WO2022251403A1 - Anticorps anti-sars-cov-2 et leurs utilisations - Google Patents

Anticorps anti-sars-cov-2 et leurs utilisations Download PDF

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WO2022251403A1
WO2022251403A1 PCT/US2022/030993 US2022030993W WO2022251403A1 WO 2022251403 A1 WO2022251403 A1 WO 2022251403A1 US 2022030993 W US2022030993 W US 2022030993W WO 2022251403 A1 WO2022251403 A1 WO 2022251403A1
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antibody
chain region
sars
cov
light chain
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Florian KRAMMER
Fatima AMANAT
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Icahn School Of Medicine At Mount Sinai
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • 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]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
    • A61K2039/541—Mucosal route
    • A61K2039/543—Mucosal route intranasal
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55511—Organic adjuvants
    • A61K2039/55561—CpG containing adjuvants; Oligonucleotide containing adjuvants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • 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
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
    • C12N2710/00011—Details
    • C12N2710/10011—Adenoviridae
    • C12N2710/10311—Mastadenovirus, e.g. human or simian adenoviruses
    • C12N2710/10341—Use of virus, viral particle or viral elements as a vector
    • C12N2710/10343—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • SARS-CoV-2 first emerged in late 2019 in the province of Hubei in China, spread rapidly throughout the globe, and has since caused the ongoing coronavirus disease 2019 (COVID- 19) pandemic (Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus I, Research T. 2020. A Novel Coronavirus from Patients with Pneumonia in China, 2019.
  • Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science 371:926–931; Hattori SI, Higashi-Kuwata N, Hayashi H, Allu SR, Raghavaiah J, Bulut H, Das D, Anson BJ, Lendy EK, Takamatsu Y, Takamune N, Kishimoto N, Murayama K, Hasegawa K, Li M, Davis DA, Kodama EN, Yarchoan R, Wlodawer A, Misumi S, Mesecar AD, Ghosh AK, Mitsuya H. 2021.
  • a small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.
  • SARS-CoV-2 a positive-sense single-stranded RNA virus from the Coronaviridae family, is closely related to SARS-CoV-1 which caused a major outbreak in 2002-2004. Both viruses use the same receptor for entry into host cells, human angiotensin converting enzyme (hACE2) (Letko M, Marzi A, Munster V. 2020. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses.
  • hACE2 human angiotensin converting enzyme
  • the receptor binding domain (RBD) which is part of the spike protein of the virus can bind to hACE2 and mediate entry and thus, the spike protein makes for an excellent target for vaccines and therapeutics (Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. 2020. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367:1260–1263).
  • N-terminal domain Another region heavily mutated in the new circulating variant viruses is the N-terminal domain (NTD) which is also a target of neutralizing antibodies(McCallum M, Marco A, Lempp F, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Caroline Foo SY, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D.
  • NTD N-terminal domain
  • N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. bioRxiv).
  • efficacy of vaccines and therapeutics could be compromised as more and more mutations in the NTD and RBD occur and persist in nature (Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, 1973, Nargi RS, Sutton RE, Sury Shawa N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE, Jr.., Bloom JD.2021.
  • an antibody that binds to the spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) or a fragment thereof (e.g., receptor binding domain (RBD)) and compositions comprising such an antibody. See, e.g., the antibodies described herein (e.g., Tables 1, 2, and 3).
  • an antibody described herein includes the amino acid sequences of the variable heavy chain region and variable light chain region of antibody 1F7, 2C3, 1H12, 2F9, and 3A7.
  • an antibody provided herein includes the amino acid sequences of the variable heavy chain region and the variable light chain region of the antibody 1F7.
  • an antibody provided herein includes the amino acid sequences of the variable heavy chain region and the variable light chain region of the antibody 2C3. In a specific aspect, an antibody provided herein includes the amino acid sequences of the variable heavy chain region and the variable light chain region of the antibody 1H12. In a specific aspect, an antibody provided herein includes the amino acid sequences of the variable heavy chain region and the variable light chain region of the antibody 2F9. In a specific aspect, an antibody provided herein includes the amino acid sequences of the variable heavy chain region and the variable light chain region of the antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 1F7; or (b) a variable light chain region comprising the variable light chain region CDRs of antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof comprises: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 2C3; or (b) a variable light chain region comprising the variable light chain region CDRs of antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 1H12; or (b) a variable light chain region comprising the variable light chain region CDRs of antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 2F9; or (b) a variable light chain region comprising the variable light chain region CDRs of antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 3A7; or (b) a variable light chain region comprising the variable light chain region CDRs of antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 1F7; and (b) a variable light chain region comprising the variable light chain region CDRs of antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 2C3; and (b) a variable light chain region comprising the variable light chain region CDRs of antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 1H12; and (b) a variable light chain region comprising the variable light chain region CDRs of antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 2F9; and (b) a variable light chain region comprising the variable light chain region CDRs of antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region comprising the variable heavy chain region complementarity determining regions (CDRs) of antibody 3A7; and (b) a variable light chain region comprising the variable light chain region CDRs of antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein wherein the antibody includes a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 1F7 and a variable light chain region including the amino acid sequence of the variable light chain region of antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein wherein the antibody includes a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 2C3 and a variable light chain region including the amino acid sequence of the variable light chain region of antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein wherein the antibody comprises a variable heavy chain region includes the amino acid sequence of the variable heavy chain region of antibody 1H12 and a variable light chain region including the amino acid sequence of the variable light chain region of antibody 1H12.
  • the antibody includes a variable heavy chain region including the amino acid sequence of the variable heavy chain region of antibody 2F9 and a variable light chain region including the amino acid sequence of the variable light chain region of antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein, wherein the antibody includes a variable heavy chain region including the amino acid sequence of the variable heavy chain region of antibody 3A7 and a variable light chain region including the amino acid sequence of the variable light chain region of antibody 3A7. See infra for the sequences of the variable heavy chain regions and the variable light chain regions of monoclonal antibodies 1F7, 2C3, 1H12, 2F9, and 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable heavy chain region antibody 1F7; or (b) a variable light chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable light chain region antibody 1F7.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 1F7.
  • the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light region of antibody 1F7.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 1F7 and the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light chain region of antibody 1F7. See infra, for the sequences of the variable heavy chain region and variable light chain region of monoclonal antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable heavy chain region antibody 2C3; or (b) a variable light chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable light chain region antibody 2C3.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 2C3.
  • the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light region of antibody 2C3.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 2C3 and the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light chain region of antibody 2C3. See infra, for the sequences of the variable heavy chain region and variable light chain region of monoclonal antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable heavy chain region antibody 1H12; or (b) a variable light chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable light chain region antibody 1H12.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 1H12.
  • the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light region of antibody 1H12.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 1H12 and the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light chain region of antibody 1H12. See infra, for the sequences of the variable heavy chain region and variable light chain region of monoclonal antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable heavy chain region antibody 2F9; or (b) a variable light chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable light chain region antibody 2F9.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 2F9.
  • the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light region of antibody 2F9.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 2F9 and the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light chain region of antibody 2F9. See infra, for the sequences of the variable heavy chain region and variable light chain region of monoclonal antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof includes: (a) a variable heavy chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable heavy chain region antibody 3A7; or (b) a variable light chain region that is at least about 90% or at least about 95% identical to the amino acid sequence of the variable light chain region antibody 3A7.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 3A7.
  • the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light region of antibody 3A7.
  • the CDRs of the variable heavy chain region of the antibody are identical to the CDRs of the variable heavy chain region of antibody 3A7 and the CDRs of the variable light chain region of the antibody are identical to the CDRs of the variable light chain region of antibody 3A7. See infra, for the sequences of the variable heavy chain region and variable light chain region of monoclonal antibody 3A7.
  • an antibody provided herein includes human-derived heavy and light chain constant regions.
  • the heavy chain constant region has an isotype selected from the group consisting of gamma1, gamma2, gamma3, and gamma4.
  • an antibody provided herein is an immunoglobulin comprising two identical heavy chains and two identical light chains.
  • an antibody provided herein is a monoclonal antibody.
  • an antibody provided herein is an antigen-binding fragment.
  • an antibody provided herein is a single-chain variable fragment (scFv).
  • an antibody provided herein is conjugated to a detectable agent or a therapeutic agent.
  • an antibody provided herein is isolated.
  • polynucleotide sequences encoding antibodies described herein See infra, for the nucleotide sequences of the variable heavy chain region and variable light chain region of antibodies 1F7, 2C3, 1H12, 2F9, and 3A7.
  • an antibody described herein is encoded by a nucleic acid sequence comprising the nucleotide sequences of the variable heavy chain region and variable light chain region of antibody 1F7.
  • an antibody described herein is encoded by a nucleic acid sequence comprising the nucleotide sequences of the variable heavy chain region and variable light chain region of antibody 2C3.
  • an antibody described herein is encoded by a nucleic acid sequence comprising the nucleotide sequences of the variable heavy chain region and variable light chain region of antibody 1H12. In a specific aspect, an antibody described herein is encoded by a nucleic acid sequence comprising the nucleotide sequences of the variable heavy chain region and variable light chain region of antibody 2F9. In a specific aspect, an antibody described herein is encoded by a nucleic acid sequence comprising the nucleotide sequences of the variable heavy chain region and variable light chain region of antibody 3A7. In a specific aspect, the nucleic acid sequences are isolated.
  • expression vectors comprising a nucleotide encoding an antibody described herein.
  • an expression vector provided herein is operably linked to one or more regulatory regions.
  • host cells comprising a nucleotide encoding an antibody described herein.
  • host cells engineered to express an antibody described herein. The host cells may be used to produce the antibody using techniques known to one of skill in the art or described herein.
  • compositions including an antibody described herein The compositions described herein may be used in the methods of prevention, treatment, or diagnosis described herein.
  • the compositions may be used to prevent COVID-19. In another particular aspect, the compositions may be used to treat a SARS-CoV-2 infection or COVID-19.
  • methods for preventing COVID-19 including administering to a subject in need thereof an antibody described herein, or a composition comprising such an antibody.
  • the subject is a human. In a specific aspect, the subject is a human infant or human toddler. In a specific aspect, the subject is an elderly human.
  • methods for treating SARS-CoV-2 infection or COVID-19 comprising administering to a subject in need thereof an antibody described herein, or composition comprising such an antibody.
  • the subject is diagnosed with SARS-CoV-2 virus infection or COVID-19. In a specific aspect, the subject is diagnosed as SARS- CoV-2 infection or COVID-19. In a specific aspect, the subject is a human. In a specific aspect, the subject is a human infant or human toddler. In a specific aspect, the subject is an elderly human. [0026] In another aspect, provided herein are methods for detecting SARS-CoV-2 or diagnosing SARS-CoV-2 infection using an antibody described herein. [0027] In another aspect, provided herein are kits including an antibody described herein.
  • kits comprising an antibody described herein, and optionally instructions for use of the antibody in the prevention or treatment of SARS-CoV-2 infection, or COVID-19, or in the detection of SARS-CoV-2 infection.
  • an isolated antigenic peptide including an epitope of an antibody described herein.
  • the peptide of the SARS-CoV-21 spike protein may be used to actively immunize a patient, or in a diagnostic to detect SARS-CoV-2.
  • FIGs. 1A-1D All mAbs bind to recombinant RBD and six mAbs neutralize SARS- COV-2.
  • the positive control used was a human antibody against SARS-CoV-1 RBD, CR3022 while the negative control used was a mouse anti- influenza H10 antibody.
  • FIG. 1D Neutralization activity of all mAbs was tested in a microneutralization assay with authentic SARS- CoV-2 (USA-WA1/2020) starting at 30 ⁇ g/ml and testing subsequent 3-fold dilutions. The cells were stained for nucleoprotein of SARS-CoV-2 and the IC50 values were calculated via non-linear regression fit. All experiments were performed with duplicates. [0031] FIGs. 2A-2B. Only neutralizing mAbs lower viral loads in vivo in an AdV-hACE2 mouse challenge model.
  • FIGs.3A-3B Immunopathological effects post mAb administration in the lungs. (FIG. 3A).
  • FIGs. 4A-4D Binding mAbs to variant RBDs as well cross-neutralization of B.1.1.7 and B.1.351 variant viruses. All fourteen antibodies (FIGs. 4A-4B) were tested in ELISA assays for binding to RBDs that contain single or multiple mutations found in new variants.
  • the line at 100% indicates binding to wild type and binding to each mutant RBD is graphed as percent binding compared to wild type.
  • a negative control mAb, anti-influenza H10 was run against all the RBDs to ensure that there is no unspecific binding.
  • Neutralizing mAbs (FIG. 4A) and non-neutralizing mAbs (FIG. 4B) are shown separately.
  • FIG. 4C a microneutralization assay was performed to test whether the neutralizing mAbs can also neutralize new variant viruses, B.1.1.7 and B.1.351.
  • FIGs.5A-5D Negative stain EM analysis of Fabs bound to SARS-CoV-2 S trimer. 3D reconstructions of Fabs (FIG. 5A) KL-S-2C3 (Boxed), (FIG. 5B) KL-S-1D2 (Boxed), (FIG. 5C) KL-S-3A7 (Boxed) and (FIG.
  • x and/or y means any element of the three-element set ⁇ (x), (y), (x, y) ⁇ . In other words, “x and/or y” means “one or both of x and y”.
  • x, y, and/or z means any element of the seven-element set ⁇ (x), (y), (z), (x, y), (x, z), (y, z), (x, y, z) ⁇ . In other words, “x, y and/or z” means “one or more of x, y and z”.
  • polyinosinic:polycytidylic acid may be abbreviated as “poly I:C or poly(I:C)”
  • poly I:C mixed with the stabilizers carboxymethylcellulose and polylysine may be abbreviated as “poly IC:LC”.
  • Antibodies can include, for example, monoclonal antibodies, recombinantly produced antibodies, monospecific antibodies, multispecific antibodies (including bispecific antibodies), human antibodies, humanized antibodies, chimeric antibodies, synthetic antibodies, tetrameric antibodies comprising two heavy chain and two light chain molecule, an antibody light chain monomer, an antibody heavy chain monomer, an antibody light chain dimer, an antibody heavy chain dimer, an antibody light chain-antibody heavy chain pair, intrabodies, heteroconjugate antibodies, single domain antibodies, monovalent antibodies, single chain antibodies or single- chain Fvs (scFv), camelized antibodies, affybodies, Fab fragments, F(ab’) fragments, disulfide- linked Fvs (sdFv), anti-idiotypic (anti-Id) antibodies (including, e.g., anti-anti-Id antibodies), and antigen-binding fragments of any of the above.
  • antibodies described herein refer to polyclonal antibody populations.
  • Antibodies can be of any type (e.g., IgG, IgE, IgM, IgD, IgA or IgY), any class, (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 or IgA2), or any subclass (e.g., IgG2a or IgG2b) of immunoglobulin molecule.
  • antibodies described herein are IgG antibodies, or a class (e.g., human IgG1 or IgG2) or subclass (e.g., IgG2a) thereof.
  • an antibody described herein is isolated or purified.
  • an antibody includes any molecule with an antigen-binding site that binds an antigen.
  • an antibody includes an antigen-binding fragment (e.g., the region(s) of an immunoglobulin that binds to an antigen or an epitope, such as a sequence comprising complementarity determining regions (e.g., the heavy and/or light chain variable regions)).
  • an antibody does not include antigen-binding fragments.
  • an antibody described herein is a monoclonal antibody.
  • the term “monoclonal antibody” refers to an antibody obtained from a population of homogenous or substantially homogeneous antibodies.
  • a “monoclonal” is not limited to any particular method for making the antibody. Generally, a population of monoclonal antibodies can be generated by cells, a population of cells, or a cell line.
  • a “monoclonal antibody,” as used herein is an antibody produced by a single cell (e.g., hybridoma or host cell producing a recombinant antibody), wherein the antibody binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) as determined, e.g., by ELISA or other antigen-binding or competitive binding assay known in the art or in the Example provided herein.
  • a monoclonal antibody can be a chimeric antibody, a human antibody, or a humanized antibody.
  • a monoclonal antibody is a monovalent antibody or multivalent (e.g., bivalent) antibody.
  • a monoclonal antibody is a monospecific or multispecific antibody (e.g., bispecific antibody).
  • Monoclonal antibodies described herein can, for example, be made by the hybridoma method as described in Kohler et al.; Nature, 256:495 (1975) or can, e.g., be isolated from phage libraries using the techniques as described herein, for example.
  • an antibody described herein is an immunoglobulin, such as an IgG, IgE, IgM, IgD, IgA or IgY.
  • an antibody described herein is an IgG2a.
  • an antibody described herein is an IgG1.
  • an antibody described herein is an IgG1 or IgG2a.
  • antibody described herein is an antigen- binding fragment, such as, e.g., an Fab fragment or F(ab’)2 fragment.
  • an antibody described herein is a scFv.
  • SARS-CoV-2 spike protein and “spike protein of SARS- CoV-2” refer to a SARS-CoV-2 spike protein known to those of skill in the art.
  • the spike protein comprises the amino acid or nucleic acid sequence found at GenBank Accession No. MN908947.3.
  • a typical spike protein comprises domains known to those of skill in the art including an S1 domain, a receptor binding domain, an S2 domain, a transmembrane domain and a cytoplasmic domain. See, e.g., Wrapp et al., 2020, Science 367: 1260-1263 for a description of SARS-CoV-2 spike protein (in particular, the structure of such protein).
  • the spike protein may be characterized as having a signal peptide (e.g. a signal peptide of 1-14 amino acid residues of the amino acid sequence of GenBank Accession No. MN908947.3), a receptor binding domain (e.g., a receptor binding domain of 319-541 amino acid residues of GenBank Accession No.
  • a fragment of a SARS-CoV-2 spike protein is at least about 8, 10, 12, 15, or 20 amino acid residues in length.
  • a fragment of a SARS-CoV-2 spike protein comprises or consists of the receptor binding domain (RBD) of the spike protein.
  • fragment of a SARS-CoV-2 spike protein consists of the RBD of the spike protein and 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues at the N-terminus, C-terminus or both.
  • fragment of a SARS-CoV-2 spike protein comprises or consists of the S1 domain or ectodomain of the spike protein.
  • fragment of a SARS-CoV-2 spike protein consists of the S1 domain or ectodomain of the spike protein and 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues at the N-terminus, C-terminus or both.
  • the antibodies provided herein bind to SARS-CoV-2 spike protein with a certain affinity.
  • Binding affinity generally refers to the strength of the sum total of non- covalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen).
  • binding affinity refers to intrinsic binding affinity, which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen).
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (KD). Affinity can be measured and/or expressed in a number of ways known in the art, including, but not limited to, equilibrium dissociation constant (K D ), equilibrium association constant (K A ), and IC 50 .
  • the K D is calculated from the quotient of k off /k on
  • K A is calculated from the quotient of kon/koff.
  • kon refers to the association rate constant of, e.g., an antibody to an antigen
  • koff refers to the dissociation of, e.g., an antibody to an antigen.
  • the kon and koff can be determined by techniques known to one of ordinary skill in the art, such as BIAcoreTM, Kinexa, or biolayer interferometry. [0050] Affinity can be measured by common methods known in the art, including those described herein.
  • individual association (kon) and dissociation (koff) rate constants can be calculated from the resulting binding curves using the BIAevaluation software available through the vendor. Data can then be fit to a 1:1 binding model, which includes a term to correct for mass transport limited binding, should it be detected. From these rate constants, the apparent dissociation binding constant (KD) for the interaction of the antibody (e.g., IgG) with the antigen (e.g., SARS-CoV-2 spike protein) can be calculated from the quotient of koff/kon.
  • KD apparent dissociation binding constant
  • Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer.
  • an antibody described herein binds to SARS-CoV-2 spike protein present in the virion particle.
  • an antibody described herein binds to a SARS- CoV-2 spike protein on the surface of a cell infected with SARS-CoV-2.
  • an antibody described herein binds to SARS-CoV-2 spike protein as assessed by techniques known in the art, e.g., ELISA, Western blot, biolayer interferometry, FACS or BIACore, or described herein.
  • an antibody described herein does not cross- react with spike protein from another type of coronavirus (e.g., other betacoronaviruses) as assessed by techniques known in the art, e.g., ELISA, Western blot, biolayer interferometry, FACS or BIACore, or described herein.
