WO2023079137A1 - Neutralizing anti-sars-cov-2 human antibodies - Google Patents

Neutralizing anti-sars-cov-2 human antibodies Download PDF

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WO2023079137A1
WO2023079137A1 PCT/EP2022/080965 EP2022080965W WO2023079137A1 WO 2023079137 A1 WO2023079137 A1 WO 2023079137A1 EP 2022080965 W EP2022080965 W EP 2022080965W WO 2023079137 A1 WO2023079137 A1 WO 2023079137A1
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antibody
seq
sars
antigen binding
binding fragment
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PCT/EP2022/080965
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French (fr)
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WO2023079137A9 (en
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Nick GEUKENS
Paul Declerck
Maya IMBRECHTS
Louanne AMPOFO
Wim Maes
Johan Neyts
Rana ABDELNABI
Hannah EECKHAUT
Nico Callewaert
Daria FIJALKOWSKA
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Katholieke Universiteit Leuven
Vib Vzw
Universiteit Gent
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Priority claimed from EP21206787.0A external-priority patent/EP4177266A1/en
Application filed by Katholieke Universiteit Leuven, Vib Vzw, Universiteit Gent filed Critical Katholieke Universiteit Leuven
Publication of WO2023079137A1 publication Critical patent/WO2023079137A1/en
Publication of WO2023079137A9 publication Critical patent/WO2023079137A9/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • 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
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • the invention relates to antibodies which are particularly suitable in the treatment of beta, delta, and omicron variant of COVID 19.
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • the spike protein of SARS-CoV-2 consists of an SI subunit that recognizes host cell receptors and an S2 subunit that promotes membrane fusion of virus and host cells.
  • the receptor binding domain Within the SI subunit, the receptor binding domain (RBD) is responsible for interaction with receptor angiotensin-converting enzyme 2 (ACE2) on host cells to mediate viral entry. Consequently, SARS-CoV-2 spike protein is the major target of neutralizing antibodies (Ab).
  • Antibodies can be elicited by natural infection and vaccination, or can be administered as recombinant monoclonal antibodies (mAbs) in a passive immunization strategy.
  • mAbs monoclonal antibodies
  • vaccines are essential tools to fight this pandemic
  • therapeutic mAbs play a crucial role as well, especially for (immune-compromised) individuals who may not generate a robust response to their vaccine, cannot be vaccinated, are at high risk for severe illness or are still awaiting their vaccine.
  • SARS-CoV-2 variants beta, gamma and delta escape from some of the currently available therapeutic mAbs.
  • REGN10933 i.e. one of the antibodies from the REGN-COV2 antibody cocktail
  • LY- CoV555 completely lost its activity against beta, gamma and delta. This demonstrates that several of the commercially available therapeutic mAbs lose their activity against the current SARS-CoV-2 variant.
  • SARS-CoV-2 omicron The latest SARS-CoV-2 variant of concern (VoC) B.1.1.529, designated omicron, was first reported to WHO from South Africa at the end of November 2021 and is rapidly spreading across many countries, replacing the already highly transmissible SARS- CoV-2 delta (B.1.617.2) VoC.
  • SARS-CoV-2 omicron has a large number of mutations compared to the pandemic founder, many of which are predicted to result in resistance towards the currently available neutralizing (therapeutic) antibodies, including those induced upon vaccination. The majority of currently available antibodies, by the end of December 2021, show a strongly reduced or no activity against the omicron variant.
  • Therapeutic monoclonal antibodies are an essential tool to combat COVID- 19 morbidity and mortality, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • mAbs have already received emergency use authorization either in the United States or South Korea.
  • SARS-CoV-2 variants escape some of these therapeutic mAbs.
  • PBMCs from convalescent patients and B cell receptor cloning we identified six mAbs, classified in four different epitope groups, that potently neutralize live SARS-CoV-2 Wuhan, alpha, beta, gamma and delta infection in vitro.
  • antibodies 3E6 and 3B8 potently cure infection with SARS-CoV-2 Wuhan, beta and delta in an in vivo hamster model when administered therapeutically at 5 mg/kg.
  • antibody 3B8 still reduced infectious viral titers after therapeutic administration at only 0.2 mg/kg, highlighting its superior potency.
  • our data mark 3B8 as a promising candidate to help fight COVID-19.
  • the 3B8 antibody binds to a novel yet unidentified specific epitope. This has unprecedented advantages in combination therapies whereby competition of different antibodies for the same antibody is avoided.
  • An antibody or antigen binding fragment thereof specifically binding to the trimeric spike protein of Wuhan Covid-SARS-2 and specifically binding to the RBD domain of all of Wuhan, alpha, beta, gamma, delta and omicron variant of Covid- SARS-2 spike protein, characterized in that: said antibody or antigen binding fragment thereof has an IC50 in a SARS-CoV-2 pseudovirus infection lower than 1 nm, lower than 0,8 nm, lower than 0,6 nm, lower than 0,4 nm or lower than 0,2 nm in a SARS-CoV-2 pseudovirus infection, and in that said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 500 pM, less than 400 pM, less than 300 pM, less than 200 pM, less than 100 pM or less than 50 pM, and in that said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with
  • the antibody or antigen binding fragment thereof according to any one of statements 1 to 3, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 24.
  • variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GVIVSRNY [SEQ ID NO: 6], IYSGGST [SEQ ID NO: 7] and ARWGPNYYGSGSDHYNSYGMDV [SEQ ID NO: 8] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGVSSSS [SEQ ID NO: 9], GAS and QQSGSSPQYT[SEQ ID NO: 10].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 26 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 28.
  • variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GFTFDDYA[SEQ ID NO: 11], VSWNSGTI [SEQ ID NO: 12] and AKDVSVYRFREQSYGMDV [SEQ ID NO: 13] and comprising - a variable light chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence SSDIGGYNF [SEQ ID NO: 14], EVT, and SSYTSSSLVV [SEQ ID NO: 15].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 30 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 32.
  • the antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GFSLDDYG [SEQ ID NO: 16], ISWNSGDR [SEQ ID NO: 17], and AKGSGAHYDIMTGARLDY [SEQ ID NO: 18] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSITNY [SEQ ID NO: 19], AAS, CDR 3: QQSYSTPWT [SEQ ID NO: 20].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 34 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 36.
  • the antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYSFTSHW [SEQ ID. NO: 37], IFPGDSKT [SEQ ID. NO: 38], and ARPNRYYDDSGNYDGSYYFDY [SEQ ID. NO: 39], a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSVNTN [SEQ ID. NO: 40], GAF, and QQYNNWPPAWT [SEQ ID. NO: 41].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 58 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 60.
  • the antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTTYY [SEQ ID. NO: 42], INSSGGST[SEQ ID. NO: 43], and ATSGWYRGAFDY [SEQ ID. NO: 44] a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SGSIDNNY [SEQ ID. NO: 45], EDN, and QSIDSNSWV [SEQ ID. NO: 46].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 62 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 64.
  • the antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGSLSVYY [SEQ ID. NO: 47], INHSGST [SEQ ID. NO: 48], and ARTSLHTWNPFDY [SEQ ID. NO: 49], and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGISSY [SEQ ID. NO: 50], AAS, and QQLNNYPLT [SEQ ID. NO: 51].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 66 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 68.
  • the antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGTFSNYA [SEQ ID. NO: 52], IIAIFGTP [SEQ ID. NO: 53], and ARRSTILERLPRHYYGMDV [SEQ ID. NO: 54], and a variable light chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence QSLLHSNGNIY [SEQ ID. NO: 55], LGS and MQTLQTLRAT [SEQ ID. NO: 56].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 70 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 72.
  • variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising a variable light chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 24.
  • the antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual comprising a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GVIVSRNY [SEQ ID NO: 6], IYSGGST [SEQ ID NO: 7] and ARWGPNYYGSGSDHYNSYGMDV [SEQ ID NO: 8] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGVSSSS [SEQ ID NO: 9], GAS and QQSGSSPQYT[SEQ ID NO: 10]
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 26 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 28.
  • the antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYSFTSHW [SEQ ID. NO: 37], IFPGDSKT [SEQ ID. NO: 38], and ARPNRYYDDSGNYDGSYYFDY [SEQ ID. NO: 39], a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSVNTN [SEQ ID. NO: 40], GAF, and QQYNNWPPAWT [SEQ ID. NO: 41].
  • a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYSFTSHW [SEQ ID. NO: 37], IFPGDSKT [SEQ ID. NO: 38], and ARPNRYYDDSGNYDGSY
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 58 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 60.
  • the antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTTYY [SEQ ID. NO: 42], INSSGGST[SEQ ID. NO: 43], and ATSGWYRGAFDY [SEQ ID. NO: 44] a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SGSIDNNY [SEQ ID. NO: 45], EDN, and QSIDSNSWV [SEQ ID. NO: 46].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 62 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 64.
  • the antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGSLSVYY [SEQ ID. NO: 47], INHSGST [SEQ ID. NO: 48], and ARTSLHTWNPFDY [SEQ ID. NO: 49], and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGISSY [SEQ ID. NO: 50], AAS, and QQLNNYPLT [SEQ ID. NO: 51].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 66 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 68.
  • the antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising: a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGTFSNYA [SEQ ID. NO: 52], IIAIFGTP [SEQ ID. NO: 53], and ARRSTILERLPRHYYGMDV [SEQ ID. NO: 54], and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSLLHSNGNIY [SEQ ID. NO: 55], LGS and MQTLQTLRAT [SEQ ID. NO: 56].
  • variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 70 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 72.
