such as leronlimab, ruxolitinib and/or anakinra are used. In some embodiments, the one or more anti-viral agents comprise nucleotide analogs or nucleotide analog prodrugs such as, for example, remdesivir, sofosbuvir, acyclovir, and zidovudine. In particular embodiments, an anti-viral agent comprises lopinavir, ritonavir, favipiravir, or any combination thereof. Other anti-inflammatory agents for use in a combination therapy of the present disclosure include non-steroidal anti-inflammatory drugs (NSAIDS). It will be appreciated that in such a combination therapy, the one or more antibody (or one or more nucleic acid, host cell, vector, or composition) and the one or more anti-inflammatory agent and/or one or the more antiviral agent can be administered in any order and any sequence, or together.
In some embodiments, an antibody (or one or more nucleic acid, host cell, vector, or composition) is administered to a subject who has previously received one or more antiinflammatory agent and/or one or more antiviral agent. In some embodiments, one or more antiinflammatory agent and/or one or more antiviral agent is administered to a subject who has previously received an antibody (or one or more nucleic acid, host cell, vector, or composition).
In certain embodiments, a combination therapy is provided that comprises two or more anti-sarbecovirus antibodies of the present disclosure. A method can comprise administering a first antibody to a subject who has received a second antibody, or can comprise administering two or more antibodies together. For example, in particular embodiments, a method is provided that comprises administering to the subject (a) a first antibody or antigen-binding fragment, when the subject has received a second antibody or antigen-binding fragment; (b) the second antibody or antigen-binding fragment, when the subject has received the first antibody or antigen-binding fragment; or (c) the first antibody or antigen-binding fragment, and the second antibody or antigen-binding fragment.
In a related aspect, uses of the presently disclosed antibodies, antigen-binding fragments, vectors, host cells, and compositions are provided.
The present disclosure further provides a kit comprising one or more of any antibodies, antigen-binding fragments, polynucleotides, nucleic acids, vectors, or other compositions disclosed herein. The kit may further include one or more of a container, such as a tube, vial, or syringe, an activator, a valve, a subcontainer, or instructions for use, such as for administering to a subject.
In certain embodiments, an antibody, antigen-binding fragment, polynucleotide, vector, host cell, or composition is provided for use in a method of treating a sarbecovirus infection in a subject.
In certain embodiments, an antibody, antigen-binding fragment, or composition is provided for use in a method of manufacturing or preparing a medicament for treating a sarbecovirus infection in a subject.
The disclosure provides the following specific embodiments:
Embodiment 1. An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (A) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO: 24, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO: 25, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID NO: 26, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to SEQ ID NO: 28, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO: 29 or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NO: 30, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid, (B) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 32 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 33, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID NO.: 34, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 38, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 39, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs. : 40, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (C) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 84 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 86 or 186, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 88 or 194, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 89, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs. : 90, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (D) (i) the CDRH1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 94, 198, or 208 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 95, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 96, 199, 202, or 205, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 98, 226, 229, 232, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 39, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs.: 99, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (E) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 104, 236, or 239, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 106 or 255, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 107, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 108 or 258, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; or (F) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 112 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 116, 273, or 283, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 117, 274, or 287, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid, wherein the substitution is optionally a substitution according to Table 2 or Table 3, and wherein the antibody or antigen-binding fragment is capable of binding to the surface glycoprotein of a sarbecovirus.
Embodiment 2. An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, having amino acid sequences according to (A) SEQ ID NOs.: 24-26 and 28-30, respectively; (B) SEQ ID NOs.: 32- 34 and 38-40, respectively; (C) SEQ ID NOs.: 84-86 or 84, 85 and 186 and 88-90 or 194, 89, and 90, respectively; (D) SEQ ID NOs.: 94-96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232, respectively; (E) SEQ ID NOs.: 103, 85, and, 104; 103, 85, and 236; or 103, 85, and 239, and 106-108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, respectively; and (F) SEQ ID NOs.: 112- 114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and
114; 112, 270, and 114; 112, 113, and 139; 112, 126, and 139; 112, 129 and 139; 112, 132, and
139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and
139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 126, and
143; 112, 129 and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129 and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and
147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and
151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and
151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and
155; 112, 126, and 155; 112, 129 and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116-118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275; 116, 117, and 280; 116, 274, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and 291; 116, 274, and 291; 116, 287, and 291; 273, 117, and 118; 273, 274, and 118; 273, 287, and 118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275; 273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 283, 117, 118; 283, 274, and 118; 283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 280; 283, 287, and 280; 283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291, respectively.
Embodiment 3. The antibody or antigen-binding fragment of Embodiment lor 2, wherein the sarbecovirus is a Clade lb sarbecovirus.
Embodiment 4. The antibody or antigen-binding fragment of Embodiment 3, wherein the sarbecovirus is SARS-CoV-2 WT, SARS-CoV-2 BA.l, RATG13, PANG/GD, or PAND/GX.
Embodiment 5. The antibody or antigen-binding fragment of any one of Embodiments 1-4, wherein the antibody or antigen-binding fragment is capable of binding to the surface glycoprotein when the surface glycoprotein is expressed on a cell surface of a host cell and/or is comprised on a virion.
Embodiment 6. The antibody or antigen-binding fragment of any one of Embodiments 1-5 which is capable of binding to a surface glycoprotein from two or more (e.g., two, three, four, five, or more) sarbecoviruses.
Embodiment 7. The antibody or antigen-binding fragment of any one of Embodiments 1-6, which is capable of neutralizing an infection by one or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
Embodiment 8. The antibody or antigen-binding fragment of any one of claims 1-7, which is capable of neutralizing an infection by two or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
Embodiment 9. The antibody or antigen-binding fragment of any one of Embodiments 1-8, wherein the VH and the VL comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in: (I) 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18) SEQ ID NOs: 183 and 193; 18) SEQ ID NOs: 185 and 87; 19) SEQ ID NOs: 185 and 193; 20) SEQ ID NOs: 188 and 87; 21) SEQ ID NOs: 188 and 193; 22) SEQ ID NOs: 190 and 87; 23) SEQ ID NOs: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 204 and 228; 39) SEQ ID NOs: 204 and 231; 40) SEQ ID NOs: 207 and 97; 41) SEQ ID NOs: 207 and 225; 42) SEQ ID NOs: 207 and 228; 43) SEQ ID NOs: 207 and 231; 44) SEQ ID NOs: 210 and 97; 45) SEQ ID NOs: 210 and 225; 46) SEQ ID NOs: 210 and 228; 47) SEQ ID NOs: 210 and 231; 48) SEQ ID NOs: 212 and 97; 49) SEQ ID NOs: 212 and 225; 50) SEQ ID NOs: 212 and 228; 51) SEQ ID NOs: 212 and 231; 52) SEQ ID NOs: 214 and 97; 53) SEQ ID NOs: 214 and 225; 54) SEQ ID NOs: 214 and 228; 55) SEQ ID NOs: 214 and 231; 56) SEQ ID NOs: 216 and 97; 57) SEQ ID NOs: 216 and 225; 58) SEQ ID NOs: 216 and 228; 59) SEQ ID NOs: 216 and 231; 60) SEQ ID NOs: 218 and 97; 61) SEQ ID NOs: 218 and 225; 62) SEQ ID NOs: 218 and 228; 63) SEQ ID NOs: 218 and 231; 64) SEQ ID NOs: 220 and 97; 65) SEQ ID NOs: 220 and 225; 66) SEQ ID NOs: 220 and 228; 67) SEQ ID NOs: 220 and 231; 68) SEQ ID NOs: 222 and 97; 69) SEQ ID NOs: 222 and 225; 70) SEQ ID NOs: 222 and 228; 71) SEQ ID NOs: 222 and 231; 72) SEQ ID NOs: 102 and 105; 73) SEQ ID NOs: 102 and 254; 74) SEQ ID NOs: 102 and 257; 75) SEQ ID NOs: 102 and 260; 76) SEQ ID NOs: 235 and 105; 77) SEQ ID NOs: 235 and 254; 78) SEQ ID NOs: 235 and 257; 79) SEQ ID NOs: 235 and 260; 80) SEQ ID NOs: 238 and 105; 81) SEQ ID NOs: 238 and 254; 82) SEQ ID NOs: 238 and 257; 83) SEQ ID NOs: 238 and 260; 84) SEQ ID NOs: 241 and 105; 85) SEQ ID NOs: 241 and 254; 86) SEQ ID NOs: 241 and 257; 87) SEQ ID NOs: 241 and 260; 88) SEQ ID NOs: 243 and 105; 89) SEQ ID NOs: 243 and 254; 90) SEQ ID NOs: 243 and 257; 91) SEQ ID NOs: 243 and 260; 92) SEQ ID NOs: 245 and 105; 93) SEQ ID NOs: 245 and 254; 94) SEQ ID NOs: 245 and 257; 95) SEQ ID NOs: 245 and 260; 96) SEQ ID NOs: 247 and 105; 97) SEQ ID NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100) SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: l l l and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NOs: 111 and 272; 112) SEQ ID NOs: 111 and 277; 113) SEQ ID NOs: 111 and 279; 114) SEQ ID NOs: 111 and 282; 115) SEQ ID NOs: 111 and 286; 116) SEQ ID NOs: 111 and 290; 117) SEQ ID NOs: 125 and 115; 118) SEQ ID NOs: 125 and 121; 119) SEQ ID NOs: 125 and 157; 120) SEQ ID NOs: 125 and 272; 121) SEQ ID NOs: 125 and 277; 122) SEQ ID NOs: 125 and 279; 123) SEQ ID NOs: 125 and 282; 124) SEQ ID NOs: 125 and 286; 125) SEQ ID NOs: 125 and 290; 126) SEQ ID NOs: 128 and 115; 127) SEQ ID NOs: 128 and 121; 128) SEQ ID NOs: 128 and 157; 129) SEQ ID NOs: 128 and 272; 129) SEQ ID NOs: 128 and 279; 130) SEQ ID NOs: 128 and 282; 131) SEQ ID NOs: 128 and 286; 132) SEQ ID NOs: 128 and 290; 133) SEQ ID NOs: 131 and 115; 134) SEQ ID NOs: 131 and 121; 135) SEQ ID NOs: 131 and 157; 136) SEQ ID NOs: 131 and 272; 137) SEQ ID NOs: 131 and 277; 138) SEQ ID NOs: 131 and 279; 139) SEQ ID NOs: 131 and 282; 140) SEQ ID NOs: 131 and 286; 141) SEQ ID NOs: 131 and 290; 142) SEQ ID NOs: 134 and 115; 143) SEQ ID NOs: 134 and 121; 144) SEQ ID NOs: 134 and 157; 145) SEQ ID NOs: 134 and 272; 146) SEQ ID NOs: 134 and 277; 147) SEQ ID NOs: 134 and 279; 148) SEQ ID NOs: 134 and 282; 149) SEQ ID NOs: 134 and 286; 150) SEQ ID NOs: 134 and 290; 151) SEQ ID NOs: 137 and 115; 152) SEQ ID NOs: 137 and 121; 153) SEQ ID NOs: 137 and 157; 154) SEQ ID NOs: 137 and 272; 155) SEQ ID NOs: 137 and 277; 156) SEQ ID NOs: 137 and 279; 157) SEQ ID NOs: 137 and 282; 158) SEQ ID NOs: 137 and 286; 159) SEQ ID NOs: 137 and 290; 160) SEQ ID NOs: 141 and 115; 161) SEQ ID NOs: 141 and 121; 162) SEQ ID NOs: 141 and 157; 162) SEQ ID NOs: 141 and 272; 162) SEQ ID NOs: 141 and 277; 163) SEQ ID NOs: 141 and 279; 164) SEQ ID NOs: 141 and 282; 165) SEQ ID NOs: 141 and 286; 166) SEQ ID NOs: 141 290; 167) SEQ ID NOs: 145 and 115; 168) SEQ ID NOs: 145 and 121; 169) SEQ ID NOs: 145 and 157; 170) SEQ ID NOs: 145 and 272; 171) SEQ ID NOs: 145 and 277; 172) SEQ ID NOs: 145 and 279; 173) SEQ ID NOs: 145 and 282; 174) SEQ ID NOs: 145 and 282; 175) SEQ ID NOs: 145 and 286; 176) SEQ ID NOs: 145 and 290; 177) SEQ ID NOs: 149 and 115; 178) SEQ ID NOs: 149 and 121; 179) SEQ ID NOs: 149 and 157; 180) SEQ ID NOs: 149 and 272; 181) SEQ ID NOs: 149 and 277; 182) SEQ ID NOs: 149 and 279; and 183) SEQ ID NOs: 149 and 282; 184) SEQ ID NOs: 149 and 286; 185) SEQ ID NOs: 149 and 290; 186) SEQ ID NOs: 153 and 115; 187) SEQ ID NOs: 153 and 121; 188) SEQ ID NOs: 153 and 157; 189) SEQ ID NOs: 153 and 272; 190) SEQ ID NOs: 153 and 277; 191) SEQ ID NOs: 153 and 279; 192) SEQ ID NOs: 153 and 282; 193) SEQ ID NOs: 153 and 286; 194) SEQ ID NOs: 153 and 290; 195) SEQ ID NOs: 264 and 115; 196) SEQ ID NOs: 264 and 121; 197) SEQ ID NOs: 264 and 157; 198) SEQ ID NOs: 264 and 272; 199) SEQ ID NOs: 264 and 277; 200) SEQ ID NOs: 264 and 279; 201) SEQ ID NOs: 264 and 282; 202) SEQ ID NOs: 264 and 286; 203) SEQ ID NOs: 264 and 290; 204) SEQ ID NOs: 266 and 115; 205) SEQ ID NOs: 266 and 121; 206) SEQ ID NOs: 266 and 157; 207) SEQ ID NOs: 266 and 272; 208) SEQ ID NOs: 266 and 277; 209) SEQ ID NOs: 266 and 279; 210) SEQ ID NOs: 266 and 282; 211) SEQ ID NOs: 266 and 286; 212) SEQ ID NOs: 266 and 290; 213) SEQ ID NOs: 269 and 115; 214) SEQ ID NOs: 269 and 121; 215) SEQ ID NOs: 269 and 157; 216) SEQ ID NOs: 269 and 157; 217) SEQ ID NOs: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290, respectively or (II) any other combinations for the same antibody type as set forth in Table 2 and Table 3.
Embodiment 10. The antibody or antigen-binding fragment of any one of
Embodiments 1-9, wherein the VH and the VL comprise or consist of amino acid sequences set forth in 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18) SEQ ID NOs: 183 and 193; 18) SEQ ID NOs: 185 and 87; 19) SEQ ID NOs: 185 and 193; 20) SEQ ID NOs: 188 and 87; 21) SEQ ID NOs: 188 and 193; 22) SEQ ID NOs: 190 and 87; 23) SEQ ID NOs: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 204 and 228; 39) SEQ ID NOs: 204 and 231; 40) SEQ ID NOs: 207 and 97; 41) SEQ ID NOs: 207 and 225; 42) SEQ ID NOs: 207 and 228; 43) SEQ ID NOs: 207 and 231; 44) SEQ ID NOs: 210 and 97; 45) SEQ ID NOs: 210 and 225; 46) SEQ ID NOs: 210 and 228; 47) SEQ ID NOs: 210 and 231; 48) SEQ ID NOs: 212 and 97; 49) SEQ ID NOs: 212 and 225; 50) SEQ ID NOs: 212 and 228; 51) SEQ ID NOs: 212 and 231; 52) SEQ ID NOs: 214 and 97; 53) SEQ ID NOs: 214 and 225; 54) SEQ ID NOs: 214 and 228; 55) SEQ ID NOs: 214 and 231; 56) SEQ ID NOs: 216 and 97; 57) SEQ ID NOs: 216 and 225; 58) SEQ ID NOs: 216 and 228; 59) SEQ ID NOs: 216 and 231; 60) SEQ ID NOs: 218 and 97; 61) SEQ ID NOs: 218 and 225; 62) SEQ ID NOs: 218 and 228; 63) SEQ ID NOs: 218 and 231; 64) SEQ ID NOs: 220 and 97; 65) SEQ ID NOs: 220 and 225; 66) SEQ ID NOs: 220 and 228; 67) SEQ ID NOs: 220 and 231; 68) SEQ ID NOs: 222 and 97; 69) SEQ ID NOs: 222 and 225; 70) SEQ ID NOs: 222 and 228; 71) SEQ ID NOs: 222 and 231; 72) SEQ ID NOs: 102 and 105; 73)
SEQ ID NOs: 102 and 254; 74) SEQ ID NOs: 102 and 257; 75) SEQ ID NOs: 102 and 260; 76)
SEQ ID NOs: 235 and 105; 77) SEQ ID NOs: 235 and 254; 78) SEQ ID NOs: 235 and 257; 79)
SEQ ID NOs: 235 and 260; 80) SEQ ID NOs: 238 and 105; 81) SEQ ID NOs: 238 and 254; 82)
SEQ ID NOs: 238 and 257; 83) SEQ ID NOs: 238 and 260; 84) SEQ ID NOs: 241 and 105; 85)
SEQ ID NOs: 241 and 254; 86) SEQ ID NOs: 241 and 257; 87) SEQ ID NOs: 241 and 260; 88)
SEQ ID NOs: 243 and 105; 89) SEQ ID NOs: 243 and 254; 90) SEQ ID NOs: 243 and 257; 91)
SEQ ID NOs: 243 and 260; 92) SEQ ID NOs: 245 and 105; 93) SEQ ID NOs: 245 and 254; 94)
SEQ ID NOs: 245 and 257; 95) SEQ ID NOs: 245 and 260; 96) SEQ ID NOs: 247 and 105; 97)
SEQ ID NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100)
SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: l l l and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NOs: 111 and 272; 112) SEQ ID NOs: 111 and 277; 113) SEQ ID NOs: 111 and 279; 114) SEQ ID NOs: 111 and 282; 115) SEQ ID NOs: 111 and 286; 116) SEQ ID NOs: 111 and 290; 117) SEQ ID NOs: 125 and 115; 118) SEQ ID NOs: 125 and 121; 119) SEQ ID NOs: 125 and 157; 120) SEQ ID NOs: 125 and 272; 121) SEQ ID NOs: 125 and 277; 122) SEQ ID NOs: 125 and 279; 123) SEQ ID NOs: 125 and 282; 124) SEQ ID NOs: 125 and 286; 125) SEQ ID NOs: 125 and 290; 126) SEQ ID NOs: 128 and 115; 127) SEQ ID NOs: 128 and 121; 128) SEQ ID NOs: 128 and 157; 129) SEQ ID NOs: 128 and 272; 129) SEQ ID NOs: 128 and 279; 130) SEQ ID NOs: 128 and 282; 131) SEQ ID NOs: 128 and 286; 132) SEQ ID NOs: 128 and 290; 133) SEQ ID NOs: 131 and 115; 134) SEQ ID NOs: 131 and 121; 135) SEQ ID NOs: 131 and 157; 136) SEQ ID NOs: 131 and 272; 137) SEQ ID NOs: 131 and 277; 138) SEQ ID NOs: 131 and 279; 139) SEQ ID NOs: 131 and 282; 140) SEQ ID NOs: 131 and 286; 141) SEQ ID NOs: 131 and 290; 142) SEQ ID NOs: 134 and 115; 143) SEQ ID NOs: 134 and 121; 144) SEQ ID NOs: 134 and 157; 145) SEQ ID NOs: 134 and 272; 146) SEQ ID NOs: 134 and 277; 147) SEQ ID NOs: 134 and 279; 148) SEQ ID NOs: 134 and 282; 149) SEQ ID NOs: 134 and 286; 150) SEQ ID NOs: 134 and 290; 151) SEQ ID NOs: 137 and 115; 152) SEQ ID NOs: 137 and 121; 153) SEQ ID NOs: 137 and 157; 154) SEQ ID NOs: 137 and 272; 155) SEQ ID NOs: 137 and 277; 156) SEQ ID NOs: 137 and 279; 157) SEQ ID NOs: 137 and 282; 158) SEQ ID NOs: 137 and 286; 159) SEQ ID NOs: 137 and 290; 160) SEQ ID NOs: 141 and 115; 161) SEQ ID NOs: 141 and 121; 162) SEQ ID NOs: 141 and 157; 162) SEQ ID NOs: 141 and 272; 162) SEQ ID NOs: 141 and 277; 163) SEQ ID NOs: 141 and 279; 164) SEQ ID NOs: 141 and 282; 165) SEQ ID NOs: 141 and 286; 166) SEQ ID NOs: 141 290; 167) SEQ ID NOs: 145 and 115; 168) SEQ ID NOs: 145 and 121; 169) SEQ ID NOs: 145 and 157; 170) SEQ ID NOs: 145 and 272; 171) SEQ ID NOs: 145 and 277; 172) SEQ ID NOs: 145 and 279; 173) SEQ ID NOs: 145 and 282; 174) SEQ ID NOs: 145 and 282; 175) SEQ ID NOs: 145 and 286; 176) SEQ ID NOs: 145 and 290; 177) SEQ ID NOs: 149 and 115; 178) SEQ ID NOs: 149 and 121; 179) SEQ ID NOs: 149 and 157; 180) SEQ ID NOs: 149 and 272; 181) SEQ ID NOs: 149 and 277; 182) SEQ ID NOs: 149 and 279; and 183) SEQ ID NOs: 149 and 282; 184) SEQ ID NOs: 149 and 286; 185) SEQ ID NOs: 149 and 290; 186) SEQ ID NOs: 153 and 115; 187) SEQ ID NOs: 153 and 121; 188) SEQ ID NOs: 153 and 157; 189) SEQ ID NOs: 153 and 272; 190) SEQ ID NOs: 153 and 277; 191) SEQ ID NOs: 153 and 279; 192) SEQ ID NOs: 153 and 282; 193) SEQ ID NOs: 153 and 286; 194) SEQ ID NOs: 153 and 290; 195) SEQ ID NOs: 264 and 115; 196) SEQ ID NOs: 264 and 121; 197) SEQ ID NOs: 264 and 157; 198) SEQ ID NOs: 264 and 272; 199) SEQ ID NOs: 264 and 277; 200) SEQ ID NOs: 264 and 279; 201) SEQ ID NOs: 264 and 282; 202) SEQ ID NOs: 264 and 286; 203) SEQ ID NOs: 264 and 290; 204) SEQ ID NOs: 266 and 115; 205) SEQ ID NOs: 266 and 121; 206) SEQ ID NOs: 266 and 157; 207) SEQ ID NOs: 266 and 272; 208) SEQ ID NOs: 266 and 277; 209) SEQ ID NOs: 266 and 279; 210) SEQ ID NOs: 266 and 282; 211) SEQ ID NOs: 266 and 286; 212) SEQ ID NOs: 266 and 290; 213) SEQ ID NOs: 269 and 115; 214) SEQ ID NOs: 269 and 121; 215) SEQ ID NOs: 269 and 157; 216) SEQ ID NOs: 269 and 157; 217) SEQ ID NOs: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290. Embodiment 11. The antibody or antigen-binding fragment of any one of Embodiments 1-10, wherein i) the VH and the VL comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in SEQ ID NOs: 111 and 157, respectively; ii) the VH and the VL comprise or consist of amino acid sequences set forth in SEQ ID NOs: 111 and 157, respectively; iii) the VH of i) or ii) comprises a CDRH1, a CDRH2, and a CDRH3, and the VL of i) or ii) comprises a CDRL1, a CDRL2, and a CDRL3, having amino acid sequences determined by any VH and VL numbering scheme; iii) the VH comprises a CDRH1, a CDRH2, and a CDRH3, and the VL comprises a CDRL1, a CDRL2, and a CDRL3, having amino acid sequences according to SEQ ID NOs: 112- 114, 116, 117, and 158, respectively; iv) the antibody or antigen-binding fragment comprises any of i)-iv) in combination with a heavy chain constant region having a sequence according to any one of SEQ ID NOs: 44-80 and a light chain constant region having a sequence according to SEQ ID NO: 292; v) the antibody or antigen-binding fragment comprises a heavy chain having a sequence according to SEQ ID NO: 293 and a light chain having a sequence according to SEQ ID NO: 294; or vi) the antibody or antigen-binding fragment comprises a heavy chain having a sequence according to SEQ ID NO: 295 and a light chain having a sequence according to SEQ ID NO: 296.