  • an antibody that selectively binds to SARS-CoV-2 spike protein relative to a spike protein of another type of coronavirus as assessed by techniques known in the art, e.g., ELISA, Western blot, biolayer interferometry, FACS or BIACore, or described herein.
  • an antibody that selectively binds to SARS-CoV-2 spike protein relative to a spike protein of other betacoronaviruses as assessed by techniques known in the art, e.g., ELISA, Western blot, biolayer interferometry, FACS or BIACore, or described herein.
  • an antibody that binds to a SARS-CoV-2 spike protein inhibits the binding of the spike protein to a host cell receptor.
  • an antibody that binds to a SARS-CoV-2 spike protein inhibits the binding of the spike protein to a host cell receptor (e.g., human receptor angiotensin converting enzyme 2 (ACE2)).
  • ACE2 human receptor angiotensin converting enzyme 2
  • an antibody provided herein has one, two or more, or all of the characteristics/properties of one of the antibodies described herein.
  • an antibody described herein has neutralizing activity as assessed by a technique known to one of skill in the art or described herein.
  • an antibody described herein binds to the spike protein of one, two or more SARS-CoV-2 variants, such as described in Example 1, infra, as assessed by a technique known to one of skill in the art or described herein.
  • an antibody described herein neutralizes SARS-CoV-2 variants, such as B.1.1.7 and B1.351, as assessed by a technique known to one of skill in the art or described herein (e.g., Example 1, infra).
  • an antibody described herein binds to the receptor binding domain of SARS-CoV-2 spike protein or a fragment thereof as assessed by a technique known to one of skill in the art or described herein.
  • an antibody described herein binds to a fragment of the SARS-CoV-2 spike protein comprising the receptor binding domain.
  • Such fragment may comprise amino acid resides 258 to 572 or amino acid residues 498 to 572 of the SARS-CoV-2 spike protein.
  • variable region typically refers to a portion of an antibody, generally, a portion of a light or heavy chain, typically about the amino-terminal 110 to 120 amino acids in a mature heavy chain and about the amino-terminal 90 to 100 amino acids in a mature light chain, which differs extensively in sequence among antibodies and is used in the binding and specificity of a particular antibody for its particular antigen.
  • the variability in sequence is concentrated in those regions called complementarity determining regions (CDRs) while the more highly conserved regions in the variable domain are called framework regions (FR). CDRs are flanked by FRs.
  • variable region is a rodent (e.g., mouse or rat) variable region.
  • variable region is a human variable region.
  • variable region comprises rodent (e.g., mouse or rat) CDRs and human framework regions (FRs).
  • variable region is a primate (e.g., non- human primate) variable region.
  • variable region comprises rodent or murine CDRs and primate (e.g., non- human primate) framework regions (FRs).
  • an antibody provided herein comprises one, two or three of the complementarity determining regions (CDRs) of the variable heavy chain region (“VH” domain) or one, two or three of the CDRs of the variable light chain region (“VL” domain) of an antibody described herein.
  • CDRs complementarity determining regions
  • an antibody provided herein comprises one, two or three of the complementarity determining regions (CDRs) of the variable heavy chain region (“VH” domain) and one, two or three of the CDRs of the variable light chain region (“VL” domain) of an antibody described herein.
  • an antibody provided herein comprises the complementarity determining regions (CDRs) of the variable heavy chain region (“VH” domain) and the CDRs of the variable light chain region (“VL” domain) of an antibody described herein.
  • the CDRs of an antibody can be determined according to the Kabat numbering system.
  • Kabat numbering and like terms are recognized in the art and refer to a system of numbering amino acid residues in the heavy and light chain variable regions of an antibody, or an antigen-binding portion thereof.
  • the CDRs of an antibody can be determined according to the Kabat numbering system (see, e.g., Kabat et al. (1971) Ann. NY Acad. Sci. 190:382-391 and, Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91- 3242).
  • the VH CDR1 is typically present at amino acid positions 31 to 35 of the heavy chain, which can optionally include one or two additional amino acids following amino acid position 35 (referred to in the Kabat numbering scheme as 35A and 35B);
  • the VH CDR2 is typically present at amino acid positions 50 to 65 of the heavy chain; and
  • the VH CDR2 is typically present at amino acid positions 95 to 102 of the heavy chain (Kabat, Elvin A. et al., Sequences of Proteins of Immunological Interest. Bethesda: National Institutes of Health, 1983).
  • the VL CDR1 is typically present at amino acid positions 24 to 34 of the light chain;
  • the VL CDR2 is typically present at amino acid positions 50 to 56 of the light chain; and
  • the VL CDR3 is typically present at amino acid positions 89 to 97 of the light chain (Kabat, Elvin A. et al., Sequences of Proteins of Immunological Interest. Bethesda: National Institutes of Health, 1983).
  • the actual linear amino acid sequence of the antibody variable domain can contain fewer or additional amino acids due to a shortening or lengthening of a FR and/or CDR and, as such, an amino acid’s Kabat number is not necessarily the same as its linear amino acid number.
  • the CDRs of an antibody can be determined according to the Chothia numbering scheme, which refers to the location of immunoglobulin structural loops (see, e.g., Chothia and Lesk, 1987, J. Mol. Biol., 196:901-917; Al-Lazikani et al., 1997, J. Mol.
  • Chothia CDRs and like terms are recognized in the art and refer to antibody CDR sequences as determined according to the method of Chothia and Lesk, 1987, J. Mol.
  • the VH CDR1 is typically present at amino acid positions 26 to 32 of the heavy chain;
  • the VH CDR2 is typically present at amino acid positions 53 to 55 of the heavy chain; and
  • the VH CDR3 is typically present at amino acid positions 96 to 101 of the heavy chain.
  • the VH CDR1 is typically present at amino acid positions 26 to 32 or 34 of the heavy chain;
  • the VH CDR2 is typically present at amino acid positions 52 to 56 (in one aspect, CDR2 is at positions 52A-56, wherein 52A follows position 52) of the heavy chain;
  • the VH CDR3 is typically present at amino acid positions 95 to 102 of the heavy chain (in one aspect, there is no amino acid at positions numbered 96-100).
  • the VL CDR1 is typically present at amino acid positions 26 to 33 of the light chain;
  • the VL CDR2 is typically present at amino acid positions 50 to 52 of the light chain; and
  • the VL CDR3 is typically present at amino acid positions 91 to 96 of the light chain.
  • the VL CDR1 is typically present at amino acid positions 24 to 34 of the light chain; (ii) the VL CDR2 is typically present at amino acid positions 50 to 56 of the light chain; and (iii) the VL CDR3 is typically present at amino acid positions 89 to 97 of the light chain (in one aspect, there is no amino acid at positions numbered 96-100).
  • Chothia CDR positions may vary depending on the antibody, and may be determined according to methods known in the art.
  • the CDRs of an antibody can be determined according to the IMGT numbering system as described in Lefranc, M.-P., 1999, The Immunologist, 7:132-136 and Lefranc, M.-P. et al., 1999, Nucleic Acids Res., 27:209-212.
  • the IMGT definition is from the IMGT (“IMGT®, the international ImMunoGeneTics information system® website imgt.org, founder and director: Marie-Paule Lefranc, adjoin, France; see, e.g., Lefranc, M.-P., 1999, The Immunologist, 7:132-136 and Lefranc, M.-P.
  • VH CDR1 is typically present at amino acid positions 25 to 35 of the heavy chain;
  • VH CDR2 is typically present at amino acid positions 51 to 57 of the heavy chain; and
  • VH CDR2 is typically present at amino acid positions 93 to 102 of the heavy chain.
  • the VL CDR1 is typically present at amino acid positions 27 to 32 of the light chain;
  • the VL CDR2 is typically present at amino acid positions 50 to 52 of the light chain; and
  • the VL CDR3 is typically present at amino acid positions 89 to 97 of the light chain.
  • the CDRs of an antibody can be determined according to MacCallum et al., 1996, J. Mol. Biol., 262:732-745. See also, e.g., Martin, A., “Protein Sequence and Structure Analysis of Antibody Variable Domains,” in Antibody Engineering, Kontermann and Dübel, eds., Chapter 31, pp.
  • the CDRs of an antibody can be determined according to the AbM numbering scheme, which refers AbM hypervariable regions which represent a compromise between the Kabat CDRs and Chothia structural loops, and are used by Oxford Molecular’s AbM antibody modeling software.
  • AbM numbering scheme refers AbM hypervariable regions which represent a compromise between the Kabat CDRs and Chothia structural loops, and are used by Oxford Molecular’s AbM antibody modeling software.
  • a person of ordinary skill in the art would be able to determine the CDRs and framework regions of the variable regions of the 1F7, 2C3, 1H12, 2F9, and 3A7 antibody sequence based on known numbering systems, such as the Kabat numbering system, Chothia system, Oxford’s AbM system, and/or contact system.
  • the position of a CDR along the VH and/or VL domain of an antibody described herein may vary by one, two, three or four amino acid positions so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • the position defining a CDR of antibody described herein may vary by shifting the N- terminal and/or C-terminal boundary of the CDR by one, two, three, or four amino acids, relative to the CDR position, so long as binding to herein SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • antibodies that bind to SARS-CoV-2 spike protein comprising one, two or three complementarity determining regions (CDRs) of the variable heavy chain region of antibody 1F7 and one, two or three CDRs of the variable light chain region of antibody 1F7.
  • antibodies that bind to SARS-CoV-2 spike protein comprising one, two or three complementarity determining regions (CDRs) of the variable heavy chain region of antibody 2C3 and one, two or three CDRs of the variable light chain region of antibody 2C3.
  • antibodies that bind to SARS-CoV-2 spike protein comprising one, two or three complementarity determining regions (CDRs) of the variable heavy chain region of antibody 1H12 and one, two or three CDRs of the variable light chain region of antibody 1H12.
  • antibodies that bind to SARS-CoV-2 spike protein comprising one, two or three complementarity determining regions (CDRs) of the variable heavy chain region of antibody 2F9 and one, two or three CDRs of the variable light chain region of antibody 2F9.
  • antibodies that bind to SARS-CoV- 2 spike protein comprising one, two or three complementarity determining regions (CDRs) of the variable heavy chain region of antibody 3A7 and one, two or three CDRs of the variable light chain region of antibody 3A7.
  • CDRs complementarity determining regions
  • an antibody that binds to a SARS-CoV-2 spike protein comprises (or alternatively, consists of) a VH CDR1 and a VL CDR1; a VH CDR1 and a VL CDR2; a VH CDR1 and a VL CDR3; a VH CDR2 and a VL CDR1; VH CDR2 and a VL CDR2; a VH CDR2 and a VL CDR3; a VH CDR3 and a VL CDR1; a VH CDR3 and a VL CDR2; a VH CDR3 and a VL CDR3; a VH1 CDR1, a VH CDR2 and a VL CDR1; a VH CDR1, a VH CDR2 and a VL CDR2; a VH CDR1, a VH CDR2 and a VL CDR3; a VH CDR2, a VH
  • an antibody that binds to SARS-CoV-2 spike protein comprising the three CDRs of the variable heavy chain region of antibody 1F7 and the three CDRs of the variable light chain region of antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising the three CDRs of the variable heavy chain region of antibody 2C4 and the three CDRs of the variable light chain region of antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein comprising the three CDRs of the variable heavy chain region of antibody 1H12 and the three CDRs of the variable light chain region of antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein comprising the three CDRs of the variable heavy chain region of antibody 2F9 and the three CDRs of the variable light chain region of antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein comprising the three CDRs of the variable heavy chain region of antibody 3A7 and the three CDRs of the variable light chain region of antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, or CDR3 of the variable heavy chain region of antibody 1F7 and CDR1, CDR2, or CDR3 of the variable light chain region of antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising two of CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1F7 and two of CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1F7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1F7 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1F7.
  • an antibody that binds to SARS- CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1F7 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1F7, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both contain one, two, three or four amino acid substitutions (e.g., a conservative amino acid substitution) so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • amino acid substitutions e.g., a conservative amino acid substitution
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1F7 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1F7, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both, may be one, two or three amino acid residues longer or shorter at the N-terminus, C-terminus or both so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, or CDR3 of the variable heavy chain region of antibody 2C3 and CDR1, CDR2, or CDR3 of the variable light chain region of antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein comprising two of CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2C3 and two of CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2C3.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2C3 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2C3.
  • an antibody that binds to SARS- CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2C3 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2C3, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both contain one, two, three or four amino acid substitutions (e.g., a conservative amino acid substitution) so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • amino acid substitutions e.g., a conservative amino acid substitution
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2C3 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2C3, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both, may be one, two or three amino acid residues longer or shorter at the N-terminus, C- terminus or both so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, or CDR3 of the variable heavy chain region of antibody 1H12 and CDR1, CDR2, or CDR3 of the variable light chain region of antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein comprising two of CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1H12 and two of CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1H12 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1H12.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1H12 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1H12, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both contain one, two, three or four amino acid substitutions (e.g., a conservative amino acid substitution) so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • amino acid substitutions e.g., a conservative amino acid substitution
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 1H12 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 1H12, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both, may be one, two or three amino acid residues longer or shorter at the N-terminus, C-terminus or both so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, or CDR3 of the variable heavy chain region of antibody 2F9 and CDR1, CDR2, or CDR3 of the variable light chain region of antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein comprising two of CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2F9 and two of CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2F9.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2F9 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2F9.
  • an antibody that binds to SARS- CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2F9 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2F9, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both contain one, two, three or four amino acid substitutions (e.g., a conservative amino acid substitution) so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • amino acid substitutions e.g., a conservative amino acid substitution
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 2F9 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 2F9, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both, may be one, two or three amino acid residues longer or shorter at the N-terminus, C-terminus or both so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, or CDR3 of the variable heavy chain region of antibody 3A7 and CDR1, CDR2, or CDR3 of the variable light chain region of antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising two of CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 3A7 and two of CDR1, CDR2, and CDR3 of the variable light chain region of antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 3A7 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 3A7.
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 3A7 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 3A7, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both contain one, two, three or four amino acid substitutions (e.g., a conservative amino acid substitution) so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • amino acid substitutions e.g., a conservative amino acid substitution
  • an antibody that binds to SARS-CoV-2 spike protein comprising CDR1, CDR2, and CDR3 of the variable heavy chain region of antibody 3A7 and CDR1, CDR2, and CDR3 of the variable light chain region of antibody 3A7, wherein one, two or three of the CDRs of the variable heavy chain region, the variable light chain region, or both, may be one, two or three amino acid residues longer or shorter at the N- terminus, C-terminus or both so long as binding to SARS-CoV-2 spike protein is maintained or substantially maintained (for example, by at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% in an assay known in the art or described herein, such as an ELISA).
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 1F7.
  • an antibody described herein which binds to SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 1F7.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises (a) a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 1F7 and (b) a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 1F7.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 2C3.
  • an antibody described herein which binds to SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 2C3.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises (a) a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 2C3 and (b) a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 2C3.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 1H12.
  • an antibody described herein which binds to SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 1H12.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises (a) a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 1H12 and (b) a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 1H12.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 2F9.
  • an antibody described herein which binds to SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 2F9.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises (a) a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 2F9 and (b) a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 2F9.
  • a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 9
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 3A7.
  • an antibody described herein which binds to SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 3A7.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises (a) a variable heavy chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable heavy chain region of antibody 3A7 and (b) a variable light chain region comprising an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97% or 98% identical to the amino acid sequence of a variable light chain region of antibody 3A7.
  • the CDRs of the antibody may, in certain aspects, be identical to one, two, three, four, five, or all six of the CDRs of the antibody described herein.
  • Techniques known to one of skill in the art can be used to determine the percent identity between two amino acid sequences or between two nucleotide sequences. Generally, to determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • a preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. U.S.A. 87:2264 2268, modified as in Karlin and Altschul, 1993, Proc. Natl. Acad. Sci. U.S.A.90:58735877.
  • Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990, J. Mol. Biol. 215:403.
  • Gapped BLAST can be utilized as described in Altschul et al., 1997, Nucleic Acids Res.25:33893402.
  • PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.).
  • BLAST Altschul BLAST
  • Gapped BLAST Altschul BLAST
  • PSI Blast programs the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., National Center for Biotechnology Information (NCBI) on the worldwide web, ncbi.nlm.nih.gov).
  • NCBI National Center for Biotechnology Information
  • Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4:1117. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
  • a PAM120 weight residue table When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. [0078] The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises the variable heavy chain region or variable light chain region of an antibody described herein (e.g., a variable heavy chain region or variable light chain region an antibody described herein) with one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20) amino acid substitutions (e.g., conservative amino acid substitutions), deletions, or additions.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises the variable heavy chain region and variable light chain region of an antibody described herein (e.g., a variable heavy chain region and variable light chain region an antibody with the same name in infra) with one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20) amino acid substitutions (e.g., conservative amino acid substitutions), deletions, or additions.
  • amino acid substitutions e.g., conservative amino acid substitutions
  • none of the amino acid substitutions are located within the CDRs.
  • all of the amino acid substitutions are in the framework regions.
  • a “conservative amino acid substitution” has the meaning known to one of skill in the art.
  • a conservative amino acid substitution is one in which the amino acid residue is replaced with an amino acid residue having a side chain with a similar charge. Families of amino acid residues having side chains with similar charges have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
  • beta- branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
  • an antibody provided herein comprises a variable heavy chain region and a variable light chain region, wherein the variable heavy chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable heavy chain region of antibody 1F7 and the variable light chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable light chain region of antibody 1F7.
  • an antibody provided herein comprises a variable heavy chain region and a variable light chain region, wherein the variable heavy chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable heavy chain region of antibody 2C3 and the variable light chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable light chain region of antibody 2C3.
  • an antibody provided herein comprises a variable heavy chain region and a variable light chain region, wherein the variable heavy chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable heavy chain region of antibody 1H12 and the variable light chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable light chain region of antibody 1H12.
  • an antibody provided herein comprises a variable heavy chain region and a variable light chain region, wherein the variable heavy chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable heavy chain region of antibody 2F9 and the variable light chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable light chain region of antibody 2F9.
  • an antibody provided herein comprises a variable heavy chain region and a variable light chain region, wherein the variable heavy chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable heavy chain region of antibody 3A7 and the variable light chain region comprises the amino acid sequence encoded by the nucleotide sequence of the variable light chain region of antibody 3A7.
  • antibodies that bind to the same or an overlapping epitope of an antibody described herein e.g., antibodies that compete for binding to SARS-CoV- 2 spike protein with an antibody described herein, or antibodies that bind to an epitope that overlaps with an epitope to which an antibody described herein binds.
  • an “epitope” is a term in the art and refers to a localized region of an antigen to which an antibody can specifically bind.
  • An epitope can be, for example, contiguous amino acids of a polypeptide (linear or contiguous epitope), or an epitope can, for example, come together from two or more non- contiguous regions of a polypeptide or polypeptides (conformational, non-linear, discontinuous, or non-contiguous epitope).
  • epitope mapping assays well known to one of skill in the art, can be performed to ascertain the epitope (e.g., conformational epitope) to which an antibody described herein binds.
  • the epitope can be determined by, e.g., structural mapping using negative electron microscopy, X-ray diffraction crystallography studies (see, e.g., Blechman et al., 1993, J. Biol. Chem.268:4399-4406; Cho et al., 2003, Nature, 421:756- 760), ELISA assays, hydrogen/deuterium exchange coupled with mass spectrometry (e.g., MALDI mass spectrometry), array-based oligo-peptide scanning assays, mutagenesis mapping (e.g., site- directed mutagenesis mapping) and/or escape binding assays.
  • structural mapping using negative electron microscopy see, e.g., Blechman et al., 1993, J. Biol. Chem.268:4399-4406; Cho et al., 2003, Nature, 421:756- 760
  • ELISA assays hydrogen/deuterium exchange coupled with mass
  • Antibodies that recognize such epitopes can be identified using routine techniques such as an immunoassay, for example, by showing the ability of one antibody to block the binding of another antibody to a target antigen, i.e., a competitive binding assay. Competition binding assays also can be used to determine whether two antibodies have similar binding specificity for an epitope. Competitive binding can be determined in an assay in which the immunoglobulin under test inhibits specific binding of a reference antibody to a common antigen, such as SARS-CoV-2 spike protein.