  • a polynucleotide comprising a sequence encoding the antibody or antigen binding fragment thereof according to any one of statements 1 to 20, for use in the treatment and prevention of COVID 19.
  • a polynucleotide can be a single polynucleotide strand comprising both the sequences encoding the light and heavy chain or fragments of these.
  • polynucleotide strands e.g. plasmids
  • one polynucleotide expresses the light chain or fragments thereof
  • a second polynucleotide expresses the heavy chain or fragments thereof.
  • polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 29 and SEQ ID NO: 31.
  • polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 57 and SEQ ID NO: 59.
  • polynucleotide for use in the treatment or prevention of COVID 19 in an individual comprising the sequence of SEQ ID NO: 61 and SEQ ID NO: 63.
  • polynucleotide for use in the treatment or prevention of COVID 19 in an individual comprising the sequence of SEQ ID NO: 65 and SEQ ID NO: 67.
  • polynucleotide for use in the treatment or prevention of COVID 19 in an individual comprising the sequence of SEQ ID NO: 69 and SEQ ID NO: 71.
  • the antibody or antigen binding fragment thereof according to statement 48 or 49, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,4, wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a K D of less than 400 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a K D of less than 300 pM.
  • the antibody or antigen binding fragment thereof according to any one of statements 48 to 50, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,05 and wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a K D of less than 250 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a K D of less than 100 pM.
  • the antibody or antigen binding fragment thereof according to any one of statements 48 to 53, which is an antibody or antigen binding fragment there of comprising:
  • variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising
  • variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
  • variable domain comprises a VH region that has outside the CDR regions at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 24.
  • the antibody or antigen binding fragment thereof according to any one of statements 48 to 56, for use in the treatment and prevention of the beta, delta or omicron variant of COVID 19 in an individual.
  • variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
  • variable domain comprises a VH region that has outside the CDR regions at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 24.
  • a polynucleotide comprising a sequence encoding the antibody or antigen binding fragment thereof according to statement 57, for use in the treatment and prevention of the beta, delta or omicron variant COVID 19.
  • polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statement 61 comprising the sequence of SEQ ID NO: 21 and SEQ ID NO: 23.
  • Figure 1 Neutralizing activity of top 8 most potent antibodies. Percentage neutralizing activity, measured via a SARS-CoV-2 D614G VSV pseudotyped assay, is given at different concentrations for the top 8 antibodies. Symbols show mean and standard deviation of 3 replicates, graph is representative for 2 independent experiments.
  • FIG. 2 in vitro neutralization of infection with live SARS-CoV-2 variants. Concentration-dependent neutralizing activity (% neutralization) was measured via CPENT assay using SARS-CoV-2 Wuhan, alpha, beta and gamma (A-D) or via PRNT assay using SARS-CoV-2 delta (E) for the 8 selected antibodies. Symbols show mean and standard deviation (only upper bar is shown for clarity) of 3 (A-D) or 2 (E) replicates.
  • Figure 3 Epitope specificity of top 8 mAbs.
  • Figure 4 Treatment of SARS-CoV-2 Wuhan infection by antibodies 3B8, 3E6, 2B2 and 1C1 (5 mg/kg) in hamsters.
  • Figure 7 gating strategy for selection of RBD-specific B cells from PBMCs of patients K-COV19-901.
  • Lymphocytes were selected based on FSC and SSC, followed by selection of single cells and live cells (Zombia Aqua negative).
  • B cells were selected as CD19+ CD3- cells and evaluated for RBD surface staining using PE as fluorophore. Fully stained sample is shown in panel A, fluorescence minus one (FMO) control for RBD fluorescence is shown in panel B.
  • FMO fluorescence minus one
  • Figure 9 Neutralizing activity of mAbs against SARS-CoV-2 delta and omicron VoC.
  • Percentage neutralizing activity measured via a SARS-CoV-2 delta (A) or omicron (B) VSV pseudotyped assay, at different concentrations of the respective mAbs tested. Symbols show mean and standard deviation of 3 replicates, measured in one experiment.
  • Figure 10 Escape plot for 3B8 ("stacked logo") with the positions V445, G446, P499 and T500 identified as crucial residues for 3B8 binding.
  • Figure 11 Summary of the 7 RBD-directed communities based on antibody competition profiles and interpreted by previous epitope studies adapted from Hastie et al 2021 ).
  • Figure 12 The antigenic landscape of the SARS-CoV-2 RBD can be divided into seven binding communities.
  • Figure 13 Escape plot for 3B8 ("stacked logo") with the positions V445, G446, P499 and T500 identified as crucial residues for 3B8 binding.
  • Figure 14 DNA and protein sequence of heavy and light chain variable regions.