Embodiment 12. The antibody or antigen-binding fragment of any one of Embodiment 1-11, which: (i) recognizes an epitope in the Spike protein of two or more, three or more, four or more, or five or more sarbecoviruses; (ii) is capable of blocking an interaction between the Spike protein of two or more, three or more, four or more, or five or more sarbecoviruses and their respective cell surface receptor(s), wherein, optionally, a cell surface receptor comprises a human ACE2; (iii) recognizes an epitope that is conserved in the Spike protein of two or more, , three or more, four or more, or five or more sarbecoviruses; (iv) is cross-reactive against two or more, three or more, four or more, or five or more sarbecoviruses, optionally comprising one or more clade lb sarbecoviruses; or (v) any combination of (i)-(iv).
Embodiment 13. The antibody or antigen-binding fragment of any one of Embodiments 1-12, which is an IgG, IgA, IgM, IgE, or IgD isotype.
Embodiment 14. The antibody or antigen-binding fragment of Embodiment 13, which is an IgG isotype selected from IgGl, IgG2, IgG3, and IgG4, and is preferably an IgGl isotype.
Embodiment 15. The antibody or antigen-binding fragment of any one of Embodiments 1-14, which is human, humanized, or chimeric.
Embodiment 16. The antibody or antigen-binding fragment of any one of Embodiments 1-15, wherein the antibody, or the antigen-binding fragment, comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab.
Embodiment 17. The antibody or antigen-binding fragment of Embodiment 16, wherein the scFv comprises more than one VH domain and more than one VL domain.
Embodiment 18. The antibody or antigen-binding fragment of any one of Embodiments 1-17, wherein the antibody or antigen-binding fragment is a multi-specific antibody or antigen-binding fragment.
Embodiment 19. The antibody or antigen-binding fragment of Embodiment 18, wherein the antibody or antigen-binding fragment is a bispecific antibody or antigen-binding fragment.
Embodiment 20. The antibody or antigen-binding fragment of Embodiment 19, comprising: a first VH and a first VL; and a second VH and a second VL, wherein the first VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs. : 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and 87 or 193, respectively; iv) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and 97, 225, 228, or 231, respectively; v) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and 105, 254, 257, or 260, respectively; or vi) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NO.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; and wherein the second VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and 87 or 193, respectively; iv) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and 97, 225, 228, or 231, respectively; v) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and 105, 254, 257, or 260, respectively; or vi) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NO.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; wherein the first VH and the second VL are different from the second VH and VL; wherein the first VH and the first VL together form a first antigen-binding site; and wherein the second VH and the second VL together form a second antigen-binding site.
Embodiment 21. The antibody or antigen-binding fragment of any one of Embodiments 1-20, wherein the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof.
Embodiment 22. The antibody or antigen-binding fragment of Embodiment 21, wherein the Fc polypeptide or fragment thereof comprises: (i) a mutation that enhances binding to a FcRn as compared to a reference Fc polypeptide that does not comprise the mutation; (ii) a mutation that enhances binding to a FcyR as compared to a reference Fc polypeptide that does not comprise the mutation; (iii) a mutation that enhances binding to human FcyRIIa and/or decreases binding to a human FcyRIIb as compared to a reference Fc polypeptide that does not comprise the mutation; and/or (iv) a mutation that enhances binding to a human Clq compared to a reference Fc polypeptide that does not comprise the mutation.
Embodiment 23. The antibody or antigen-binding fragment of Embodiment 22, wherein the Fc polypeptide comprises the substitution mutations M428L/N434S, M428L/N434A, G236A/A330L/I332E/M428L/N434S, or G236A/A330L/I332E/M428L/N434A, wherein, optionally, the antibody or antigen-binding fragment is an IgGl isotype, and comprises or consists of a Fc polypeptide or fragment thereof that comprises or consists of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NOs: 44-80, optionally other than naturally occurring variants thereof, or that comprises or consists of, the amino acid sequences set forth in SEQ ID NOs: 52-80.
Embodiment 24. An isolated polynucleotide encoding the antibody or antigenbinding fragment of any one of Embodiments 1-23.
Embodiment 25. The polynucleotide of Embodiment 24, wherein the polynucleotide comprises or consists of a nucleic acid sequence having at least 85% (/.< ., 85%, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%) identity to the nucleic acid sequence according to one or more of SEQ ID NOs: 81, 82, 91, 92, 100, 101, 109, 110, 119, 120, 123, 127, 130, 133,
136, 140, 144, 148, 152, 156, 159, 180, 182, 184, 187, 189, 191, 192, 195, 196, 200, 203, 206,
209, 211, 213, 215, 217, 219, 221, 223, 224, 227, 230, 233, 234, 237, 240, 242, 244, 246,248,
250, 252, 253, 256, 259, 261, 262, 263, 265, 268, 271, 276, 278, 281, 285, or 289.
Embodiment 26. The polynucleotide of Embodiment 24 or Embodiment 25, wherein the polynucleotide comprises deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), wherein the RNA optionally comprises messenger RNA (mRNA).
Embodiment 27. The polynucleotide of any one of Embodiments 24-26, which is codon-optimized for expression in a host cell.
Embodiment 28. A recombinant vector comprising the polynucleotide of any one of Embodiments 24-27.
Embodiment 29. A host cell comprising the polynucleotide of any one of Embodiments 24-27 and/or the vector of Embodiment 28, wherein the polynucleotide is heterologous to the host cell.
Embodiment 30. A human B cell comprising the polynucleotide of any one of Embodiments 24-27 and/or the vector of Embodiment 28, wherein polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized.
Embodiment 31. A composition comprising: (i) the antibody or antigen-binding fragment of any one of Embodiments 1-23; (ii) the polynucleotide of any one of Embodiments 24-27; (iii) the recombinant vector of Embodiment 28; (iv) the host cell of Embodiment 29; and/or (v)the human B cell of Embodiment 30, and a pharmaceutically acceptable excipient, carrier, or diluent.
Embodiment 32. The composition of Embodiment 31, comprising two or more antibodies or antigen-binding fragments, wherein the first antibody or antigen-binding fragment and second antibody or antigen-binding fragment, respectively, or the multispecific antibody or antigen-binding fragment, comprise(s) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, according to (i) any S3A3 antibody and any S3A19 antibody; (ii) any S3A3 antibody and sotrovimab; (iii) any S3 A3 antibody and S2K146; (iv) any S3 A3 antibody and S2X259; (v) any S3 A3 antibody and any S2X324 antibody; (vi) any S3 A3 antibody and S309; (vi) any S3A19 antibody and sotrovimab; (vii) any S3A19 antibody and S2K146; (viii) any S3A19 antibody and S2X259; (ix) any S3A19 antibody and any S2X324 antibody; (x) any S3A19 antibody and S309; (xi) any S3I2 antibody and any S3A3 antibody; (xii) any S3I2 antibody and any S3 Al 9 antibody; (xiii) any S3I2 antibody and sotrovimab; (xiv) any S3I2 antibody and S2K146; (xv) any S3I2 antibody and S2X259; (xvi) any S3I2 antibody and any S2X324 antibody; (xvii) any S3I2 antibody and S309; (xviii) any S3I2 antibody and any S3O13 antibody; (xix) any S3I2 antibody and any S3L17 antibody; (xx) any S3O13 antibody and any S3A3 antibody; (xxi) any S3O13 antibody and any S3A19 antibody; (xxii) any S3O13 antibody and sotrovimab; (xxiii) any S3O13 antibody and S2K146; (xxiv) any S3O13 antibody and S2X259; (xxv) any S3O13 antibody and any S2X324 antibody; (xxvi) any S3O13 antibody and S309; (xxvii) any S3O13 antibody and any S3L17 antibody; (xxviii) any S3L17 antibody and any S3 A3 antibody; (xxix) any S3L17 antibody and any S3 Al 9 antibody; (xxx) any S3L17 antibody and sotrovimab; (xxxi) any S3L17 antibody and S2K146; (xxxii) any S3L17 antibody and S2X259; (xxxiii) any S3L17 antibody and any S2X324 antibody; (xxxiv) any S3L17 antibody and S309; (xxxv) any S2V29 antibody and any S3 A3 antibody; (xxxvi) any S2V29 antibody and any S3 Al 9 antibody; (xxxvii) any S2V29 antibody and sotrovimab; (xxxviii) any S2V29 antibody and S2K146; (xxxix) any S2V29 antibody and S2X259; (xl) any S2V29 antibody and any S2X324 antibody; (xli) any S2V29 antibody and S309; (Ixlii) any S2V29 antibody and any S3L17 antibody; and (xliii) any S2V29 antibody and any S3O13 antibody, or any antigen-binding fragments thereof.
Embodiment 33. The composition of Embodiment 31, where the first antibody or antigen-binding fragment comprises a S3L17 antibody or antigen-binding fragment and the second antibody or antigen-binding fragment comprises a S2V29 antibody.
Embodiment 34. A composition of Embodiment 33, wherein the first antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 103, 85, and, 104; 103, 85, and 236; or 103, 85, and 239, and 106-108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, respectively, and the second antibody or antigen-binding fragment comprises CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3 amino acid sequences according to SEQ ID NOs.: 112- 114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and
114; 112, 270, and 114; 112, 113, and 139; 112, 126, and 139; 112, 129 and 139; 112, 132, and
139; 112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and
139; 112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 126, and
143; 112, 129 and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129 and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and
147; 112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and
151; 112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and
151; 112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and
155; 112, 126, and 155; 112, 129 and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116-118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122; 116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and
275; 116, 117, and 280; 116, 274, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and
284; 116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and
291; 116, 274, and 291; 116, 287, and 291; 273, 117, and 118; 273, 274, and 118; 273, 287, and
118; 273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and
275; 273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273, 117, and 284; 273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and
288; 273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 283, 117, 118; 283, 274, and 118;
283, 287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158;
283, 274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 280; 283, 287, and 280;
283, 117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288;
283, 287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291, respectively Embodiment 35. The composition of Embodiment 33, wherein the first antibody or antigen-binding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 104, 236, or 239, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 106 or 255, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 107, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 108 or 258, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid, and wherein the second antibody or antigenbinding fragment comprises a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein: (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 112 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs. : 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 116, 273, or 283, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 117, 274, or 287, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid.
Embodiment 36. The composition of Embodiment 33, wherein the first antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and a VL sequence according to any one of SEQ ID NOs.: 105, 254, 257, or 260, and wherein the second antibody or antigen-binding fragment comprises a VH sequence according to any one of SEQ ID NOs.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and a VL sequence according to any one of SEQ ID NOs.: 115, 121, 157, 272, 277, 279, 282, 286, or 290.
Embodiment 37. A composition comprising the polynucleotide of any one of Embodiments 24-27 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform.
Embodiment 38. A method of treating a sarbecovirus infection (e.g. infection by a SARS-CoV-2) in a subject, the method comprising administering to the subject an effective amount of (i) the antibody or antigen-binding fragment of any one of Embodiments 1-23; (ii) the polynucleotide of any one of Embodiments 24-27; (iii) the recombinant vector of Embodiment 28; (iv) the host cell of Embodiment 29; and/or (v) the human B cell of Embodiment 30, and/or
(vi) the composition of any one of Embodiments 31-37.
Embodiment 39. The antibody or antigen-binding fragment of any one of Embodiments 1-23, the polynucleotide of any one of Embodiments 24-27, the recombinant vector of Embodiment 28, the host cell of Embodiment 29, the human B cell of Embodiment 30, and/or the composition of any one of Embodiments 31-37 for use in a method of treating a sarbecovirus infection (e.g. infection by a SARS-CoV-2) in a subject.
Embodiment 40. The antibody or antigen-binding fragment of any one of Embodiments 1-23, the polynucleotide of any one of Embodiments 24-27, the recombinant vector of Embodiment 28, the host cell of Embodiment 29, the human B cell of Embodiment 30, and/or the composition of any one of Embodiments 31-37 for use in the preparation of a medicament for the treatment of a sarbecovirus infection (e.g. infection by a SARS-CoV-2) in a subject.
Embodiment 41. The antibody or antigen-binding fragment of any one of Embodiments 1-23 or 39-40 wherein the antibody or antigen-binding fragment binds to two or more sarbecovirus S proteins, as measured using biolayer interferometry.
Embodiment 42. A kit comprising a liquid composition comprising and antibody or antigen-binding fragment of any one of Embodiments 1-23 or 39-40 and instructions for use thereof in treating a SARS-CoV-2 infection in a subject.
Embodiment 43. The kit of Embodiment 42, wherein the instructions for use are for the method of Embodiment 38 or the use according to any one of Embodiments 39-40.
Embodiment 44. A method for in vitro diagnosis of a sarbecovirus infection (e.g. infection by a SARS-CoV-2), the method comprising: (i) contacting a sample from a subject with an antibody or antigen-binding fragment of any one of Embodiments 1-23; and (ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigenbinding fragment.
Embodiment 45. A method for producing an antibody or antigen-binding fragment of any one of Embodiments 1-23 or 39-40, wherein the method comprises culturing a host cell expressing the antibody or antigen-binding fragment under conditions and for a time sufficient to produce the antibody, or the antigen-binding fragment.
Embodiment 46. The method for producing an antibody or antigen-binding fragment of Embodiment 45, wherein the host cell comprises a recombinant vector of Embodiment 28.
Embodiment 47. The method for producing an antibody or antigen-binding fragment of Embodiment 46, wherein the host cell is a mammalian cell. Table 2. Sequences
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000120_0001
Figure imgf000121_0001
Figure imgf000122_0001
Figure imgf000123_0001
Figure imgf000124_0001
Figure imgf000125_0001
Figure imgf000126_0001
Figure imgf000127_0001
Figure imgf000128_0001
Figure imgf000129_0001
Figure imgf000130_0001
Figure imgf000131_0001
Figure imgf000132_0001
Figure imgf000133_0001
Figure imgf000134_0001
Figure imgf000135_0001
Figure imgf000136_0001
Figure imgf000137_0001
Figure imgf000138_0001
Figure imgf000139_0001
Figure imgf000140_0001
*Table 2 indicates CDRH1, CDRH2 and CDRH3d (IMGT definition), in that order, in bold in each corresponding VH sequence; and CDRL1, CDRL2, CDRL3, in that order, in bold in each corresponding VL sequence. Table 3: S3A3, S3A19 and Variants, S3I2, S3O13, and S3L17, and S2V29 and Variants
(amino acid SEP ID NOs.)
Figure imgf000140_0002
Figure imgf000141_0001
EXAMPLES
EXAMPLE 1
ANTIBODY PRODUCTION AND MATERIALS
The following materials and methods were used in Example 1 and, unless otherwise noted, in Example 2 and Example 3.
Cell lines
Cell lines used in Example 1 were obtained from ATCC (HEK293T, Vero and Vero-E6), ThermoFisher Scientific (Expi293F™ cells).
Recombinant protein production Wild-type SARS-CoV-2 RBD (with N-terminal signal peptide and ‘ETGT’, and C- terminal 8xHis-tag) was expressed in Expi293F cells at 37°C and 8% CO2 in the presence of 10 pM kifunensine. Transfection was performed using the ExpiFectamine 293 Transfection Kit (Thermo Fisher Scientific). Cell culture supernatant was collected four days after transfection and supplemented with lOx PBS to a final concentration of 2.5x PBS (342.5 mM NaCl, 6.75 mM KC1 and 29.75 mM phosphates). SARS-CoV-2 S hexapro protein, used for cryo-EM single particle studies, was expressed and purified using known methods.
Antibody isolation and recombinant production
Antigen specific IgG+ memory B cells were isolated and cloned from PBMC of convalescent individuals who were previously vaccinated for or infected with SARS-CoV-2, then later were infected with a SARS-CoV-2 Omicron variant. Briefly, CD19+ B cells were enriched by staining with CD 19 PE-Cy7 and anti -PE microbeads (Milteniy), followed by positive selection using LS columns. Enriched B cells were stained with anti-IgD, anti-IgM, anti-IgA, anti-CD14, all PE labelled and prefusion SARS-CoV-2 S-Avi tag conjugated with streptavidin Alexa-Fluor 647 (Life Technologies). SARS-CoV-2-specific IgG+ memory B cells were sorted and seeded on MSC (mesenchymal stromal cells) at 0.5 cell/well in the presence of CpG2006, IL-2, IL6, IL- 10 and IL-21 using known methods. After 7 days, B cell supernatants were screened by ELISA for binding to a panel of RBDs representative of different sarbecovirus clades as well as by neutralization using high-throughput VSV SARS-CoV-2 S-based microneutralization. Abs VH and VL sequences were obtained by reverse transcription PCR (RT-PCR) and mAbs were expressed as recombinant human IgGl, carrying the half-life extending M428L/N434S (“LS”, or “MLNS”) mutation in the Fc region fragment. ExpiCHO cells were transiently transfected with heavy and light chain expression vectors using known methods. Using the Database IMGT, the VH and VL gene family and the number of somatic mutations were determined by analyzing the homology of the VH and VL sequences to known human V, D and J genes. UCA sequences of heavy and light variable regions were constructed using IMGT/V-QUEST.
MAbs affinity purification was performed on AKTA Xpress FPLC (Cytiva) operated by UNICORN software version 5.11 (Build 407) using HiTrap Protein A columns (Cytiva) for full length human and hamster mAbs and CaptureSelect CH1-XL MiniChrom columns (ThermoFisher Scientific) for Fab fragments, using PBS as mobile phase. Buffer exchange to the appropriate formulation buffer was performed with a HiTrap Fast desalting column (Cytiva). The final products were sterilized by filtration through 0.22 pm filters and stored at 4°C.
Various comparator anti-SARS-CoV-2 antibodies are used in these Examples. S2X259 is described in Tortorici, M.A., et al. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature 597, 103-108 (2021). https://doi.org/10.1038/s41586-021-03817-4. S2K146 is described in Park, Y-J., et al. Science https://doi.org/10.1126/science.abm8143 (2022). S2X324 is described in WO2021/226560. S309 is described in Pinto, D., et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290-295 (2020). https://doi.org/10.1038/s41586-020-2349-y. Sotrovimab (VIR-7831) was developed from S309 and is described in Cathcart, A., et al. The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2; bioRxiv 2021.03.09.434607; doi: https://doi.org/10.1101/2021.03.09.434607. Sotrovimab, in addition to having the VH and VL sequences noted in Table 4, is an IgGl antibody with MLNS F mutations.
The antigen-binding site of certain antibodies used in the examples is provided in Figure 3 and Table 4.