  • RIA solid phase direct or indirect radioimmunoassay
  • EIA solid phase direct or indirect enzyme immunoassay
  • sandwich competition assay see Stahli et al., (1983) Methods in Enzymology 9:242
  • solid phase direct biotin-avidin EIA see Kirkland et al., (1986) J. Immunol. 137:3614
  • solid phase direct labeled assay solid phase direct labeled sandwich assay
  • solid phase direct label RIA using I-125 label see Morel et al., (1988) Mol. Immunol.
  • Such an assay involves the use of purified antigen (e.g., SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD)) bound to a solid surface or cells bearing either of these, an unlabeled test immunoglobulin and a labeled reference immunoglobulin.
  • purified antigen e.g., SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD)
  • RBD fragment thereof
  • test immunoglobulin is present in excess.
  • competing antibody when a competing antibody is present in excess, it will inhibit specific binding of a reference antibody to a common antigen by at least about 50-55%, 55-60%, 60-65%, 65-70%, 70-75% or more.
  • a competition binding assay can be configured in a large number of different formats using either labeled antigen or labeled antibody.
  • the antigen is immobilized on a 96-well plate. The ability of unlabeled antibodies to block the binding of labeled antibodies to the antigen is then measured using radioactive or enzyme labels. For further details, see, for example, Wagener et al., J.
  • competition binding assays can be used to determine whether an antibody is competitively blocked, e.g., in a dose dependent manner, by another antibody, for example, an antibody binds essentially the same epitope, or overlapping epitopes, as a reference antibody, when the two antibodies recognize identical or sterically overlapping epitopes in competition binding assays such as competition ELISA assays, which can be configured in all number of different formats, using either labeled antigen or labeled antibody.
  • competition binding assays such as competition ELISA assays, which can be configured in all number of different formats, using either labeled antigen or labeled antibody.
  • an antibody can be tested in competition binding assays with an antibody described herein.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g.
  • RBD comprises framework regions (e.g., framework regions of the VL domain and/or VH domain) that are human framework regions or derived from human framework regions.
  • the framework region may be naturally occurring or consensus framework regions (see, e.g., Sui et al., 2009, Nature Structural & Molecular Biology 16:265-273).
  • Non- limiting examples of human framework regions are described in the art, e.g., see Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242).
  • an antibody described herein comprises framework regions (e.g., framework regions of the VL domain and/or VH domain) that are primate (e.g., non-human primate) framework regions or derived from primate (e.g., non- human primate) framework regions.
  • an antibody comprising an antibody light chain and heavy chain, e.g., a separate light chain and heavy chain.
  • the light chain of an antibody described herein is a kappa light chain.
  • the light chain of an antibody described herein is a lambda light chain.
  • the light chain of an antibody described herein is a human kappa light chain or a human lambda light chain.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a light chain wherein the amino acid sequence of the variable light chain region can comprise any amino acid sequence described herein (e.g., variable light chain region of antibody 1F7, 2C3, 1H12, 2F9, and 3A7), and wherein the constant region of the light chain comprises the amino acid sequence of a human kappa or lambda light chain constant region.
  • the constant region of the light chain comprises the amino acid sequence of a human kappa or lambda light chain constant region.
  • Non-limiting examples of human constant region sequences have been described in the art, e.g., see U.S.
  • an antibody described herein comprises (i) a heavy chain comprising a variable heavy chain region described herein and a constant region; or (ii) a light chain comprising a variable light chain region described herein and a constant region.
  • a heavy chain comprising a variable heavy chain region described herein and a constant region
  • a light chain comprising a variable light chain region described herein and a constant region.
  • the term “constant region” or “constant domain” is interchangeable and has its meaning common in the art.
  • the constant region refers to an antibody portion, e.g., a carboxyl terminal portion of a light and/or heavy chain which is not directly involved in binding of an antibody to antigen but which can exhibit various effector functions, such as interaction with the Fc receptor.
  • the terms refer to a portion of an immunoglobulin molecule having a generally more conserved amino acid sequence relative to an immunoglobulin variable domain.
  • the term “heavy chain” when used in reference to an antibody can refer to any distinct types, e.g., alpha ( ⁇ ), delta ( ⁇ ), epsilon ( ⁇ ), gamma ( ⁇ ) and mu ( ⁇ ), based on the amino acid sequence of the constant domain, which give rise to IgA, IgD, IgE, IgG and IgM classes of antibodies, respectively, including subclasses of IgG, e.g., IgG1, IgG2, IgG3 and IgG4.
  • the term “light chain” when used in reference to an antibody can refer to any distinct types, e.g., kappa ( ⁇ ) of lambda ( ⁇ ) based on the amino acid sequence of the constant domains. Light chain amino acid sequences are well known in the art. In specific aspects, the light chain is a human light chain. With respect to the heavy chain, in a specific aspect, the heavy chain of an antibody described herein can be an alpha ( ⁇ ), delta ( ⁇ ), epsilon ( ⁇ ), gamma ( ⁇ ) or mu ( ⁇ ) heavy chain.
  • the heavy chain of an antibody described can comprise a human alpha ( ⁇ ), delta ( ⁇ ), epsilon ( ⁇ ), gamma ( ⁇ ) or mu ( ⁇ ) heavy chain.
  • an antibody described herein, which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) comprises a heavy chain wherein the amino acid sequence of the variable heavy chain region can comprise any amino acid sequence described herein (e.g., variable heavy chain region of antibody 1F7, 2C3, 1H12, 2F9, and 3A7), and wherein the constant region of the heavy chain comprises the amino acid sequence of a human gamma ( ⁇ ) heavy chain constant region.
  • Non-limiting examples of human constant region sequences have been described in the art, e.g., see U.S. Patent No. 5,693,780 and Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region and a variable light chain region comprising any amino acid sequences described herein, and wherein the constant regions comprise the amino acid sequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule, or a human IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule.
  • an antibody described herein which binds SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), comprises a variable heavy chain region and a variable light chain region comprising any amino acid sequences described herein, and wherein the constant regions comprise the amino acid sequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgY immunoglobulin molecule, any class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2), or any subclass (e.g., IgG2a and IgG2b) of immunoglobulin molecule.
  • any class e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2
  • subclass e.g., IgG2a and IgG2b
  • an antibody described herein is an IgG2a antibody, and optionally comprises a kappa light chain.
  • an antibody described herein is an IgG1 antibody.
  • the antibodies described can be chimeric.
  • a chimeric antibody is a molecule in which different portions of the antibody are derived from different immunoglobulin molecules.
  • a chimeric antibody can contain a variable region of a mouse monoclonal antibody fused to a constant region of a human antibody. Methods for producing chimeric antibodies are known in the art.
  • a humanized antibody is an antibody that is capable of binding to a predetermined antigen and which comprises a framework region having substantially the amino acid sequence of a human immunoglobulin and a CDR having substantially the amino acid sequence of a non-human immunoglobulin.
  • a humanized antibody comprises substantially all of at least one, and typically two, variable domains (Fab, Fab', F(ab')2, Fab, Fv) in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin (i.e., donor antibody) and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence.
  • a humanized antibody also comprises at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • the antibody will contain both the light chain as well as at least the variable domain of a heavy chain.
  • the antibody also may include the CHI, hinge, CH2, CHS, and CH4 regions of the heavy chain.
  • the humanized antibody can be selected from any class of immunoglobulins, including IgM, IgG, IgD, IgA and IgE, and any isotype, including IgGl, IgG2, IgG3 and IgG4.
  • the constant domain is a complement fixing constant domain where it is desired that the humanized antibody exhibits cytotoxic activity, and the class is typically IgGl. Where such cytotoxic activity is not desirable, the constant domain may be of the IgG2 class.
  • VL and VH constant domains that can be used in certain aspects include, but are not limited to, C-kappa and C-gamma-1 (nGlm) described in Johnson et al. (1997) J. Infect. Dis.
  • the humanized antibody may comprise sequences from more than one class or isotype, and selecting particular constant domains to optimize desired effector functions is within the ordinary skill in the art.
  • the framework and CDR regions of a humanized antibody need not correspond precisely to the parental sequences, e.g., the donor CDR or the consensus framework may be mutagenized by substitution, insertion or deletion of at least one residue so that the CDR or framework residue at that site does not correspond to either the consensus or the import antibody. Such mutations, however, will not be extensive. Usually, at least about 75% of the humanized antibody residues will correspond to those of the parental framework and CDR sequences, more often 90%, and most preferably greater than 95%.
  • a humanized antibody comprising the VHCDR1, VHCDR2, VHCDR3, VLCDR1, VLCDR2, and VLCDR3 of the 1F7 antibody described herein.
  • a humanized antibody comprising the VHCDR1, VHCDR2, VHCDR3, VLCDR1, VLCDR2, and VLCDR3 of the 2C3 antibody described herein.
  • a humanized antibody comprising the VHCDR1, VHCDR2, VHCDR3, VLCDR1, VLCDR2, and VLCDR3 of the 1H12 antibody described herein.
  • a humanized antibody comprising the VHCDR1, VHCDR2, VHCDR3, VLCDR1, VLCDR2, and VLCDR3 of the 2F9 antibody described herein.
  • a humanized antibody comprising the VHCDR1, VHCDR2, VHCDR3, VLCDR1, VLCDR2, and VLCDR3 of the 3A7 antibody described herein.
  • the antibodies described herein can be affinity matured using techniques known to one of skill in the art.
  • the antibodies provided herein include derivatives that are chemically modified, i.e., by the covalent attachment of any type of molecule to the antibody.
  • the antibody derivatives include antibodies that have been chemically modified, e.g., by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to, specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. Additionally, the derivative may contain one or more non-classical amino acids.
  • the glycosylation of antibodies described herein in particular, glycosylation of a variable region of an antibody described herein, is modified.
  • an aglycoslated antibody can be made (i.e., the antibody lacks glycosylation) or an antibody comprising a mutation or substitution at one or more glycosylation sites to eliminate glycosylation at the one or more glycosylation sites can be made.
  • Glycosylation can be altered to, for example, increase the affinity of the antibody for SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • Such carbohydrate modifications can be accomplished by, for example, altering one or more sites of glycosylation within the antibody sequence.
  • one or more amino acid substitutions can be made that result in elimination of one or more variable region (e.g., variable heavy chain region CDRS and/or variable light chain region CDRs or variable heavy chain region FRs and/or variable light chain region FRs) glycosylation sites to thereby eliminate glycosylation at that site.
  • variable region e.g., variable heavy chain region CDRS and/or variable light chain region CDRs or variable heavy chain region FRs and/or variable light chain region FRs
  • Such aglycosylation can increase the affinity of the antibody for SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • RBD fragment thereof
  • Glycosylation can occur via N-linked (or asparagine-linked) glycosylation or O- linked glycosylation.
  • N-linked glycosylation involves carbohydrate modification at the side- chain NH 2 group of an asparagine amino acid in a polypeptide.
  • O-linked glycosylation involves carbohydrate modification at the hydroxyl group on the side chain of a serine, threonine, or hydroxylysine amino acid.
  • aglycosylated antibodies can be produced in bacterial cells which lack the necessary glycosylation machinery. Cells with altered glycosylation machinery have been described in the art and can be used as host cells in which to express recombinant antibodies described herein to thereby produce an antibody with altered glycosylation. See, for example, Shields, R.L. et al. (2002) J. Biol. Chem.
  • Antibodies with reduced fucose content have been reported to have an increased affinity for Fc receptors, such as, e.g., Fc ⁇ RIIIa. Accordingly, in certain aspects, the antibodies described herein have reduced fucose content or no fucose content. Such antibodies can be produced using techniques known to one skilled in the art. For example, the antibodies can be expressed in cells deficient or lacking the ability to fucosylate.
  • cell lines with a knockout of both alleles of ⁇ 1,6-fucosyltransferase can be used to produce antibodies with reduced fucose content.
  • the Potelligent® system (Lonza) is an example of such a system that can be used to produce antibodies with reduced fucose content.
  • one, two or more mutations are introduced into the Fc region of an antibody described herein or a fragment thereof (e.g., CH2 domain (residues 231-340 of human IgG1) and/or CH3 domain (residues 341-447 of human IgG1) and/or the hinge region, with numbering according to the Kabat numbering system (e.g., the EU index in Kabat)) to increase the affinity of the antibody for an Fc receptor (e.g., an activated Fc receptor) on the surface of an effector cell.
  • an Fc receptor e.g., an activated Fc receptor
  • Mutations in the Fc region of an antibody or fragment thereof that increase the affinity of an antibody for an Fc receptor and techniques for introducting such mutations into the Fc receptor or fragment thereof are known to one of skill in the art. Examples of mutations in the Fc receptor of an antibody that can be made to increase the affinity of the antibody for an Fc receptor are described in, e.g., Smith, P., et al. (2012) PNAS. 109:6181- 6186, which is incorporated herein by reference. [00101] In some aspects, provided herein are antibodies, conjugated or recombinantly fused to a diagnostic, detectable or therapeutic agent or any other molecule.
  • the conjugated or recombinantly fused antibodies can be useful, e.g., for monitoring or prognosing the onset, development, progression and/or severity of COVID-19 as part of a clinical testing procedure, such as determining the efficacy of a particular therapy.
  • the conjugated or recombinantly fused antibodies can be useful in preventing, treating, or both COVID-19.
  • Antibodies described herein can also be conjugated to a molecule (e.g., polyethylene glycol) which can affect one or more biological and/or molecular properties of the antibodies, for example, stability (e.g., in serum), half-life, solubility, and antigenicity.
  • a conjugate comprises an antibody described herein and a molecule (e.g., therapeutic or drug moiety), wherein the antibody is linked directly to the molecule, or by way of one or more linkers.
  • an antibody is covalently conjugated to a molecule.
  • an antibody is noncovalently conjugated to a molecule.
  • an antibody-drug conjugate comprising an antibody moiety and a drug (e.g., therapeutic or prophylactic agent), wherein the antibody moiety is an antibody described herein and wherein the conjugate may comprise one or more linkers.
  • an antibody described herein is conjugated to one or more molecules (e.g., therapeutic or drug moiety) directly or indirectly via one or more linker molecules.
  • a linker comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20 amino acid residues.
  • a linker consists of 1 to 10 amino acid residues, 1 to 15 amino acid residues, 5 to 20 amino acid residues, 10 to 25 amino acid residues, 10 to 30 amino acid residues, or 10 to 50 amino acid residues.
  • a linker is an enzyme-cleavable linker or a disulfide linker.
  • the cleavable linker is cleavable via an enzyme such an aminopeptidase, an aminoesterase, a dipeptidyl carboxy peptidase, or a protease of the blood clotting cascade.
  • the linker that may be conjugated to the antibody does not interfere with the antibody binding to either recombinant SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), the virion of SARS-CoV-2, or both, using techniques known in the art or described herein.
  • diagnosis and detection can be accomplished, for example, by coupling the antibody to a detectable substance(s) including, but not limited to, various enzymes, such as, but not limited to, horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; prosthetic groups, such as, but not limited to, streptavidin/biotin and avidin/biotin; fluorescent materials, such as, but not limited to, umbelliferone, fluorescein, fluorescein isothiocynate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; luminescent materials, such as, but not limited to, luminol; bioluminescent materials, such as but not limited to, luciferase, luciferin, and aequorin; radioactive materials, such as, but not limited to, iod
  • antibodies described herein conjugated or recombinantly fused to a therapeutic moiety or one or more therapeutic moieties
  • the antibody can be conjugated or recombinantly fused to a therapeutic moiety, such as a cytotoxin, e.g., a cytostatic or cytocidal agent, a therapeutic agent or a radioactive metal ion, e.g., alpha- emitters.
  • a cytotoxin e.g., a cytostatic or cytocidal agent
  • a therapeutic agent or a radioactive metal ion e.g., alpha- emitters.
  • uses of the antibodies conjugated or recombinantly fused to a therapeutic moiety or drug moiety that modifies a given biological response.
  • Therapeutic moieties or drug moieties are not to be construed as limited to classical chemical therapeutic agents.
  • the drug moiety may be a protein, peptide, or polypeptide possessing a desired biological activity.
  • an antibody described herein can be conjugated to therapeutic moieties such as a radioactive metal ion, such as alpha-emitters such as 213 Bi or macrocyclic chelators useful for conjugating radiometal ions, including but not limited to, 131 In, 131 LU, 131 Y, 131 Ho, 131 Sm, to polypeptides.
  • therapeutic moieties such as a radioactive metal ion, such as alpha-emitters such as 213 Bi or macrocyclic chelators useful for conjugating radiometal ions, including but not limited to, 131 In, 131 LU, 131 Y, 131 Ho, 131 Sm, to polypeptides.
  • antibodies can be fused to marker sequences, such as a peptide to facilitate purification.
  • the marker amino acid sequence is a hexa-histidine peptide (i.e., His-tag), such as the tag provided in a pQE vector (QIAGEN, Inc.), among others, many of which are commercially available.
  • His-tag a hexa-histidine peptide
  • QIAGEN, Inc. a pQE vector
  • hexa-histidine provides for convenient purification of the fusion protein.
  • peptide tags useful for purification include, but are not limited to, the hemagglutinin (“HA”) tag, which corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson et al., 1984, Cell 37:767), and the “flag” tag.
  • HA hemagglutinin
  • Methods for fusing or conjugating therapeutic moieties (including polypeptides) to antibodies are well known, see, e.g., Arnon et al., “Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy”, in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss, Inc.
  • fusion proteins may be generated, for example, through the techniques of gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling (collectively referred to as “DNA shuffling”).
  • DNA shuffling may be employed to alter the activities of the monoclonal antibodies described herein (or an antigen-binding fragment thereof) (e.g., antibodies with higher affinities and lower dissociation rates).
  • monoclonal antibodies described herein or an antigen-binding fragment thereof
  • DNA shuffling may be employed to alter the activities of the monoclonal antibodies described herein (or an antigen-binding fragment thereof) (e.g., antibodies with higher affinities and lower dissociation rates).
  • U.S. Patent Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252, and 5,837,458 Patten et al., 1997, Curr. Opinion Biotechnol. 8:724-33; Harayama, 1998, Trends Biotechnol. 16(2):76-82; Hansson, et al., 1999, J. Mol. Biol.
  • Antibodies, or the encoded antibodies may be altered by being subjected to random mutagenesis by error-prone PCR, random nucleotide insertion or other methods prior to recombination.
  • a polynucleotide encoding a monoclonal antibody described herein (or an antigen-binding fragment thereof) may be recombined with one or more components, motifs, sections, parts, domains, fragments, etc. of one or more heterologous molecules.
  • An antibody can also be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Patent No. 4,676,980, which is incorporated herein by reference in its entirety.
  • An antibody can also be linked directly or indirectly to one or more antibodies to produce bispecific/multispecific antibodies.
  • An antibody can also be attached to solid supports, which are particularly useful for immunoassays or purification of an antigen. Such solid supports include, but are not limited to, glass, cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene.
  • polynucleotides comprising a nucleotide sequence encoding an antibody described herein or a fragment thereof (e.g., a variable heavy chain region and/or variable light chain region) that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), and vectors, e.g., vectors comprising such polynucleotides for recombinant expression in host cells (e.g., E. coli and mammalian cells).
  • host cells e.g., E. coli and mammalian cells.
  • polynucleotides comprising nucleotide sequences encoding any of the antibodies provided herein, as well as vectors comprising such polynucleotide sequences, e.g., expression vectors for their efficient expression in host cells, e.g., mammalian cells.
  • an “isolated” polynucleotide or nucleic acid molecule is one that is separated from other nucleic acid molecules that are present in the natural source (e.g., in a mouse or a human) of the nucleic acid molecule.
  • an “isolated” nucleic acid molecule such as a cDNA molecule
  • the language “substantially free” includes preparations of polynucleotide or nucleic acid molecule having less than about 15%, 10%, 5%, 2%, 1%, 0.5%, or 0.1% (in particular less than about 10%) of other material, e.g., cellular material, culture medium, other nucleic acid molecules, chemical precursors and/or other chemicals.
  • a nucleic acid molecule(s) encoding an antibody described herein is isolated or purified.
  • polynucleotide(s)” “nucleic acid” and “nucleotide” include deoxyribonucleotides, deoxyribonucleic acids, ribonucleotides, and ribonucleic acids, and polymeric forms thereof, and includes either single- or double-stranded forms.
  • the terms “polynucleotide(s)” “nucleic acid” and “nucleotide” include known analogues of natural nucleotides, for example, peptide nucleic acids (“PNA”s), that have similar binding properties as the reference nucleic acid.