  • antibody 3B8 is an ultrapotent therapeutic antibody, with treatment at a dose of 1 mg/kg resulting in undetectable infectious viral titers. Even when administered at 0.2 mg/kg, viral replication was reduced, with median infectious viral titers of the treatment group being 67 times lower compared to the isotype control group. This further highlights the potency of antibody 3B8 in a therapeutic setting [Andreano et al. Cell 184, 1821-1835. el6 (2021)]. High potencies are crucial to decrease cost of goods, enable sustainable manufacturability and increase the number of doses produced annually, and may therefore also facilitate the availability of therapeutic mAbs to low- and middle-income countries.
  • K D values observed for our antibodies were consistently between 3- and 200-fold lower than values reported for marketed antibodies of Vir Biotechnology, Regeneron Pharmaceuticals or Eli Lilly.
  • K D values of REGN-COV2 antibodies 10933 and 10987 in our own experiments for benchmarking purposes K D values were similar to values observed for our mAbs (data not shown).
  • antibodies 3B8 and 3E6 each performed equally well as monotherapy (when administered at 5 mg/kg) to treat SARS-CoV-2 infection beta and delta in hamsters when compared to the marketed REGN-COV2 antibody cocktail, which consists of two different antibodies [FDA Fact Sheet for Health Care Providers Emergency Use Authorization Of REGEN-COV. (2021).].
  • therapeutic efficacy of antibody 3B8 in vivo at a dose of only 0.2 mg/kg.
  • no in vivo therapeutic mAb efficacy data have been published yet for SARS-CoV-2 delta infection in hamsters.
  • REGN-COV2 only for REGN-COV2 some therapeutic efficacy was reported in hamsters at such low mAb doses, although after infection of hamsters with SARS-CoV-2 Wuhan and using different readouts 32 .
  • the present invention discloses the in vitro neutralizing activity against SARS-CoV-2 delta and omicron.
  • the results reported here for neutralization of SARS-CoV-2 delta are in line with those previously described using another assay format (VSV pseudotyped assay versus plaque reduction assay respectively), thereby indicating a high reliability of the current data.
  • the phrases “specifically binds to” refers to a binding reaction which is determinative of the presence of a target protein in the presence of a heterogeneous population of proteins and other biologies.
  • the specified binding moieties bind preferentially to a particular target protein and do not bind in a significant amount to other components present in a test sample. Specific binding to a target protein under such conditions may require a binding moiety that is selected for its specificity for a particular target antigen.
  • a variety of assay formats may be used to select ligands that are specifically reactive with a particular protein, for example, solid-phase ELISA immunoassays, or immunoprecipitation.
  • a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 times background.
  • antibodies and antibody fragments of the invention preferentially bind to the RBD domain of the spike protein SI subunit of Sars-Cov-2, whereby by “preferentially binding”, “preferentially recognizing” or “preferentially reacting with” is meant that the antibodies or antibody fragments show greater binding capacity for RBD domain of the spike protein SI subunit of Sars-Cov-2 as compared to any other antigen.
  • the binding capacity of an antibody or antibody fragment to an antigen is reflective of its affinity and/or avidity for that antigen.
  • Binding specificity can be expressed by association and dissociation constants as determined by ELISA or BIACORE.
  • antibody and “antibodies” are recognized in the art and refer to proteins also known as immunoglobulins that bind to antigens. It is to be understood that these terms encompass conventional vertebrate antibodies like IgA, IgD, IgE, IgG, IgM, IgT, IgX and IgY, composed of at least two heavy and two light chains, as well as antibodies only composed of two heavy chains (VHH antibodies, IgNAR, heavychain antibodies, single-domain antibodies or nanobodies), and single-chain antibodies. In the case of conventional antibodies, the antigen binding sites are contributed to by the variable domains of both the heavy and light chains (VH and VL).
  • variable domain refers to the part or domain of an antibody which is partially or fully responsible for antigen binding.
  • variable domains will be amino acid sequences that essentially consist of 4 framework regions (FRI to FR4 respectively) and 3 complementarity determining regions (CDR1 to CDR3 respectively), or any suitable fragment of such an amino acid sequence which usually contains at least some of the amino acid residues that form at least one of the CDR's.
  • Such variable domains and fragments are most preferably such that they comprise an immunoglobulin fold or are capable for forming, under suitable conditions, an immunoglobulin fold.
  • Each CDR may contribute to a greater or lesser extent to antigen binding by the antibody.
  • Single domain antibodies or heavy-chain antibodies can be found in camelids and sharks, and each of the antigen-binding sites of these antibodies is formed by a single heavy chain variable domain (VHH) only. Therefore, only three CDRs contribute to a greater or lesser extent to each antigen-binding site.
  • Single chain antibodies (scFv) are derived from conventional antibodies by translational fusion of the VH and VL domains, separated by a flexible linker, into a single antigen-binding domain. Framework sequences of an antibody may be altered without altering the antigenic specificity of the antibody, or in order to change the binding affinity of the antibody. Furthermore, conventional antibodies may switch classes or isotypes without substantially affecting antigen-binding characteristics.