Table 4: Characteristics of certain comparator antibodies
Figure imgf000143_0001
Sequences of Antibodies or DNA Encoding Antibodies Used in the Examples
S3A3
S3A3-VH
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSSISWNSGSLGYADSVKGRF
TISRDNAKNSLYLQMNTLRAEDTALYYCAKDTGYEILTIAYGMDVWGQGTTVTVSS
S3A3-VL
QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTS
ASLAITGLQAEDEADYYCQSLDSSLSGLYVFGTGTKVTVL
S3L17
VH
GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGC
AGCCTCTGAGATTATTGTCAGTAGTAACTACATGAATTGGGTCCGCCAGGCTCCAGGGAAGGGGCTG
GAGTGGGTCTCAGTTATTTATGCCGGTGGTAGCACATTCTACGCAGACTCCGTGAGGGGCCGATTCA
CCATCTCCAGAGACAATTCCAAGAACACACTGTACCTTCAAATGAACAGCCTGAGACCTGATGACACG
GCTATATACTACTGTGCGAGAGATCTCGGGCCCTGGGGTATGGACGTCTGGGGCCAAGGGACCACG
GTCACCGTCTCCTCA
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPWGMDVWGQGTTVTVSS
VK
GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCGCCATCACTTGC
CGGGCGAGTCACGGCATTAACAATGATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGC
TCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGG
ACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAACATTAT
AGCAGTGACCCTCGATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC
DIQMTQSPSSLSASVGDRVAITCRASHGINNDLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFT
LTISSLQPEDVATYYCQHYSSDPRFTFGPGTKVDIK
S3A19 (VH.l + VK) and S3A19 dev, variants (VH.2 or VH.3 + VK)
S3A19-VH.1
EVQLVESGGGLVQPGGSLRLSCAVSGFTVSRNYMCWFRQAPGKGLEWVSLIYPGGSTFYADSVKGRLTIS
RDNSNNTLYLQMNSLRAEDTAVYFCAREGGTARPLYSFWGQGTLVTVSS
S3A19-VH.2
EVQLVESGGGLVQPGGSLRLSCAVSGFTVSRNYMSWFRQAPGKGLEWVSLIYPGGSTFYADSVKGRLTIS RDNSKNTLYLQMNSLRAEDTAVYFCAREGGTARPLYSFWGQGTLVTVSS
S3A19-VH.3
EVQLVESGGGLVQPGGSLRLSCAVSGFTVSRNYMSWFRQAPGKGLEWVSLIYPGGSTFYADSVKGRLTIS
RDNSDNTLYLQMNSLRAEDTAVYFCAREGGTARPLYSFWGQGTLVTVSS
S3A19-VK
DIRMTQSPSSLSASVGDRVTITCQASQDITTFLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTF
TISSLQPEDIATYYCQQYDNLPITFGQGTRLEIK
VH
GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGC
AGTCTCTGGATTCACCGTCAGTAGGAACTACATGTGCTGGTTCCGCCAGGCTCCAGGGAAGGGGCTG
GAATGGGTCTCACTTATTTATCCCGGTGGTAGCACATTCTACGCAGACTCCGTGAAGGGCAGATTGA CCATCTCCAGAGACAATTCCAACAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACG GCCGTGTATTTCTGTGCGAGAGAAGGCGGGACAGCTCGTCCCCTTTACAGCTTCTGGGGCCAGGGA
ACCCTGGTCACCGTCTCCTCAG
VK
GACATCCGGATGACCCAGTCTCCATCCTCCCTGTCTGCTTCTGTAGGGGACAGAGTCACCATCACTTGC
CAGGCGAGTCAGGACATTACCACCTTTTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGC TCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGG ACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATCGCAACATATTACTGTCAACAGTA
TGATAATCTCCCCATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC
S3L17-VH, 1 parental codon optimized
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPWGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTGGTGCAGCCTGGCGGATCTCTGAGACTGTCTTGTGC
TGCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTCAGACAGGCCCCCGGCAAGGGCCTGG AATGGGTGTCTGTGATCTATGCTGGCGGCTCTACCTTCTACGCCGATTCCGTGCGGGGCAGATTCACCA TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATAGCCTGCGGCCTGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTCGGCCCTTGGGGCATGGACGTGTGGGGACAAGGCACCACCGTGAC AGTGTCCAGC
S3L17-VH.2 (W102F)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPFGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGAGGCAGCCTGAGACTGTCTTGTGC
TGCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTGCGGCAAGCCCCTGGCAAGGGCCTGG AATGGGTCTCTGTGATCTATGCTGGCGGATCTACATTCTACGCCGATTCCGTGAGAGGCAGATTCACCA TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATTCTCTGCGGCCTGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTGGGCCCCTTTGGCATGGACGTGTGGGGCCAGGGCACCACCGTGAC CGTGTCCAGC
S3L17-VH.3 (W102Y)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPYGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGAGGAAGCCTGAGACTGTCTTGTGC
TGCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTGCGGCAAGCCCCTGGCAAGGGCCTGG AATGGGTCTCTGTGATCTATGCTGGCGGCTCTACCTTCTACGCCGATTCCGTGAGAGGCAGATTCACCA TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATTCTCTGCGGCCCGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTGGGCCCTTACGGCATGGACGTGTGGGGCCAGGGCACCACAGTGAC CGTGTCCAGC
S3L17-VH.4 (D61Q)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYAQSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPWGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGAGGCTCTCTGAGACTGTCTTGTGC
TGCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTGCGGCAGGCCCCTGGCAAGGGCCTGG AATGGGTCTCCGTGATCTATGCTGGCGGATCTACCTTCTACGCCCAATCTGTGAGAGGCAGATTCACCA TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATAGCCTGCGGCCCGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTGGGCCCTTGGGGCATGGACGTGTGGGGCCAGGGCACCACCGTGAC AGTGTCCAGC
S3L17-VH.5 (S62A)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADAVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPWGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGCGGCTCTCTGCGGCTGAGCTGTGC
TGCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTCAGACAGGCCCCCGGCAAGGGCCTGG AATGGGTGTCCGTGATCTATGCTGGAGGCTCCACCTTCTACGCCGATGCCGTGCGGGGCAGATTCACCA TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATAGCCTGAGACCTGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTGGGCCCTTGGGGCATGGACGTGTGGGGACAAGGCACAACCGTGAC CGTGTCTTCT
S3L17-VH.6 (D61Q; W102F)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYAQSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPFGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGCGGATCTCTGAGACTGTCTTGTGC
TGCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTGCGGCAGGCCCCCGGCAAGGGCCTGG AATGGGTCTCCGTGATCTATGCTGGCGGATCTACCTTCTACGCCCAATCTGTGAGAGGCAGATTCACCA TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATAGCCTGCGGCCTGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTGGGCCCTTTTGGCATGGACGTGTGGGGCCAGGGCACCACAGTGAC CGTGTCCAGC
S3L17-VH.7 (S62A; W102F)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADAVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPFGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGAGGATCTCTGAGACTGTCTTGTGC
TGCCTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTGCGGCAAGCTCCTGGCAAGGGCCTGG AATGGGTCTCCGTGATCTATGCTGGCGGCTCCACCTTCTACGCCGATGCCGTGAGAGGCAGATTCACCA TCAGCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATTCCCTGCGGCCCGACGACACCGCC
ATCTACTACTGCGCCAGAGATCTGGGCCCTTTTGGCATGGACGTGTGGGGCCAGGGCACCACAGTGAC CGTGTCTAGC
S3L17-VH.8 (D61Q; W102Y)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYAQSVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPYGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGCGGCTCTCTGAGACTGTCTTGTGCT GCTTCTGAGATCATCGTGTCCTCCAACTACATGAACTGGGTGCGGCAGGCCCCCGGCAAGGGACTGGA ATGGGTCAGCGTGATCTATGCTGGCGGATCTACCTTCTACGCCCAATCCGTGAGAGGCAGATTCACCAT
CTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATAGCCTGCGGCCTGACGACACCGCCA TCTACTACTGCGCCAGAGATCTGGGCCCTTACGGCATGGACGTGTGGGGCCAGGGCACCACCGTGACA GTGTCCTCT
S3L17-VH.9 (S62A; W102Y)
EVQLVESGGGLVQPGGSLRLSCAASEIIVSSNYMNWVRQAPGKGLEWVSVIYAGGSTFYADAVRGRFTISR
DNSKNTLYLQMNSLRPDDTAIYYCARDLGPYGMDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTGGTCTCGTGCAGCCTGGCGGATCTCTGAGACTGTCTTGTGC TGCTTCCGAGATCATCGTGTCCTCCAACTACATGAACTGGGTCAGACAAGCCCCCGGCAAGGGCCTGG AATGGGTGTCCGTGATCTATGCTGGCGGCTCTACCTTCTACGCCGATGCCGTGCGGGGAAGATTCACCA
TCTCCCGGGACAACTCCAAGAACACCCTGTACCTGCAGATGAATAGCCTGCGGCCTGACGACACCGCC ATCTACTACTGCGCCAGAGATCTGGGCCCTTACGGCATGGACGTGTGGGGCCAGGGCACCACCGTGAC AGTGTCTAGC
S3L17-VK, 1 parental codon optimized
DIQMTQSPSSLSASVGDRVAITCRASHGINNDLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFT
LTISSLQPEDVATYYCQHYSSDPRFTFGPGTKVDIK
GATATCCAAATGACTCAAAGTCCAAGTAGTCTCTCCGCCTCCGTGGGCGACAGAGTGGCCATCACCTG TAGAGCCTCTCACGGCATCAACAACGACCTGGCTTGGTATCAGCAGAAGCCTGGCAAAGTGCCCAAGC TGCTGATCTACGCCGCTTCTACCCTGCAAAGCGGCGTGCCATCTCGGTTCTCCGGCTCTGGATCTGGCA
CCGACTTCACACTGACCATCTCCTCCCTGCAGCCTGAGGATGTCGCTACCTACTACTGCCAGCACTACT CCAGCGATCCTCGGTTTACCTTCGGCCCTGGAACCAAGGTGGACATCAAG
S3L17-VK.2 (N30S)
DIQMTQSPSSLSASVGDRVAITCRASHGISNDLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFT LTISSLQPEDVATYYCQHYSSDPRFTFGPGTKVDIK
GATATCCAAATGACTCAAAGTCCAAGTAGTCTGTCTGCCTCCGTGGGCGACAGAGTGGCTATCACATG
TAGAGCCTCTCACGGCATCTCCAACGACCTCGCCTGGTATCAGCAGAAACCTGGCAAGGTCCCAAAGC
TGCTGATCTACGCCGCTAGCACCCTGCAATCTGGCGTGCCCAGCCGGTTCTCCGGCTCCGGATCTGGCA
CCGACTTTACACTGACCATCTCCTCTCTGCAGCCTGAGGATGTGGCTACCTACTACTGCCAGCACTACT
CCTCCGATCCTCGGTTCACCTTCGGCCCTGGAACCAAGGTGGACATCAAG
S3L17-VK.3 (D94A)
DIQMTQSPSSLSASVGDRVAITCRASHGINNDLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFT
LTISSLQPEDVATYYCQHYSSAPRFTFGPGTKVDIK
GATATCCAAATGACTCAAAGTCCAAGTAGTCTCTCCGCCTCCGTGGGCGATAGAGTGGCCATCACCTGT
AGAGCCTCTCACGGCATCAACAACGACCTGGCCTGGTATCAGCAGAAGCCCGGCAAAGTGCCTAAGCT
GCTGATCTACGCCGCTAGCACACTGCAATCTGGCGTCCCATCTCGGTTCTCCGGCTCCGGCTCTGGAAC
AGACTTCACCCTGACCATCTCCAGCCTGCAGCCTGAGGACGTGGCTACCTACTACTGCCAGCACTACTC
CTCTGCTCCTCGGTTTACCTTCGGACCTGGCACCAAGGTGGACATCAAG
S3L17-VK.4 (N30S; D94A)
DIQMTQSPSSLSASVGDRVAITCRASHGISNDLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFT
LTISSLQPEDVATYYCQHYSSAPRFTFGPGTKVDIK
GATATCCAAATGACTCAAAGTCCAAGTAGTCTCTCCGCCTCCGTGGGCGACAGAGTGGCCATCACCTG
TAGAGCCTCTCACGGCATCTCCAACGACCTGGCCTGGTACCAGCAGAAGCCTGGCAAAGTGCCTAAGC
TGCTGATCTACGCCGCTTCTACCCTGCAAAGCGGCGTGCCCTCCCGGTTCTCCGGCTCTGGATCTGGCA
CCGACTTCACACTGACCATCAGCTCCCTGCAGCCTGAGGATGTCGCTACCTATTACTGCCAGCACTACT
CCTCTGCTCCTCGGTTTACCTTCGGCCCAGGCACCAAGGTGGACATCAAG
S3O13
VH
CAGGTCCAGCTTGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAA
GGCCTCTGGATACACCTTCACTATGTCTGCTATGCATTGGGTGCGCCAGGCCCCCGGACAAAGGCCT
GAGTGGATGGGATGGATCACCGCTGGCACTGGTGACACAAAATATTCACAGAAGTTCCAAGGCAGA
GTCACCATTACCAGTGACACATCCGCGACCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGA
CACGGCTGTCTATTACTGTGCGAAGGACGGTGACTACGCCGCTGAATACTTCCAGCACTGGGGCCA
GGGCACCCTGGTCACCGTCTCCTCAG
OVOLVOSGAEVKKPGASVKVSCKASGYTFTMSAMHWVROAPGORPEWMGWITAGTGDTKYSOKFQGR
VTITSDTSATTAYMELSSLRSEDTAVYYCAKDGDYAAEYFQHWGQGTLVTVSS
VK
GACATCGTGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGC
CGGGCCAGTCAGAGTATTAATAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAACC
TCCTGATCTCTGATGCCTCCAATTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGG
ACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTAT
AATACTTACCCCTCGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC
DIVMTQSPSTLSASVGDRVTITCRASQSINSWLAWYQQKPGKAPNLLISDASNLESGVPSRFSGSGSGTEFTL
TIS SLQPDDFATYYCQQYNTYPSFGQGTKVEIK
S3I2
VH
GAGGTGCAACTGGTGGAGACTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGACACTCTCCTGTGC
AGCCTCTGGGTTAGTTGTCAGTTACAACTACATGACTTGGGTCCGTCAGGCTCCAGGGAAGGGCCTG
GAGTGGCTTTCAGTCATTTATGCCGGTGGTAGCACATTCTACGCAGACTCCGTGAAGGGCCGATTCA
CCGTCTCCAGAGACAATTCCAACAACACCCTGTATCTTCAAATGAACAACCTGAGAGCCGAGGACACG
GCCGTGTATTTCTGTGCGAGATGGGGACAGGTACGGTTCACTAGTGAGGAGGCCTACTATAAATA
CGGTTTGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCA
EVOLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVROAPGKGLEWLSVIYAGGSTFYADSVKGRFTVS
RDNSNNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGLDVWGQGTTVTVSS
VK
GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGC
CGGGCCAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAAAGACCAGGGAAAGCCCCTAAGC
TCCTGATCTTCACTGCATCCACTTTGCAAAGTGGGGTGTCATCAAGGTTCAGCGGCAGTGGATCTGGG
ACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATCTTGCAACTTATTACTGTCAACAACT
TAATAGTAACCTCCAGGGAACGTTCGGCCAAGGGACCAGGGTGGAAATCAAAC
DIQLTQSPSFLSASVGDRVTITCRASQGISNYLAWYQQRPGKAPKLLIFTASTLQSGVSSRFSGSGSGTEFTL TIS SLQPEDL AT Y YCQQLN SN LQGTFGQGTR VE IK
S3I2-VH.2 (N75K)
EVQLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVRQAPGKGLEWLSVIYAGGSTFYADSVKGRFTVS
RDNSKNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGLDVWGQGTTVTVSS
GAGGTGCAGCTGGTGGAGACCGGCGGAGGACTGATCCAGCCAGGAGGATCTCTGACACTGTCCTGCGC
TGCTAGCGGACTGGTGGTGTCCTACAACTATATGACCTGGGTGAGGCAGGCTCCTGGCAAGGGACTGG
AGTGGCTGAGCGTGATCTACGCCGGCGGCAGCACATTCTATGCTGACTCTGTGAAGGGCAGGTTTACC GTGTCTCGGGATAACTCCAAGAATACACTGTACCTGCAGATGAACAATCTGAGAGCCGAGGACACCGC CGTGTACTTCTGTGCCAGATGGGGCCAGGTGCGCTTTACATCTGAGGAGGCTTACTATAAGTACGGACT
GGACGTGTGGGGACAGGGAACCACAGTGACCGTGTCCAGC
S3I2-VH.3 (N75K S62A)
EVQLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVRQAPGKGLEWLSVIYAGGSTFYADAVKGRFTVS
RDNSKNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGLDVWGQGTTVTVSS
GAGGTGCAGCTGGTGGAGACCGGCGGAGGACTGATCCAGCCAGGAGGATCTCTGACACTGTCCTGCGC
TGCTAGCGGACTGGTGGTGTCCTACAACTATATGACCTGGGTGAGGCAGGCTCCTGGCAAGGGACTGG
AGTGGCTGAGCGTGATCTACGCCGGCGGCAGCACATTCTATGCTGACGCCGTGAAGGGCAGGTTTACC GTGTCTCGGGATAACTCCAAGAATACACTGTACCTGCAGATGAACAATCTGAGAGCCGAGGACACCGC CGTGTACTTCTGTGCCAGATGGGGCCAGGTGCGCTTTACATCTGAGGAGGCTTACTATAAGTACGGACT
GGACGTGTGGGGACAGGGAACCACAGTGACCGTGTCCAGC
S3I2-VH.4 (N75K D61Q)
EVQLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVRQAPGKGLEWLSVIYAGGSTFYAQSVKGRFTVS
RDNSKNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGLDVWGQGTTVTVSS
GAGGTGCAGCTGGTGGAGACCGGCGGAGGACTGATCCAGCCAGGAGGATCTCTGACACTGTCCTGCGC
TGCTAGCGGACTGGTGGTGTCCTACAACTATATGACCTGGGTGAGGCAGGCTCCTGGCAAGGGACTGG
AGTGGCTGAGCGTGATCTACGCCGGCGGCAGCACATTCTATGCTCAGTCTGTGAAGGGCAGGTTTACC GTGTCTCGGGATAACTCCAAGAATACACTGTACCTGCAGATGAACAATCTGAGAGCCGAGGACACCGC CGTGTACTTCTGTGCCAGATGGGGCCAGGTGCGCTTTACATCTGAGGAGGCTTACTATAAGTACGGACT
GGACGTGTGGGGACAGGGAACCACAGTGACCGTGTCCAGC
S3I2-VH.5 (N75K LI 141)
EVQLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVRQAPGKGLEWLSVIYAGGSTFYADSVKGRFTVS
RDNSKNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGIDVWGQGTTVTVSS
GAGGTGCAGCTGGTGGAGACCGGCGGAGGACTGATCCAGCCAGGAGGATCTCTGACACTGTCCTGCGC
TGCTAGCGGACTGGTGGTGTCCTACAACTATATGACCTGGGTGAGGCAGGCTCCTGGCAAGGGACTGG
AGTGGCTGAGCGTGATCTACGCCGGCGGCAGCACATTCTATGCTGACTCTGTGAAGGGCAGGTTTACC GTGTCTCGGGATAACTCCAAGAATACACTGTACCTGCAGATGAACAATCTGAGAGCCGAGGACACCGC CGTGTACTTCTGTGCCAGATGGGGCCAGGTGCGCTTTACATCTGAGGAGGCTTACTATAAGTACGGAAT
CGACGTGTGGGGACAGGGAACCACAGTGACCGTGTCCAGC
S3I2-VH.6 (N75K S62A LI 141)
EVQLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVRQAPGKGLEWLSVIYAGGSTFYADAVKGRFTVS
RDNSKNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGIDVWGQGTTVTVSS
GAGGTGCAGCTGGTGGAGACCGGCGGAGGACTGATCCAGCCAGGAGGATCTCTGACACTGTCCTGCGC
TGCTAGCGGACTGGTGGTGTCCTACAACTATATGACCTGGGTGAGGCAGGCTCCTGGCAAGGGACTGG
AGTGGCTGAGCGTGATCTACGCCGGCGGCAGCACATTCTATGCTGACGCCGTGAAGGGCAGGTTTACC GTGTCTCGGGATAACTCCAAGAATACACTGTACCTGCAGATGAACAATCTGAGAGCCGAGGACACCGC CGTGTACTTCTGTGCCAGATGGGGCCAGGTGCGCTTTACATCTGAGGAGGCTTACTATAAGTACGGAAT
CGACGTGTGGGGACAGGGAACCACAGTGACCGTGTCCAGC
S3I2-VH.7 (N75K D61Q L114I)
EVQLVETGGGLIQPGGSLTLSCAASGLWSYNYMTWVRQAPGKGLEWLSVIYAGGSTFYAQSVKGRFTVS
RDNSKNTLYLQMNNLRAEDTAVYFCARWGQVRFTSEEAYYKYGIDVWGQGTTVTVSS
GAGGTGCAGCTGGTGGAGACCGGCGGAGGACTGATCCAGCCAGGAGGATCTCTGACACTGTCCTGCGC
TGCTAGCGGACTGGTGGTGTCCTACAACTATATGACCTGGGTGAGGCAGGCTCCTGGCAAGGGACTGG
AGTGGCTGAGCGTGATCTACGCCGGCGGCAGCACATTCTATGCTCAGTCTGTGAAGGGCAGGTTTACC GTGTCTCGGGATAACTCCAAGAATACACTGTACCTGCAGATGAACAATCTGAGAGCCGAGGACACCGC CGTGTACTTCTGTGCCAGATGGGGCCAGGTGCGCTTTACATCTGAGGAGGCTTACTATAAGTACGGAAT
CGACGTGTGGGGACAGGGAACCACAGTGACCGTGTCCAGC
S3I2-VK.1 parental codon optimized DIQLTQSPSFLSASVGDRVTITCRASQGISNYLAWYQQRPGKAPKLLIFTASTLQSGVSSRFSGSGSGTEFTL TIS SLQPEDLATYYCQQLNSNLQGTFGQGTRVEIK
GACATCCAGCTGACCCAGAGCCCATCTTTCCTGTCCGCCAGCGTGGGCGATAGGGTGACCATCACATG CCGGGCCTCTCAGGGCATCTCCAACTACCTGGCTTGGTATCAGCAGAGACCCGGCAAGGCCCCTAAGC TGCTGATCTTTACCGCTAGCACACTGCAGTCTGGCGTGTCCAGCCGCTTCTCTGGATCCGGAAGCGGAA CCGAGTTTACCCTGACAATCTCTTCCCTGCAGCCCGAGGACCTGGCTACATACTATTGTCAGCAGCTGA ACTCCAATCTGCAGGGCACCTTCGGCCAGGGCACAAGGGTGGAGATCAAG
S3I2-VK.2 (N31Q)
DIQLTQSPSFLSASVGDRVTITCRASQGISQYLAWYQQRPGKAPKLLIFTASTLQSGVSSRFSGSGSGTEFTLT ISSLQPEDLATYYCQQLNSNLQGTFGQGTRVEIK
GACATCCAGCTGACCCAGAGCCCATCTTTCCTGTCCGCCAGCGTGGGCGATAGGGTGACCATCACATG CCGGGCCTCTCAGGGCATCTCCCAGTACCTGGCTTGGTATCAGCAGAGACCCGGCAAGGCCCCTAAGC TGCTGATCTTTACCGCTAGCACACTGCAGTCTGGCGTGTCCAGCCGCTTCTCTGGATCCGGAAGCGGAA CCGAGTTTACCCTGACAATCTCTTCCCTGCAGCCCGAGGACCTGGCTACATACTATTGTCAGCAGCTGA ACTCCAATCTGCAGGGCACCTTCGGCCAGGGCACAAGGGTGGAGATCAAG
S3O13
S3O13-VH.1 parental codon optimized
OVOLVOSGAEVKKPGASVKVSCKASGYTFTMSAMHWVROAPGORPEWMGWITAGTGDTKYSOKFQGR VTITSDTSATTAYMELSSLRSEDTAVYYCAKDGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCTGGCGCTTCTGTGAAAGTGTCCTGCAA GGCCTCTGGCTACACCTTCACCATGTCCGCCATGCACTGGGTGCGGCAGGCTCCTGGACAGCGGCCCG AGTGGATGGGCTGGATCACCGCTGGAACCGGCGATACCAAGTACTCCCAGAAGTTCCAAGGCAGAGTG ACCATCACCTCCGACACCTCTGCTACAACAGCCTACATGGAACTGTCCAGCCTGAGATCCGAGGACAC AGCCGTGTACTACTGTGCCAAGGACGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGCA CCCTGGTGACCGTGTCTAGC
S3O13-VH.2 (M31S D99E)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV TITSDTSATTAYMELSSLRSEDTAVYYCAKEGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTGAAGAAGCCTGGCGCTTCCGTGAAGGTGTCCTGCAA GGCCTCTGGCTACACCTTCACCAGCTCTGCCATGCACTGGGTCAGACAGGCCCCTGGACAGCGGCCCG AATGGATGGGCTGGATCACAGCTGGAACTGGCGATACCAAGTACTCCCAGAAGTTCCAAGGCAGAGTG ACCATCACCTCCGACACATCTGCTACCACCGCCTACATGGAACTGTCCAGCCTGCGGTCCGAGGACAC CGCTGTGTACTACTGTGCCAAAGAGGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGCA CCCTGGTGACCGTGTCTTCT
S3O13-VH.3 (M31S D99Q)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV TITSDTSATTAYMELSSLRSEDTAVYYCAKQGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCCGGAGCTTCCGTGAAAGTGTCCTGCAA GGCCTCTGGCTACACCTTCACCAGCTCTGCCATGCACTGGGTGCGGCAGGCTCCTGGCCAGCGGCCTG AGTGGATGGGCTGGATCACAGCTGGAACTGGCGATACCAAGTACTCCCAGAAGTTCCAGGGCAGAGTG ACCATCACCTCCGACACCTCTGCTACCACCGCCTACATGGAACTGTCCTCTCTGAGATCCGAGGACACA GCCGTGTACTACTGTGCCAAGCAGGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAAGGCAC CCTGGTGACCGTGTCTAGC
S3O13-VH.4 (M31S G100A)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV TITSDTSATTAYMELSSLRSEDTAVYYCAKDADYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCCGGCGCTTCCGTGAAAGTGTCCTGCAA GGCCTCTGGCTACACCTTCACCTCTTCTGCCATGCACTGGGTGCGGCAGGCTCCTGGCCAGCGGCCTGA GTGGATGGGCTGGATCACCGCTGGAACAGGCGACACCAAGTACTCCCAGAAGTTCCAAGGAAGAGTG ACAATCACCTCCGACACAAGCGCTACCACCGCCTACATGGAACTGTCCTCTCTGAGATCCGAGGATAC CGCCGTGTACTACTGTGCCAAGGACGCCGACTACGCCGCTGAGTATTTTCAGCACTGGGGCCAGGGCA CCCTGGTGACCGTGTCTAGC
S3O13-VH.5 (M3 II D99E)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTISAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV TITSDTSATTAYMELSSLRSEDTAVYYCAKEGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCCGGAGCTTCCGTGAAGGTGTCCTGCAA GGCCTCTGGCTACACCTTCACCATCTCCGCCATGCACTGGGTGCGGCAGGCCCCTGGCCAGCGGCCTG AGTGGATGGGCTGGATCACCGCTGGAACCGGCGATACCAAGTACAGCCAGAAGTTCCAAGGCAGAGT GACAATCACATCCGACACCTCTGCTACCACCGCCTACATGGAACTGTCCTCTCTGAGATCCGAGGACA CAGCCGTGTACTACTGTGCTAAAGAAGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGC
ACCCTGGTGACCGTGTCTAGC
S3O13-VH.6 (M3 II D99Q)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTISAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV
TITSDTSATTAYMELSSLRSEDTAVYYCAKQGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCTGGCGCTTCTGTGAAAGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCATCTCCGCCATGCACTGGGTGCGGCAGGCTCCTGGACAGCGGCCCG
AGTGGATGGGCTGGATCACAGCTGGCACCGGCGATACCAAGTACTCCCAGAAGTTCCAAGGCAGAGTG ACCATCACCTCCGACACCTCTGCTACCACCGCCTACATGGAACTGTCCAGCCTGAGATCCGAGGACAC AGCCGTGTACTACTGTGCCAAGCAGGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGAA
CACTGGTGACCGTGTCTAGC
S3O13-VH.7 (M3 II G100A)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTISAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV
TITSDTSATTAYMELSSLRSEDTAVYYCAKDADYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTGAAGAAGCCTGGCGCTTCCGTGAAAGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCATCTCCGCCATGCACTGGGTCCGGCAGGCTCCTGGACAACGGCCCG