  • PNA peptide nucleic acids
  • polynucleotide(s)” “nucleic acid” and “nucleotide” refer to deoxyribonucleic acids (e.g., cDNA or DNA). In other aspects, the terms “polynucleotide(s)” “nucleic acid” and “nucleotide” refer to ribonucleic acids (e.g., mRNA or RNA).
  • polynucleotides comprising nucleotide sequences encoding antibodies, which bind to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) and comprise an amino acid sequence as described herein, as well as antibodies which compete with such antibodies for binding to SARS-CoV-2 spike protein or a fragment thereof (e.g., in a dose-dependent manner), or which bind to the same epitope as that of such antibodies.
  • a polynucleotide described herein an antibody which comprises a variable heavy chain region and/or variable light chain region of an antibody described herein (e.g., the variable heavy chain region and/or variable light chain region of antibody 1F7; the variable heavy chain region and/or variable light chain region of antibody 2C3; the variable heavy chain region and/or variable light chain region of antibody 1H12; the variable heavy chain region and/or variable light chain region of antibody 2F9; or the variable heavy chain region and/or variable light chain region of antibody 3A7).
  • a variable heavy chain region and/or variable light chain region of an antibody described herein e.g., the variable heavy chain region and/or variable light chain region of antibody 1F7; the variable heavy chain region and/or variable light chain region of antibody 2C3; the variable heavy chain region and/or variable light chain region of antibody 1H12; the variable heavy chain region and/or variable light chain region of antibody 2F9; or the variable heavy chain region and/or variable light chain region of antibody 3A7.
  • a polynucleotide described herein comprises a nucleotide sequence encoding an antibody which comprises a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 1F7 and/or a variable light chain region comprising the amino acid sequence of the variable light chain region of antibody in 1F7.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs and/or 1, 2, or 3 VL CDRs of antibody 1F7.
  • a polynucleotide described herein comprises a nucleotide sequence encoding an antibody which comprises a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 2C3 and/or a variable light chain region comprising the amino acid sequence of the variable light chain region of antibody in 2C3.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs and/or 1, 2, or 3 VL CDRs of antibody 2C3.
  • a polynucleotide described herein comprises a nucleotide sequence encoding an antibody which comprises a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 1H12 and/or a variable light chain region comprising the amino acid sequence of the variable light chain region of antibody in 1H12.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs and/or 1, 2, or 3 VL CDRs of antibody 1H12.
  • a polynucleotide described herein comprises a nucleotide sequence encoding an antibody which comprises a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 2F9 and/or a variable light chain region comprising the amino acid sequence of the variable light chain region of antibody in 2F9.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs and/or 1, 2, or 3 VL CDRs of antibody 2F9.
  • a polynucleotide described herein comprises a nucleotide sequence encoding an antibody which comprises a variable heavy chain region comprising the amino acid sequence of the variable heavy chain region of antibody 3A7 and/or a variable light chain region comprising the amino acid sequence of the variable light chain region of antibody in 3A7.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs and/or 1, 2, or 3 VL CDRs of antibody 3A7.
  • a polynucleotide described herein comprises the nucleotide sequence of the variable heavy chain region of antibody 1F7 (SEQ ID NO:1). In some aspects, a polynucleotide described herein comprises the nucleotide sequence of the variable light chain region of antibody 1F7 (SEQ ID NO:3). In some aspects, a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs of antibody 1F7.
  • SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VL CDRs of antibody 1F7.
  • a polynucleotide described herein comprises the nucleotide sequence of the variable heavy chain region of antibody 2C3 (SEQ ID NO:5).
  • a polynucleotide described herein comprises the nucleotide sequence of the variable light chain region of antibody 2C3 (SEQ ID NO:7).
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs of antibody 2C3.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VL CDRs of antibody 2C3.
  • a polynucleotide described herein comprises the nucleotide sequence of the variable heavy chain region of antibody 1H12 (SEQ ID NO:9). In some aspects, a polynucleotide described herein comprises the nucleotide sequence of the variable light chain region of antibody 1H12 (SEQ ID NO:11). In some aspects, a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs of antibody 1H12.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VL CDRs of antibody 1H12.
  • a polynucleotide described herein comprises the nucleotide sequence of the variable heavy chain region of antibody 2F9 (SEQ ID NO:13).
  • a polynucleotide described herein comprises the nucleotide sequence of the variable light chain region of antibody 2F9 (SEQ ID NO:15).
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs of antibody 2F9.
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VL CDRs of antibody 2F9.
  • a polynucleotide described herein comprises the nucleotide sequence of the variable heavy chain region of antibody 3A7 (SEQ ID NO:17). In some aspects, a polynucleotide described herein comprises the nucleotide sequence of the variable light chain region of antibody 3A7 (SEQ ID NO:19). In some aspects, a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VH CDRs of antibody 3A7.
  • SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • a polynucleotide described herein comprises a nucleotide sequence encoding for an antibody that binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), wherein the antibody comprises 1, 2, or 3 VL CDRs of antibody 3A7.
  • RBD SARS-CoV-2 spike protein
  • the antibody comprises 1, 2, or 3 VL CDRs of antibody 3A7.
  • polynucleotides comprising a nucleotide sequence encoding the light chain or heavy chain of an antibody described herein.
  • the polynucleotides can comprise nucleotide sequences encoding a light chain or a VL domain, comprising the VL FRs and CDRs of an antibody described herein.
  • the polynucleotides can comprise nucleotide sequences encoding a heavy chain, or a VH domain, comprising the VH FRs and CDRs of antibodies described herein.
  • a polynucleotide described herein encodes a variable heavy chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 1F7.
  • a polynucleotide described herein encodes a variable light chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of a variable light chain region of antibody 1F7.
  • the variable heavy chain region and/or variable light chain region encoded the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 1F7, and/or the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 1F7.
  • a polynucleotide described herein encodes a variable heavy chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 2C3.
  • a polynucleotide described herein encodes a variable light chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of a variable light chain region of antibody 2C3.
  • the variable heavy chain region and/or variable light chain region encoded the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 2C3, and the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 2C3.
  • a polynucleotide described herein encodes a variable heavy chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 1H12.
  • a polynucleotide described herein encodes a variable light chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of a variable light chain region of antibody 1H12.
  • the variable heavy chain region and/or variable light chain region encoded the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 1H12, and/or the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 1H12.
  • a polynucleotide described herein encodes a variable heavy chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 2F9.
  • a polynucleotide described herein encodes a variable light chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of a variable light chain region of antibody 2F9.
  • the variable heavy chain region and/or variable light chain region encoded the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 2F9, and/or the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 2F9.
  • a polynucleotide described herein encodes a variable heavy chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 3A7.
  • a polynucleotide described herein encodes a variable light chain region, wherein the polynucleotide comprises a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of a variable light chain region of antibody 3A7.
  • the variable heavy chain region and/or variable light chain region encoded the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • a polynucleotide described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide comprises (i) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 1F7 (SEQ ID NO:1), and (ii) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable light chain region of antibody 1F7 (SEQ ID NO:1), and (ii) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable light chain region of antibody
  • variable heavy chain region and/or variable light chain region encoded by the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 1F7, and the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 1F7.
  • a polynucleotide described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide comprises (i) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 2C3 (SEQ ID NO:5), and (ii) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable light chain region of antibody 2C3 (SEQ ID NO:7).
  • variable heavy chain region and/or variable light chain region encoded by the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 2C3, and the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 2C3.
  • a polynucleotide described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide comprises (i) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 1H12 (SEQ ID NO:9), and (ii) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable light chain region of antibody 1H12 (SEQ ID NO:11).
  • variable heavy chain region and/or variable light chain region encoded by the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 1H12, and the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 1H12.
  • a polynucleotide described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide comprises (i) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 2F9 (SEQ ID NO:13), and (ii) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable light chain region of antibody 2F9 (SEQ ID NO:15).
  • variable heavy chain region and/or variable light chain region encoded by the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 2F9, and the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 2F9.
  • a polynucleotide described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide comprises (i) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable heavy chain region of antibody 3A7 (SEQ ID NO:17), and (ii) a nucleic acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% identical to the nucleic acid sequence of the variable light chain region of antibody 3A7 (SEQ ID NO:19).
  • variable heavy chain region and/or variable light chain region encoded by the polynucleotide(s) does not affect the amino acid sequence of the variable heavy chain region and/or variable light chain region.
  • the CDRs of the variable heavy chain region are identical to the variable heavy chain region CDRs of antibody 3A7, and the CDRs of the variable light chain region are identical to the variable light chain region CDRs of antibody 3A7.
  • a polynucleotide(s) described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide(s) comprises (i) a nucleic acid sequence identical to the nucleic acid sequence of the variable heavy chain region of antibody 1F7 (SEQ ID NO:1), and (ii) a nucleic acid sequence identical to the nucleic acid sequence of the variable light chain region of antibody 1F7 (SEQ ID NO:3).
  • a polynucleotide(s) described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide(s) comprises (i) a nucleic acid sequence identical to the nucleic acid sequence of the variable heavy chain region of antibody 2C3 (SEQ ID NO:5), and (ii) a nucleic acid sequence identical to the nucleic acid sequence of the variable light chain region of antibody 2C3 (SEQ ID NO:7).
  • a polynucleotide(s) described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide(s) comprises (i) a nucleic acid sequence identical to the nucleic acid sequence of the variable heavy chain region of antibody 1H12 (SEQ ID NO:9), and (ii) a nucleic acid sequence identical to the nucleic acid sequence of the variable light chain region of antibody 1H12 (SEQ ID NO:11).
  • a polynucleotide(s) described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide(s) comprises (i) a nucleic acid sequence identical to the nucleic acid sequence of the variable heavy chain region of antibody 2F9 (SEQ ID NO:13), and (ii) a nucleic acid sequence identical to the nucleic acid sequence of the variable light chain region of antibody 2F9 (SEQ ID NO:15).
  • a polynucleotide(s) described herein encodes a variable heavy chain region and a variable light chain region, wherein the polynucleotide(s) comprises (i) a nucleic acid sequence identical to the nucleic acid sequence of the variable heavy chain region of antibody 3A7 (SEQ ID NO:17), and (ii) a nucleic acid sequence identical to the nucleic acid sequence of the variable light chain region of antibody 3A7 (SEQ ID NO:19).
  • a polynucleotide provided herein comprises a nucleotide sequence encoding a kappa light chain (e.g., human kappa light chain).
  • a polynucleotide provided herein comprises a nucleotide sequence encoding a lambda light chain (e.g., human lambda light chain).
  • a polynucleotide provided herein comprises a nucleotide sequence encoding an IgG1 heavy chain (e.g., human IgG1 heavy chain) of an antibody described herein.
  • a polynucleotide provided herein comprises a nucleotide sequence encoding IgG4 heavy chain (e.g., human IgG4 heavy chain).
  • a polynucleotide provided herein comprises a nucleotide sequence encoding IgG2 heavy chain (e.g., human IgG2 heavy chain).
  • a polynucleotide provided herein encodes an antigen- binding domain, e.g., a Fab or F(ab’) 2 .
  • a polynucleotide described herein hybridizes under high stringency, or intermediate stringency hybridization conditions to an antisense polynucleotide of a polynucleotide encoding a variable light chain region, provided herein. In other specific aspects, a polynucleotide described herein hybridizes under high stringency, or intermediate stringency hybridization conditions to an antisense polynucleotide of a polynucleotide encoding a variable heavy chain region, provided herein. [00144] Hybridization conditions have been described in the art and are known to one of skill in the art.
  • hybridization under stringent conditions can involve hybridization to filter- bound DNA in 6x sodium chloride/sodium citrate (SSC) at about 45° C followed by one or more washes in 0.2xSSC/0.1% SDS at about 50-65° C; hybridization under highly stringent conditions can involve hybridization to filter-bound nucleic acid in 6xSSC at about 45° C followed by one or more washes in 0.1xSSC/0.2% SDS at about 68° C.
  • Hybridization under other stringent hybridization conditions are known to those of skill in the art and have been described, see, for example, Ausubel, F.M. et al., eds., 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc.
  • polynucleotides encoding an antibody that are optimized, e.g., by codon/RNA optimization, replacement with heterologous signal sequences, and elimination of mRNA instability elements.
  • Methods to generate optimized nucleic acids encoding an antibody or a fragment thereof (e.g., light chain, heavy chain, a variable heavy chain region, or a variable light chain region) for recombinant expression by introducing codon changes and/or eliminating inhibitory regions in the mRNA can be carried out by adapting the optimization methods described in, e.g., U.S.
  • potential splice sites and instability elements e.g., A/T or A/U rich elements
  • the alterations utilize the degeneracy of the genetic code, e.g., using an alternative codon for an identical amino acid.
  • Such methods can increase expression of an antibody or fragment thereof by at least about 1 fold, 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, or 100 fold or more relative to the expression of an antibody encoded by polynucleotides that have not been optimized.
  • an optimized polynucleotide sequence encoding an antibody described herein or a fragment thereof can hybridize to an antisense polynucleotide of an unoptimized polynucleotide encoding an antibody described herein or a fragment thereof (e.g., a variable light chain region and/or a variable heavy chain region).
  • an optimized nucleotide sequence encoding an antibody described herein or a fragment thereof hybridizes under high stringency conditions to an antisense polynucleotide of an unoptimized polynucleotide encoding an antibody described herein or a fragment thereof (e.g., a variable light chain region and/or a variable heavy chain region).
  • an optimized nucleotide sequence encoding an antibody described herein or a fragment thereof hybridizes under intermediate or lower stringency hybridization conditions to an antisense polynucleotide of an unoptimized polynucleotide encoding an antibody described herein or a fragment thereof (e.g., a variable light chain region and/or a variable heavy chain region).
  • an antisense polynucleotide of an unoptimized polynucleotide encoding an antibody described herein or a fragment thereof e.g., a variable light chain region and/or a variable heavy chain region.
  • the polynucleotides can be obtained, and the nucleotide sequence of the polynucleotides determined, by any method known in the art. Nucleotide sequences encoding antibodies described herein, and modified forms of these antibodies can be determined using methods well known in the art, i.e., nucleotide codons known to encode particular amino acids are assembled in such a way to generate a nucleic acid that encodes the antibody.
  • Such a polynucleotide encoding the antibody can be assembled from chemically synthesized oligonucleotides (e.g., as described in Kutmeier et al., 1994, BioTechniques 17:242), which, briefly, involves the synthesis of overlapping oligonucleotides containing portions of the sequence encoding the antibody, annealing and ligating of those oligonucleotides, and then amplification of the ligated oligonucleotides by PCR.
  • chemically synthesized oligonucleotides e.g., as described in Kutmeier et al., 1994, BioTechniques 17:242
  • oligonucleotides e.g., as described in Kutmeier et al., 1994, BioTechniques 17:242
  • a polynucleotide encoding an antibody described herein can be generated from nucleic acid from a suitable source (e.g., a hybridoma) using methods well known in the art (e.g., PCR and other molecular cloning methods). For example, PCR amplification using synthetic primers hybridizable to the 3’ and 5’ ends of a known sequence can be performed using genomic DNA obtained from hybridoma cells producing the antibody of interest. Such PCR amplification methods can be used to obtain nucleic acids comprising the sequence encoding the light chain and/or heavy chain of an antibody.
  • a suitable source e.g., a hybridoma
  • methods well known in the art e.g., PCR and other molecular cloning methods.
  • PCR amplification using synthetic primers hybridizable to the 3’ and 5’ ends of a known sequence can be performed using genomic DNA obtained from hybridoma cells producing the antibody of interest.
  • Such PCR amplification methods can
  • Such PCR amplification methods can be used to obtain nucleic acids comprising the sequence encoding the variable light domain and/or the variable heavy domain of an antibody.
  • the amplified nucleic acids can be cloned into vectors for expression in host cells and for further cloning, for example, to generate chimeric and humanized antibodies.
  • a nucleic acid encoding the immunoglobulin can be chemically synthesized or obtained from a suitable source (e.g., an antibody cDNA library or a cDNA library generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any tissue or cells expressing the antibody, such as hybridoma cells selected to express an antibody described herein) by PCR amplification using synthetic primers hybridizable to the 3’ and 5’ ends of the sequence or by cloning using an oligonucleotide probe specific for the particular gene sequence to identify, e.g., a cDNA clone from a cDNA library that encodes the antibody.
  • a suitable source e.g., an antibody cDNA library or a cDNA library generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any tissue or cells expressing the antibody, such as hybridoma cells selected to express an antibody described herein
  • Amplified nucleic acids generated by PCR can then be cloned into replicable cloning vectors using any method well known in the art.
  • DNA encoding an antibody can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody).
  • Hybridoma cells can serve as a source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as E.
  • phage display methods functional antibody domains are displayed on the surface of phage particles which carry the polynucleotide sequences encoding them.
  • a library of DNA sequences encoding a variable light chain region and/or a variable heavy chain region are generated (e.g., amplified from animal cDNA libraries such as human cDNA libraries or random libraries are generated by chemical synthesis).
  • the DNA encoding the variable light chain region and a variable heavy chain region are recombined together with a scFv linker by PCR and cloned into a phagemid vector.
  • the vector is electroporated in E. coli and the E. coli is infected with helper phage.
  • Phage expressing an antigen-binding domain that binds to a particular antigen can be selected or identified with antigen, e.g., using labeled antigen or antigen bound or captured to a solid surface or bead.
  • the antibody coding regions from the phage can be isolated and used to generate whole antibodies, including human antibodies, or any other desired antigen-binding fragment, and expressed in any desired host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, e.g., as described below.
  • Techniques to recombinantly produced Fab, Fab′, and F(ab′) 2 fragments can also be employed using methods known in the art such as those disclosed in PCT Publication No.
  • Antibodies can be isolated from antibody phage libraries generated using the techniques described in McCafferty et al., Nature, 348:552-554 (1990). Clackson et al., Nature, 352:624-628 (1991). Marks et al., J. Mol. Biol., 222:581-597 (1991) describe the isolation of murine and human antibodies, respectively, using phage libraries.
  • Chain shuffling can be used in the production of high affinity (nM range) human antibodies (Marks et al., Bio/Technology, 10:779-783 (1992)), as well as combinatorial infection and in vivo recombination as a strategy for constructing very large phage libraries (Waterhouse et al., Nuc. Acids. Res., 21:2265-2266 (1993)).
  • PCR primers including a variable light chain region and a variable heavy chain region nucleotide sequences, a restriction site, and a flanking sequence to protect the restriction site can be used to amplify the VH or VL sequences in scFv clones.
  • the PCR amplified VH domains can be cloned into vectors expressing a heavy chain constant region, e.g., the human gamma 4 constant region, and the PCR amplified VL domains can be cloned into vectors expressing a light chain constant region, e.g., human kappa or lambda constant regions.
  • the vectors for expressing the VH or VL domains comprise a promoter, a secretion signal, a cloning site for the variable domain, constant domains, and a selection marker such as neomycin.
  • VH and VL domains can also be cloned into one vector expressing the necessary constant regions.
  • the heavy chain conversion vectors and light chain conversion vectors are then co-transfected into cell lines to generate stable or transient cell lines that express full-length antibodies, e.g., IgG, using techniques known to those of skill in the art.
  • two vectors e.g., plasmids or viruses
  • one vector comprises the variable heavy chain region of an antibody described herein
  • the second vector comprises the variable light chain region of an antibody described herein.
  • the Dyax (Cambridge, MA) technology platform can be used to convert Fab-phage or Fabs to complete IgG antibodies, such as the Dyax pR rapid reformatting vectors (RR).
  • a Fab-encoding DNA fragment is inserted into a Dyax pR-RRV between a eukaryotic leader sequence and an IgG heavy chain constant region cDNA.
  • Antibody expression is driven by the human cytomegalovirus (hCMV).
  • hCMV human cytomegalovirus
  • bacterial regulatory elements are replaced by the appropriate eukaryotic sequences (i.e., the IRES (internal ribosome entry site) motif).
  • the expression vector can also include the SV40 origin of replication.
  • the Dyax pRh1(a,z), pRh1(f), pRh4 and pRm2a are expression vectors allowing expression of reformatted FAbs as human IgG1 (isotype a,z), human IgG1 (isotype F), human IgG4, and mouse IgG2a, respectively.
  • Expressing vectors can be introduced into a suitable host cell (e.g., HEK293T cells, CHO cells)) for expression and purification.
  • a polynucleotide(s) encoding an antibody provided herein is isolated.