  • CDR complementarity determining region
  • VH and VL variable regions of either H (heavy) or L (light) chains (abbreviated as VH and VL, respectively) and contains the amino acid sequences capable of specifically binding to antigenic targets.
  • CDR regions account for the specificity of the antibody for a particular antigenic determinant structure. Such regions are also referred to as “hypervariable regions.”
  • the CDRs represent non-contiguous stretches of amino acids within the variable regions but, regardless of species, the positional locations of these critical amino acid sequences within the variable heavy and light chain regions have been found to have similar locations within the amino acid sequences of the variable chains.
  • the accepted CDR regions and variable domains of an antibody are known to the skilled person and have been described by Padlan et al. (1995) FASEB J. 9, 133-139.
  • antibody fragment is meant a fragment of an antibody that largely retains antigen-binding capacity of the antibody from which it is derived. Therefore, an antibody fragment of the invention is capable of preferentially binding to RBD domain of the spike protein SI subunit of Sars-Cov-2. Antigen-binding capacity is determined by the variable domain or domains, more particularly by 1, 2, 3, 4, 5 or 6 CDRs located in the VH and/or VL domains in the case of conventional and singlechain antibodies, and 1, 2 or 3 CDRs in the case of single-domain antibodies. Preferred antibody fragments of the invention therefore comprise antigen-binding sites comprising 1, 2, 3, 4, 5 or 6 CDRs.
  • Two or more CDRs may be physically separated from each other by connecting regions to provide a framework structure for the CDRs.
  • More preferred antibody fragments of the invention comprise antigenbinding sites comprising 1 or 2 variable domains. Examples of antibody fragments are well-known to the skilled person and include the monovalent antigen-binding fragments (Fab), bivalent F(ab')2 fragments, Fv fragments (e.g. single chain antibodies scFv), miniaturized antibodies, single-domain antibody fragments like nanobodies (Nelson (2010) mAbs 2, 77-83).
  • Antibody fragments of the invention may be obtained by enzymatic or chemical proteolysis, or by recombinant DNA technology techniques well known to the skilled person.
  • Antibodies and antibody fragments of the invention may be further chemically conjugated, non-covalently bound, or translationally fused to other proteins.
  • Single chain antibodies scFv are an example of translational fusion between a VH and a VL domain.
  • Further examples are albumin-conjugated antibodies or antibody fragments, bivalent diabodies, and monospecific and bispecific tandem svFcs (Nelson et al. cited above).
  • a single-chain antibody (also referred to as "scFv") can be prepared by linking a heavy chain V region and a light chain V region of an antibody.
  • Methods for preparing single-chain antibodies are known in the art (US5,455,030).
  • the heavy chain V region and the light chain V region are linked together via a linker, preferably, a polypeptide linker.
  • the heavy chain V region and the light chain V region in a scFv may be derived from the same antibody, or from different antibodies.
  • an “Fv” fragment is the smallest antibody fragment, and contains a complete antigen recognition site and a binding site.
  • This region is a dimer (VH-VL dimer) wherein the variable regions of each of the heavy chain and light chain are strongly connected by a noncovalent bond.
  • the three CDRs of each of the variable regions interact with each other to form an antigen binding site on the surface of the VH-VL dimer.
  • a total of six CDRs from the heavy and light chains function together as an antibody's antigen-binding site.
  • variable region or a half Fv, which contains only three antigen-specific CDRs
  • a preferred antibody fragment of the present invention is an Fv fragment, but is not limited thereto.
  • Such an antibody fragment may be a polypeptide which comprises an antibody fragment of heavy or light chain CDRs which are conserved, and which can recognize and bind its antigen.
  • a Fab fragment also contains a light chain constant region and heavy chain constant region (CHI).
  • CHI heavy chain constant region
  • a Fab fragment also contains a light chain constant region and heavy chain constant region (CHI).
  • CHI heavy chain constant region
  • papain digestion of an antibody produces the two kinds of fragments: an antigen-binding fragment, called a Fab fragment, containing the variable regions of a heavy chain and light chain, which serve as a single antigen-binding domain; and the remaining portion, which is called an "Fc" because it is readily crystallized.
  • a Fab' fragment is different from a Fab fragment in that a Fab' fragment also has several residues derived from the carboxyl terminus of a heavy chain CHI region, which contains one or more cysteine residues from the hinge region of an antibody.
  • a Fab' fragment is, however, structurally equivalent to Fab in that both are antigenbinding fragments which comprise the variable regions of a heavy chain and light chain, which serve as a single antigen-binding domain.
  • an antigen-binding fragment comprising the variable regions of a heavy chain and light chain which serve as a single antigen-binding domain, and which is equivalent to that obtained by papain digestion, is referred to as a "Fab-like antibody", even when it is not identical to an antibody fragment produced by protease digestion.
  • Fab'-SH is Fab' with one or more cysteine residues having free thiol groups in its constant region.