AGTGGATGGGCTGGATCACCGCTGGCACCGGCGACACCAAGTACTCCCAGAAGTTTCAGGGAAGAGTG ACCATCACATCTGACACCTCTGCTACCACCGCCTACATGGAACTGTCCTCTCTGAGATCCGAGGATACT GCCGTGTACTATTGTGCTAAGGACGCCGACTACGCCGCCGAGTACTTCCAGCACTGGGGCCAGGGCAC
ACTGGTGACCGTGAGCAGC
S3O13-VH.8 (D99E)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTMSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGR
VTITSDTSATTAYMELSSLRSEDTAVYYCAKEGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCTGGCGCTTCCGTGAAGGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCATGTCCGCCATGCACTGGGTGCGGCAGGCCCCCGGACAGCGGCCTG
AGTGGATGGGCTGGATCACAGCTGGCACCGGCGATACCAAGTACAGCCAGAAGTTCCAAGGCAGAGT GACCATCACCTCCGACACCTCTGCTACCACCGCCTACATGGAACTGTCCAGCCTGAGATCCGAGGACA CAGCCGTGTACTACTGTGCTAAAGAAGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGA
ACTCTGGTGACCGTGTCTTCT
S3O13-VH.9 (D99Q)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTMSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGR
VTITSDTSATTAYMELSSLRSEDTAVYYCAKQGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCCGGCGCTTCCGTGAAAGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCATGTCCGCCATGCACTGGGTGCGGCAGGCCCCTGGCCAGCGGCCTG
AGTGGATGGGCTGGATCACAGCTGGCACCGGCGATACCAAGTATAGCCAGAAGTTTCAGGGCAGAGT GACTATCACCTCCGACACATCTGCTACCACCGCCTACATGGAACTGTCCTCTCTGAGATCCGAGGACAC CGCTGTGTACTACTGTGCCAAGCAGGGCGACTACGCCGCCGAGTACTTCCAGCACTGGGGACAAGGAA
CCCTGGTGACCGTGTCTAGC
S3O13-VH.1Q (G100A)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTMSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGR
VTITSDTSATTAYMELSSLRSEDTAVYYCAKDADYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCCGGCGCTTCCGTGAAAGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCATGTCCGCCATGCACTGGGTGCGGCAGGCTCCTGGCCAGCGGCCTG
AGTGGATGGGCTGGATCACCGCTGGCACCGGCGACACCAAGTACTCCCAGAAGTTCCAGGGCAGAGT
GACCATCACCTCTGATACATCTGCTACAACAGCCTACATGGAACTGTCCAGCCTGAGATCCGAGGACA CCGCCGTGTACTACTGTGCCAAGGACGCCGACTACGCCGCTGAGTATTTTCAGCACTGGGGCCAAGGA ACCCTGGTGACCGTGTCTAGC
S3O13-VH.il (M31S)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV
TITSDTSATTAYMELSSLRSEDTAVYYCAKDGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCCGGAGCTTCCGTGAAAGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCTCTTCTGCCATGCACTGGGTGCGGCAGGCTCCTGGACAGCGGCCTGA
GTGGATGGGCTGGATCACAGCTGGCACCGGCGATACCAAGTACTCCCAGAAGTTCCAAGGCAGAGTGA CCATCACCTCCGACACATCTGCTACCACCGCCTACATGGAACTGTCCAGCCTGAGATCCGAGGACACA GCCGTGTACTACTGTGCCAAGGACGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGCAC CCTGGTGACCGTGTCTAGC
S3O13-VH.12 (M31D
QVQLVQSGAEVKKPGASVKVSCKASGYTFTISAMHWVRQAPGQRPEWMGWITAGTGDTKYSQKFQGRV
TITSDTSATTAYMELSSLRSEDTAVYYCAKDGDYAAEYFQHWGQGTLVTVSS
CAAGTGCAACTAGTGCAAAGTGGTGCAGAAGTCAAGAAGCCTGGAGCTTCCGTGAAAGTGTCCTGCAA
GGCCTCTGGCTACACCTTCACCATCTCCGCCATGCACTGGGTGCGGCAGGCTCCTGGACAGCGGCCCG
AGTGGATGGGCTGGATCACTGCTGGCACCGGCGATACCAAGTACAGCCAGAAGTTCCAAGGCAGAGT
GACAATCACCTCCGACACCTCTGCTACCACCGCCTACATGGAACTGTCCAGCCTGAGATCCGAGGACA CAGCCGTGTACTACTGTGCCAAGGACGGCGACTACGCCGCCGAGTATTTTCAGCACTGGGGCCAGGGC ACCCTGGTGACCGTGTCTTCT
S3O13-VK.1 parental codon optimized
DIVMTQSPSTLSASVGDRVTITCRASQSINSWLAWYQQKPGKAPNLLISDASNLESGVPSRFSGSGSGTEFTL
TIS SLQPDDFATYYCQQYNTYPSFGQGTKVEIK
GATATCGTGATGACTCAAAGTCCAAGTACTCTGTCTGCTTCCGTGGGCGACAGAGTGACAATCACCTGT
AGAGCCTCTCAGTCCATCAACTCCTGGCTGGCTTGGTACCAGCAAAAACCTGGCAAGGCCCCTAATCT
GCTGATCTCTGATGCCTCCAACCTGGAAAGCGGCGTGCCCTCTCGGTTCTCCGGCTCTGGCTCCGGAAC
CGAGTTCACCCTGACCATCTCCAGCCTCCAGCCTGACGACTTCGCCACCTACTACTGCCAGCAGTACAA
CACCTATCCAAGCTTTGGCCAGGGCACCAAGGTCGAGATCAAG
S3O13-VK.2 (W32Y)
DIVMTQSPSTLSASVGDRVTITCRASQSINSYLAWYQQKPGKAPNLLISDASNLESGVPSRFSGSGSGTEFTL
TISSLQPDDFATYYCQQYNTYPSFGQGTKVEIK
GATATCGTGATGACTCAAAGTCCAAGTACTCTGTCTGCTTCCGTGGGCGACAGAGTGACCATCACCTGT
AGAGCCTCTCAGTCCATCAACTCCTACCTGGCTTGGTACCAGCAAAAACCTGGCAAGGCCCCTAATCT
GCTGATCAGCGATGCCTCCAACCTGGAATCCGGCGTGCCATCTCGGTTCTCCGGATCTGGCTCTGGCAC
AGAGTTCACCCTGACCATCTCCAGCCTCCAGCCTGACGACTTCGCCACCTACTACTGCCAGCAGTACAA
CACCTATCCCAGCTTTGGCCAGGGCACCAAGGTCGAGATCAAG
S3O13-VK.3 (N30S)
DIVMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPNLLISDASNLESGVPSRFSGSGSGTEFTL
TIS SLQPDDFATYYCQQYNTYPSFGQGTKVEIK
GATATCGTGATGACTCAAAGTCCAAGTACTCTGTCCGCCTCCGTGGGCGACAGAGTGACAATCACCTG
TAGAGCCTCTCAGTCCATCTCCTCCTGGCTGGCTTGGTACCAGCAAAAACCTGGCAAGGCCCCTAACCT
CCTGATCTCTGATGCTTCCAACCTGGAATCCGGCGTGCCATCTCGGTTCTCCGGATCTGGCTCTGGCAC
CGAGTTCACCCTGACCATCAGCTCTCTGCAGCCTGACGACTTCGCCACATACTACTGCCAGCAGTACAA
CACCTATCCCAGCTTTGGCCAGGGCACCAAGGTCGAGATCAAG
S3O13-VK.4 (N30S; W32Y) pVIR-Kappa
DIVMTQSPSTLSASVGDRVTITCRASQSISSYLAWYQQKPGKAPNLLISDASNLESGVPSRFSGSGSGTEFTLT
ISSLQPDDFATYYCQQYNTYPSFGQGTKVEIK
GATATCGTGATGACTCAAAGTCCAAGTACTCTGTCTGCTTCCGTGGGCGACAGAGTGACAATCACCTGT
AGAGCCTCTCAGTCCATCTCCTCCTACCTGGCTTGGTACCAGCAAAAACCTGGCAAGGCCCCTAACCTG
CTCATCAGCGATGCCTCCAACCTGGAATCTGGCGTGCCATCTCGGTTCTCCGGCTCTGGCTCCGGAACC
GAGTTCACCCTGACCATCTCCTCTCTGCAGCCTGACGACTTCGCCACCTACTACTGCCAGCAGTACAAC
ACCTATCCCAGCTTTGGCCAGGGCACAAAGGTCGAGATCAAG
S2V29
VH
IGHV3-30*18, IGHJ6*02, IGHD2-2*01
GAGGTGCAGCTGGTGGAGTCTGGGGGAAGTGTGGTCCAGCCTGGGAGGGCCCTGAGACTCTCCTGTGC
AGCCTCTGGAATCACCTTCAGTAGCTTTGGCATGTACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTG
GAGTGGCTGGGAGTTATAGCGTATGATGGAAGTAATACATACTATGCAGACTCCGTGAAGGGCCGAT
TCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATTTGCAAATGAACAGCCTGAGAATTGAGGAC
ACGGCTGTCTATTATTGTGCGAAAGATTATTACCCGCTGCTATCGTACTACTACGGTTTGGACGTC
TGGGGCCAAGGGACCACGGTCACCGTATCCTCA
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDGSNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
VL-S2V29a
IGLV2-ll*01, IGLJ3*02
CAGTCTGTGCTGACTCAGCCTCGCTCAGTGTCCGGGTCTCCTGGACAGTCAGTCACCATTTCCTGCACT GGAACCAGCAGTGATGTCGGTGCTTATAACTATGTCTCCTGGTACCAACAACACCCAGGCAAAGCC CCCAAATTCATGATTTATGATGTCGATCAGCGGCCCTCAGGGGTCCCTGATCGCTTCTCTGGCTCCAA GTCTGGCAACACGGCCTCCCTGATCATCTCTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCTG CTCATATGCTGGCAGCTACATTTGGGTGTTCGGCGGAGGGACCCAACTGACCGTCCTAG
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCCSYAGSYIWVFGGGTQLTVL
VL-S2V29b
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCSSYAGSYIWVFGGGTQLTVL
S2V29-VH, 1 parental codon optimized
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDGSNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACGACGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTGGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.2 (D54K)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYKGSNTYYADSVKGRFTI SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACAAGGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTGGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.3 (54S)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYSGSNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACTCCGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCAC AATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACCG CCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTGGACGTGTGGGGCC
AGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.4 (D54E)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYEGSNTYYADSVKGRFTI SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACGAGGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTGGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.5 (G55A)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDASNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACGACGCCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCAC AATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACCG CCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTGGACGTGTGGGGCC
AGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.6 (D54S-L110D
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYSGSNTYYADSVKGRFTIS RDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGIDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACTCCGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCAC AATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACCG CCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCATCGACGTGTGGGGCC
AGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.7 (D54E-L110D
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYEGSNTYYADSVKGRFTIS
RDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGIDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACGAGGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCATCGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.8 (D54K-L110D
EVQLVESGGSVVQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYKGSNTYYADSVKGRFTIS
RDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGIDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACAAGGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCATCGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.9 (G55A-L110D
EVQLVESGGSVVQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDASNTYYADSVKGRFTIS
RDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGIDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACGACGCCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCAC AATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACCG CCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCATCGACGTGTGGGGCC
AGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.10 (L110F)
EVQLVESGGSVVQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDDSNTYYADSVKGRFTIS
RDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGIDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA ATGGCTGGGCGTGATCGCCTACGACGACTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCATCGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VL, 1 parental codon optimzed
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCCSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTGTT
CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.2 (C91S)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCSSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGAGCGGCTCTCCTGGCCAGTCCGTGACCATCTCCTGTACC GGCACCTCTAGCGATGTGGGCGCTTACAACTACGTGTCCTGGTATCAACAGCACCCCGGCAAGGCCCC TAAGTTCATGATCTACGACGTGGACCAGCGGCCATCTGGCGTGCCTGATAGATTCTCCGGCTCCAAATC CGGCAACACCGCTTCTCTGATCATCTCTGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCCTC
CTACGCCGGATCTTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.3 (C91A)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCASYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC
CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCGCCT
CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.4 (C91V)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCVSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC
CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCGTGT
CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.5 (C91Y)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCYSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC
CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTACT
CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.6 (C91G)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCGSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC
CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCGGCT
CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.7 (C91deD
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC
CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGTTCTT
ATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.8 (C90S)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYSCSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC
CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTCCTGTT
CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.9 (C90A)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYACSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGACAATCCGTGACCATCTCCTGCACC
GGCACCTCCAGCGATGTGGGCGCCTACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCTTCTGGCGTGCCCGATAGATTCTCCGGCAGCAAATC CGGCAACACCGCTTCTCTGATCATCAGCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACGCCTGTT CTTATGCTGGCTCCTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VH.1 (parental)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDGSNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTCAGACTGAGCTGTGC
TGCTTCTGGCATCACCTTCTCCTCTTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGACTGGA
ATGGCTGGGCGTGATCGCCTACGACGGCTCTAATACCTACTACGCCGATTCCGTGAAGGGCCGCTTCA CAATCTCCAGAGATAACTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTGGACGTGTGGGGC
CAGGGCACCACAGTGACCGTGTCCAGC
S2V29-VH.il (V50F)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGFIAYDGSNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGCAGAGCCCTGAGACTGTCTTGTGC
TGCTTCTGGCATCACCTTCAGCAGCTTTGGCATGTACTGGGTGCGGCAAGCTCCCGGAAAAGGCCTGG
AATGGCTGGGCTTCATCGCCTACGACGGCTCCAACACCTACTACGCCGACTCCGTGAAGGGCCGCTTC
ACCATCTCCAGAGATAATTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACAC CGCCGTGTACTACTGCGCCAAGGACTACTACCCTCTGCTGTCCTACTACTATGGACTCGATGTGTGGGG CCAGGGCACAACCGTGACCGTGTCCTCT
S2V29-VH.12 (D54N)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYNGSNTYYADSVKGRFTI
SRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTGGTGCAGCCTGGCAGAGCTCTGAGACTGTCTTGTGC
TGCTTCTGGCATCACCTTTTCTTCTTTCGGCATGTACTGGGTCAGACAGGCCCCCGGCAAGGGCCTGGA
ATGGCTGGGAGTGATCGCCTACAACGGCTCCAACACCTACTACGCCGACTCCGTGAAAGGACGGTTCA CCATCTCCCGGGACAACTCCAAGAATACACTGTACCTGCAGATGAACAGCCTGCGCATCGAGGACACC GCCGTGTACTACTGCGCCAAGGACTACTATCCTCTGCTGTCCTACTACTACGGCCTCGATGTGTGGGGC
CAAGGCACCACCGTGACCGTGTCCAGC
S2V29-VH.13 (I51D-A52K)
EVQLVESGGSWQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVDKYDGSNTYYADSVKGRFT
ISRDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
GAAGTGCAACTAGTGGAAAGTGGTGGTAGTGTCGTGCAGCCTGGACGCGCCCTGAGACTCTCTTGTGC
TGCTTCTGGCATCACCTTCAGCAGCTTCGGCATGTACTGGGTGCGGCAAGCTCCTGGAAAAGGCCTGG
AATGGCTGGGCGTGGACAAGTACGACGGCTCCAACACCTACTACGCCGATTCCGTGAAGGGCAGATTT
ACAATCTCCAGAGATAATTCCAAGAACACCCTGTACCTGCAGATGAACTCTCTGCGGATCGAGGACAC CGCCGTGTACTACTGCGCCAAGGACTACTACCCCCTGCTGTCCTACTATTACGGCCTGGACGTGTGGGG CCAGGGCACCACCGTGACCGTGTCCTCT
S2V29-VL.2 (C91S)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCSSYAGSYIWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGAGCGGCTCTCCTGGCCAGTCCGTGACCATCTCCTGTACC
GGCACCTCTAGCGATGTGGGCGCTTACAACTACGTGTCCTGGTATCAACAGCACCCCGGCAAGGCCCC
TAAGTTCATGATCTACGACGTGGACCAGCGGCCATCTGGCGTGCCTGATAGATTCTCCGGCTCCAAATC CGGCAACACCGCTTCTCTGATCATCTCTGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCCTC CTACGCCGGATCTTACATCTGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL, 10 (Y32H-I50M-D52N-C91S-S92V-Y93D-I98R)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAHNYVSWYQQHPGKAPKFMMYNVDQRPSGVPDRFSGSKSG
NTASLIISGLQAEDEADYYCSVDAGSYRWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCAGGCCAGTCCGTGACCATCTCTTGTACC
GGCACATCCTCCGACGTGGGCGCTCACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC
TAAGTTCATGATGTACAACGTGGATCAACGGCCTTCTGGCGTGCCCGACAGATTTAGCGGAAGCAAAA GCGGCAACACCGCCTCTCTGATCATCTCCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCC GTCGATGCTGGCTCCTATAGATGGGTGTTCGGCGGCGGAACCCAGCTGACCGTGCTG
S2V29-VL, 11 (Y32H-D52N-C91S-S92V-Y93D-I98R)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAHNYVSWYQQHPGKAPKFMIYNVDQRPSGVPDRFSGSKSGN TASLIISGLQAEDEADYYCSVDAGSYRWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCTGGCCAGTCCGTGACCATCAGCTGTACC GGCACCTCCTCCGACGTGGGCGCTCACAACTACGTGTCCTGGTACCAGCAGCACCCCGGCAAGGCCCC TAAGTTCATGATCTACAACGTGGATCAACGGCCATCTGGCGTGCCTGACAGATTTAGCGGATCTAAAA GCGGCAACACCGCCTCTCTGATCATCTCCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCC GTCGATGCTGGCTCCTATAGATGGGTGTTCGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.12 (I50M-D52N-O55H-C91S-S92G-Y93N-I98R)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMMYNVDHRPSGVPDRFSGSKSG NTASLIISGLQAEDEADYYCSGNAGSYRWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCTGGCTCTCCTGGCCAATCCGTGACCATCTCCTGTACC GGCACAAGCTCCGACGTGGGCGCCTATAACTACGTGTCCTGGTACCAGCAGCACCCCGGCAAGGCCCC TAAATTCATGATGTACAACGTGGACCACCGGCCTTCTGGCGTGCCAGATAGATTCAGCGGATCCAAGT CCGGCAACACCGCTTCTCTGATCATCTCTGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCC GGCAATGCTGGCAGCTACAGATGGGTCTTTGGTGGAGGCACCCAGCTGACCGTGCTG
S2V29-VL.13 (Y32N-I50M-D52N-O55K-C91S-S92V-Y93D-I98K)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGANNYVSWYQQHPGKAPKFMMYNVDKRPSGVPDRFSGSKSG NTASLIISGLQAEDEADYYCSVDAGSYKWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGAGCGGCTCTCCAGGACAATCTGTGACCATCTCCTGTAC CGGCACCTCCTCCGACGTGGGCGCCAACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAAGCTC CTAAGTTCATGATGTACAACGTGGACAAGCGGCCTTCTGGCGTGCCCGATAGATTTAGCGGCTCCAAG TCCGGCAATACCGCCTCTCTGATCATCTCTGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCC GTCGATGCTGGCAGCTATAAGTGGGTGTTCGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-VL.14 (Y32H-I50M-D52G-C91S-S92F-Y93D-I98R)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAHNYVSWYQQHPGKAPKFMMYGVDQRPSGVPDRFSGSKSG NTASLIISGLQAEDEADYYCSFDAGSYRWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGAGCGGCTCTCCTGGCCAGTCCGTGACCATCTCTTGTACC GGCACAAGCTCCGACGTGGGCGCTCACAACTACGTGTCCTGGTACCAGCAGCACCCCGGCAAGGCCCC TAAGTTCATGATGTACGGCGTGGACCAACGGCCTTCTGGTGTCCCAGATAGATTCTCCGGATCTAAAAG CGGCAACACCGCCTCTCTGATCATCTCCGGCCTGCAGGCCGAGGACGAAGCCGACTACTACTGCTCCTT TGATGCTGGCTCCTATAGATGGGTGTTCGGCGGAGGCACCCAGCTGACCGTGCTG
S2V29-VL,15(Y32H-I50M-D52N-C91S-S92D-Y93D-I98R)
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAHNYVSWYQQHPGKAPKFMMYNVDQRPSGVPDRFSGSKSG NTASLIISGLQAEDEADYYCSDDAGSYRWVFGGGTQLTVL
CAAAGTGTGCTAACTCAACCACGAAGTGTGTCCGGCTCTCCAGGCCAGTCCGTGACCATCTCCTGTACC GGCACCAGCTCTGACGTGGGCGCTCACAACTACGTGTCCTGGTACCAGCAGCACCCTGGCAAGGCCCC TAAGTTCATGATGTACAACGTGGACCAACGGCCTTCTGGCGTGCCCGATAGATTCAGCGGATCTAAAT CCGGCAACACCGCCTCTCTGATCATCAGCGGCCTGCAGGCCGAGGATGAAGCCGACTACTACTGCTCC GACGACGCTGGCTCCTATAGATGGGTCTTTGGCGGCGGAACACAGCTGACCGTGCTG
S2V29-yl.2-IgGlml7.l-LS
Variable Heavy Chain
EVQLVESGGSVVQPGRALRLSCAASGITFSSFGMYWVRQAPGKGLEWLGVIAYDGSNTYYADSVKGRFTIS RDNSKNTLYLQMNSLRIEDTAVYYCAKDYYPLLSYYYGLDVWGQGTTVTVSS
Constant region Heavy Chain (Glml7,l-LS) LS, Glm3->Glml7,l
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSWTVP
SSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCV
WDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPA
PIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGS
FFLYSKLTVDKSRWQQGNVFSCSVLHEALHSHYTQKSLSLSPGK
Variable Light Chain
QSVLTQPRSVSGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKFMIYDVDQRPSGVPDRFSGSKSGN
TASLIISGLQAEDEADYYCSSYAGSYIWVFGGGTQLTVL
Light Chain Lambda Constant region
GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS S2V29-yl.2-IgGlml7 Lamda
Light Chain QSVLTQPRSV SGSPGQSVTI SCTGTSSDVG AYNYVSWYQQ HPGKAPKFMI YDVDQRPSGV PDRFSGSKSG NTASLIISGL QAEDEADYYC SSYAGSYIWVFGGGTQLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS
Heavy Chain EVQLVESGGS WQPGRALRL SCAASGITFS SFGMYWVRQA PGKGLEWLGV IAYDGSNTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRIED TAVYYCAKDY YPLLSYYYGL DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS WTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS RTPEVTCVW DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRWS VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPS RDELTKNQVS LTCLVKGFYP SDIAVEWESN GQPENNYKTT PPVLDSDGSF FLYSKLTVDK SRWQQGNVFS CSVLHEALHS HYTQKSLSLS PGK
EXAMPLE 2
TESTING OF S3A3 AND S3A19 MONOCLONAL ANTIBODIES
All testing was conducted as indicated in Example 1 unless provided otherwise in this Example 2.