  • a polynucleotide(s) encoding an antibody provided herein is not isolated.
  • a polynucleotide(s) encoding an antibody provided herein is integrated, e.g., into chromosomal DNA or an expression vector.
  • a polynucleotide(s) encoding an antibody provided herein is not integrated into chromosomal DNA.
  • an antibody described herein e.g., an antigen-binding fragment
  • SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • an antibody described herein may be prepared, expressed, created or isolated by any means that involves creation, e.g., via synthesis or genetic engineering of sequences.
  • such an antibody comprises sequences that are encoded by DNA sequences that do not naturally exist within the antibody germline repertoire of an animal or mammal (e.g., a human).
  • a method for making an antibody described herein, which binds to SARS-CoV-2 or fragment thereof comprises the step of culturing a cell (e.g., host cell or hybridoma cell) that expresses the antibody.
  • the method for making an antibody described herein further comprises the step of purifying the antibody expressed by the cell.
  • a method for making an antibody described herein comprises the step of culturing a cell (e.g., host cell or hybridoma cell) that comprises polynucleotides or vectors encoding the antibody.
  • a cell e.g., host cell or hybridoma cell
  • methods for producing an antibody described herein comprising expressing such antibody from a host cell.
  • cells e.g., host cells
  • cells expressing (e.g., recombinantly expressing) the antibodies described herein (e.g., an antigen-binding fragment thereof) and related expression vectors.
  • vectors e.g., expression vectors
  • polynucleotides comprising nucleotide sequences encoding antibodies (e.g., an antigen-binding fragment) for recombinant expression in host cells, preferably in mammalian cells.
  • host cells comprising a polynucleotide encoding an antibody, or vectors comprising a polynucleotide encoding an antibody for recombinantly expressing an antibody described herein.
  • a host cell comprising two vectors, wherein the first vector comprises a polynucleotide of a variable heavy chain region of antibody 1F7 and the second vector comprises a polynucleotide of a variable light chain region of antibody 1F7 for recombinantly expressing an antibody described herein.
  • a host cell comprising two vectors, wherein the first vector comprises a polynucleotide of a variable heavy chain region of antibody 2C3 and the second vector comprises a polynucleotide of a variable light chain region of antibody 2C3 for recombinantly expressing an antibody described herein.
  • the cells may be primary cells or cell lines.
  • a host cell comprising two vectors, wherein the first vector comprises a polynucleotide of a variable heavy chain region of antibody 1H12 and the second vector comprises a polynucleotide of a variable light chain region of antibody 1H12 for recombinantly expressing an antibody described herein.
  • a host cell comprising two vectors, wherein the first vector comprises a polynucleotide of a variable heavy chain region of antibody 2F9 and the second vector comprises a polynucleotide of a variable light chain region of antibody 2F9 for recombinantly expressing an antibody described herein.
  • a host cell comprising two vectors, wherein the first vector comprises a polynucleotide of a variable heavy chain region of antibody 3A7 and the second vector comprises a polynucleotide of a variable light chain region of antibody 3A7 for recombinantly expressing an antibody described herein.
  • hybridoma cells expressing an antibody described herein In a particular aspect, provided herein are hybridoma cells expressing an antibody described herein. In a particular aspect, the host cell is isolated from other cells. In another aspect, the host cell is not found within the body of a subject.
  • Antibodies described herein e.g., monoclonal antibodies, such as chimeric or humanized antibodies, or an antigen-binding fragment thereof
  • SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • RBD fragment thereof
  • Monoclonal antibodies can be prepared using a wide variety of techniques known in the art, including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof.
  • monoclonal antibodies can be produced using hybridoma techniques including those known in the art and taught, for example, in Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563 681 (Elsevier, N.Y., 1981).
  • the term “monoclonal antibody” as used herein is not limited to antibodies produced through hybridoma technology.
  • a mouse or other appropriate host animal such as a sheep, goat, rabbit, rat, hamster or macaque monkey
  • lymphocytes that produce or are capable of producing antibodies that will bind to the protein (e.g., SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD)) used for immunization.
  • lymphocytes may be immunized in vitro.
  • Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986)).
  • a suitable fusing agent such as polyethylene glycol
  • a RIMMS (repetitive immunization multiple sites) technique can be used to immunize an animal (Kilptrack et al., 1997 Hybridoma 16:381-9, incorporated by reference in its entirety).
  • the hybridoma cells thus prepared are seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells.
  • the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
  • HAT medium hypoxanthine, aminopterin, and thymidine
  • myeloma cell lines are murine myeloma lines, such as those derived from MOPC-21 and MPC-11 mouse tumors available from the Salk Institute Cell Distribution Center, San Diego, CA, USA, and SP-2 or X63-Ag8.653 cells available from the American Type Culture Collection, Rockville, MD, USA.
  • Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987)).
  • Culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • the binding specificity of monoclonal antibodies produced by hybridoma cells is determined by methods known in the art, for example, immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA).
  • RIA radioimmunoassay
  • ELISA enzyme-linked immunoabsorbent assay
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986)). Suitable culture media for this purpose include, for example, D-MEM or RPMI 1640 medium. Alternatively, clonal cells can be isolated using a semi-solid agar supplemented with HAT (Stemcell Technologies). In addition, the hybridoma cells may be grown in vivo as ascites tumors in an animal.
  • the monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
  • mice or other animals, such as rats, monkeys, donkeys, pigs, sheep, goats, hamsters, or dogs
  • an antigen e.g., SARS-CoV-2 spike protein fragment thereof (e.g., RBD)
  • an immune response e.g., antibodies specific for the antigen are detected in the mouse serum
  • the mouse spleen is harvested and splenocytes isolated.
  • the splenocytes are then fused by well-known techniques to any suitable myeloma cells, for example, cells from cell line SP2/0 available from the American Type Culture Collection (ATCC®) (Manassas, VA), to form hybridomas.
  • ATCC® American Type Culture Collection
  • Hybridomas are selected and cloned by limited dilution.
  • lymph nodes of the immunized mice are harvested and fused with NS0 myeloma cells.
  • the hybridoma clones are then assayed by methods known in the art for cells that secrete antibodies capable of binding a polypeptide of the antigen. Ascites fluid, which generally contains high levels of antibodies, can be generated by immunizing mice with positive hybridoma clones.
  • described herein are methods of making antibodies described herein by culturing a hybridoma cell secreting an antibody.
  • the method of making an antibody described herein further comprises the step of purifying the antibody.
  • the hybridoma is generated by fusing splenocytes isolated from a mouse (or other animal, such as rat, monkey, donkey, pig, sheep, or dog) immunized with SARS- CoV-2 spike proteina fragment thereof (e.g., RBD) with myeloma cells and then screening the hybridomas resulting from the fusion for hybridoma clones that secrete an antibody able to bind to the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • SARS- CoV-2 spike proteina fragment thereof e.g., RBD
  • the hybridoma is generated by fusing lymph nodes isolated from a mouse (or other animal, such as rat, monkey, donkey, pig, sheep, or dog) immunized with a SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) with myeloma cells, and then screening the hybridomas resulting from the fusion for hybridoma clones that secrete an antibody able to bind to the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • a SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • Antibodies described herein include antibody fragments that recognize SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) and can be generated by any technique known to those of skill in the art.
  • Fab and F(ab’) 2 fragments described herein can be produced by proteolytic cleavage of immunoglobulin molecules, using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab’) 2 fragments).
  • a Fab fragment corresponds to one of the two identical arms of an antibody molecule and contains the complete light chain paired with the VH and CH1 domains of the heavy chain.
  • a F(ab’) 2 fragment contains the two antigen-binding arms of an antibody molecule linked by disulfide bonds in the hinge region.
  • the antibodies described herein can also be generated using various phage display methods known in the art. Examples of phage display methods that can be used to make the antibodies described herein include those disclosed in Brinkman et al., 1995, J. Immunol. Methods 182:41-50; Ames et al., 1995, J. Immunol. Methods 184:177-186; Kettleborough et al., 1994, Eur. J. Immunol.
  • the antibody coding regions from the phage can be isolated and used to generate whole antibodies, including human antibodies, or any other desired antigen-binding fragment, and expressed in any desired host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, e.g., as described below.
  • PCR primers including variable heavy chain region or variable light chain region nucleotide sequences, a restriction site, and a flanking sequence to protect the restriction site can be used to amplify the variable heavy chain region or variable light chain region sequences from a template, e.g., scFv clones.
  • a template e.g., scFv clones.
  • the PCR amplified variable heavy chain region can be cloned into vectors expressing a heavy chain constant region
  • the PCR amplified variable light chain region can be cloned into vectors expressing a light chain constant region, e.g., human kappa or lambda constant regions.
  • variable heavy chain region and variable light chain region can also be cloned into one vector expressing the necessary constant regions.
  • the heavy chain conversion vectors and light chain conversion vectors are then co-transfected into cell lines to generate stable or transient cell lines that express full-length antibodies, e.g., IgG, using techniques known to those of skill in the art.
  • full-length antibodies e.g., IgG
  • Human antibodies can be made by a variety of methods known in the art, including phage display methods described above using antibody libraries derived from human immunoglobulin sequences. See also U.S.
  • a chimeric antibody is a molecule in which different portions of the antibody are derived from different immunoglobulin molecules.
  • a chimeric antibody can contain a variable region of a mouse monoclonal antibody fused to a constant region of a human antibody. Methods for producing chimeric antibodies are known in the art.
  • humanized antibodies are produced.
  • a humanized antibody is capable of binding to a predetermined antigen and comprises a framework region having substantially the amino acid sequence of a human immunoglobulin and CDRs having substantially the amino acid sequence of a non-human immunoglobulin (e.g., a murine immunoglobulin).
  • Humanized antibodies can be produced using a variety of techniques known in the art, including but not limited to, CDR-grafting (European Patent No. EP 239,400; International publication No. WO 91/09967; and U.S. Patent Nos. 5,225,539, 5,530,101, and 5,585,089), veneering or resurfacing (European Patent Nos. EP 592,106 and EP 519,596; Padlan, 1991, Molecular Immunology 28(4/5):489-498; Studnicka et al., 1994, Protein Engineering 7(6):805-814; and Roguska et al., 1994, PNAS 91:969- 973), chain shuffling (U.S. Patent No.
  • an antibody described herein which binds to the same epitope of a SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) as antibody 1F7, 2C3, 1H12, 2F9, and 3A7, is a humanized antibody.
  • an antibody described herein, which competitively blocks (e.g., in a dose- dependent manner) antibody 1F7, 2C3, 1H12, 2F9, and 3A7 from binding to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) is a humanized antibody.
  • an antibody described herein which binds to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), is a humanized antibody derived from antibody 1F7, 2C3, 1H12, 2F9, and 3A7.
  • a humanized antibody comprises a VL domain comprising VL CDR1, VL CDR2, and VL CDR3, and/or a VH domain comprising VH CDR1, VH CDR2, and VH CDR3, of the antibody from which it was derived (e.g., antibody 1F7, 2C3, 1H12, 2F9, and 3A7).
  • Human antibodies can be produced using any method known in the art.
  • transgenic mice which are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes
  • the human heavy and light chain immunoglobulin gene complexes can be introduced randomly or by homologous recombination into mouse embryonic stem cells.
  • the human variable region, constant region, and diversity region can be introduced into mouse embryonic stem cells in addition to the human heavy and light chain genes.
  • the mouse heavy and light chain immunoglobulin genes can be rendered non-functional separately or simultaneously with the introduction of human immunoglobulin loci by homologous recombination. In particular, homozygous deletion of the J H region prevents endogenous antibody production.
  • the modified embryonic stem cells are expanded and microinjected into blastocysts to produce chimeric mice.
  • the chimeric mice are then bred to produce homozygous offspring, which express human antibodies.
  • the transgenic mice are immunized in the normal fashion with a selected antigen, e.g., all or a portion of an antigen (e.g., SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • Monoclonal antibodies directed against the antigen can be obtained from the immunized, transgenic mice using conventional hybridoma technology.
  • the human immunoglobulin transgenes harbored by the transgenic mice rearrange during B cell differentiation, and subsequently undergo class switching and somatic mutation.
  • human antibodies can be produced using mouse–human hybridomas.
  • human antibodies can be generated by inserting polynucleotides encoding human CDRs (e.g., VL CDRs and/or VH CDRs) of an antibody into an expression vector containing nucleotide sequences encoding human framework region sequences.
  • expression vectors further comprise nucleotide sequences encoding a constant region of a human light and/or heavy chain.
  • human antibodies can be generated by inserting human CDRs (e.g., VL CDRs and/or VH CDRs) of an antibody obtained from a phage library into such human expression vectors.
  • a human antibody can be generated by selecting human CDR sequences that are homologous (or substantially homologous) to non-human CDR sequences of a non-human antibody and selecting human framework sequences that are homologous (or substantially homologous) to non-human framework sequences of a non-human antibody.
  • Single domain antibodies for example, antibodies lacking the light chains, can be produced by methods well-known in the art. See Riechmann et al., 1999, J. Immunol. 231:25- 38; Nuttall et al., 2000, Curr. Pharm. Biotechnol. 1(3):253-263; Muylderman, 2001, J. Biotechnol.
  • Bispecific antibodies are antibodies that have binding specificities for at least two different epitopes. Exemplary bispecific antibodies may bind to two different epitopes of an antigen or to two different epitopes of two different antigens. In specific aspects, a bispecific antibody has two distinct antigen-binding domains, wherein each domain specifically binds to a different antigen.
  • bispecific antibodies can be prepared as full-length antibodies or antibody fragments (e.g., F(ab’): bispecific antibodies).
  • Methods for making bispecific antibodies are known in the art. (See, for example, Millstein et al., Nature, 305:537-539 (1983); Traunecker et al., EMBO J., 10:3655-3659 (1991); Suresh et al., Methods in Enzymology, 121:210 (1986); Kostelny et al., J.
  • antibodies that bind to SARS-CoV-2 spike protein or a fragment thereof can, in turn, be utilized to generate anti-idiotype antibodies that “mimic” an antigen using techniques well known to those skilled in the art. (See, e.g., Greenspan & Bona, 1989, FASEB J.
  • Recombinant expression of an antibody described herein e.g., a full-length antibody, heavy and/or light chain of an antibody, or a single-chain antibody described herein
  • SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • vectors e.g., expression vectors
  • a polynucleotide that encodes the antibody or fragments thereof (e.g., VL domain and/or VH domain).
  • a vector for the production of the antibody molecule can be produced by recombinant DNA technology using techniques well-known in the art. Methods for preparing a protein by expressing a polynucleotide containing an antibody encoding nucleotide sequence are described herein. Methods that are well known to those skilled in the art can be used to construct expression vectors containing antibody coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination.
  • replicable vectors comprising a nucleotide sequence encoding an antibody molecule described herein, a heavy or light chain of an antibody, a heavy or light chain variable domain of an antibody or a fragment thereof, or a heavy or light chain CDR, operably linked to a promoter.
  • Such vectors can, for example, include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., International Publication Nos. WO 86/05807 and WO 89/01036; and U.S. Patent No. 5,122,464) and the variable domain of the antibody can be cloned into such a vector for expression of the entire heavy, the entire light chain, or both the entire heavy and light chains.
  • An expression vector can be transferred to a cell (e.g., host cell) by conventional techniques and the resulting cells can then be cultured by conventional techniques to produce an antibody described herein or a fragment thereof.
  • a cell e.g., host cell
  • host cells containing a polynucleotide encoding an antibody described herein, or fragments thereof, or a heavy or light chain thereof, or antigen-binding fragment thereof, or a single-chain antibody described herein, operably linked to a promoter for expression of such sequences in the host cell.
  • vectors encoding both the heavy and light chains individually can be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.
  • a host cell contains a vector comprising a polynucleotide encoding both the heavy chain and light chain of an antibody described herein, or a fragment thereof.
  • a host cell contains two different vectors, a first vector comprising a polynucleotide encoding a heavy chain of an antibody described herein, or a fragment thereof, and a second vector comprising a polynucleotide encoding a light chain of an antibody described herein, or a fragment thereof.
  • a first host cell comprises a first vector comprising a polynucleotide encoding a heavy chain of an antibody described herein, or a fragment thereof
  • a second host cell comprises a second vector comprising a polynucleotide encoding a light chain of an antibody described herein.
  • microorganisms such as bacteria (e.g., E. coli and B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing antibody coding sequences; plant cell systems (e.g.,green algae such as Chlamydomonas reinhardtii) infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing antibody coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, MD
  • a mammalian expression vector is pOptiVECTM or pcDNA3.3.
  • bacterial cells such as Escherichia coli, and more preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule, are used for the expression of a recombinant antibody molecule.
  • mammalian cells such as Chinese hamster ovary (CHO) cells, in conjunction with a vector such as the major intermediate early gene promoter element from human cytomegalovirus is an effective expression system for antibodies (Foecking et al., 1986, Gene 45:101; and Cockett et al., 1990, Bio/Technology 8:2).
  • antibodies described herein are produced by CHO cells or NS0 cells.
  • the expression of nucleotide sequences encoding antibodies described herein (or fragments thereof) which bind to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) is regulated by a constitutive promoter, inducible promoter or tissue specific promoter.
  • a number of expression vectors can be advantageously selected depending upon the use intended for the antibody molecule being expressed. For example, when a large quantity of such an antibody is to be produced, for the generation of pharmaceutical compositions of an antibody molecule, vectors that direct the expression of high levels of fusion protein products that are readily purified can be desirable.
  • Such vectors include, but are not limited to, the E. coli expression vector pUR278 (Ruther et al., 1983, EMBO 12:1791), in which the antibody coding sequence can be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13:3101-3109; Van Heeke & Schuster, 1989, J. Biol. Chem. 24:5503-5509); and the like.
  • pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione 5-transferase (GST).
  • fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to matrix glutathione agarose beads followed by elution in the presence of free glutathione.
  • the pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.
  • AcNPV Autographa californica nuclear polyhedrosis virus
  • the virus grows in Spodoptera frugiperda cells.
  • the antibody coding sequence can be cloned individually into non-essential regions (for example, the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example, the polyhedrin promoter).
  • an AcNPV promoter for example, the polyhedrin promoter.
  • the antibody coding sequence of interest can be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene can then be inserted in the adenovirus genome by in vitro or in vivo recombination.
  • Insertion in a non-essential region of the viral genome will result in a recombinant virus that is viable and capable of expressing the antibody molecule in infected hosts (e.g., see Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 8 1:355-359).
  • Specific initiation signals can also be required for efficient translation of inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert.
  • These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic.
  • the term “host cell” refers to any type of cell, e.g., a primary cell or a cell from a cell line.
  • the term “host cell” refers to a cell transfected with a polynucleotide and the progeny or potential progeny of such a cell.
  • Progeny of such a cell may not be identical to the parent cell transfected with the polynucleotide due to mutations or environmental influences that may occur in succeeding generations or integration of the polynucleotide into the host cell genome.
  • a host cell strain can be chosen that modulates the expression of the inserted sequences or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products can be important for the function of the protein.
  • Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed.
  • eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product can be used.
  • mammalian host cells include but are not limited to CHO, VERO, BHK, Hela, COS, MDCK, HEK 293, NIH 3T3, W138, BT483, Hs578T, HTB2, BT2O and T47D, NS0 (a murine myeloma cell line that does not endogenously produce any immunoglobulin chains), CRL7O3O and HsS78Bst cells.
  • humanized monoclonal antibodies described herein are produced in mammalian cells, such as CHO cells.
  • cell lines that stably express the antibody molecule can be engineered.
  • host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker.
  • appropriate expression control elements e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.
  • engineered cells can be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media.
  • the selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines.
  • This method can advantageously be used to engineer cell lines that express the antibody molecule.
  • Such engineered cell lines can be particularly useful in screening and evaluation of compositions that interact directly or indirectly with the antibody molecule.
  • a number of selection systems can be used, including but not limited to, the herpes simplex virus thymidine kinase (Wigler et al., 1977, Cell 11:223), hypoxanthineguanine phosphoribosyltransferase (Szybalska & Szybalski, 1992, Proc. Natl. Acad. Sci. USA 48:202), and adenine phosphoribosyltransferase (Lowy et al., 1980, Cell 22:8-17) genes can be employed in tk- , hgprt- or aprt-cells, respectively.
  • antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler et al., 1980, Natl. Acad. Sci. USA 77:357; O’Hare et al., 1981, Proc. Natl. Acad. Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, which confers resistance to the aminoglycoside G-418 (Wu and Wu, 1991, Biotherapy 3:87-95; Tolstoshev, 1993, Ann. Rev. Pharmacol.