  • a F(ab') fragment is produced by cleaving the disulfide bond between the cysteine residues in the hinge region of F(ab')2.
  • Other chemically crosslinked antibody fragments are also known to those skilled in the art.
  • Pepsin digestion of an antibody yields two fragments; one is a F(ab')2 fragment which comprises two antigen-binding domains and can cross-react with antigens, and the other is the remaining fragment (referred to as pFc').
  • an antibody fragment equivalent to that obtained by pepsin digestion is referred to as a "F(ab')2-like antibody" when it comprises two antigen-binding domains and can cross-react with antigens.
  • Such antibody fragments can also be produced, for example, by genetic engineering.
  • Such antibody fragments can also be isolated, for example, from the antibody phage library described above.
  • F(ab')2-SH fragments can be recovered directly from hosts, such as E. coli, and then allowed to form F(ab')2 fragments by chemical crosslinking.
  • Antibodies and antibody fragments of the invention may be further modified. Examples of such modifications include the addition of detectable enzymatic, fluorescent, luminescent, or radioactive marker groups or molecules that act in detection such as streptavidin. Other examples include the chemical modification to alter the half-life of antibodies and antibody fragments, such as PEGylation. Still other examples add effector moieties to antibodies and antibody fragments, such as toxins, radioisotopes, enzymes, cytokines, and antigens (Nelson (2010) mAbs 2, 77-83). Antibodies or antibody fragments may be further modified into an antibody-derived scaffold or antibody-like scaffolds that largely retains antigen-binding capacity of the antibody or antibody fragments from which it is derived.
  • antibody- derived scaffolds or antibody-like scaffolds are domain antibodies (dAb) that selectively or preferentially bind the same epitope as a natural antibody, for instance dAb with fully human frameworks, for instance dAb fused to a human Fc domain or for instance nanobodies engineered in a molecule that has an IgG-like circulating half-life in humans or antibody fragments with retained antigen-binding capacity or domain antibody with active scaffolds for controlled and cell delivery.
  • dAb domain antibodies
  • Single domain antibodies can be engineered into antibody like fragments.
  • Single domain antibodies are antibodies whose complementary determining regions are part of a single domain polypeptide. Examples include, but are not limited to, heavy chain antibodies, antibodies naturally devoid of light chains, single domain antibodies derived from conventional 4-chain antibodies, engineered antibodies and single domain scaffolds other than those derived from antibodies.
  • Single domain antibodies may be any of the art, or any future single domain antibodies.
  • Single domain antibodies may be derived from any species including, but not limited to mouse, human, camel, llama, goat, rabbit, bovine.
  • a single domain antibody as used herein is a naturally occurring single domain antibody known as heavy chain antibody devoid of light chains. Such single domain antibodies are disclosed in WO9404678 for example.
  • variable domain derived from a heavy chain antibody naturally devoid of light chain is known herein as a VHH or nanobody to distinguish it from the conventional VH of four chain immunoglobulins.
  • a VHH molecule can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, alpaca and guanaco or Elasmobranchii species for instance skates, rays (batoidea), and sharks (selachii).
  • Other species besides Camelidae may produce heavy chain antibodies naturally devoid of light chain; such VHHs are within the scope of the invention.
  • the singlechain polypeptide may be produced by various methods well known in the art such as genetic engineering technique and chemical synthesis.
  • the genetic engineering technique includes constructing a replicable cloning vector or expression vector, transforming the host cell with the vector, culturing the transformed host cell to express the nucleic acid in it, collecting and purifying the single-chain polypeptide.
  • the vector usually comprises the nucleic acid encoding one of the two single-chain polypeptides constituting the diabody-type bispecific antibody according to the present invention. In such case, the resulting two kinds of the vectors are preferably introduced into the same host cell.
  • the two kinds of nucleic acid encoding the different single-chain polypeptides from each other may be comprised in the same vector.
  • the term "replicable expression vector” or "expression vector” as used herein refers to a piece of DNA (usually double-stranded) that may comprise a fragment of a foreign DNA fragment inserted therein.
  • the foreign DNA is also defined as a "heterologous DNA", which cannot be found naturally in a host cell in interest.
  • the vector is used to carry or convey the foreign or heterologous DNA into an appropriate host cell. Once the vector is introduced into the host cell, it may be replicated independently from a chromosomal DNA of the host cell to produce copies of the vector and foreign DNA inserted therein.
  • the vector also comprises elements essential for translating the foreign DNA into a polypeptide so that the polypeptide molecules encoded by the foreign DNA will be synthesized very quickly.
  • the above vector means a DNA construct comprising an appropriate control sequence and DNA sequence that are operably linked together (i.e., linked together so that the foreign DNA can be expressed).
  • the control sequence includes a promoter for transcription, an optional operator sequence to regulate the transcription, a sequence encoding an appropriate mRNA ribosome-biding site, an enhancer, a polyadenylation sequence, and a sequence controlling the termination of transcription and translation.