Spike Protein Binding ELISAs
Binding of various monoclonal antibodies to the spike protein RBD of different sarbecoviruses was measured by enzyme-linked immunoabsorbant assay (ELISA).
96 half area well-plates (Corning, 3690) were coated over-night at 4°C with 25 pl of sarbecoviruses RBD proteins, prepared at 5 pg/ml in PBS pH 7.2. After a blocking step of 60 min at room temperature with PBS 1% BSA (Sigma-Aldrich, A3059), plates were incubated with mAb serial dilutions for 60 min at room temperature. After 4 washing steps with PBS 0.05% Tween 20 (PBS-T) (Sigma-Aldrich, 93773), goat anti-human IgG secondary antibody (Southern Biotech, 2040-04) was added and incubated for 45 min at room temperature. Plates were then washed 4 times with PBS-T and 4-NitroPhenyl phosphate (pNPP, Sigma-Aldrich, 71768) substrate was added. After 45 min incubation, absorbance at 405 nm was measured by a plate reader (Biotek) and data plotted using Prism GraphPad. IC50 was determined for each antibody/virus combination.
ELISA assays were conducted to test the ability of S3 A3 and S3 Al 9, along with other antibodies including comparator antibodies S2X259 and S2K146, to bind the RDB of various sarbecoviruses representing Clades la, lb, 2 and 3, as well as several variants of SARS-CoV-2 (Figure 4). Results are summarized in Figure 5 (right-hand portion).
Neutralization Assays
To evaluate neutralization potency S3A3 and S3A19, dose-response inhibition assays were carried out using a vesicular stomatitis virus (VSV) pseudotyping platform.
Pseudotyped viruses were prepared using Lenti-X 293 cells seeded in 15-cm dishes. Briefly, cells in culture medium (DMEM supplemented with 10% heat-inactivated FBS, 1% PenStrep) were transfected with 25 pg of plasmid encoding for the corresponding S glycoprotein using TransIT-Lenti (Minis) as transfectant reagent. One day post-transfection, cells were infected with vesicular stomatitis virus (VSV) (G*AG-luciferase) for 1 h, washed 3 times in PBS with Ca2+/Mg2+ (Thermo Fisher) before adding 25 ml of culture medium/dish. Particles were harvested after 18-24 h, clarified from cellular debris by centrifugation at 2,000 x g for 20 min at 4°C, aliquoted and stored at -80°C until use in neutralization experiments.
For neutralization experiments, Vero E6 cells were seeded at 20,000 cells/well in culture medium into white 96-well plates (PerkinElmer, 6005688) and cultured overnight at 37°C 5% CO2. Ten-point 3-fold mAb serial dilutions were prepared in culture medium and mixed 1 : 1 with pseudotyped VSV prepared in culture medium in order to infect cells with the desired MOI. After 60 min incubation at 37 °C, cell culture medium was aspirated and 50 pl of PVs/mAb mixture was added onto cells and incubated 60 min at 37°C 5% CO2. After 60 min, 100 pl of culture medium was added to the cells and incubation at 37°C 5% CO2 followed in the next 16- 24 h. At the end of the incubation time, culture medium was removed from the cells and 50 pl/well of Steadylite (PerkinElmer) diluted 1 :2 with PBS with Ca2+Mg2+ was added to the cells and incubated in the dark for 10 min.
Luminescence signals were read using a Synergy Hl Hybrid Multi-Mode plate reader (Biotek). Measurements were done in duplicate and at least six wells per plate contained untreated infected cells (defining the 0% of neutralization, “MAX RLU” value) and infected cells in the presence of controls defining the 100% of neutralization, “MIN RLU” value. Average of Relative light units (RLUs) of untreated infected wells (MAX RLUave) was subtracted by the average of MIN RLU (MIN RLUave) and used to normalize percentage of neutralization of individual RLU values of experimental data according to the following formula: (l-(RLUx - MIN RLUave) / (MAX RLUave - MIN RLUave)) x 100. Data were analyzed and visualized with Prism (Version 9.1.1). IC50 values were calculated from the interpolated value from the log(inhibitor) versus response, using variable slope (four parameters) nonlinear regression with an upper constraint of <100, and a lower constraint equal to 0.
Results for variants of SARS-CoV-2, along with results for other sarbecoviruses, are presented in Figure 5 (left-hand portion) and Table 5.
Table 5: IC50 (ng/ml) of Various Antibodies
Figure imgf000157_0001
Figure imgf000158_0001
S3 A3 and S3 Al 9 neutralized Omicron variants of SARS-CoV-2 at low IC5Os. The fold change in neutralization as compared to comparator antibody S2X324 is presented in Table 6. Table 6: Fold Change of IC50 (ng/ml) of Various Antibodies Compared to S2X324
Figure imgf000158_0002
Additional neutralization tests against SARS-CoV-2 variants of concern were conducted and results are presented in Figure 6.
Results from additional neutralization testing for antibodies including S3 A3 and S3 Al 9 are presented in Figure 7. A summary of the results is presented in Table 7.
Table 7: Neutralization Test Results for Various Antibodies
Figure imgf000158_0003
Figure imgf000159_0001
ND = Not Neutralized
Biolayer Interferometry and KD
Biolayer Interferometry (BLI) experiments were carried out using an Octet Red96 (ForteBio) and all reagents were prepared in Kinetics buffer (KB) (PBS 0.01% BSA).
To assess competition with S2X259, S309, S2K146, and S2X324, His-tagged SARS- CoV-2 RBD was prepared at 8 pg/ml in Kinetics buffer (PBS 0.01% BSA) and loaded on prehydrated anti-penta-HIS biosensors (Sartorius) for 2.5 min. Biosensors were then moved into a solution containing 20 pg/ml S3 A3 or S3 Al 9 mAb and association recorded for 5 min. A second association step was subsequently performed into S2X259, S309, S2K146, or S2X324 mAbs solutions at 20 pg/ml and recorded for 5 min. Response values were exported and plotted using GraphPad Prism (version 9.1.1).
Results from binding competition assays using antibodies including AS3A3 and S3A19 are presented in Table 8.
Table 8: Binding Competition Assay Results for Various Antibodies
Figure imgf000159_0002
The antibodies listed across the top row were tested for competitive (“C”) or noncompetitive (“NC”) binding against the antibodies listed in the left-most column. S3 A3 competed with S2X324 and S309, but not S2K146 or S2X259, indicating that its binding site is similar to (e.g. overlaps with) that of S2X324 and S309 (Figure 8). S3A19 competed with S2K146 and S2X259 one-way only, but not S2X324 and S309, indicating that its binding site is similar to (e.g. overlaps with) that of S2K146 and S2X259 (Figure 9).
To assess binding affinities, S3 A3 and comparator antibody S2X324 were prepared at 3 ug/ml and immobilized on pre-hydrated protein- A biosensors (Sartorius) for 75 sec. After a 30 sec stabilization step in KB, biosensors were moved in SARS-CoV-2 :2 dilution series (starting concentration: 18.5 nM) for the 600 sec association step, and then moved back in KB to record dissociation signals for 540 sec. The data were baseline subtracted, results fitted using the Pall ForteBio/Sartorius analysis software (version 12.0) and plotted using GraphPad Prism (version 9.1.1). Biolayer interferometry showed that S3 A3 binds to SARS-CoV-2 RBD with nanomolar affinities similar to those observed with S2X324-v3.1 (Figure 10).
A similar assay was conducted with S3 Al 9 and results are presented in Figure 11. A summary of KD values for S3 A3, S3A19, and comparator antibody S2X324-v3.1 as determined in these assays is presented at Table 9.
Table 9: KD(M) of Various Antibodies
Figure imgf000160_0001
ACE2 Binding and FcR Activation
The ability of S3 A3 to bind to the RBD of various sarbecoviruses was assayed by competition ELISA and results are presented in Figure 12. Results for S3 Al 9 are presented in Figure 13.
The ability of S3 A3 and S3 Al 9 to block ACE2 receptor binding to the SARS-CoV-2 RBD (Wuhan-Hu-1), as compared to S2X324, was also evaluated by competition ELISA. SARS-CoV-2 mouse/rabbit Fc-tagged RBDs (final concentration 20 ng/ml) were incubated with serially diluted recombinant mAbs (from 25 pg/ml) and incubated for 1 h 37°C. The complex RBD:mAbs was then added to a pre-coated hACE2 (2 pg/ml in PBS) 96-well plate MaxiSorp (Nunc) and incubated 1 hour at room temperature. Subsequently, the plates were washed and a goat anti-mouse/rabbit IgG (Southern Biotech) coupled to alkaline phosphatase (Jackson Immunoresearch) added to detect mouse Fc-tagged RBDs binding. After further washing, the substrate (p-NPP, Sigma) was added, and plates read at 405 nm using a microplate reader (Biotek). The percentage of inhibition was calculated as follows: (1-((OD sample-OD neg ctr)/(OD pos. ctr-OD neg. ctr))*100. S3 A3 and S3A19 inhibited binding of the SARS-CoV-2 RBD to human ACE2 in a concentration-dependent manner (Figure 14).
Neutralization Against SARS-CoV-2 Variants of Concern and S2X324 Escape Mutants
The ability of S3 A3 and S3 Al 9 to neutralize SARS-CoV-2 WT and variants was tested in comparison to antibody S2X324 v.3.1, and results are presented in Figure 15 and Figure 16.
The ability of S3 A3 and S2X324 v.3.1 to neutralize SARS-CoV-2 variants generate using a BA.2 backbone that escape S2X324 was also assayed and results are presented in Figure 17 and summarized in Table 10. Results indicate that S3 A3 may be effective against S2X324 escape mutants.
Table 10: Escape Variant Neutralization Fold Change
Figure imgf000161_0001
Antibody Combinations
The ability of antibody combinations to neutralize SARS-CoV-2 BA.5 in VSV-PVs was also assayed and potential synergy at different concentrations was evaluated. Results for S3 A3 and S3A19 combined at the indicated concentrations are presented in Figure 18. In Figure 18, synergy/antagonism volumes of <25 pM 2% were defined as additive, those between 25 and 50 pM 2% were defined as minor, those between 50 and 100 pM 2% were defined as moderate and those of >100 pM 2% were defined as strong. Confidence for results was 95% and the synergy score was 101.9.
Results for S3 A3 and sotrovimab combined at the indicated concentrations are presented in Figure 19. In Figure 19, synergy/antagonism volumes of <25 pM 2% were defined as additive, those between 25 and 50 pM 2% were defined as minor, those between 50 and 100 pM 2% were defined as moderate and those of >100 pM 2% were defined as strong. Confidence for results was 95% and the synergy score was 2.6.
Results for S3 A3 and S2K146 combined at the indicated concentrations are presented in Figure 20. In Figure 20, synergy/antagonism volumes of <25 pM 2% were defined as additive, those between 25 and 50 pM 2% were defined as minor, those between 50 and 100 pM 2% were defined as moderate and those of >100 pM 2% were defined as strong. Confidence for results was 95% and the synergy score was 104.
Results for S3 Al 9 and sotrovimab combined at the indicated concentrations are presented in Figure 21. In Figure 21, synergy/antagonism volumes of <25 pM 2% were defined as additive, those between 25 and 50 pM 2% were defined as minor, those between 50 and 100 pM 2% were defined as moderate and those of >100 pM 2% were defined as strong. Confidence for results was 95% and the synergy score was 125.5.
Results for S3A19 and S2K146 combined at the indicated concentrations are presented in Figure 22. In Figure 22, synergy/antagonism volumes of <25 pM 2% were defined as additive, those between 25 and 50 pM 2% were defined as minor, those between 50 and 100 pM 2% were defined as moderate and those of >100 pM 2% were defined as strong. Confidence for results was 95% and the synergy score was 11.1.
EXAMPLE 3
TESTING OF S2V29, S3O13, S3L17, S3I2, S2X259, S2X324 AND CERTAIN OTHER MONOCLONAL ANTIBODIES
Table 11 is a table summarizing characteristics for variant antibodies S2V29vl.2, S3O13, S3L17, S3I2v2.1, S2X259v50 AM, S309 AM, SVB, and S2X324.
Table 11: Antibody Characteristics
Figure imgf000162_0001
The antibodies were isolated from memory B cells. The below shows V gene usage and load of somatic mutations for select variant antibodies:
1. S3I2 (IGHV3-53*02; VH identity = 92.1%; CDR3 lenght = 21 aa)
2. S3L17 (IGHV3-66*02; VH identity = 93.1%; CDR3 length = 11 aa)
3. S2V29 (IGHV3-30*18; VH identity = 94%; CDR3 length = 16 aa)
4. S3O13 (IGHV1-3*O2; VH identity = 95.5%; CDR3 length = 13 aa)
Testing was conducted on certain variant antibodies. The following results were obtained.
Binding and Neutralization Testing
Figure 23 shows binding by S2V29 to various sarbecoviruses, and neutralization against SARS-CoV-2 variants by S2V29. The monoclonal antibody isolated from an Omicron infected donor (BA.5) previously vaccinated (3 doses) shows an unprecedented combination of breadth and potency. Covers escapes of S2K146, S2X259, sotrovimab and S2X324 (on BA.2 and BA.5). A sequence liability (unpaired cysteine in VL) was fixed.
S2V29-vl.2 retains the neutralization profile of the parent antibody (S2V29-vl.l) against a panel of VSV SARS-CoV-2 viruses, as shown in Figure 24. S2V29-vl.2 variant solves a high- impact sequence liability in the VL-CDR3 (Cysl05 Ser).
Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2V29-vl.2. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Fold change is indicated in Table 12 and Table 13. Average fold change vs D614G is 0.9x (1 :10 viral stock).
Table 12: Neutralization Test Results for Various Antibodies- Fold Change to WT
Figure imgf000163_0001
Table 13: Neutralization Test Results for Various Antibodies- Fold Change to BA.2
Figure imgf000163_0002
S2V29 and S2V29-vl.2 were tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647. S2V29 and S2V29-vl.2 retain binding activity against SARS-CoV-2 BQ.1.1 (Figure 26).
Binding and neutralization were also tested for S2X324. Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2X324. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Fold change is indicated in Table 12 and Table 13. Average fold change vs D614G is 0.9x (1 : 10 viral stock). S2X324 does not neutralize BQ.1.1 (1 : 10 viral stock).
S2X324 was also tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647. S2X324 displays weak binding to SARS-CoV-2 BQ 1.1 Spike (Figure 27).
Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S2X259v50. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Fold change is indicated in Table 12 and Table 13. Average fold change vs D614G is 28.7x (1 : 10 viral stock) and 2.3x vs BA.2.
Binding and neutralization were also tested for S3O13 and for S3L17. Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3O13. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Fold change is indicated in Table 12 and Table 13. Unexpectedly, S3O13 does not neutralize BQ.1.1 (1 : 10 viral stock).
Figure 25 also shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3L17. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Fold change is indicated in Table 12 and Table 13. S3L17 potently neutralizes BQ.1.1 (1 : 10 viral stock).
S2X324-v3.1, S3L17 and S3O13 were tested in hamsters infected with BA.5. All tested variant antibodies were human monoclonal antibodies with LS modification. Table 14 shows experimental details of the testing in hamsters.
Table 14: Hamster Testing BA.4 Variant 1E+04 TCIDso
Figure imgf000164_0001
Figure 28 shows log TCID values for S2X324-v3.1, S3L17 and S3O13, with an isotype control. S3L17 was found to potently protect hamsters from BA.5 infection.
Binding and neutralization were further tested for S3I2v2.1. Figure 25 shows in vitro neutralization of infection of WT (Wuhan-1 D614G) and Omicron BA.2 and BQ.1.1 VSV-pp by S3I2v2.1. VSV-pp carries 38 mutations. Curves shown on the left are data using Omicron viral stock dilution of 1 : 10 selected based on RLU counts. Fold change is indicated in Table 12 and Table 13. S3I2v2.1 potently neutralizes BQ.1.1 (1 : 10 viral stock). EC50s were found higher as compared to previous results.
Figure 29 summarizes neutralizing activity against SARS-CoV-2 Omicron variants for certain variant antibodies.
Table 15 shows potential combinations of variant antibodies for treatment.
Table 15: Variant Antibody Combinations
Figure imgf000165_0001
Figure 30 shows neutralization of Wuhan-Hu-1 D614 and G614 mediated by sotrovimab and VIR-7832.
Figure 31 illustrates antigenic sites on SARS-CoV-2 RBD recognized by certain variant antibodies of the present disclosure.
Figure 32 shows the results of BLI studies testing S3I2, S3L17, S3O10, and S2V29 against S2K146, S2X259, S2X324, and S309.
Figure 33 shows the results of biolayer interferometry (BLI) competition studies testing the indicated antibodies. Table 16 shows a summary of results from the binding competition assays. The antibodies listed across the top row were tested for competitive (“C”), partial competition (“PC”) or non-competitive (“NC”) binding against the antibodies listed in the leftmost column.
Table 16: Binding Competition Assay Results
Figure imgf000165_0002
Figure 34 shows binding results versus a panel of RBDs from sarbecoviruses (ELISA) for S3I1, S3L17, S2V29, and S3O13.
Figure 35 shows VSV-PV neutralizations against BA.2-escape mutants for S3I2, S3L17, and S2V29. BA.2-G504D is an escape mutant of S2X259. Figure 36 shows additional neutralization results against BA.2-escape mutants, including S2X324 escape mutants, S309 escape mutants, and S2K146 escape mutants, for S3O13. Fold change is relative to BA.2 variant.
Figure 37 shows VSV-PV neutralizations against BA.5-escape mutants for S2V29, S3L17, S3I2, and S3O13.
Table 17 summarizes neutralization (IC50) against BA.5 escape mutants and fold changes relative to BA.5 variant.