  • the expression levels of an antibody molecule can be increased by vector amplification (for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol. 3 (Academic Press, New York, 1987)).
  • vector amplification for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol. 3 (Academic Press, New York, 1987)).
  • a marker in the vector system expressing antibody is amplifiable
  • increase in the level of inhibitor present in culture of host cell will increase the number of copies of the marker gene. Since the amplified region is associated with the antibody gene, production of the antibody will also increase (Crouse et al., 1983, Mol. Cell. Biol. 3:257).
  • the host cell can be co-transfected with two or more expression vectors described herein, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide.
  • a host cell comprises two expression vectors: one vector comprising a polynucleotide sequence comprising a nucleotide sequence encoding a heavy chain variable region of an antibody described herein and a second vector comprising a polynucleotide sequence comprising a nucleotide sequence encoding a light chain variable region of an antibody described herein.
  • a single vector can be used which encodes, and is capable of expressing, both heavy and light chain polypeptides.
  • the coding sequences for the heavy and light chains can comprise cDNA or genomic DNA.
  • the expression vector can be monocistronic or multicistronic.
  • a multicistronic nucleic acid construct can encode 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, or in the range of 2-5, 5-10 or 10-20 genes/nucleotide sequences.
  • a bicistronic nucleic acid construct can comprise in the following order a promoter, a first gene (e.g., heavy chain of an antibody described herein), and a second gene and (e.g., light chain of an antibody described herein).
  • a promoter e.g., a promoter
  • a first gene e.g., heavy chain of an antibody described herein
  • a second gene and e.g., light chain of an antibody described herein.
  • the transcription of both genes can be driven by the promoter, whereas the translation of the mRNA from the first gene can be by a cap-dependent scanning mechanism and the translation of the mRNA from the second gene can be by a cap- independent mechanism, e.g., by an IRES.
  • an antibody molecule described herein can be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins.
  • chromatography e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography
  • centrifugation e.g., ion exchange, affinity, particularly by affinity for the specific antigen after Protein A, and sizing column chromatography
  • differential solubility e.g., differential solubility, or by any other standard technique for the purification of proteins.
  • the antibodies described herein can be fused to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification.
  • an antibody e.g., a monoclonal antibody, such as a humanized or chimeric antibody or an antigen-binding fragment thereof
  • an isolated antibody is one that is substantially free of other antibodies with different antigenic specificities than the isolated antibody.
  • a preparation of an antibody described herein is substantially free of cellular material and/or chemical precursors. The language “substantially free of cellular material” includes preparations of an antibody in which the antibody is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • an antibody that is substantially free of cellular material includes preparations of antibody having less than about 30%, 20%, 10%, 5%, 2%, 1%, 0.5%, or 0.1% (by dry weight) of heterologous protein (also referred to herein as a “contaminating protein”) and/or variants of an antibody, for example, different post-translational modified forms of an antibody or other different versions of an antibody (e.g., antibody fragments).
  • heterologous protein also referred to herein as a “contaminating protein”
  • variants of an antibody for example, different post-translational modified forms of an antibody or other different versions of an antibody (e.g., antibody fragments).
  • the antibody is recombinantly produced, it is also generally substantially free of culture medium, i.e., culture medium represents less than about 20%, 10%, 2%, 1%, 0.5%, or 0.1% of the volume of the protein preparation.
  • compositions e.g., pharmaceutical compositions
  • an antibody having the desired degree of purity in a physiologically acceptable carrier, excipient, or stabilizer (Remington’s Pharmaceutical Sciences (1990) Mack Publishing Co., Easton, PA).
  • a composition comprises an antibody described herein and an acceptable carrier or excipient.
  • a composition comprises two or more antibodies described herein and an acceptable carrier or excipient.
  • the compositions comprise an antibody conjugated to a moiety such as described herein.
  • Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, histidine, and other organic acids; antioxidants; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEENTM, PLURONICSTM or polyethylene glycol (PEG).
  • buffers such as phosphate, citrate, histidine, and other organic acids
  • antioxidants amino acids such as glycine, glutamine, asparagine, histidine, arginine
  • compositions comprise an antibody, and optionally one or more additional prophylactic or therapeutic agents, in a pharmaceutically acceptable carrier.
  • pharmaceutical compositions comprise an effective amount of an antibody, and optionally one or more additional prophylactic of therapeutic agents, in a pharmaceutically acceptable carrier.
  • the antibody is the only active ingredient included in the pharmaceutical composition.
  • pharmaceutical compositions comprise an antibody conjugated to a moiety such as described herein, and optionally one or more additional prophylactic or therapeutic agents, in a pharmaceutically acceptable carrier.
  • the antibody conjugated to a moiety such as described herein is the only active ingredient included in the pharmaceutical composition.
  • compositions described herein can be useful in the prevention and/or treatment of SARS-CoV-2 infection, or disease associated therewith.
  • a pharmaceutical compositions described herein can be useful in the prevention and/or treatment of COVID-19.
  • Pharmaceutically acceptable carriers used in parenteral preparations include aqueous vehicles, nonaqueous vehicles, antimicrobial agents, isotonic agents, buffers, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents and other pharmaceutically acceptable substances.
  • aqueous vehicles examples include Sodium Chloride Injection, Ringers Injection, Isotonic Dextrose Injection, Sterile Water Injection, Dextrose and Lactated Ringers Injection.
  • Nonaqueous parenteral vehicles include fixed oils of vegetable origin, cottonseed oil, corn oil, sesame oil and peanut oil.
  • Antimicrobial agents in bacteriostatic or fungistatic concentrations can be added to parenteral preparations packaged in multiple-dose containers, which include phenols or cresols, mercurials, benzyl alcohol, chlorobutanol, methyl and propyl p-hydroxybenzoic acid esters, thimerosal, benzalkonium chloride and benzethonium chloride.
  • Isotonic agents include sodium chloride and dextrose. Buffers include phosphate and citrate. Antioxidants include sodium bisulfate. Local anesthetics include procaine hydrochloride. Suspending and dispersing agents include sodium carboxymethylcelluose, hydroxypropyl methylcellulose and polyvinylpyrrolidone. Emulsifying agents include Polysorbate 80 (TWEEN®80). A sequestering or chelating agent of metal ions includes EDTA. Pharmaceutical carriers also include ethyl alcohol, polyethylene glycol and propylene glycol for water miscible vehicles; and sodium hydroxide, hydrochloric acid, citric acid or lactic acid for pH adjustment.
  • a pharmaceutical composition may be formulated for any route of administration to a subject.
  • routes of administration include intranasal, oral, pulmonary, transdermal, intradermal, parenteral, and mucosal.
  • the composition is formulated for intranasal or intramuscular administration.
  • the composition is formulated for intramuscular administration.
  • the composition is formulated for mucosal administration.
  • the composition is formulated for intranasal administration.
  • the composition may be formulated as an aerosol.
  • Parenteral administration characterized by either subcutaneous, intramuscular or intravenous injection, is also contemplated herein.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions.
  • the injectables, solutions and emulsions also contain one or more excipients. Suitable excipients are, for example, water, saline, dextrose, glycerol or ethanol.
  • Topical mixtures comprising an antibody are prepared as described for the local and systemic administration.
  • the resulting mixture can be a solution, suspension, emulsions or the like and can be formulated as creams, gels, ointments, emulsions, solutions, elixirs, lotions, suspensions, tinctures, pastes, foams, aerosols, irrigations, sprays, suppositories, bandages, dermal patches or any other formulations suitable for topical administration.
  • An antibody can be formulated as an aerosol for topical application, such as by inhalation (see, e.g., U.S. Patent Nos. 4,044,126, 4,414,209, and 4,364,923, which describe aerosols for delivery of a steroid useful for treatment of inflammatory diseases, particularly asthma).
  • formulations for administration to the respiratory tract can be in the form of an aerosol or solution for a nebulizer, or as a microfine powder for insufflations, alone or in combination with an inert carrier such as lactose.
  • the particles of the formulation will, in one aspect, have diameters of less than 50 microns, in one aspect less than 10 microns.
  • a pharmaceutical composition comprising an antibody is a lyophilized powder, which can be reconstituted for administration as solutions, emulsions and other mixtures. It may also be reconstituted and formulated as solids or gels.
  • the lyophilized powder is prepared by dissolving an antibody provided herein, or a pharmaceutically acceptable derivative thereof, in a suitable solvent.
  • the lyophilized powder is sterile.
  • the solvent may contain an excipient that improves the stability or other pharmacological component of the powder or reconstituted solution, prepared from the powder. Excipients that may be used include, but are not limited to, dextrose, sorbitol, fructose, corn syrup, xylitol, glycerin, glucose, sucrose or other suitable agent.
  • the solvent may also contain a buffer, such as citrate, sodium or potassium phosphate or other such buffer known to those of skill in the art at, in one aspect, about neutral pH.
  • the resulting solution will be apportioned into vials for lyophilization.
  • Each vial will contain a single dosage or multiple dosages of the compound.
  • the lyophilized powder can be stored under appropriate conditions, such as at about 4°C to room temperature. Reconstitution of this lyophilized powder with water for injection provides a formulation for use in parenteral administration. For reconstitution, the lyophilized powder is added to sterile water or other suitable carrier. The precise amount depends upon the selected compound. Such amount can be empirically determined.
  • An antibody or a nucleic acid sequence encoding an antibody can, for example, be formulated in liposomes.
  • Liposomes containing the molecule of interest are prepared by methods known in the art, such as described in Epstein et al. (1985) Proc. Natl. Acad. Sci. USA 82:3688; Hwang et al. (1980) Proc. Natl. Acad. Sci. USA 77:4030; and U.S. Patent Nos. 4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Patent No. 5,013,556.
  • liposomal suspensions may also be suitable as pharmaceutically acceptable carriers.
  • liposome formulations can be prepared as described in U.S. Patent No. 4,522,811. Briefly, liposomes such as multilamellar vesicles (MLV’s) may be formed by drying down egg phosphatidyl choline and brain phosphatidyl serine (7:3 molar ratio) on the inside of a flask. A solution of a compound comprising an antibody described herein in phosphate buffered saline lacking divalent cations (PBS) is added and the flask shaken until the lipid film is dispersed.
  • MLV multilamellar vesicles
  • An antibody can also be entrapped in a microcapsule prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano- particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano- particles and nanocapsules
  • sustained-release preparations can also be prepared.
  • suitable examples of sustained- release preparations include semipermeable matrices of solid hydrophobic polymers, which matrices are in the form of shaped articles, e.g., films, or microcapsule.
  • sustained- release matrices include polyesters, hydrogels (for example, poly(2- hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Patent No.
  • copolymers of L-glutamic acid and ethyl-L-glutamate can be sterile.
  • non-degradable ethylene-vinyl acetate non-degradable ethylene-vinyl acetate
  • degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOTTM (injectable microspheres composed of lactic acid- glycolic acid copolymer and leuprolide acetate)
  • poly- D-(-)-3-hydroxybutyric acid While polymers such as ethylene-vinyl acetate and lactic acid- glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods.
  • the compositions to be used for in vivo administration can be sterile.
  • nucleic acids comprising sequences encoding an antibody described herein are administered to a subject by way of gene therapy.
  • Gene therapy refers to therapy performed by the administration to a subject of an expressed or expressible nucleic acid.
  • Encompassed herein are any of the methods for gene therapy available in the art. For general review of the methods of gene therapy, see Goldspiel et al., 1993, Clinical Pharmacy 12:488- 505; Wu and Wu, 1991, Biotherapy 3:87-95; Tolstoshev, 1993, Ann. Rev. Pharmacol.
  • PROPHYLACTIC AND THERAPEUTIC USES OF ANTIBODIES are methods for preventing COVID-19 comprising administering an antibody described herein.
  • a method for preventing COVID-19 in a subject comprising administering to the subject an effective amount of an antibody described herein.
  • a method for preventing COVID-19 in a subject comprising administering to the subject a pharmaceutical composition comprising an effective amount of an antibody described herein.
  • the antibody is a protein or a protein conjugate.
  • the antibody is administered to the subjects as polynucleotide sequence comprising a nucleotide sequence encoding the antibody.
  • the antibody administered to the subject is a conjugated moiety such as described herein.
  • the administration of an effective amount of the antibody to the subject inhibits or reduces in the development or onset of COVID-19.
  • a method for preventing COVID-19 in a subject comprising administering to the subject an effective amount of an antibody described herein and another therapy, such as known to one of skill in the art or described herein.
  • the administration of an effective amount of the antibody to the subject inhibits or reduces the development or onset of COVID-19.
  • the administration of an effective amount of the antibody to the subject inhibits or reduces onset, development and/or severity of a symptom thereof (e.g., fever, myalgia, cough, difficulty breathing, tiredness) of COVID-19.
  • the administration of an effective amount of the antibody inhibits or reduces the recurrence of COVID-19 or a symptom associated therewith.
  • the administration of an effective amount of an antibody to a subject results in one, two, three, four, or more of the following: (i) the reduction or inhibition of the spread of SARS-CoV-2 from one cell to another cell; (ii) the reduction or inhibition of the spread of SARS-CoV-2 from one organ or tissue to another organ or tissue; (iii) the reduction or inhibition of the spread of SARS-CoV-2 from one region of an organ or tissue to another region of the organ or tissue (e.g., the reduction in the spread of SARS-CoV-2 from the upper to lower respiratory tract); (iv) the prevention of COVID-19 after exposure to SARS-CoV-2; (v) the reduction or inhibition in SARS-CoV-2 infection and/or replication; (vi) prevention of the onset or development of one or more symptoms associated with COVID-19 or SARS
  • provided herein are methods for treating a SARS-CoV-2 infection or COVID-19 comprising administering an antibody described herein.
  • a method for treating SARS-CoV-2 infection or COVID-19 in a subject comprising administering to the subject an effective amount of an antibody described herein.
  • a method for treating SARS-CoV-2 infection or COVD-19 in a subject comprising administering to the subject a pharmaceutical composition comprising an effective amount of an antibody described herein.
  • provided herein is a method for treating SARS-CoV-2 infection or COVID-19 comprising administering to the subject an effective amount of an antibody described herein and another therapy, such as known to one of skill in the art or described herein.
  • a method for treating SARS-CoV-2 infection or COVID-19 in a subject comprising administering to the subject a pharmaceutical composition comprising an effective amount of an antibody described herein, and another therapy, such as known to one of skill in the art or described herein.
  • the antibody is administered as a polynucleotide sequence comprising a nucleotide sequence encoding the antibody.
  • the antibody that is administered to the subject is conjugated to a moiety such as described herein.
  • the administration of an effective amount of the antibody to the subject inhibits or reduces the development of COVID-19.
  • the administration of an effective amount of the antibody to the subject inhibits or reduces onset, development and/or severity of a symptom thereof (e.g., fever, myalgia, cough, difficulty breathing, tiredness) of COVID-19.
  • the administration of an effective amount of the antibody inhibits or reduces duration of COVID-19 or a symptom associated therewith.
  • the administration of an effective amount of the antibody reduces organ failure associated with COVID-19.
  • the administration of an effective amount of the antibody reduces the hospitalization of the subject. In another aspect, the administration of an effective amount of the antibody reduces the length of hospitalization of the subject. In another aspect, the administration of an effective amount of the antibody increases the overall survival of subjects with COVID-19. In another aspect, the administration of an effective amount of the antibody prevents the onset or progression of a secondary infection associated with SARS-CoV-2 infection.
  • administration of an antibody(ies) to a subject reduces the incidence of hospitalization by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to the incidence of hospitalization in the absence of administration of said antibody(ies).
  • administering reduces mortality by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to the mortality in the absence of administration of said antibody(ies).
  • administering prevents or inhibits SARS-CoV- 2 from binding to its host cell receptor (e.g., ACE-2) by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to SARS-CoV-2 binding to its host cell receptor in the absence of said antibody(ies) or in the presence of a negative control in an assay known to one of skill in the art or described herein.
  • its host cell receptor e.g., ACE-2
  • administering inhibits or reduces SARS-CoV- 2 replication by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to replication of SARS-CoV-2 in the absence of said antibody(ies) or in the presence of a negative control in an assay known to one of skill in the art or described herein.
  • Inhibition of SARS-CoV-2 replication can be determined by detecting the SARS-CoV-2 titer in a biological specimen from a subject using methods known in the art (e.g., Northern blot analysis, RT-PCR, Western Blot analysis, etc.).
  • administration of an antibody(ies) results in reduction of about 1- fold, about 1.5-fold, about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 8-fold, about 10- fold, about 15-fold, about 20-fold, about 25-fold, about 30-fold, about 35-fold, about 40-fold, about 45-fold, about 50-fold, about 55-fold, about 60-fold, about 65-fold, about 70-fold, about 75- fold, about 80-fold, about 85-fold, about 90-fold, about 95-fold, about 100-fold, about 105 fold, about 110-fold, about 115-fold, about 120 fold, about 125-fold or higher in SARS-CoV-2 titer in the subject.
  • the fold-reduction in SARS-CoV-2 titer may be as compared to a negative control, as compared to another treatment, or as compared to the titer in the patient prior to antibody administration.
  • administration of an antibody(ies) results in a reduction of approximately 1 log or more, approximately 2 logs or more, approximately 3 logs or more, approximately 4 logs or more, approximately 5 logs or more, approximately 6 logs or more, approximately 7 logs or more, approximately 8 logs or more, approximately 9 logs or more, approximately 10 logs or more, 1 to 5 logs, 2 to 10 logs, 2 to 5 logs, or 2 to 10 logs in SARS-CoV- 2 titer in the subject.
  • the log-reduction in SARS-CoV-2 titer may be as compared to a negative control, as compared to another treatment, or as compared to the titer in the patient prior to antibody administration.
  • administration of an antibody(ies) inhibits or reduces SARS-CoV- 2 infection of a subject by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to SARS-CoV-2 infection of a subject in the absence of said antibody(ies) or in the presence of a negative control in an assay known to one of skill in the art or described herein.
  • administering inhibits or reduces the spread of SARS-CoV-2 in a subject by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to the spread of SARS-CoV-2 in a subject in the absence of said an antibody(ies) or in the presence of a negative control in an assay known to one of skill in the art or described herein.
  • administering inhibits or reduces the spread of SARS-CoV-2 between a subject and at least one other subject by at least about 99%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 60%, at least about 50%, at least about 45%, at least about 40%, at least about 45%, at least about 35%, at least about 30%, at least about 25%, at least about 20%, or at least about 10% relative to the spread of SARS-CoV-2 between a subject and at least one other subject in the absence of said antibody(ies) or in the presence of a negative control in an assay known to one of skill in the art or described herein.
  • administering reduces the number of and/or the frequency of symptoms of a SARS-CoV-2 infection in the subject (exemplary symptoms of a SARS-CoV-2 infection include, but are not limited to, body aches (especially joints and throat), fever, nausea, headaches, fatigue, sore throat, and difficulty breathing).
  • administration of an antibody(ies) to a subject reduces the number of and/or the frequency of symptoms of COVID-19 in the subject (exemplary symptoms of COVID-19 include, but are not limited to, body aches (especially joints and throat), fever, nausea, headaches, fatigue, sore throat, and difficulty breathing).
  • an antibody(ies) may be administered alone or in combination with another/other type of therapy known in the art.
  • an antibody described herein may be used as any line of therapy, including, but not limited to, a first, second, third, fourth and/or fifth line of therapy.
  • Encompassed herein are methods for administering one or more antibodies described herein to prevent the onset of a disease associated with SARS-CoV-2 infection and/or to treat or lessen the recurrence of a disease associated with SARS-CoV-2 infection.
  • an antibody described herein may be used as any line of therapy, including, but not limited to, a first, second, third, fourth and/or fifth line of therapy.
  • Encompassed herein are methods for administering one or more antibodies described herein to prevent the onset of COVID-19 and/or to treat or lessen the recurrence of COVID-19.
  • Further encompassed herein are methods for preventing and/or treating a disease associated with SARS-CoV-2 infection (e.g., COVID-19) and/or a symptom relating thereto for which no other antiviral therapy is available.
  • a disease associated with SARS-CoV-2 infection e.g., COVID-19
  • a symptom relating thereto for which no other antiviral therapy is available.
  • An antibody e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof
  • composition described herein may be delivered to a subject by a variety of routes.