  • the vector may further comprise various sequences known in the art, such as a restriction enzyme cleaving site, a marker gene (selection gene) such as a drugresistant gene, a signal sequence, and a leader sequence. These sequences and elements may be optionally selected by those skilled in the art depending on the kinds of the foreign DNA and host cell, and conditions of culture medium.
  • the vector may be in any form such as a plasmid, phage particle, or just simply genomic insert. Once the appropriate host cell is transformed with the vector, the vector will be replicated or function independently from the genome of the host cell, or the vector will alternatively be integrated into the genome of the cell. Any cell known in the art may be used as the host cell, for example, there may be mentioned procaryotic cells such as including E. coli, eucaryotic cells such as mammalian cells such Chinese hamster ovary (CHO) cell and human cells, yeast, and insect cells.
  • procaryotic cells such as including E. coli
  • eucaryotic cells such as mammalian cells such Chinese hamster ovary (CHO) cell and human cells, yeast, and insect cells.
  • the single-chain polypeptide obtained by the expression in the host cell is usually secreted and collected from the culture medium, it may be also collected from cell lysate when it is directly expressed without a secretion signal.
  • the singlechain polypeptide may be released from the membrane with an appropriate surfactant such as Triton-XIOO.
  • Purification of the polypeptide may be carried out by any method known to those skilled in the art such as centrifugation, hydroxyapatite chromatography, gel electrophoresis, dialysis, separation on ion-exchange chromatography, ethanol precipitation, reverse phase HPLC, silica chromatography, heparin-sepharose chromatography, anion-or cation-resin chromatography such as polyaspartic acid column, chromato-focusing, SDS-PAGE, precipitation with ammonium sulfate, and affinity chromatography.
  • the affinity chromatography which utilizes affinity with a peptide tag of the single-chain polypeptide, is one of the preferred purification techniques with a high efficiency.
  • the polypeptide is preferably purified after being solubilized and denatured.
  • the solubilization treatment may be carried out with the use of any agent known in the art, including alcohol such ethanol, a dissolving agent such as guanidine hydrochloride and urea.
  • the antibody-like fragments according to the present invention are produced by assembling the single-chain polypeptides, eventually on a scaffold, and separating and collecting the thus formed antibody-like fragments.
  • Assembling treatment brings the single-chain polypeptides back in an appropriate spatial arrangement in which a desired biological activity is shown. Thus, since this treatment brings the polypeptides or domains back into an assembling state, it may be considered “re-assembling.” It may be also called “re-constitution” or “refolding” in view of gaining the desired biological activity.
  • the assembling treatment may be carried out by any method known in the art preferably by gradually lowering the concentration of a denaturing agent such as guanidine hydrochloride in a solution comprising the single-chain polypeptide by means of dialysis.
  • a denaturing agent such as guanidine hydrochloride
  • an anti-coagulant or oxidizing agent may be optionally added in a reaction system in order to promote the oxidation.
  • the separation and collection of the formed antibody-like fragment may be done by any method known in the art as well.
  • VHHs are heavy chain variable domains derived from immunoglobulins naturally devoid of light chains such as those derived from Camelidae as described in WO9404678 (and referred to hereinafter as VHH domains or nanobodies).
  • VHH molecules are about lOx smaller than IgG molecules. They are single polypeptides and very stable, resisting extreme pH and temperature conditions. Moreover, they are resistant to the action of proteases which is not the case for conventional antibodies. Furthermore, in vitro expression of VHHs produces high yield, properly folded functional VHHs.
  • antibodies generated in Camelids will recognize epitopes other than those recognised by antibodies generated in vitro through the use of antibody libraries or via immunization of mammals other than Camelids or Elasmobranchii species (WO 9749805).
  • anti-albumin VHH's may interact in a more efficient way with serum albumin which is known to be a carrier protein.
  • serum albumin which is known to be a carrier protein.
  • some of the epitopes of serum albumin may be inaccessible by bound proteins, peptides and small chemical compounds. Since VHH's are known to bind into 'unusual' or non- conventional epitopes such as cavities (WO9749805), the affinity of such VHH's to circulating albumin may be increased.
  • the antibodies and antibody fragments of the invention are humanized.
  • Antibody fragments derived from an antibody of the invention can be fused to the Fc region of a human antibody, in order to obtain humanized antibodies and antibody fragments.
  • Humanized antibodies or antibody fragments can also be obtained by grafting of one or more CDRs or only their specificity-determining residues (SDRs), optionally together with one or more framework residues important for optimal CDR functionality, of a non-human antibody having the desired antigenbinding specificity, into framework polypeptide sequences of a human antibody or 1 antibody fragment, or even into a universal humanized nanobody scaffold.
  • SDRs specificity-determining residues
  • humanized antibody as used herein means a human immunoglobulin (a recipient antibody) in which at least part of the residues of complementary- determining region (CDR) is replaced with residues derived from the CDR of a nonhuman animal antibody (a donor antibody) that has a desired specificity, affinity and capability, such as those of mouse, rat, and rabbit.