Table 17: Neutralization and Fold Changes
Figure imgf000166_0001
Figure 38 summarizes ACE2 binding inhibition to RBDs of SARS-CoV-2 and SARS- CoV.
Figure 39 shows SI staining over time, gated on pos cells. SI shedding is shown to be induced by variant antibodies of the present disclosure.
Figure 40 shows luminescence results for activation of FcgRIIa and FcgRIIIa.
Figure 41 summarizes binding affinity versus a panel of RBDs (BLI), for S3L17 and S3O13. Table 18 shows the KD, ka and kdis values against the RBDs for S3L17 and S3O13.
Table 18: Binding Affinity For S3L17, S3O13, and S2V29
Figure imgf000166_0002
Figure 42 shows binding affinity versus the same panel of RBDs (BLI) for S2V29. Table 18 shows the KD, ka and kdis values against the RBDs for S2V29.
Figure 43 shows binding affinity (BLI) versus a panel of RBDs representative of different sarbecovirus clades.
Figure 44 illustrates antibody-dependent cellular cytotoxicity (ADCC) and antibodydependent cellular phagocytsosis (ADCP).
S3L17 was tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647 (Figure 45). S3L17 retained binding activity against SARS-CoV-2 BQ.1.1.
S3I2-v2.1 was tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647 (Figure 46). S3I2-v2.1 retained binding activity against SARS-CoV-2 BQ.1.1.
S3O13 was tested at different concentrations on ExpiCHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins (Wuhan D614, BQ.1.1 or BA.2). Binding to S proteins was detected using a secondary antibody labeled with Alexa Fluor 647 (Figure 47). S3O13 did not retain binding activity against SARS-CoV-2 BQ.1.1.
S2V29 was tested at different concentration on Expi-CHO-S cells transiently transfected with SARS-CoV-2 spike glycoproteins from the variants, Wuhan D614, BA.2, BQ.1.1, XBB. l, and E340A (Figure 48). Specifically, Expi-CHO-S cells were harvested 24-48 hours after transfection, washed, and stained with the indicated antibody concentrations to assess binding to the cell surface. S2V29 exhibited potent and equal neutralizing activity against all pseudoviruses tested.
Further S3L17 and S2V29 Testing
S3L17, S2V29, REGEN-COV and Evusheld were tested for neutralization against pre- Omicron and Omicron SARS-CoV-2 variants and additional escape mutants, including sotrovimab escape mutants, bebtelovimab escape mutants, S2K146 escape mutants, and S2X259 escape mutants (Figure 49). IC50s for REGEN-COV and Evusheld from Stanford database as of Jan 22, 2023: https://covdb.stanford.edu/susceptibility-data/table-mab-susc/ and Park et al. Science 2022.
S3L17 and S2V29 were further tested for additional neutralization results against SARS- CoV-2 variants and escape mutants (Figure 50 and Table 19). Table 19: Neutralization Against Escape Mutants
Figure imgf000168_0001
Additional testing of S2V29-vl.2 against SARS-CoV and SARS-CoV-2 variants was also performed (Figure 68).
No rVSV escape mutants were identified for S3L17 and all S2V29 escape mutants were only partial escapes. Full escape mutants for both antibodies were determined and marked as unfit (Figure 50). All full escape mutants had less than 5 counts combined out of >14 million sequences in GISAID, which indicates that such mutants are very unlikely to occur. All full escape mutants required two or three nucleotide mutations.
Results of similar testing with S2V29-vl.2 are provided in Figure 51, which shows neutralization mutations with >100 counts in a GISAID VS pseudovirus assay out of 13.5 million total sequences. Further, in an assay using serial passing with rVSV, in a in two separate replicates, full escape with S2V29-vl.2 was not observed until P5 or higher. Further testing in SARS-CoV (SARS1) and SARS-CoV-2 strains showed breadth and barrier to escape in still further strains (Figure 51).
Analysis of S3L17 and S2V29 data shows that escape mutants for these antibodies are not likely to occur. Figure 52 summarizes escape mutant neutralization and binding data and analysis for S2V29 and S3L17. GISAID counts are as of January 26, 2023 and are out of >14 million sequences, >3 years of SARS-CoV-2 evolution, including antigenic shift. S2V29 total escape counts were < 0.01%. S3L17 total escape counts were < 0.00006% (below sequencing error). For comparison, escape frequency for the stem helix mAb S2P6 is 0.1%. ACE2 binding and RBD expression from DMS data was obtained from <https://jbloomlab.github.io/SARS- CoV-2-RBD_DMS_Omicron/RBD-heatmaps/>. Spread probability was calculated using a machine learning model for predicting likelihood of a mutation to spread (>0.03-0.05 indicates likely to spread). ACE contact residues were identified using published structure PDB ID 6M0J. Putative single-nucleotide mutation intermediates that lead to escape mutants were also determined (Figure 52). A list was determined of intermediate mutants that would be required for an identified escape to be generated in a stepwise process: i.e., if 2 or 3 mutations in the codon are required to from amino acid xx to yy. Then all the possible intermediate AA changes were listed (yet to be tested). Reported are only the DMS data from bloom on the effect of these mutations on ACE2 binding and RBD expression (both proxies for fitness).
Further live virus testing was conducted for S2V29-vl.2 (S2V29) and S3L17 (Figure 53 and Table 20). Table 20: Live Virus IC50 (ng/ml)
Figure imgf000169_0001
In vivo efficacy of S2V29-vl.2 (S2V29) and S3L17 was also determined. Antibodies were dosed 24 hours prior to SARS-CoV-2 BA.5 infection. Infectious viral loads in the lung were quantified on day 4. Both S2V29 and S3L17 reduced the lung infectious viral load in a dose-dependent manner (Figure 54).
Binding affinity tests for S2V29-vl.2 (S2V29) and S3L17 for the Wuhan and BA.5 SARS-Co-V-2 RBDs, and a second test for S2V29-vl.2 and Wuhan and XBB1.5 (Figure 55) showed picomolar binding activity and dissociation at the limit of detection for many variants (Table 21) A connection between high affinity and a high barrier to escape mutants was observed. Binding affinity of S2V29-vl.2 Fabs to recombinant RBDs carrying escape mutations of BQ.l. lwas also assessed using SPR (Figure 65), as was binding affinity to recombinant RBDs from other sarbecoviruses (Figure 66).
Table 21: Binding Affinity
Figure imgf000169_0002
Evolutionary breadth testing demonstrated that S3L17 binds to all clase lb RBDs and S2V29-1.2 binds to all clades 1-3 RBDs (Figure 56). This is unexpectedly high breadth for ACE2-competing antibodies. Likely binding configurations for S2V29-V.2 and S3L17 on the RBD were determined (Figure 57). The epitopes were partially overlapping, but the antibodies showed different escape profiles and no functional antagonism, such that there is likely a benefit to combining these two receptor-mimic antibodies.
Serial passaging with Wuhan rVSV through up to seven passages (P7) showed no escape from either S3L17 or S2V29-vl.2 (Table 22), whereas escape was observed for all other tested antibodies.
Table 22: Escape Mutant Data for Various Antibodies
Figure imgf000170_0001
S3L17 and S2V29 are ACE mimics as demonstrated through testing for critical RBD binding residues. Those residues determined to be critical for S3L17 and S2V29 using deep mutational scanning (DMS) were also critical for ACE (Figure 58). Most mutations that lost antibody binding (letters on Figure 58) also lost ACE 2 binding (lighter color). All escape mutations, except L455W, required two or three nucleotide substitutions.
Analysis of binding contacts of S3L17 and S2V29 with the SARS-CoV-2 RBD showed that these contacts overlap with strong Omicron RBD-ACE2 contacts (Figure 59). Figure 60 illustrates how S2V29 likely competes with ACE2 for binding to the RBD of SARS-CoV-2 BQ.1.1. The S2V29 epitope is outlined in black and binding residues are differentially shaded, as are RBD contact residues.
ADCP tests were conducted using PBMC (monocyte) effector cells and ExpiCHO target cells expressing SARS-CoV-2 to evaluate the effector function of S3L17 and S2V29-vl.2 (Figure 61). S3L17 and S2V29-V.12 both exhibit ADCP as measured using flow cytometry. Results for the BQ.1.1 variant were consistent with those for the Wuhan strain.
ADCC tests were conducted using purified NK cells to further the effector function of S3L17 and S2V29-vl.2 (Figure 62). Weak antibody-dependent phagocytosis was observed.
FcgR activation testing in Jurkat reporter cells was also conducted using S3L17-vl.2 and S2V29-vl (Figure 63).
Figure 64 shows a comparison of results obtained with authentic virus vs. VSV pseudovirus for S2V29-vl.2. Authentic virus data are consistent with VSV pseudovirus data.
Figure 67 shows the results of pharmokinetic studies in Tg32 SCID mice through 3 weeks post injection. Based on this data, it is expected that S2V29-vl.2 would provide both suitable therapeutic effect and six moths of prophylactic effect following a single IM injection.
Table 23 summarizes selected properties of S2V29-V.12 and S3L17 that indicate the suitability of these antibodies or variants thereof for SARS-CoV-2 binding, for therapy, prophylaxis, and testing.
Table 23: S2V29 and S3L17 Properties
Figure imgf000171_0001
The various embodiments described above can be combined to provide further embodiments. All of the U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet including U.S. Provisional Application No. 63/357,574, filed June 30, 2022, U.S. Provisional Application No. 63/359,718, filed July 8, 2022, U.S. Provisional Application No. 63/412,208, filed Sep. 30, 2022, U.S. Provisional Application No. 63/414,333, filed Oct. 7, 2022, U.S. Provisional Application No. 63/427,392, filed Nov. 22, 2022, U.S. Provisional Application No. 63/431,261, filed Dec. 8, 2022, U.S. Provisional Application No. 63/480,268, filed Jan. 17, 2023 and U.S. Provisional Application No. 63/483,251, filed Feb. 3, 2023 are incorporated herein by reference, in their entirety. Aspects of the embodiments can be modified, if necessary to employ concepts of the various patents, applications and publications to provide yet further embodiments.
These and other changes can be made to the embodiments in light of the above-detailed description. In general, in the following claims, the terms used should not be construed to limit the claims to the specific embodiments disclosed in the specification and the claims, but should be construed to include all possible embodiments along with the full scope of equivalents to which such claims are entitled. Accordingly, the claims are not limited by the disclosure.

Claims

1. An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, wherein:
(A) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO: 24, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO: 25, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID NO: 26, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iv) the CDRL1 comprises or consists of the amino acid sequence according to SEQ ID NO: 28, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO: 29 or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or
(vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NO: 30, or a functional variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(B) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 32 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 33, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iii) the CDRH3 comprises or consists of the amino acid sequence according to SEQ ID NO.: 34, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iv) the CDRL1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 38, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 39, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or
(vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs.: 40, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(C) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 84 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 86 or 186, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 88 or 194, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 89, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or
(vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs.: 90, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(D) (i) the CDRH1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 94, 198, or 208 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 95, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 96, 199, 202, or 205, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 98, 226, 229, 232, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 39, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or
(vi) the CDRL3 comprises or consists of the amino acid sequence according to SEQ ID NOs.: 99, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(E) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 104, 236, or 239, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 106 or 255, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 107, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or
(vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 108 or 258, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or;
(E) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 103 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(ii) the CDRH2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 85, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 104, 236, or 239, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NO.: 106 or 255, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(v) the CDRL2 comprises or consists of the amino acid sequence according to SEQ ID NO.: 107, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or
(vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 108 or 258, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid;
(F) (i) the CDRH1 comprises or consists of the amino acid sequence according to SEQ ID NO.: 112 or a sequence variant thereof comprising one, two, or three acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (ii) the CDRH2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 113, 126, 129, 132, 135, 138, 142, 146, 150, 154, 267, or 270, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (iii) the CDRH3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 114, 139, 143, 147, 151, or 155, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline- encoded amino acid; (iv) the CDRL1 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 116, 273, or 283, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; (v) the CDRL2 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 117, 274, or 287, or a sequence variant thereof comprising one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid; and/or (vi) the CDRL3 comprises or consists of the amino acid sequence according to any one of SEQ ID NOs.: 118, 122, 158, 275, 280, 284, 288, or 291, or a sequence variant thereof comprising having one, two, or three amino acid substitutions, one or more of which substitutions is optionally a conservative substitution and/or is a substitution to a germline-encoded amino acid, wherein the substitution is optionally a substitution according to Table 2 or Table 2, and wherein the antibody or antigen-binding fragment is capable of binding to the surface glycoprotein of a sarbecovirus.
2. An antibody, or an antigen-binding fragment thereof, comprising a heavy chain variable domain (VH) comprising a CDRH1, a CDRH2, and a CDRH3, and a light chain variable domain (VL) comprising a CDRL1, a CDRL2, and a CDRL3, having amino acid sequences according to (A) SEQ ID NOs.: 24-26 and 28-30, respectively; (B) SEQ ID NOs.: 32-34 and 38- 40, respectively; (C) SEQ ID NOs.: 84-86 or 84, 85 and 186 and 88-90 or 194, 89, and 90, respectively; (D) SEQ ID NOs.: 94-96; 198, 95 and 96; 208, 95 and 96; 94, 95, and 199; 198, 95 and 199; 208, 95, and 199; 94, 95, and 202; 198, 95, and 205; 208, 95, and 199; 205, 95, and 202; or 208, 95, and 205, and 98, 39, and 99; 226, 39, and 99; or 229, 39, and 232, respectively; (E) SEQ ID NOs.: 103, 85, and, 104; 103, 85, and 236; or 103, 85, and 239, and 106-108; 106, 107, and 258; 255, 107, and 108; or 255, 107, or 258, respectively; and (F) SEQ ID NOs.: 112-114; 112, 126, and 114; 112, 129 and 114; 112, 132, and 114; 112, 135, and 114; 112, 138, and 114; 112, 142, and 114; 112, 146, and 114; 112, 150, and 114; 112, 154, and 114; 112, 267, and 114;
112, 270, and 114; 112, 113, and 139; 112, 126, and 139; 112, 129 and 139; 112, 132, and 139;
112, 135, and 139; 112, 138, and 139; 112, 142, and 139; 112, 146, and 139; 112, 150, and 139;
112, 154, and 139; 112, 267, and 139; 112, 270, and 139; 112, 113, and 143; 112, 126, and 143;
112, 129 and 143; 112, 132, and 143; 112, 135, and 143; 112, 138, and 143; 112, 142, and 143; 112, 146, and 143; 112, 150, and 143; 112, 154, and 143; 112, 267, and 143; 112, 270, and 143; 112, 113, and 147; 112, 126, and 147; 112, 129 and 147; 112, 132, and 147; 112, 135, and 147; 112, 138, and 147; 112, 142, and 147; 112, 146, and 147; 112, 150, and 147; 112, 154, and 147;
112, 267, and 147; 112, 270, and 147; 112, 113, and 151; 112, 126, and 151; 112, 129 and 151;
112, 132, and 151; 112, 135, and 151; 112, 138, and 151; 112, 142, and 151; 112, 146, and 151;
112, 150, and 151; 112, 154, and 151; 112, 267, and 151; 112, 270, and 151; 112, 113, and 155;
112, 126, and 155; 112, 129 and 155; 112, 132, and 155; 112, 135, and 155; 112, 138, and 155; 112, 142, and 155; 112, 146, and 1551; 112, 150, and 155; 112, 154, and 155; 112, 267, and 155; or 112, 270, and 155; and 116-118; 116, 274, and 118; 116, 287, and 118; 116, 117, and 122;
116, 274, and 122; 116, 287, and 122; 116, 117, and 158; 116, 274, and 275; 116, 287, and 275;
116, 117, and 280; 116, 274, and 280; 116, 287, and 280; 116, 117, and 284; 116, 274, and 284;
116, 287, and 284; 116, 117, and 288; 116, 274, and 288; 116, 287, and 288; 116, 117, and 291;
116, 274, and 291; 116, 287, and 291; 273, 117, and 118; 273, 274, and 118; 273, 287, and 118;
273, 117, and 122; 273, 274, and 122; 273, 287, and 122; 273, 117, and 158; 273, 274, and 275;
273, 287, and 275; 273, 117, and 280; 273, 274, and 280; 1273, 287, and 280; 273, 117, and 284;
273, 274, and 284; 273, 287, and 284; 273, 117, and 288; 273, 274, and 288; 273, 287, and 288;
273, 117, and 291; 273, 274, and 291; 273, 287, and 291; 283, 117, 118; 283, 274, and 118; 283,
287, and 118; 283, 117, and 122; 283, 274, and 122; 283, 287, and 122; 283, 117, and 158; 283,
274, and 275; 283, 287, and 275; 283, 117, and 280; 283, 274, and 280; 283, 287, and 280; 283,
117, and 284; 283, 274, and 284; 283, 287, and 284; 283, 117, and 288; 283, 274, and 288; 283,
287, and 288; 283, 117, and 291; 283, 274, and 291; or 283, 287, and 291, respectively.
3. The antibody or antigen-binding fragment of claim 1 or claim 2, wherein the sarbecovirus is a Clade lb sarbecovirus.
4. The antibody or antigen-binding fragment of claim 3, wherein the sarbecovirus is SARS-CoV-2 WT, SARS-CoV-2 BA. l, RATG13, PANG/GD, or PAND/GX.
5. The antibody or antigen-binding fragment of any one of claims 1-4, wherein the antibody or antigen-binding fragment is capable of binding to the surface glycoprotein when the surface glycoprotein is expressed on a cell surface of a host cell and/or is comprised on a virion.
6. The antibody or antigen-binding fragment of any one of claims 1-5 which is capable of binding to a surface glycoprotein from two or more (e.g., two, three, four, five, or more) sarbecoviruses.
7. The antibody or antigen-binding fragment of any one of claims 1-6, which is capable of neutralizing an infection by one or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
8. The antibody or antigen-binding fragment of any one of claims 1-7, which is capable of neutralizing an infection by two or more sarbecoviruses in an in vitro model of infection and/or in an in vivo animal model of infection and/or in a human.
9. The antibody or antigen-binding fragment of any one of claims 1-8, wherein the VH and the VL comprise or consist of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to, or comprising or consisting of, the amino acid sequences set forth in: (I) 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18)
SEQ ID NOs: 183 and 193; 18) SEQ ID NOs: 185 and 87; 19) SEQ ID NOs: 185 and 193; 20)
SEQ ID NOs: 188 and 87; 21) SEQ ID NOs: 188 and 193; 22) SEQ ID NOs: 190 and 87; 23)
SEQ ID NOs: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ
ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 204 and 228; 39) SEQ ID NOs: 204 and 231; 40) SEQ ID NOs: 207 and 97; 41) SEQ ID
NOs: 207 and 225; 42) SEQ ID NOs: 207 and 228; 43) SEQ ID NOs: 207 and 231; 44) SEQ ID
NOs: 210 and 97; 45) SEQ ID NOs: 210 and 225; 46) SEQ ID NOs: 210 and 228; 47) SEQ ID NOs: 210 and 231; 48) SEQ ID NOs: 212 and 97; 49) SEQ ID NOs: 212 and 225; 50) SEQ ID NOs: 212 and 228; 51) SEQ ID NOs: 212 and 231; 52) SEQ ID NOs: 214 and 97; 53) SEQ ID
NOs: 214 and 225; 54) SEQ ID NOs: 214 and 228; 55) SEQ ID NOs: 214 and 231; 56) SEQ ID
NOs: 216 and 97; 57) SEQ ID NOs: 216 and 225; 58) SEQ ID NOs: 216 and 228; 59) SEQ ID NOs: 216 and 231; 60) SEQ ID NOs: 218 and 97; 61) SEQ ID NOs: 218 and 225; 62) SEQ ID NOs: 218 and 228; 63) SEQ ID NOs: 218 and 231; 64) SEQ ID NOs: 220 and 97; 65) SEQ ID
NOs: 220 and 225; 66) SEQ ID NOs: 220 and 228; 67) SEQ ID NOs: 220 and 231; 68) SEQ ID
NOs: 222 and 97; 69) SEQ ID NOs: 222 and 225; 70) SEQ ID NOs: 222 and 228; 71) SEQ ID NOs: 222 and 231; 72) SEQ ID NOs: 102 and 105; 73) SEQ ID NOs: 102 and 254; 74) SEQ ID
NOs: 102 and 257; 75) SEQ ID NOs: 102 and 260; 76) SEQ ID NOs: 235 and 105; 77) SEQ ID
NOs: 235 and 254; 78) SEQ ID NOs: 235 and 257; 79) SEQ ID NOs: 235 and 260; 80) SEQ ID
NOs: 238 and 105; 81) SEQ ID NOs: 238 and 254; 82) SEQ ID NOs: 238 and 257; 83) SEQ ID NOs: 238 and 260; 84) SEQ ID NOs: 241 and 105; 85) SEQ ID NOs: 241 and 254; 86) SEQ ID NOs: 241 and 257; 87) SEQ ID NOs: 241 and 260; 88) SEQ ID NOs: 243 and 105; 89) SEQ ID NOs: 243 and 254; 90) SEQ ID NOs: 243 and 257; 91) SEQ ID NOs: 243 and 260; 92) SEQ ID NOs: 245 and 105; 93) SEQ ID NOs: 245 and 254; 94) SEQ ID NOs: 245 and 257; 95) SEQ ID NOs: 245 and 260; 96) SEQ ID NOs: 247 and 105; 97) SEQ ID NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100) SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: l l l and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NOs: 111 and 272; 112) SEQ ID NOs: 111 and 277; 113) SEQ ID NOs: 111 and 279; 114) SEQ ID NOs: 111 and 282; 115) SEQ ID NOs: 111 and 286; 116) SEQ ID NOs: 111 and 290; 117) SEQ ID NOs: 125 and 115; 118) SEQ ID NOs: 125 and 121; 119) SEQ ID NOs: 125 and 157; 120) SEQ ID NOs: 125 and 272; 121) SEQ ID NOs: 125 and 277; 122) SEQ ID NOs: 125 and 279; 123) SEQ ID NOs: 125 and 282; 124) SEQ ID NOs: 125 and 286; 125) SEQ ID NOs: 125 and 290; 126) SEQ ID NOs: 128 and 115; 127) SEQ ID NOs: 128 and 121; 128) SEQ ID NOs: 128 and 157; 129) SEQ ID NOs: 128 and 272; 129) SEQ ID NOs: 128 and 279; 130) SEQ ID NOs: 128 and 282; 131) SEQ ID NOs: 128 and 286; 132) SEQ ID NOs: 128 and 290; 133) SEQ ID NOs: 131 and 115; 134) SEQ ID NOs: 131 and 121; 135) SEQ ID NOs: 131 and 157; 136) SEQ ID NOs: 131 and 272; 137) SEQ ID NOs: 131 and 277; 138) SEQ ID NOs: 131 and 279; 139) SEQ ID NOs: 131 and 282; 140) SEQ ID NOs: 131 and 286; 141) SEQ ID NOs: 131 and 290; 142) SEQ ID NOs: 134 and 115; 143) SEQ ID NOs: 134 and 121; 144) SEQ ID NOs: 134 and 157; 145) SEQ ID NOs: 134 and 272; 146) SEQ ID NOs: 134 and 277; 147) SEQ ID NOs: 134 and 279; 148) SEQ ID NOs: 134 and 282; 149) SEQ ID NOs: 134 and 286; 150) SEQ ID NOs: 134 and 290; 151) SEQ ID NOs: 137 and 115; 152) SEQ ID NOs: 137 and 121; 153) SEQ ID NOs: 137 and 157; 154) SEQ ID NOs: 137 and 272; 155) SEQ ID NOs: 137 and 277; 156) SEQ ID NOs: 137 and 279; 157) SEQ ID NOs: 137 and 282; 158) SEQ ID NOs: 137 and 286; 159) SEQ ID NOs: 137 and 290; 160) SEQ ID NOs: 141 and 115; 161) SEQ ID NOs: 141 and 121; 162) SEQ ID NOs: 141 and 157; 162) SEQ ID NOs: 141 and 272; 162) SEQ ID NOs: 141 and 277; 163) SEQ ID NOs: 141 and 279; 164) SEQ ID NOs: 141 and 282; 165) SEQ ID NOs: 141 and 286; 166) SEQ ID NOs: 141 290; 167) SEQ ID NOs: 145 and 115; 168) SEQ ID NOs: 145 and 121; 169) SEQ ID NOs: 145 and 157; 170) SEQ ID NOs: 145 and 272; 171) SEQ ID NOs: 145 and 277; 172) SEQ ID NOs: 145 and 279; 173) SEQ ID NOs: 145 and 282; 174) SEQ ID NOs: 145 and 282; 175) SEQ ID NOs: 145 and 286; 176) SEQ ID NOs: 145 and 290; 177) SEQ ID NOs: 149 and 115; 178) SEQ ID NOs: 149 and 121; 179) SEQ ID NOs: 149 and 157; 180) SEQ ID NOs: 149 and 272; 181) SEQ ID NOs: 149 and 277; 182) SEQ ID NOs: 149 and 279; and 183) SEQ ID NOs: 149 and 282; 184) SEQ ID NOs: 149 and 286; 185) SEQ ID NOs: 149 and 290; 186) SEQ ID NOs: 153 and 115; 187) SEQ ID NOs: 153 and 121; 188) SEQ ID NOs: 153 and 157; 189) SEQ ID NOs: 153 and 272; 190) SEQ ID NOs: 153 and 277; 191) SEQ ID NOs: 153 and 279; 192) SEQ ID NOs: 153 and 282; 193) SEQ ID NOs: 153 and 286; 194) SEQ ID NOs: 153 and 290; 195) SEQ ID NOs: 264 and 115; 196) SEQ ID NOs: 264 and 121; 197) SEQ ID NOs: 264 and 157; 198) SEQ ID NOs: 264 and 272; 199) SEQ ID NOs: 264 and 277; 200) SEQ ID NOs: 264 and 279; 201) SEQ ID NOs: 264 and 282; 202) SEQ ID NOs: 264 and 286; 203) SEQ ID NOs: 264 and 290; 204) SEQ ID NOs: 266 and 115; 205) SEQ ID NOs: 266 and 121; 206) SEQ ID NOs: 266 and 157; 207) SEQ ID NOs: 266 and 272; 208) SEQ ID NOs: 266 and 277; 209) SEQ ID NOs: 266 and 279; 210) SEQ ID NOs: 266 and 282; 211) SEQ ID NOs: 266 and 286; 212) SEQ ID NOs: 266 and 290; 213) SEQ ID NOs: 269 and 115; 214) SEQ ID NOs: 269 and 121; 215) SEQ ID NOs: 269 and 157; 216) SEQ ID NOs: 269 and 157; 217) SEQ ID NOs: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290, respectively, or (II) any other combinations for the same antibody type as set forth in Table 2 and Table 3.