  • an antibody conjugated to a moiety such as described herein, or a polynucleotide encoding a sequence encoding an antibody may be administered to a subject by a variety of routes. These include, but are not limited to, intranasal, intratracheal, oral, intradermal, intramuscular, intraperitoneal, transdermal, intravenous, conjunctival and subcutaneous routes. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent for use as a spray. In a specific aspect, an antibody described herein is administered to a subject intranasally or intramuscularly.
  • an antibody e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof
  • antibody conjugate or composition which will be effective in the treatment and/or prevention of SARS-CoV-2 infection, or a disease associated therewith (e.g., COVID-19) will depend on the nature of the disease.
  • the precise dose to be employed in a composition will also depend on the route of administration, and the seriousness of the infection or disease caused by it, and should be decided according to the judgment of the practitioner and each subject’s circumstances.
  • an antibody e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen- binding fragment thereof
  • the dosage ranges from about 0.0001 to 100 mg/kg, and more usually 0.01 to 5 mg/kg, of the patient body weight.
  • human antibodies have a longer half-life within the human body than antibodies from other species due to the immune response to the foreign polypeptides. Thus, lower dosages of human antibodies and less frequent administration is often possible.
  • An exemplary treatment regime entails administration once per every two weeks or once a month or once every 3 to 6 months for a period of one year or over several years, or over several year-intervals.
  • two or more antibodies with different binding specificities are administered simultaneously to a subject.
  • An antibody is usually administered on multiple occasions. Intervals between single dosages can be weekly, monthly, every 3 months, every 6 months or yearly. Intervals can also be irregular as indicated by measuring blood levels of antibody to the SARS-CoV-2 antigen in the patient.
  • the plasma level of an antibody described herein in a patient is measured prior to administration of a subsequent dose of an antibody described herein, or a composition thereof.
  • the plasma level of the antibody may be considered in determining the eligibility of a patient to receive a subsequent dose of an antibody described herein.
  • a patient’s plasma level of an antibody described herein may suggest not administering an antibody described herein; alternatively, a patient’s plasma level of an antibody described herein may suggest administering an antibody described herein at a particular dosage, at a particular frequency, and/or for a certain period of time.
  • the route of administration for a dose of an antibody described herein, or a composition thereof to a patient is intranasal, intramuscular, intravenous, or a combination thereof, but other routes described herein are also acceptable. Each dose may or may not be administered by an identical route of administration.
  • an antibody described herein, or composition thereof may be administered via multiple routes of administration simultaneously or subsequently to other doses of the same or a different antibody described herein.
  • an antibody described herein or a nucleic acid encoding such an antibody may be administered to a subject in combination with one or more other therapies (e.g., antiviral or immunomodulatory therapies).
  • an antibody conjugated to a moiety such as described herein may be administered to a subject with one or more other therapies.
  • a pharmaceutical composition described herein may be administered to a subject in combination with one or more therapies.
  • the one or more other therapies may be in the same composition or a different composition as an antibody described herein.
  • the one or more other therapies that are supportive measures such as pain relievers, anti-fever medications, or therapies that alleviate or assist with breathing.
  • supportive measures include humidification of the air by an ultrasonic nebulizer, aerolized racemic epinephrine, oral dexamethasone, intravenous fluids, intubation, fever reducers (e.g., ibuprofen, acetometaphin), and antibiotic and/or antifungal therapy (i.e., to prevent or treat secondary bacterial and/or fungal infections).
  • the therapies are administered less than 5 minutes apart, less than 30 minutes apart, 1 hour apart, at about 1 hour apart, at about 1 to about 2 hours apart, at about 2 hours to about 3 hours apart, at about 3 hours to about 4 hours apart, at about 4 hours to about 5 hours apart, at about 5 hours to about 6 hours apart, at about 6 hours to about 7 hours apart, at about 7 hours to about 8 hours apart, at about 8 hours to about 9 hours apart, at about 9 hours to about 10 hours apart, at about 10 hours to about 11 hours apart, at about 11 hours to about 12 hours apart, at about 12 hours to 18 hours apart, 18 hours to 24 hours apart, 24 hours to 36 hours apart, 36 hours to 48 hours apart, 48 hours to 52 hours apart, 52 hours to 60 hours apart, 60 hours to 72 hours apart, 72 hours to 84 hours apart, 84 hours to 96 hours apart, or 96 hours to 120 hours part.
  • two or more therapies are administered within the same patent visit. In some aspects, two or more therapies are administered concurrently. The two or more therapies can be administered in the same composition or a different composition. Further, the two or more therapies can be administered by the same route of administration of a different route of administration.
  • PATIENT POPULATIONS [00247]
  • the terms “subject” and “patient” are used interchangeably to refer to an animal (e.g., birds, reptiles, and mammals).
  • a patient treated in accordance with the methods provided herein is a na ⁇ ve subject, i.e., a subject that does not have COVID-19 or has not been and is not currently infected with SARS-CoV-2.
  • a patient treated in accordance with the methods provided herein is a subject that is at risk of acquiring SARS-CoV- 2 infection.
  • a patient treated in accordance with the methods provided herein is a patient suffering from or expected to suffer from COVID-19.
  • a patient treated in accordance with the methods provided herein is a patient diagnosed with SARS-CoV-2 infection or COVID-19.
  • a patient treated in accordance with the methods provided herein is a patient infected with SARS-CoV-2 that does not manifest any symptoms of COVID-19.
  • a patient treated in accordance with the methods provided herein is a patient infected with SARS-CoV-2 that manifests moderate to severe symptoms of COVID-19.
  • a patient treated in accordance with the methods provided herein is a patient experiencing one or more symptoms of COVID-19.
  • Symptoms of COVID-19 include, but are not limited to, body aches (especially joints and throat), fever, nausea, headaches, fatigue, sore throat, and difficulty breathing.
  • a patient treated in accordance with the methods provided herein is a patient with COVID-19 who does not manifest symptoms of the disease that are severe enough to require hospitalization.
  • a patient treated in accordance with the methods provided herein is a human.
  • a patient treated in accordance with the methods provided herein is a human infant.
  • a patient treated in accordance with the methods provided herein is a human toddler.
  • a patient treated in accordance with the methods provided herein is a human child.
  • a patient treated in accordance with the methods provided herein is a human adult.
  • a patient treated in accordance with the methods provided herein is an elderly human.
  • a patient treated in accordance with the methods provided herein is patient that is pregnant.
  • a patient treated in accordance with the methods provided herein is any subject at increased risk of SARS-CoV-2 infection or COVID-19 (e.g., an immunocompromised or immunodeficient individual).
  • a patient treated in accordance with the methods provided herein is any subject in close contact with an individual with increased risk of SARS-CoV-2 infection or COVID-19 (e.g., immunocompromised or immunosuppressed individuals).
  • a patient treated in accordance with the methods provided herein is a subject affected by any condition that increases susceptibility to SARS-CoV-2 infection or complications or COVID-19.
  • a patient treated in accordance with the methods provided herein is a subject in which SARS-CoV-2 infection has the potential to increase complications of another condition that the individual is affected by, or for which they are at risk.
  • such conditions that increase susceptibility to SARS-CoV-2 complications or for which SARS-CoV-2 increases complications associated with the condition are, e.g., conditions that affect the lung, such as cystic fibrosis, asthma, chronic obstructive pulmonary disease, emphysema, or bacterial infections; cardiovascular disease; or diabetes.
  • Other conditions that may increase SARS-CoV-2 complications include kidney disorders; blood disorders (including anemia or sickle cell disease); or weakened immune systems (including immunosuppression caused by medications, malignancies such as cancer, organ transplant, or HIV infection).
  • a patient treated in accordance with the methods provided herein is a subject that resides in a group home, such as a nursing home or orphanage.
  • a patient treated in accordance with the methods provided herein is subject that works in, or spends a significant amount of time in, a group home, e.g., a nursing home or orphanage.
  • a patient treated in accordance with the methods provided herein is a health care worker (e.g., a doctor or nurse).
  • a patient treated in accordance with the methods provided herein resides in a dormitory (e.g., a college dormitory).
  • a patient treated in accordance with the methods provided herein is a member of the military.
  • a patient treated in accordance with the methods provided herein is a child that attends school or daycare.
  • patients treated in accordance with the methods provided herein are patients already being treated with antibiotics, antivirals, antifungals, or other biological therapy/immunotherapy.
  • the antibodies described herein e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof
  • DIAGNOSTIC USES Provided herein are methods for the detection of SARS-CoV-2 infection comprising: (a) detecting the expression of SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) in a biological specimen (e.g., sputum, nasal drippings, cells or tissue samples) from a subject using an antibody described herein (e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof); and (b) comparing the level of the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) with a control level, e.g., levels in a biological specimen from a subject not infected with SARS-CoV-2, wherein an increase in the assayed level of SARS- CoV-2 spike protein c or a fragment thereof (e.g., RBD) compared to the control level of the SARS-CoV-2
  • a biological specimen e
  • a diagnostic assay for diagnosing SARS-Co-2 infection comprising: (a) assaying for the level of SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) in a biological specimen from a subject using an antibody described herein (e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof); and (b) comparing the level of the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) with a control level, e.g., levels in a biological specimen from a subject not infected with SARS-CoV- 2, wherein an increase in the assayed SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) level compared to the control level of the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) is indicative of SARS-CoV-2 infection.
  • an antibody described herein e.g.,
  • a more definitive diagnosis of SARS-CoV-2 infection may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the SARS-CoV-2 infection.
  • a biological sample e.g., cells, sputum, nasal swab, mucous, etc.
  • SARS-CoV-2 spike protein or a fragment thereof e.g., RBD
  • SARS-CoV-2 is detected if the level of binding of the antibody to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) is greater than the level of binding of the antibody to non-SARS-CoV-2 infected cells or a biological sample not infected with SARS-CoV-2.
  • the detection is done in vitro. In other aspects, the detection is done in vivo. Techniques known to one of skill in the art may be used to detect the binding of the antibody to the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • Antibodies described herein can be used to assay SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) levels in a biological sample using classical immunohistological methods as described herein or as known to those of skill in the art (e.g., see Jalkanen et al., 1985, J. Cell. Biol.101:976-985; and Jalkanen et al., 1987, J. Cell. Biol.105:3087- 3096).
  • classical immunohistological methods as described herein or as known to those of skill in the art (e.g., see Jalkanen et al., 1985, J. Cell. Biol.101:976-985; and Jalkanen et al., 1987, J. Cell. Biol.105:3087- 3096).
  • Antibody-based methods useful for detecting protein expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA).
  • ELISA enzyme linked immunosorbent assay
  • RIA radioimmunoassay
  • An antibody described herein or generated in accordance with the methods described herein may be labeled with a detectable label or a secondary antibody that binds to such an antibody may be labeled with a detectable label.
  • Suitable antibody assay labels include enzyme labels, such as, glucose oxidase; radioisotopes, such as iodine ( 125 I, 121 I), carbon ( 14 C), sulfur (35 S), tritium ( 3 H), indium ( 121 In), and technetium ( 99 Tc); luminescent labels, such as luminol; and fluorescent labels, such as fluorescein and rhodamine, and biotin. See, above for examples of antibody conjugates that might be useful in the detection and diagnosis of SARS- CoV-2 infection.
  • enzyme labels such as, glucose oxidase
  • radioisotopes such as iodine ( 125 I, 121 I), carbon ( 14 C), sulfur (35 S), tritium ( 3 H), indium ( 121 In), and technetium ( 99 Tc)
  • luminescent labels such as luminol
  • fluorescent labels such as fluorescein and rhodamine, and biotin. See, above for examples of antibody conjugates that might
  • monitoring of SARS-CoV-2 infection is carried out by repeating the method for diagnosing the SARS-CoV-2 infection, for example, one day, two days, one week, two weeks, or one month after initial diagnosis.
  • BIOLOGICAL ASSAYS An antibody described herein (e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof) may be characterized using any assay known to one of skill in the art or described herein. In a specific aspect, an antibody described herein is characterized as described in herein.
  • An antibody may be characterized in a variety of ways known to one of skill in the art (e.g., ELISA, biolayer interferometry, surface plasmon resonance display (BIAcore kinetic), Western blot, immunofluorescence, immunostaining, plaque reduction assays, and/or microneutralization assays). In some aspects, an antibody is assayed for its ability to bind to SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • an antibody is assayed for its ability to inhibit or reduce the interaction of SARS-CoV-2 with its host cell receptor (e.g., ACE-2) using techniques known to one of skill in the art.
  • SARS-CoV-2 e.g., ACE-2
  • the ability of an antibody to inhibit or reduce the interaction of SARS-CoV-2 spike protein with ACE-2 may be tested using techniques known to one of skill in the art.
  • the specificity or selectivity of an antibody for SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) and cross-reactivity with other antigens can be assessed by any method known in the art or described herein.
  • Immunoassays that can be used to analyze specific binding and cross-reactivity include, but are not limited to, competitive and non-competitive assay systems using techniques such as Western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, to name but a few.
  • competitive and non-competitive assay systems using techniques such as Western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement
  • a competitive binding assay is a radioimmunoassay comprising the incubation of labeled antigen (e.g., 3 H or 125 I) with the antibody of interest in the presence of increasing amounts of unlabeled antigen, and the detection of the antibody bound to the labeled antigen.
  • labeled antigen e.g., 3 H or 125 I
  • the affinity of the antibody for a SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) and the binding off-rates can be determined from the data by Scatchard plot analysis. Competition with a second antibody can also be determined using radioimmunoassays.
  • a SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) or SARS-CoV-2 is incubated with the test antibody conjugated to a detectable labeled (e.g., 3 H or 125 I) in the presence of increasing amounts of an unlabeled second antibody.
  • a detectable labeled e.g., 3 H or 125 I
  • surface plasmon resonance (e.g., BIAcore kinetic) analysis is used to determine the binding on and off rates of an antibody to SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD), or SARS-CoV-2.
  • an antibody described herein is tested for its ability to neutralize SARS-CoV-2 or SARS-CoV-2 spike protein expressing pseudotyped viruses, such as described herein.
  • CYTOTOXICITY ASSAYS Many assays well-known in the art can be used to assess viability of cells (infected or uninfected) or cell lines following exposure to an antibody or composition thereof and, thus, determine the cytotoxicity of the antibody or composition thereof. For example, cell proliferation can be assayed by measuring Bromodeoxyuridine (BrdU) incorporation (See, e.g., Hoshino et al., 1986, Int. J.
  • protein can be quantitated by known immunodiagnostic methods such as ELISA, Western blotting or immunoprecipitation using antibodies, including commercially available antibodies.
  • mRNA can be quantitated using methods that are well known and routine in the art, for example, using northern analysis, RNase protection, or polymerase chain reaction in connection with reverse transcription.
  • Cell viability can be assessed by using trypan-blue staining or other cell death or viability markers known in the art.
  • the level of cellular ATP is measured to determined cell viability.
  • cell viability is measured in three-day and seven-day periods using an assay standard in the art, such as the CellTiter-Glo Assay Kit (Promega), which measures levels of intracellular ATP. A reduction in cellular ATP is indicative of a cytotoxic effect.
  • cell viability can be measured in the neutral red uptake assay.
  • visual observation for morphological changes may include enlargement, granularity, cells with ragged edges, a filmy appearance, rounding, detachment from the surface of the well, or other changes.
  • the cells used in the cytotoxicity assay are animal cells, including primary cells and cell lines. In some aspects, the cells are human cells.
  • cytotoxicity is assessed in one or more of the following cell lines: U937, a human monocyte cell line; primary peripheral blood mononuclear cells (PBMC); Huh7, a human hepatoblastoma cell line; 293T, a human embryonic kidney cell line; and THP-1, monocytic cells.
  • cytotoxicity is assessed in one or more of the following cell lines: MDCK, MEF, Huh 7.5, Detroit, or human tracheobronchial epithelial (HTBE) cells.
  • An antibody or composition thereof can be tested for in vivo toxicity in animal models.
  • animal models used to test the activities of an antibody or composition thereof can also be used to determine the in vivo toxicity of these antibodies.
  • animals are administered a range of concentrations of an antibody. Subsequently, the animals are monitored over time for lethality, weight loss or failure to gain weight, and/or levels of serum markers that may be indicative of tissue damage (e.g., creatine phosphokinase level as an indicator of general tissue damage, level of glutamic oxalic acid transaminase or pyruvic acid transaminase as indicators for possible liver damage).
  • tissue damage e.g., creatine phosphokinase level as an indicator of general tissue damage, level of glutamic oxalic acid transaminase or pyruvic acid transaminase as indicators for possible liver damage.
  • These in vivo assays may also be adapted to test the toxicity of various administration mode and/or regimen in addition to dosages.
  • the toxicity and/or efficacy of an antibody or composition thereof can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio LD 50 /ED 50 .
  • An antibody or composition thereof that exhibits large therapeutic indices is preferred. While an antibody or composition thereof that exhibits toxic side effects may be used, care should be taken to design a delivery system that targets such agents to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage of an antibody or composition thereof for use in humans.
  • the dosage of such antibodies lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the effective dose can be estimated initially from cell culture assays.
  • a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50 (i.e., the concentration of the antibody that achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans.
  • Levels in plasma may be measured, for example, by high- performance liquid chromatography. Additional information concerning dosage determination is provided herein.
  • any assays known to those skilled in the art can be used to evaluate the prophylactic and/or therapeutic utility of an antibody or composition thereof, for example, by measuring viral infection or a condition or symptoms associated therewith.
  • IN VIVO ASSAYS [00279] Antibodies and compositions thereof are preferably assayed in vivo for the desired therapeutic or prophylactic activity prior to use in humans. For example, in vivo assays can be used to determine whether it is preferable to administer an antibody or composition thereof and/or another therapy.
  • the antibody or composition can be administered before the animal is infected with SARS-CoV-2.
  • an antibody or composition thereof can be administered to the animal at the same time that the animal is infected with SARS-CoV-2.
  • the antibody or composition may be administered after infecting the animal with SARS-CoV-2.
  • an antibody or composition thereof is administered to the animal more than one time.
  • animals are infected with SARS-CoV-2 and concurrently or subsequently treated with an antibody or composition thereof, or placebo.
  • animals are treated with an antibody or composition thereof or placebo and subsequently infected with SARS-CoV-2.
  • Samples obtained from these animals can be tested for viral replication via well-known methods in the art, e.g., those that measure altered viral titers (as determined, e.g., by plaque formation), the production of viral proteins (as determined, e.g., by Western blot, ELISA, or flow cytometry analysis) or the production of viral nucleic acids (as determined, e.g., by RT-PCR or northern blot analysis).
  • tissue samples are homogenized in phosphate-buffered saline (PBS), and dilutions of clarified homogenates are adsorbed for a time period (e.g., 20 minutes or 1 hour) at 37°C onto monolayers of cells (e.g., Vero, CEF or MDCK cells).
  • PBS phosphate-buffered saline
  • histopathologic evaluations are performed after infection, preferably evaluations of the organ(s) the virus is known to target for infection.
  • Virus immunohistochemistry can be performed using a viral-specific monoclonal antibody.
  • the effect of an antibody or composition thereof on the infectious disease process or pathogenicity of a given virus can also be determined using in vivo assays in which the titer of the virus in an infected subject administered an antibody or composition thereof, the length of survival of an infected subject administered an antibody or composition thereof, the immune response in an infected subject administered an antibody or composition thereof, the number, duration and/or severity of the symptoms in an infected subject administered an antibody or composition thereof, and/or the time period before onset of one or more symptoms in an infected subject administered an antibody or composition thereof, is assessed. Techniques known to one of skill in the art can be used to measure such effects.
  • histopathologic evaluations are performed after infection of an animal model subject.
  • Nasal turbinates and trachea may be examined for epithelial changes and subepithelial inflammation.
  • the lungs may be examined for bronchiolar epithelial changes and peribronchiolar inflammation in large, medium, and small or terminal bronchioles.
  • the alveoli are also evaluated for inflammatory changes.
  • Virus immunohistochemistry may be performed using a viral-specific monoclonal antibody (e.g. spike-specific monoclonal antibodies).
  • the ability of an antibody or composition thereof to treat SARS- CoV-2 infection or a disease associated therewith is assessed by determining the ability of the antibody to confer passive immunity to a disease associated with SARS-CoV-2 infection (e.g., COVID-19) in a subject.
  • the ability of an antibody described herein to confer passive immunity to a disease associated with SARS-CoV-2 infection (e.g., COVID-19) in a subject can be assessed using any methods known in the art.