10. The antibody or antigen-binding fragment of any one of claims 1-9, wherein the
VH and the VL comprise or consist of amino acid sequences set forth in 1) SEQ ID NOs: 23 and 27; 2) SEQ ID NOs: 23 and 37; 3) SEQ ID NOs: 31 and 27; 4) SEQ ID NOs: 31 and 37; 5) SEQ ID NOs: 35 and 27; 6) SEQ ID NOs: 35 and 37; 7) SEQ ID NOs: 36 and 27; 8) SEQ ID NOs: 36 and 37; 9) SEQ ID NOs: 43 and 27; 10) SEQ ID NOs: 43 and 37; 11) SEQ ID NOs: 83 and 87; 12) SEQ ID NOs: 83 and 193; 13) SEQ ID NOs: 179 and 87; 14) SEQ ID NOs: 179 and 193; 15) SEQ ID NOs: 181 and 87; 16) SEQ ID NOs: 181 and 193; 17) SEQ ID NOs: 183 and 87; 18)
SEQ ID NOs: 183 and 193; 18) SEQ ID NOs: 185 and 87; 19) SEQ ID NOs: 185 and 193; 20)
SEQ ID NOs: 188 and 87; 21) SEQ ID NOs: 188 and 193; 22) SEQ ID NOs: 190 and 87; 23)
SEQ ID NOs: 190 and 193; 24) SEQ ID NOs: 93 and 97; 25) SEQ ID NOs: 93 and 225; 26) SEQ
ID NOs: 93 and 228; 27) SEQ ID NOs: 93 and 231; 28) SEQ ID NOs: 197 and 97; 29) SEQ ID NOs: 197 and 225; 30) SEQ ID NOs: 197 and 228; 31) SEQ ID NOs: 197 and 231; 32) SEQ ID NOs: 201 and 97; 33) SEQ ID NOs: 201 and 225; 34) SEQ ID NOs: 201 and 228; 35) SEQ ID NOs: 201 and 231; 36) SEQ ID NOs: 204 and 97; 37) SEQ ID NOs: 204 and 225; 38) SEQ ID NOs: 204 and 228; 39) SEQ ID NOs: 204 and 231; 40) SEQ ID NOs: 207 and 97; 41) SEQ ID NOs: 207 and 225; 42) SEQ ID NOs: 207 and 228; 43) SEQ ID NOs: 207 and 231; 44) SEQ ID NOs: 210 and 97; 45) SEQ ID NOs: 210 and 225; 46) SEQ ID NOs: 210 and 228; 47) SEQ ID NOs: 210 and 231; 48) SEQ ID NOs: 212 and 97; 49) SEQ ID NOs: 212 and 225; 50) SEQ ID NOs: 212 and 228; 51) SEQ ID NOs: 212 and 231; 52) SEQ ID NOs: 214 and 97; 53) SEQ ID NOs: 214 and 225; 54) SEQ ID NOs: 214 and 228; 55) SEQ ID NOs: 214 and 231; 56) SEQ ID NOs: 216 and 97; 57) SEQ ID NOs: 216 and 225; 58) SEQ ID NOs: 216 and 228; 59) SEQ ID NOs: 216 and 231; 60) SEQ ID NOs: 218 and 97; 61) SEQ ID NOs: 218 and 225; 62) SEQ ID NOs: 218 and 228; 63) SEQ ID NOs: 218 and 231; 64) SEQ ID NOs: 220 and 97; 65) SEQ ID NOs: 220 and 225; 66) SEQ ID NOs: 220 and 228; 67) SEQ ID NOs: 220 and 231; 68) SEQ ID NOs: 222 and 97; 69) SEQ ID NOs: 222 and 225; 70) SEQ ID NOs: 222 and 228; 71) SEQ ID NOs: 222 and 231; 72) SEQ ID NOs: 102 and 105; 73) SEQ ID NOs: 102 and 254; 74) SEQ ID NOs: 102 and 257; 75) SEQ ID NOs: 102 and 260; 76) SEQ ID NOs: 235 and 105; 77) SEQ ID NOs: 235 and 254; 78) SEQ ID NOs: 235 and 257; 79) SEQ ID NOs: 235 and 260; 80) SEQ ID NOs: 238 and 105; 81) SEQ ID NOs: 238 and 254; 82) SEQ ID NOs: 238 and 257; 83) SEQ ID NOs: 238 and 260; 84) SEQ ID NOs: 241 and 105; 85) SEQ ID NOs: 241 and 254; 86) SEQ ID NOs: 241 and 257; 87) SEQ ID NOs: 241 and 260; 88) SEQ ID NOs: 243 and 105; 89) SEQ ID NOs: 243 and 254; 90) SEQ ID NOs: 243 and 257; 91) SEQ ID NOs: 243 and 260; 92) SEQ ID NOs: 245 and 105; 93) SEQ ID NOs: 245 and 254; 94) SEQ ID NOs: 245 and 257; 95) SEQ ID NOs: 245 and 260; 96) SEQ ID NOs: 247 and 105; 97) SEQ ID NOs: 247 and 254; 98) SEQ ID NOs: 247 and 257; 99) SEQ ID NOs: 247 and 260; 100) SEQ ID NOs: 249 and 105; 101) SEQ ID NOs: 249 and 254; 102) SEQ ID NOs: 249 and 257; 103) SEQ ID NOs: 249 and 260; 104) SEQ ID NOs: 251 and 105; 105) SEQ ID NOs: 251 and 254; 106) SEQ ID NOs: 251 and 257; 107) SEQ ID NOs: 251 and 260; 108) SEQ ID NOs: l l l and 115; 109) SEQ ID NOs: 111 and 121; 110) SEQ ID NOs: 111 and 157; 111) SEQ ID NOs: 111 and 272; 112) SEQ ID NOs: 111 and 277; 113) SEQ ID NOs: 111 and 279; 114) SEQ ID NOs: 111 and 282; 115) SEQ ID NOs: 111 and 286; 116) SEQ ID NOs: 111 and 290; 117) SEQ ID NOs: 125 and 115; 118) SEQ ID NOs: 125 and 121; 119) SEQ ID NOs: 125 and 157; 120) SEQ ID NOs: 125 and 272; 121) SEQ ID NOs: 125 and 277; 122) SEQ ID NOs: 125 and 279; 123) SEQ ID NOs: 125 and 282; 124) SEQ ID NOs: 125 and 286; 125) SEQ ID NOs: 125 and 290; 126) SEQ ID NOs: 128 and 115; 127) SEQ ID NOs: 128 and 121; 128) SEQ ID NOs: 128 and 157; 129) SEQ ID NOs: 128 and 272; 129) SEQ ID NOs: 128 and 279; 130) SEQ ID NOs: 128 and 282; 131) SEQ ID NOs: 128 and 286; 132) SEQ ID NOs: 128 and 290; 133) SEQ ID NOs: 131 and 115; 134) SEQ ID NOs: 131 and 121; 135) SEQ ID NOs: 131 and 157; 136) SEQ ID NOs: 131 and 272; 137) SEQ ID
NOs: 131 and 277; 138) SEQ ID NOs: 131 and 279; 139) SEQ ID NOs: 131 and 282; 140) SEQ ID NOs: 131 and 286; 141) SEQ ID NOs: 131 and 290; 142) SEQ ID NOs: 134 and 115; 143) SEQ ID NOs: 134 and 121; 144) SEQ ID NOs: 134 and 157; 145) SEQ ID NOs: 134 and 272; 146) SEQ ID NOs: 134 and 277; 147) SEQ ID NOs: 134 and 279; 148) SEQ ID NOs: 134 and 282; 149) SEQ ID NOs: 134 and 286; 150) SEQ ID NOs: 134 and 290; 151) SEQ ID NOs: 137 and 115; 152) SEQ ID NOs: 137 and 121; 153) SEQ ID NOs: 137 and 157; 154) SEQ ID NOs: 137 and 272; 155) SEQ ID NOs: 137 and 277; 156) SEQ ID NOs: 137 and 279; 157) SEQ ID NOs: 137 and 282; 158) SEQ ID NOs: 137 and 286; 159) SEQ ID NOs: 137 and 290; 160) SEQ ID NOs: 141 and 115; 161) SEQ ID NOs: 141 and 121; 162) SEQ ID NOs: 141 and 157; 162) SEQ ID NOs: 141 and 272; 162) SEQ ID NOs: 141 and 277; 163) SEQ ID NOs: 141 and 279; 164) SEQ ID NOs: 141 and 282; 165) SEQ ID NOs: 141 and 286; 166) SEQ ID NOs: 141 290; 167) SEQ ID NOs: 145 and 115; 168) SEQ ID NOs: 145 and 121; 169) SEQ ID NOs: 145 and 157; 170) SEQ ID NOs: 145 and 272; 171) SEQ ID NOs: 145 and 277; 172) SEQ ID NOs: 145 and 279; 173) SEQ ID NOs: 145 and 282; 174) SEQ ID NOs: 145 and 282; 175) SEQ ID NOs: 145 and 286; 176) SEQ ID NOs: 145 and 290; 177) SEQ ID NOs: 149 and 115; 178) SEQ ID NOs: 149 and 121; 179) SEQ ID NOs: 149 and 157; 180) SEQ ID NOs: 149 and 272; 181) SEQ ID NOs: 149 and 277; 182) SEQ ID NOs: 149 and 279; and 183) SEQ ID NOs: 149 and 282; 184) SEQ ID NOs: 149 and 286; 185) SEQ ID NOs: 149 and 290; 186) SEQ ID NOs: 153 and 115; 187) SEQ ID NOs: 153 and 121; 188) SEQ ID NOs: 153 and 157; 189) SEQ ID NOs: 153 and 272; 190) SEQ ID NOs: 153 and 277; 191) SEQ ID NOs: 153 and 279; 192) SEQ ID NOs: 153 and 282; 193) SEQ ID NOs: 153 and 286; 194) SEQ ID NOs: 153 and 290; 195) SEQ ID NOs: 264 and 115; 196) SEQ ID NOs: 264 and 121; 197) SEQ ID NOs: 264 and 157; 198) SEQ ID NOs: 264 and 272; 199) SEQ ID NOs: 264 and 277; 200) SEQ ID NOs: 264 and 279; 201) SEQ ID NOs: 264 and 282; 202) SEQ ID NOs: 264 and 286; 203) SEQ ID NOs: 264 and 290; 204) SEQ ID NOs: 266 and 115; 205) SEQ ID NOs: 266 and 121; 206) SEQ ID NOs: 266 and 157; 207) SEQ ID NOs: 266 and 272; 208) SEQ ID NOs: 266 and 277; 209) SEQ ID NOs: 266 and 279; 210) SEQ ID NOs: 266 and 282; 211) SEQ ID NOs: 266 and 286; 212) SEQ ID NOs: 266 and 290; 213) SEQ ID NOs: 269 and 115; 214) SEQ ID NOs: 269 and 121; 215) SEQ ID NOs: 269 and 157; 216) SEQ ID NOs: 269 and 157; 217) SEQ ID NOs: 269 and 272; 218) SEQ ID NOs: 269 and 277; 219) SEQ ID NOs: 269 and 279; 219) SEQ ID NOs: 269 and 282; 220) SEQ ID NOs: 269 and 286; or 221) SEQ ID NOs: 269 and 290, respectively.
11. The antibody or antigen-binding fragment of any one of claims 1-10, which:
(i) recognizes an epitope in the Spike protein of two or more, three or more, four or more, or five or more sarbecoviruses;
(ii) is capable of blocking an interaction between the Spike protein of two or more, three or more, four or more, or five or more sarbecoviruses and their respective cell surface receptor(s), wherein, optionally, a cell surface receptor comprises a human ACE2;
(iii) recognizes an epitope that is conserved in the Spike protein of two or more, , three or more, four or more, or five or more sarbecoviruses;
(iv) is cross-reactive against two or more, three or more, four or more, or five or more sarbecoviruses, optionally comprising one or more clade lb sarbecoviruses; or
(v) any combination of (i)-(iv).
12. The antibody or antigen-binding fragment of any one of claims 1-11, which is an IgG, IgA, IgM, IgE, or IgD isotype.
13. The antibody or antigen-binding fragment of claim 12, which is an IgG isotype selected from IgGl, IgG2, IgG3, and IgG4, and is preferably an IgGl isotype.
14. The antibody or antigen-binding fragment of any one of claims 1-13, which is human, humanized, or chimeric.
15. The antibody or antigen-binding fragment of any one of Claims 1-14, wherein the antibody, or the antigen-binding fragment, comprises a human antibody, a monoclonal antibody, a purified antibody, a single chain antibody, a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, or a scFab.
16. The antibody or antigen-binding fragment of Claim 15, wherein the scFv comprises more than one VH domain and more than one VL domain.
17. The antibody or antigen-binding fragment of any one of Claims 1-16, wherein the antibody or antigen-binding fragment is a multi-specific antibody or antigen-binding fragment.
18. The antibody or antigen-binding fragment of Claim 17, wherein the antibody or antigen-binding fragment is a bispecific antibody or antigen-binding fragment.
19. The antibody or antigen-binding fragment of Claim 18, comprising: a first VH and a first VL; and a second VH and a second VL, wherein the first VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and 87 or 193, respectively; iv) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and 97, 225, 228, or 231, respectively; v) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and 105, 254, 257, or 260, respectively; or vi) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NO.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; and wherein the second VH and VL comprise i) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in SEQ ID NOs.: 23 and 27, respectively; ii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 31, 35, 36, or 43 and 37, respectively; 14 and 15, respectively; 16 and 17, respectively; 18 and 19, respectively; 20 and 21, respectively; 20 and 22, respectively; iii) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 83, 179, 181, 183, 185, 188, or 190 and 87 or 193, respectively; iv) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 93, 197, 201, 204, 207, 210, 212, 214, 216, 218, 220, or 222 and 97, 225, 228, or 231, respectively; v) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 102, 235, 238, 241, 243, 245, 247, 249, or 251 and 105, 254, 257, or 260, respectively; or vi) an amino acid sequence having at least 85% (i.e., 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) identity to the amino acid sequence set forth in any one of SEQ ID NO.: I l l, 125, 128, 131, 134, 137, 141, 145, 149, 153, 264, 266, or 269 and 115, 121, 157, 272, 277, 279, 282, 286, or 290, respectively; wherein the first VH and the second VL are different from the second VH and VL; wherein the first VH and the first VL together form a first antigen-binding site; and wherein the second VH and the second VL together form a second antigen-binding site.
20. The antibody or antigen-binding fragment of any one of claims 1-19, wherein the antibody or antigen-binding fragment comprises a Fc polypeptide or a fragment thereof comprising the substitution mutations M428L/N434S, M428L/N434A, G236A/A330L/I332E/M428L/N434S, or G236A/A330L/I332E/M428L/N434A, wherein, optionally, the antibody or antigen-binding fragment is an IgGl isotype, and comprises or consists of a Fc polypeptide or fragment thereof that comprises or consists of amino acid sequences having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NOs: 44-80, optionally other than naturally occurring variants thereof, or that comprises or consists of, the amino acid sequences set forth in SEQ ID NOs: 52-80.
21. An isolated polynucleotide encoding the antibody or antigen-binding fragment of any one of claims 1-20.
22. A recombinant vector comprising the polynucleotide of any claim 21.
23. A host cell comprising the polynucleotide of claim 21 and/or the vector of claim 22, wherein the polynucleotide is heterologous to the host cell.
24. A human B cell comprising the polynucleotide of claim 21 and/or the vector of claim 22, wherein polynucleotide is heterologous to the human B cell and/or wherein the human B cell is immortalized.
25. A composition comprising:
(i) the antibody or antigen-binding fragment of any one of claims 1-20;
(ii) the polynucleotide of claim 21;
(iii) the recombinant vector of claim 22;
(iv) the host cell of claim 23; and/or
(v) the human B cell of claim 24, and a pharmaceutically acceptable excipient, carrier, or diluent.
26. The composition of claim 25, comprising two or more antibodies or antigenbinding fragments, wherein the first antibody or antigen-binding fragment and second antibody or antigen-binding fragment, respectively, or the multispecific antibody or antigen-binding fragment, comprise(s) CDRH1, CDRH2, CDRH3, CDRL1, CDRL2, and CDRL3, and optionally VH and VL, according to (i) any S3 A3 antibody and any S3 Al 9 antibody; (ii) any S3 A3 antibody and sotrovimab; (iii) any S3A3 antibody and S2K146; (iv) any S3A3 antibody and S2X259; (v) any S3 A3 antibody and any S2X324 antibody; (vi) any S3 A3 antibody and S309;
(vi) any S3A19 antibody and sotrovimab; (vii) any S3A19 antibody and S2K146; (viii) any
S3 Al 9 antibody and S2X259; (ix) any S3 Al 9 antibody and any S2X324 antibody; (x) any S3A19 antibody and S309; (xi) any S3I2 antibody and any S3A3 antibody; (xii) any S3I2 antibody and any S3 Al 9 antibody; (xiii) any S3I2 antibody and sotrovimab; (xiv) any S3I2 antibody and S2K146; (xv) any S3I2 antibody and S2X259; (xvi) any S3I2 antibody and any S2X324 antibody; (xvii) any S3I2 antibody and S309; (xviii) any S3I2 antibody and any S3O13 antibody; (xix) any S312 antibody and any S3L17 antibody; (xx) any S3O13 antibody and any S3A3 antibody; (xxi) any S3O13 antibody and any S3A19 antibody; (xxii) any S3O13 antibody and sotrovimab; (xxiii) any S3O13 antibody and S2K146; (xxiv) any S3O13 antibody and S2X259; (xxv) any S3O13 antibody and any S2X324 antibody; (xxvi) any S3O13 antibody and S309; (xxvii) any S3O13 antibody and any S3L17 antibody; (xxviii) any S3L17 antibody and any S3 A3 antibody; (xxix) any S3L17 antibody and any S3A19 antibody; (xxx) any S3L17 antibody and sotrovimab; (xxxi) any S3L17 antibody and S2K146; (xxxii) any S3L17 antibody and S2X259; (xxxiii) any S3L17 antibody and any S2X324 antibody; (xxxiv) any S3L17 antibody and S309; (xxxv) any S2V29 antibody and any S3 A3 antibody; (xxxvi) any S2V29 antibody and any S3 Al 9 antibody; (xxxvii) any S2V29 antibody and sotrovimab; (xxxviii) any S2V29 antibody and S2K146; (xxxix) any S2V29 antibody and S2X259; (xl) any S2V29 antibody and any S2X324 antibody; (xli) any S2V29 antibody and S309; (Ixlii) any S2V29 antibody and any S3L17 antibody; and (xliii) any S2V29 antibody and any S3O13 antibody, or any antigen-binding fragments thereof.
27. A composition comprising the polynucleotide of claim 25 or claim 26 encapsulated in a carrier molecule, wherein the carrier molecule optionally comprises a lipid, a lipid-derived delivery vehicle, such as a liposome, a solid lipid nanoparticle, an oily suspension, a submicron lipid emulsion, a lipid microbubble, an inverse lipid micelle, a cochlear liposome, a lipid microtubule, a lipid microcylinder, lipid nanoparticle (LNP), or a nanoscale platform.
28. A method of treating a sarbecovirus infection in a subject, the method comprising administering to the subject an effective amount of
(i) the antibody or antigen-binding fragment of any one of claims 1-20;
(ii) the polynucleotide of claim 21;
(iii) the recombinant vector of claim 22;
(iv) the host cell of claim 23; and/or
(v) the human B cell of claim 24, and/or
(vi) the composition of any one of claims 25-27.
29. The antibody or antigen-binding fragment of any one of claims 1-20, the polynucleotide of claim 21, the recombinant vector of claim 22, the host cell of claim 23, the human B cell of claim 24, and/or the composition of any one of claims 25-27 for use in a method of treating a sarbecovirus infection in a subject.
30. The antibody or antigen-binding fragment of any one of claims 1-20, the polynucleotide of claim 21, the recombinant vector of claim 22, the host cell of claim 23, the human B cell of claim 24, and/or the composition of any one of claims 25-27 for use in the preparation of a medicament for the treatment of a sarbecovirus infection in a subject.
31. A kit comprising a liquid composition comprising and antibody or antigen-binding fragment of any one of claims 1-20 or 29-30 and instructions for use thereof in treating a SARS- CoV-2 infection in a subject.
32. A method for in vitro diagnosis of a sarbecovirus infection (e.g. infection by a SARS-CoV-2), the method comprising:
(i) contacting a sample from a subject with an antibody or antigen-binding fragment of any one of claims 1-20; and
(ii) detecting a complex comprising an antigen and the antibody, or comprising an antigen and the antigen-binding fragment.
33. A method for producing an antibody or antigen-binding fragment of any one of claims 1-20 or 29-30, wherein the method comprises culturing a host cell expressing the antibody or antigen-binding fragment under conditions and for a time sufficient to produce the antibody, or the antigen-binding fragment.
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Citations (28)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4751180A (en) 1985-03-28 1988-06-14 Chiron Corporation Expression using fused genes providing for protein product
US4816567A (en) 1983-04-08 1989-03-28 Genentech, Inc. Recombinant immunoglobin preparations
US4935233A (en) 1985-12-02 1990-06-19 G. D. Searle And Company Covalently linked polypeptide cell modulators
US5283173A (en) 1990-01-24 1994-02-01 The Research Foundation Of State University Of New York System to detect protein-protein interactions
US5530101A (en) 1988-12-28 1996-06-25 Protein Design Labs, Inc. Humanized immunoglobulins
US5648237A (en) 1991-09-19 1997-07-15 Genentech, Inc. Expression of functional antibody fragments
US5770429A (en) 1990-08-29 1998-06-23 Genpharm International, Inc. Transgenic non-human animals capable of producing heterologous antibodies
US5789199A (en) 1994-11-03 1998-08-04 Genentech, Inc. Process for bacterial production of polypeptides
US5840523A (en) 1995-03-01 1998-11-24 Genetech, Inc. Methods and compositions for secretion of heterologous polypeptides
US5959177A (en) 1989-10-27 1999-09-28 The Scripps Research Institute Transgenic plants expressing assembled secretory antibodies
US6040498A (en) 1998-08-11 2000-03-21 North Caroline State University Genetically engineered duckweed
US6420548B1 (en) 1999-10-04 2002-07-16 Medicago Inc. Method for regulating transcription of foreign genes
US6596541B2 (en) 2000-10-31 2003-07-22 Regeneron Pharmaceuticals, Inc. Methods of modifying eukaryotic cells
WO2004076677A2 (en) 2003-02-26 2004-09-10 Institute For Research In Biomedicine Monoclonal antibody production by ebv transformation of b cells
US7049426B2 (en) 1999-06-10 2006-05-23 Abgenix, Inc. Transgenic animals for producing specific isotypes of human antibodies via non-cognate switch regions
US7125978B1 (en) 1999-10-04 2006-10-24 Medicago Inc. Promoter for regulating expression of foreign genes
US7498415B2 (en) 2003-09-24 2009-03-03 Kyowa Hakko Kogyo Co., Ltd. Recombinant antibody against human insulin-like growth factor
US8119772B2 (en) 2006-09-29 2012-02-21 California Institute Of Technology MART-1 T cell receptors
US8258268B2 (en) 2005-08-19 2012-09-04 Abbott Laboratories Dual variable domain immunoglobulin and uses thereof
WO2015103072A1 (en) 2013-12-30 2015-07-09 Epimab Biotherapeutics Fabs-in-tandem immunoglobulin and uses thereof
WO2016181357A1 (en) 2015-05-13 2016-11-17 Zumutor Biologics, Inc. Afucosylated protein, cell expressing said protein and associated methods
WO2019024979A1 (en) 2017-07-31 2019-02-07 Institute For Research In Biomedicine Antibodies with functional domains in the elbow region
WO2019057122A1 (en) 2017-09-22 2019-03-28 Wuxi Biologics (Shanghai) Co., Ltd. Novel bispecific polypeptide complexes
WO2019125846A1 (en) * 2017-12-19 2019-06-27 The Rockefeller University HUMAN IgG Fc DOMAIN VARIANTS WITH IMPROVED EFFECTOR FUNCTION
WO2021186190A1 (en) * 2020-03-19 2021-09-23 Imperial College Innovations Limited Coronavirus antibody
WO2021226560A1 (en) 2020-05-08 2021-11-11 Vir Biotechnology, Inc. Antibodies against sars-cov-2
CN114031685A (en) * 2022-01-10 2022-02-11 中国人民解放军军事科学院军事医学研究院 Fully human anti-new coronavirus broad-spectrum neutralizing antibody ZW2G10 and application thereof
WO2022251119A2 (en) 2021-05-24 2022-12-01 Vir Biotechnology, Inc. Engineered polypeptides

Patent Citations (31)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4816567A (en) 1983-04-08 1989-03-28 Genentech, Inc. Recombinant immunoglobin preparations
US4751180A (en) 1985-03-28 1988-06-14 Chiron Corporation Expression using fused genes providing for protein product
US4935233A (en) 1985-12-02 1990-06-19 G. D. Searle And Company Covalently linked polypeptide cell modulators
US5530101A (en) 1988-12-28 1996-06-25 Protein Design Labs, Inc. Humanized immunoglobulins
US5959177A (en) 1989-10-27 1999-09-28 The Scripps Research Institute Transgenic plants expressing assembled secretory antibodies
US6417429B1 (en) 1989-10-27 2002-07-09 The Scripps Research Institute Transgenic plants expressing assembled secretory antibodies
US5468614A (en) 1990-01-24 1995-11-21 The Research Foundation Of State University Of New York System to detect protein-protein interactions
US5283173A (en) 1990-01-24 1994-02-01 The Research Foundation Of State University Of New York System to detect protein-protein interactions
US5770429A (en) 1990-08-29 1998-06-23 Genpharm International, Inc. Transgenic non-human animals capable of producing heterologous antibodies
US5648237A (en) 1991-09-19 1997-07-15 Genentech, Inc. Expression of functional antibody fragments
US5789199A (en) 1994-11-03 1998-08-04 Genentech, Inc. Process for bacterial production of polypeptides
US5840523A (en) 1995-03-01 1998-11-24 Genetech, Inc. Methods and compositions for secretion of heterologous polypeptides
US6040498A (en) 1998-08-11 2000-03-21 North Caroline State University Genetically engineered duckweed
US7049426B2 (en) 1999-06-10 2006-05-23 Abgenix, Inc. Transgenic animals for producing specific isotypes of human antibodies via non-cognate switch regions
US6420548B1 (en) 1999-10-04 2002-07-16 Medicago Inc. Method for regulating transcription of foreign genes
US7125978B1 (en) 1999-10-04 2006-10-24 Medicago Inc. Promoter for regulating expression of foreign genes
US6596541B2 (en) 2000-10-31 2003-07-22 Regeneron Pharmaceuticals, Inc. Methods of modifying eukaryotic cells
WO2004076677A2 (en) 2003-02-26 2004-09-10 Institute For Research In Biomedicine Monoclonal antibody production by ebv transformation of b cells
US7498415B2 (en) 2003-09-24 2009-03-03 Kyowa Hakko Kogyo Co., Ltd. Recombinant antibody against human insulin-like growth factor
US8258268B2 (en) 2005-08-19 2012-09-04 Abbott Laboratories Dual variable domain immunoglobulin and uses thereof
US8119772B2 (en) 2006-09-29 2012-02-21 California Institute Of Technology MART-1 T cell receptors
WO2015103072A1 (en) 2013-12-30 2015-07-09 Epimab Biotherapeutics Fabs-in-tandem immunoglobulin and uses thereof
WO2016181357A1 (en) 2015-05-13 2016-11-17 Zumutor Biologics, Inc. Afucosylated protein, cell expressing said protein and associated methods
WO2019024979A1 (en) 2017-07-31 2019-02-07 Institute For Research In Biomedicine Antibodies with functional domains in the elbow region
WO2019025391A1 (en) 2017-07-31 2019-02-07 Institute For Research In Biomedicine Antibodies with functional domains in the elbow region between variable adn constant domain
WO2019057122A1 (en) 2017-09-22 2019-03-28 Wuxi Biologics (Shanghai) Co., Ltd. Novel bispecific polypeptide complexes
WO2019125846A1 (en) * 2017-12-19 2019-06-27 The Rockefeller University HUMAN IgG Fc DOMAIN VARIANTS WITH IMPROVED EFFECTOR FUNCTION
WO2021186190A1 (en) * 2020-03-19 2021-09-23 Imperial College Innovations Limited Coronavirus antibody
WO2021226560A1 (en) 2020-05-08 2021-11-11 Vir Biotechnology, Inc. Antibodies against sars-cov-2
WO2022251119A2 (en) 2021-05-24 2022-12-01 Vir Biotechnology, Inc. Engineered polypeptides
CN114031685A (en) * 2022-01-10 2022-02-11 中国人民解放军军事科学院军事医学研究院 Fully human anti-new coronavirus broad-spectrum neutralizing antibody ZW2G10 and application thereof

Non-Patent Citations (87)

* Cited by examiner, † Cited by third party
Title
"GenBank", Database accession no. QHD43416.1
"Remington: The Science and Practice of Pharmacy", 2000, PHILADELPHIA COLLEGE OF PHARMACY AND SCIENCE
ABHINANDANMARTIN, MOL IMMUNOL, vol. 45, 2008, pages 3832 - 8
AHMED ET AL., J. STRUC. BIOL, vol. 194, no. 1, 2016, pages 78
ALTSCHUL ET AL., NUCLEIC ACIDS RES., vol. 25, 1997, pages 3389 - 3402
ARMOUR, K. L ET AL., EUR. J. IMMUNOL., vol. 29, 1999, pages 2613 - 2624
BAUM ALINA ET AL: "Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies", SCIENCE, vol. 369, no. 6506, 21 August 2020 (2020-08-21), US, pages 1014 - 1018, XP093069117, ISSN: 0036-8075, DOI: 10.1126/science.abd0831 *
BIOINFORMATICS, vol. 15, 2016, pages 298 - 300
BRINKMANNKONTERMANN, MABS, vol. 9, no. 2, 2017, pages 182 - 212
BRUHNS ET AL., BLOOD, vol. 113, 2009, pages 3716 - 3725
BURTON, D. R, MOL. IMMUNOL, vol. 22, 1985, pages 161 - 206
CAMERONI ELISABETTA ET AL: "Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift", CLEO: APPLICATIONS AND TECHNOLOGY 2019 SAN JOSE, CALIFORNIA UNITED STATES 5-10 MAY 2019, OPTICA, vol. 602, no. 7898, 23 December 2021 (2021-12-23), pages 664 - 670, XP037700797, DOI: 10.1038/S41586-021-04386-2 *
CAPEL, P. J ET AL., IMMUNOMETHODS, vol. 113, 1994, pages 269 - 315
CATHCART ANDREA L. ET AL: "The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2", BIORXIV, 10 March 2021 (2021-03-10), pages 1 - 44, XP055841313, Retrieved from the Internet <URL:https://www.biorxiv.org/content/10.1101/2021.03.09.434607v1.full.pdf> [retrieved on 20210915], DOI: 10.1101/2021.03.09.434607 *
CATHCART, A. ET AL.: "The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2", BIORXIV 2021.03.09.434607
CHAUDHARY ET AL., PROC. NATL. ACAD. SCI. USA, vol. 87, 1990, pages 1066 - 1070
CHOTHIALESK: "J. Mol. Biol.", vol. 196, 1987, pages: 901 - 917
CHU, S. Y ET AL.: "Inhibition of B cell receptor-mediated activation of primary human B cells by coengagement of CD19 and FcgammaRIIb with Fc-engineered antibodies", MOLECULAR IMMUNOLOGY, vol. 45, 2008, pages 3926 - 3933, XP002498116, DOI: 10.1016/j.molimm.2008.06.027
CLACKSON ET AL., NATURE, vol. 352, 1991, pages 624 - 628
COFFIN, J. M ET AL.: "Fundamental Virology", 1996, LIPPINCOTT-RAVEN PUBLISHERS, article "Retroviridae: The viruses and their replication"
DELILLORAVETCH, CELL, vol. 161, no. 5, 2015, pages 1035 - 1045
DUNCAN, A. RWINTER, G, NATURE, vol. 332, 1988, pages 323 - 327
ELLIOTT ET AL., NPJ VACCINES, 2017, pages 18
ENGELS ET AL., HUM. GENE THER, vol. 14, 2003, pages 1155
FLINGAI ET AL., SCI REP, vol. 5, 2015, pages 12616
FRECHA ET AL., MOL. THER, vol. 18, 2010, pages 1748
GANESAN, L. P ET AL.: "2012: FcyRIIb on liver sinusoidal endothelium clears small immune complexes", JOURNAL OF IMMUNOLOGY, vol. 189, pages 4981 - 4988, XP002724347, DOI: 10.4049/jimmunol.1202017
GANESAN, L. P ET AL.: "FcyRIIb on liver sinusoidal endothelium clears small immune complexes", JOURNAL OF IMMUNOLOGY, vol. 189, 2012, pages 4981 - 4988, XP002724347, DOI: 10.4049/jimmunol.1202017
GESSNER, J. E ET AL., ANN. HEMATOL, vol. 76, 1998, pages 231 - 248
GEURTS ET AL., MOL. THER, vol. 8, 2003, pages 108
HAAS, M ET AL., J LAB. CLIN. MED, vol. 126, 1995, pages 330 - 341
HE WAN-TING ET AL: "Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses", NATURE IMMULOGY, NATURE PUBLISHING GROUP US, NEW YORK, vol. 23, no. 6, 1 June 2022 (2022-06-01), pages 960 - 970, XP037898007, ISSN: 1529-2908, [retrieved on 20220602], DOI: 10.1038/S41590-022-01222-1 *
HONEGGERPLUCKTHUN, J. MOL. BIO, vol. 309, 2001, pages 657 - 670
HUANG ET AL., MABS, vol. 6, 2018, pages 1 - 12
JOLLY, D J, EMERGING VIRAL VECTORS, 1999, pages 209 - 40
JONES ET AL., NATURE, vol. 321, 1986, pages 522 - 525
KOHLER ET AL., NATURE, vol. 256, 1975, pages 495
KOSE ET AL., SCI. IMMUNOL, 2019, pages 4
KRISKY ET AL., GENE THER, vol. 5, 1998, pages 1517
LEFRANC ET AL., DEV. COMP. IMMUNOL, vol. 27, 2003, pages 55
LEFRANC, M.-P., LEFRANC, G: "Immunogenetics", HUMANA PRESS, article " Human Gm, Km and Am allotypes and their molecular characterization: a remarkable demonstration of polymorphism"
LI ET AL., NAT. BIOTECH., vol. 24, 2006, pages 210 - 215
LI ET AL., WILERY INTERDISCIP REV. NANOMED NANOBIOTECHNOL, vol. 77, no. 2, 2019, pages el530
LIU ET AL., MABS, vol. 6, no. 5, 2014, pages 1145 - 1154
LIU LIHONG ET AL: "An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses", SCI. TRANSL. MED., 25 May 2022 (2022-05-25), XP055925624, Retrieved from the Internet <URL:https://www.science.org/doi/10.1126/scitranslmed.abn6859> [retrieved on 20220530], DOI: 10.1126/scitranslmed.abn6859 *
MARATEA ET AL., GENE, vol. 40, 1985, pages 39 46
MARKS ET AL., J. MOL. BIOL., vol. 222, 1991, pages 581 - 597
MATES ET AL., NAT. GENET., vol. 41, 2009, pages 753
METHODS MOL. BIOL, vol. 882, 2012, pages 635 - 680
MORRISON ET AL., PROC. NATL. ACAD. SCI. USA, vol. 81, 1984, pages 6851 - 6855
MURPHY ET AL., PROC. NATL. ACAD. SCI. USA, vol. 83, 1986, pages 8258 8262
MUTHUMANI ET AL., HUM VACCIN IMMUNOTHER, vol. 9, 2013, pages 2253 - 2262
MUTHUMANI ET AL., J INFECT DIS, vol. 214, no. 3, 2016, pages 369 - 378
NAT. BIOTECH., vol. 22, 2004, pages 1409 - 1414
NORTH ET AL., J MOL BIOL., vol. 406, 2011, pages 228 - 56
PALMBERGER ET AL., J. BIOTECHNOL, vol. 152, no. 3-4, 2011, pages 160 - 166
PARDI ET AL., J CONTROL RELEASE, 2015, pages 217345 - 351
PARK ET AL.: "REGEN-COV and Evusheld from Stanford", SCIENCE 2022, 22 January 2023 (2023-01-22), Retrieved from the Internet <URL:https://covdb.stanford.edu/susceptibility-data/table-mab-susc>
PARK YOUNG-JUN ET AL: "Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry", SCIENCE, vol. 375, no. 6579, 6 January 2022 (2022-01-06), US, pages 449 - 454, XP055930660, ISSN: 0036-8075, Retrieved from the Internet <URL:https://www.science.org/doi/10.1126/science.abm8143> DOI: 10.1126/science.abm8143 *
PARK YOUNG-JUN ET AL: "Suppl Material Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry", SCIENCE, vol. 375, no. 6579, 6 January 2022 (2022-01-06), US, pages 449 - 454, XP055930662, ISSN: 0036-8075, Retrieved from the Internet <URL:https://www.science.org/doi/10.1126/science.abm8143> DOI: 10.1126/science.abm8143 *
PARK, Y-J. ET AL., SCIENCE, 2022, Retrieved from the Internet <URL:https://doi.org/10.1126/science.abm8143>
PINTO, D. ET AL.: "Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody", NATURE, vol. 583, 2020, pages 290 - 295, XP037289888, Retrieved from the Internet <URL:https://doi.org/10.1038/s41586-020-2349-y> DOI: 10.1038/s41586-020-2349-y
PLUCKTHUN, A, BIO/TECHNOLOGY, vol. 9, 1991, pages 545 - 551
PRESTA, CURR. OP. STRUCT. BIOL, vol. 2, 1992, pages 593 - 596
RAVETCH, J. VKINET, J. P, ANNU. REV. IMMUNOL, vol. 9, 1991, pages 457 - 492
SABNIS ET AL., MOL. THER, vol. 26, 2018, pages 1509 - 1519
SAMBROOK ET AL.: "Molecular Cloning: A Laboratory Manual", 1989, COLD SPRING HARBOR LABORATORY
SCATCHARD ET AL.: "Ann. N.Y. Acad. Sci", vol. 51, 1949, pages: 660
SCHOLTEN ET AL., CLIN. IMMUNOL., vol. 119, 2006, pages 135
SHIELDS, R. L ET AL., J. BIOL. CHEM., vol. 276, 2001, pages 6591 - 6604
SPIESS ET AL., MOL. IMMUNOL, vol. 67, no. 2, 2015, pages 95
SUZUKI, CANCER RES., vol. 13, no. 6, 2007, pages 1875 - 82
THESS ET AL., MOL THER, vol. 23, 2015, pages 1456 - 1464
THRAN ET AL., EMBO MOL MED, vol. 9, no. 10, 2017, pages 1434 - 1448
TORTORICI, M.A ET AL.: "Broad sarbecovirus neutralization by a human monoclonal antibody", NATURE, vol. 597, 2021, pages 103 - 108, XP037552984, Retrieved from the Internet <URL:https://doi.org/10.1038/s41586-021-03817-4> DOI: 10.1038/s41586-021-03817-4
URLAUB ET AL., PNAS, vol. 77, 1980, pages 4216
VAN DE WINKEL, J. G.ANDERSON, C. L, J. LEUKOC. BIOL, vol. 49, 1991, pages 511 - 524
VERHOEYEN ET AL., METHODS MOL. BIOL, vol. 506, 2009, pages 97
VERHOEYEN ET AL., SCIENCE, vol. 239, 1988, pages 1534 - 1536
WALCHLI ET AL., PLOS ONE, vol. 6, 2011, pages 327930
WARD, E. SGHETIE, V, THER. IMMUNOL, vol. 2, 1995, pages 77 - 94
WILSON, SCIENCE, vol. 295, 2002, pages 2103
WINES, B.D ET AL., J. IMMUNOL., vol. 164, 2000, pages 5313 - 5318
WOLFF ET AL., CANCER RES., vol. 55, 1993, pages 2560
XIANG YUFEI ET AL: "Superimmunity by pan-sarbecovirus nanobodies", CELL REPORTS, vol. 39, no. 13, 1 June 2022 (2022-06-01), US, pages 111004, XP093090210, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2022.111004 *
YAZAKIWU: "Methods in Molecular Biology", vol. 248, 2003, HUMANA PRESS, pages: 255 - 268
ZHAO ET AL., J. IMMUNOL., vol. 174, 2005, pages 4415

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