  • an animal experiment e.g., an animal challenge experiment to assess any antibody described herein is conducted as described in Example 1, infra.
  • an antibody or composition thereof that modulates replication of SARS- CoV-2 is assessed in infected human subjects.
  • an antibody or composition thereof is administered to the human subject, and the effect of the antibody and/or composition on viral replication is determined by, e.g., analyzing the level of the virus or viral nucleic acids in a biological sample (e.g., serum or plasma).
  • a biological sample e.g., serum or plasma.
  • An antibody or composition thereof that alters virus replication can be identified by comparing the level of virus replication in a subject or group of subjects treated with a control antibody to that in a subject or group of subjects treated with an antibody or composition thereof.
  • alterations in viral replication can be identified by comparing the level of the virus replication in a subject or group of subjects before and after the administration of an antibody or composition thereof. Techniques known to those of skill in the art can be used to obtain the biological sample and analyze the mRNA or protein expression. [00288] In another aspect, the effect of an antibody or composition thereof on the severity of one or more symptoms associated with SARS-CoV-2 infection/COVID-19 are assessed in an infected subject. In accordance with this aspect, an antibody or composition thereof or a control antibody is administered to a human subject suffering from SARS-CoV-2 infection, and the effect of the antibody or composition on one or more symptoms of the virus infection is determined.
  • An antibody or composition thereof that reduces one or more symptoms can be identified by comparing the subjects treated with a control antibody to the subjects treated with the antibody or composition. Techniques known to physicians familiar with infectious diseases can be used to determine whether an antibody or composition thereof reduces one or more symptoms associated with a SARS-CoV-2 infection (e.g., COVID-19).
  • KITS in another aspect, provided herein is a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of a composition (e.g., pharmaceutical compositions) described herein, such as one or more antibodies provided herein (e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof), one or more polynucleotides described herein, or one or more antibody conjugates described herein.
  • a composition e.g., pharmaceutical compositions
  • a compositions e.g., pharmaceutical compositions described herein, such as one or more antibodies provided herein (e.g., a monoclonal antibody, such as a chimeric or humanized antibody, or an antigen-binding fragment thereof), one or more polynucleotides described herein, or one or more antibody conjugates described herein.
  • a composition e.g., pharmaceutical compositions described herein, such as one or more antibodies provided herein (e.g.,
  • kits encompassed herein can be used in the above methods.
  • a kit comprises an antibody described herein, preferably an isolated antibody, in one or more containers.
  • An antibody described herein included in a kit may be attached to a solid support (e.g., a microtiter plate or bead).
  • the kits encompassed herein contain an isolated SARS-CoV2 antigen that the antibodies encompassed herein react with (e.g., the antibody binds to the antigen) as a control.
  • the kits provided herein further comprise a control antibody which does not react with SARS-CoV-2 spike protein or a fragment thereof (e.g,. RBD) (such as a control IgG).
  • kits provided herein contain a means for detecting the binding of an antibody to SARS-CoV-2 spike protein or a fragment thereof (e.g., the antibody may be conjugated to a detectable substrate such as a fluorescent compound, an enzymatic substrate, a radioactive compound, a luminescent compound, or another antibody that is conjugated to a detectable substrate (e.g., the antibody may be conjugated to a second antibody which recognizes/binds to the first antibody)).
  • the kits comprise a second antibody which is labeled with a detectable substance and which binds to an antibody described herein.
  • the kit may include a recombinantly produced or chemically synthesized SARS- CoV-2 spike protein or a fragment thereof (e.g., RBD).
  • the SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) provided in the kit may also be attached to a solid support.
  • the detecting means of the above described kit includes a solid support to which SARS-CoV-2 spike protein or a fragment thereof (e.g., RBD) is attached.
  • Such a kit may also include a non-attached reporter-labeled antibody.
  • Example 1 Murine monoclonal antibodies against RBD of SARS-CoV-2 neutralize authentic wild type SARS-CoV-2 as well as B.1.1.7 and B.1.351 viruses and protect in vivo in a mouse model in a neutralization dependent manner.
  • SARS-CoV-2 severe acute respiratory syndrome 2
  • Vaccines have been developed and authorized but supply of these vaccines is currently limited.
  • This example describes the generation mouse monoclonal antibodies (mAbs) against different epitopes on the RBD and the assessment of binding and neutralization against authentic SARS-CoV-2.
  • mAbs monoclonal antibodies
  • this example describes the isolation and characterization of fourteen mouse mAbs against the RBD of SARS-CoV-2 and the assessment of their binding to recombinant RBD and spike protein as well as tested their ability to neutralize live virus.
  • this example describes testing if non-neutralizing mAbs can lower viral loads in a mouse challenge model.
  • Vero.E6 cells ATCC CRL-1586 were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies), which was supplemented with 10% fetal bovine serum (FBS; Corning) as well as antibiotics (100 units/ml penicillin–100 ⁇ g/ml streptomycin [Pen-Strep; Gibco]), and buffer solution [1 M 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES); Gibco].
  • DMEM Dulbecco’s modified Eagle’s medium
  • FBS fetal bovine serum
  • antibiotics 100 units/ml penicillin–100 ⁇ g/ml streptomycin [Pen-Strep; Gibco]
  • buffer solution [1 M 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES); Gibco].
  • SARS-CoV-2 was exclusively handled in a BSL3 facility and passaged in Vero.E6 for three days and the supernatant from infected cells was clarified via centrifugation at 1000 g for 5 minutes. The virus stock was titered in Vero.E6 cells as well.
  • Generation of monoclonal antibodies All animal work was performed by adhering to institutional regulation as well as Institutional Animal Care and Use Committee (IACUC) guidelines. Six to eight weeks old, female, mice (Jackson Laboratories) were immunized with 3 ⁇ gs of purified RBD of SARS-CoV-2 mixed with 10 ⁇ gs of poly I:C (Invivogen) twice with 3 weeks interval [17, 29].
  • mice were immunized again with 100 ⁇ gs of RBD along with 10 ⁇ gs of poly I:C.
  • mice were immunized again with 100 ⁇ gs of RBD along with 10 ⁇ gs of poly I:C.
  • the splenocytes were washed with phosphate buffered saline (Life Technologies; PBS) and then fused with SP2/o myeloma cells (ATCC) using polyethylene glycol (Sigma-Aldrich catalog # P7181).
  • Hybridoma supernatants were screened in an enzyme-linked immunosorbent assay (ELISA) assay as described in the below section. Desirable hybridomas that secreted IgG were selected and expanded.
  • ELISA enzyme-linked immunosorbent assay
  • ELISA Ninety-six well, flat-bottom, Immulon 4 HBX plates (Thermo Scientific) were coated overnight at 4°C with 50 ⁇ ls/well of a 2 ⁇ g/ml solution of each respective protein in PBS. The next day, coating solution was discarded. One hundred ⁇ ls per well of 3% non-fat milk prepared in PBS containing 0.1% of Tween-20 (Fisher Bioreagents; T-PBS) was added to the plates for one hour at room temperature (RT) to block the plates.
  • Tween-20 Fisher Bioreagents
  • Antibody dilutions were prepared in 1% non-fat milk in T-PBS. The starting concentration used for each antibody was 30 ⁇ g/ml and three-fold dilutions were subsequently prepared. After the blocking solution had been on the plates for 1 hour, the antibody dilutions were added for 1 hour at RT. Next, the plates were washed thrice with 250 ⁇ ls per well of T-PBS. The secondary solution was also prepared in 1% non-fat milk in T-PBS. For mouse antibodies, anti-mouse IgG conjugated to horseradish peroxidase (Rockland) was used at a dilution of 1:3000. For human antibodies, anti-human IgG Fab was used at the same dilution.
  • Microneutralization assay All antibodies were tested for neutralization capability in a neutralization assay with authentic SARS-CoV-2 isolate USA-WA1/2020 (BEI Resources NR- 52281), isolate hCoV-19/South Africa/KRISP-K005325/2020 (BEI Resources NR-54009), and hCoV-19/England/204820464/2020 (BEI Resources NR-54000) in the BSL-3 facility. All viruses were obtained from BEI resources and propagated in Vero.E6 cells. Twenty-thousand Vero.E6 cells were seeded in a 96-well cell culture plate and used the next day.
  • Antibody dilutions were prepared starting at 30 ⁇ g/ml and 3-fold subsequent dilutions were prepared. The protocol has been described earlier (21, 29, 35, 36). Cells were stained for the nucleoprotein and quantified. Percent inhibition was calculated and IC 50 S were obtained (35). All viruses were subjected to deep sequencing to ensure that no mutations had taken place in culture. The polybasic cleavage site changed to WRAR in the B.1.351 during passage in cell culture (as known for this virus at BEI Resources) and no other unexpected mutations occurred. [00302] In vivo mouse challenge studies: All work with SARS-CoV-2 was performed in a BSL-3 facility.
  • mice Six -to 8-weeks old, female, BALB/c mice (Jackson Laboratories) were administered an adenovirus containing human ACE2 (AdV-hACE2) via the intranasal route at 2.5 ⁇ 10 8 plaque forming units (PFUs) per mouse in a final volume of 50 ⁇ ls. Five days later, each respective antibody was administered via the intraperitoneal route at 10 mg/kg in 100 ⁇ ls volume. Two hours later, mice were infected with 10 5 PFUs of SARS-CoV-2 intranasally. Mice were humanely sacrificed on day 3 and day 5 to assess viral titer in the lungs. Lungs were homogenized using a BeadBlaster 24 (Benchmark) homogenizer.
  • BeadBlaster 24 Benchmark
  • Plaque assay To assess viral titer in the lungs, each homogenate was diluted in 1X minimal essential medium (10X MEM; Life Technologies) supplemented with glutamine, 35% bovine serum albumin (BSA; MP Biomedicals), antibiotics, and HEPES as described earlier (29, 37). Three-hundred thousand Vero.E6 cells were seeded per well in a 12-well cell culture plate and used the next day when the cells were approximately 90% confluent. Media was removed from cells and dilutions were added to the plates and incubated at 37 degree C incubator for 1 hour.
  • 1X minimal essential medium (10X MEM; Life Technologies) supplemented with glutamine, 35% bovine serum albumin (BSA; MP Biomedicals), antibiotics, and HEPES as described earlier (29, 37).
  • BSA bovine serum albumin
  • HEPES HEPES
  • Sections were analyzed, images were taken, and sections were also scored by a pathologist. Scores were assigned by the pathologist based on six parameters, as mentioned in the results section. Both H&E staining as well as IHC was performed. An anti-SARS-CoV nucleoprotein antibody (Novus Biologicals cat. NB100–56576) was used for IHC.
  • the SARS-CoV-2 spike construct used for EM studies contains the mammalian- codon-optimized gene encoding residues 1-1208 of the spike followed by a C-terminal T4 fibritin trimerization domain, a HRV3C cleavage site and an 8x-His tag subcloned into the eukaryotic- expression vector pcDNA3.4. Amino acid mutations were introduced in the S1/S2 cleavage site (RRAR to GSAS) along with other stabilizing mutations including the HexaPro mutations (38). The spike trimers were expressed and purified as described previously (39).
  • Negative stain EM sample preparation and data collection Spike protein was complexed with purified Fab at three times molar excess per trimer and incubated for thirty minutes at room temperature. Complexes were diluted to 0.02 mg/ml in TBS and 3 ⁇ l applied to a 400mesh Cu grid, blotted with filter paper, and stained with 2% uranyl formate for 30 seconds. Images were collected on a Tecnai Spirit microscope operating at 120 kV with a FEI Eagle CCD (4k) camera. Particles were picked using DogPicker and 3D classification was done using Relion 3.0 (40, 41).
  • results [00308] Generation of monoclonal antibodies: After two vaccinations of BALB/c mice with recombinant RBD protein supplemented with poly I:C, murine hybridoma technology was used to generate hybridoma cell lines that secreted RBD-specific monoclonal antibodies (17–19). Fourteen unique hybridoma lines were isolated and picked that produced IgGs (Tables 1 and 2). Twelve monoclonal antibodies belonged to the IgG1 isotype, while two monoclonal antibodies were from the IgG2a subclass.
  • Table 1 [00310] Table 2: Characteristics of MAbs * ND, not detected [00311] All antibodies bind the RBD of SARS-CoV-2 and six mAbs can neutralize live virus: Once all antibodies were purified from hybridoma supernatant, a standard enzyme-linked immunosorbent assay (ELISA) was performed to assess binding of the monoclonal antibodies to the RBD of SARS-CoV-2 (Figure 1A), full spike of SARS-CoV-2 ( Figure 1B), and RBD of SARS-CoV-1 ( Figure 1C). All antibodies bound well to SARS-CoV-2 RBD and most had very low minimal binding concentrations (MBC).
  • ELISA enzyme-linked immunosorbent assay
  • KL-S-3A7 is extraordinarily low IC 50 values lower than 1 ⁇ g/ml.
  • Antibodies can lower viral titers in vivo in a mouse challenge model: To further study the biological functionality of these mAbs, all mAbs were tested in vivo. Hence, an animal model was utilized to test if antibodies are able to block viral entry and thus lower titers in the lung. Since mouse ACE2 does not facilitate entry of SARS-CoV-2, an adenovirus that expresses the human ACE2 gene was used to first transduce mice (20, 21).
  • the negative control used here was an irrelevant purified antibody, binding to influenza virus H10 hemagglutinin (18).
  • groups that received the six neutralizing mAbs had little to no virus in their lungs ( Figure 2B).
  • One mouse in the KL-S-2C3 group and one mouse in the KL-S-2F9 showed residual virus in the lungs which could be a caveat of animal model used. None of the non- neutralizing antibodies conferred any protective benefit and all of these mAbs belonged to the IgG1 isotype.
  • pathological analysis such as hematoxylin and eosin (H&E) staining
  • IHC immunohistochemistry
  • mice from all groups treated with antibodies displayed some pulmonary histopathological lesions of interstitial pneumonia (FIGs.3A-3B). This could be a result of the high dose (10 5 PFU per mouse) of SARS-CoV-2 used.
  • the group that received only the AdV-hACE2 exhibited some microscopic lesions of perivascular, peri-bronchiolar and alveolar inflammation and had much lower scores compared to the antibody groups that received AdV-hACE2 plus SARS-CoV-2 (FIGURE 6).
  • Histopathological lesions were uniformly absent in the mock group that received no treatment and were basically just na ⁇ ve mice.
  • Clinical scores were slightly higher for groups KL-S-1E10, KL-S-2A5 and KL-S-3A5. Both of these antibodies are non-neutralizing, but this could be a result of external variables in the experimental setup.
  • RBDs were expressed including N439K, Y453F, E484K, N501Y (B.1.1.7) and the RBDs of B.1.351 and P.1 and ELISAs were performed on them using the mAbs.
  • Such analysis can demonstrate the epitope of the antibody or the single amino acid that is crucial in its native state for binding.
  • the neutralizing mAbs and non-neutralizing mAbs are shown separately (FIG. 4A and FIG. 4B)
  • KL- S-1D2 maintained binding to all RBDs but lost complete binding to K487R RBD.
  • KL-S-2C3 bound at only 30% to the N487R RBD compared to wild-type RBD.
  • KL-S-1H12 lost a lot of binding to E484K, F486A, F490K and the B.1.351 RBD (FIG. 4A).
  • KL-S-1D11, KL-S-1F7, KL- S-2F9, KL-S-2G9 and KL-S-3A7 were able to bind all mutant RBDs at a level of 50% or even more compared to wild type RBD (FIG. 4A).
  • KL-S-1E10 and KL-S-2A1 lost binding to a large number of mutant RBDs (FIG. 4B).
  • the ability to bind all RBDs could be a function of antibody affinity which, when high, can allow the antibody to maintain its footprint.
  • neutralizing mAbs had comparable binding to both wild type and most mutant RBDs.
  • an anti-histidine antibody was used as a positive control.
  • Four mAbs maintain neutralizing activity to B.1.351 virus while all six mAbs neutralize B.1.1.7 virus: Since binding may not be directly related to neutralization, we wanted to assess if antibodies that were generated by vaccination of mice with wild type RBD can neutralize new variant viruses. These variant viruses carry mutations in the RBD and can escape neutralization by monoclonal antibodies easily if their native epitope has been disrupted (6, 16).
  • KL-S-1H12 showed much lower binding to E484K RBD as well as the B.1.351 RBD and this lower binding capability might be the reason for the loss of neutralization.
  • the IC50 value for KL-S-1F7 was 1.7 ⁇ g/ml for the wild-type virus, 1.4 ⁇ g/ml for the B.1.1.7 virus and 4.3 ⁇ g/ml for the B.1.351 virus.
  • the IC50 value for KL-S-2C3 was 1.1 ⁇ g/ml for the wild-type virus, 2.2 for the B.1.1.7 virus, and 5.5 ⁇ g/ml for the B.1.351 virus (FIG. 4C).
  • KLS-1F7 binds lower on the RBD to a similar epitope as S309 (FIG. 5D) (24).
  • the RBD of the spike protein of SARS-CoV-2 is relatively plastic and can tolerate extensive mutations, at least in vitro. The plasticity of the RBD is alarming because extensive changes in the RBD could reduce the efficacy of current vaccines and additional booster vaccinations with updated vaccines may be needed for protection in the future (15, 16). All 14 isolated mAbs were tested for binding to a whole panel of mutant RBDs.
  • KL-S-1D2 and KL-S-2C3 are both of the IgG2a subtype. While KL-S-1D2 showed the best in vitro neutralization of all isolated mAbs, which could cause this phenotype, KL-S-2C3’s in vitro activity was lower but still showed stronger activity in vivo than other mAbs. This could be seen as evidence that Fc-FcR interactions, especially engagement with activating FcRs, which is an important component of protection.
  • McCallum M Marco A, Lempp F, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Caroline Foo SY, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SPJ, Virgin HW, Corti D, Pizzuto MS, Veesler D. 2021.
  • N-terminal domain antigenic mapping reveals a site of vulnerability for SARS- CoV-2.
  • Rathnasinghe R Strohmeier S, Amanat F, Gillespie VL, Krammer F, Garcia-Sastre A, Coughlan L, Schotsaert M, Uccellini MB. 2020. Comparison of transgenic and adenovirus hACE2 mouse models for SARS-CoV-2 infection. Emerg Microbes Infect 9:2433–2445. 21. Amanat F, Strohmeier S, Rathnasinghe R, Schotsaert M, Coughlan L, Garcia-Sastre A, Krammer F. 2020.
  • Newcastle disease virus expressing the spike protein of SARS-CoV-2 as a live virus vaccine candidate.

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Abstract

L'invention concerne des anticorps qui se lient à la protéine de spicule du SARS-CoV-2 ou à un fragment de celle-ci (par exemple, le domaine de liaison au récepteur (RBD)), des cellules hôtes pour produire de tels anticorps, et des kits comprenant de tels anticorps. L'invention concerne également des compositions comprenant des anticorps qui se lient à la protéine de spicule du SARS-CoV-2 ou à un fragment de celle-ci (par exemple, le domaine de liaison au récepteur) et des méthodes d'utilisation de ces anticorps pour diagnostiquer, prévenir ou traiter une infection par le SARS-CoV-2, ou la COVID-19.
PCT/US2022/030993 2021-05-28 2022-05-26 Anticorps anti-sars-cov-2 et leurs utilisations WO2022251403A1 (fr)

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013040358A2 (fr) * 2011-09-14 2013-03-21 University Of Washington Through Its Center For Commercialization Procede et compositions pour la détection d'agr2
CN108948198A (zh) * 2018-07-18 2018-12-07 博奥信生物技术（南京）有限公司 抗人csf-1r单克隆抗体及其应用
US10975139B1 (en) * 2020-04-02 2021-04-13 Regeneron Pharmaceuticals, Inc. Anti-SARS-CoV-2-Spike glycoprotein antibodies and antigen-binding fragments

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013040358A2 (fr) * 2011-09-14 2013-03-21 University Of Washington Through Its Center For Commercialization Procede et compositions pour la détection d'agr2
CN108948198A (zh) * 2018-07-18 2018-12-07 博奥信生物技术（南京）有限公司 抗人csf-1r单克隆抗体及其应用
US10975139B1 (en) * 2020-04-02 2021-04-13 Regeneron Pharmaceuticals, Inc. Anti-SARS-CoV-2-Spike glycoprotein antibodies and antigen-binding fragments

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