  • CDR complementary- determining region
  • a nonhuman animal antibody a donor antibody
  • the residue(s) of a Fv framework (FR) in the human immunoglobulin is replaced with residue(s) of the corresponding non-human antibody.
  • the humanized antibody may further comprise a residue that is not found in the recipient antibody or the introduced CDR or framework.
  • the antibody fragments of the present invention can also be generated using various phage display methods known in the art.
  • phage display methods functional antibody domains are displayed on the surface of phage particles which carry the polynucleotide sequences encoding them.
  • phage can be utilized to display epitope-binding domains expressed from a repertoire or combinatorial antibody library (e.g., human or murine).
  • Phage expressing an epitope-binding domain that binds the antigen of interest can be selected or identified with antigen, e.g., using labeled antigen bound or captured to a solid surface or bead.
  • Phages used in these methods are typically filamentous phage including fd and M13 binding domains expressed from phage with antigen-binding antibody domains recombinantly fused to either the phage gene III or gene VIII protein.
  • Examples of phage display methods that can be used to make the antibodies or antibody fragments of the present invention include those disclosed in Persic et al. Gene 187, 9-18 (1997).
  • the regions of the phage encoding the fragments can be isolated and used to generate the epitope-binding fragments through expression in a chosen host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, using recombinant DNA technology.
  • a chosen host including mammalian cells, insect cells, plant cells, yeast, and bacteria
  • techniques to recombinantly produce antigen-binding fragments can also be employed using methods known in the art such as those disclosed in Sawai et al. AJRI, 34, 2634 (1995). Examples of techniques which can be used to produce single-chain Fvs and antibodies include those described in Shu et al. PNAS 90, 7995-7999 (1993).
  • Changes may be made to the residues that comprise the CDRs without interfering with the ability of the antibody to recognize and bind its cognate epitope. For example, changes that do not affect epitope recognition, yet increase the binding affinity of the antibody for the epitope may be made.
  • Several studies have surveyed the effects of introducing one or more amino acid changes at various positions in the sequence of an antibody, based on the knowledge of the primary antibody sequence, on its properties such as binding and level of expression [Rader et al., Proc Natl Acad Sci U.S.A. 95, 8910-8915 (1998)].
  • altered versions of the antibody have been generated by changing the sequences of the encoding genes in the CDR1, CDR2, CDR3, or framework regions, using methods such as oligonucleotide-mediated site-directed mutagenesis, cassette mutagenesis, error-prone PCR, DNA shuffling, or mutator-strains of E. coli (Vaughan et al. Nat Biotechnol. 16, 535-539 (1998)).
  • methods of changing the sequence of the antibody have resulted in improved affinities of the resulting antibodies [e.g. Short et al. J Biol Chem. 277, 16365-16370 (2002)].
  • the antibody of the invention is monoclonal.
  • the term "monoclonal antibody” is well recognized in the art and refers to an antibody or a homogenous population of antibodies that is derived from a single clone. Individual antibodies from a monoclonal antibody population are essentially identical, in that minor naturally occurring mutations may be present. Antibodies from a monoclonal antibody population show a homogenous binding specificity and affinity for a particular epitope.
  • percentage identity or percent sequence identity between two or more amino acid sequences or two or more nucleotide sequences refers to the ratio, expressed in %, of : the number of amino acids or nucleotides in an optimal alignment of the amino acid sequences or nucleotide sequences that are identical in both sequences (i.e. match), to the length of the alignment, i.e. the number of aligned positions, including gaps if any.
  • nucleic acid is intended to include DNA molecules and RNA molecules.
  • a nucleic acid can be single-stranded or double-stranded.
  • the nucleic acids of the invention are present in whole cells, in a cell lysate, or in a partially purified or substantially pure form.
  • a nucleic acid is "isolated” or “rendered substantially pure” when purified away from other cellular components or other contaminants, e.g., other cellular nucleic acids or proteins, by standard techniques, including alkaline/SDS treatment, CsCI banding, column chromatography, agarose gel electrophoresis and others well known in the art. see, e.g., Sambrook, Tijssen and Ausubel.
  • nucleic acid sequences of the invention and other nucleic acids used to practice this invention may be isolated from a variety of sources, genetically engineered, amplified, and/or expressed recombinantly. Any recombinant expression system can be used, including, in addition to bacterial, e.g., yeast, insect or mammalian systems. Alternatively, these nucleic acids can be chemically synthesized in vitro. Techniques for the manipulation of nucleic acids, such as, e.g., subcloning into expression vectors, labeling probes, sequencing, and hybridization are well described in the scientific and patent literature, see, e.g., Sambrook, Tijssen and Ausubel.
  • Nucleic acids can be analyzed and quantified by any of a number of general means well known to those of skill in the art. These include, e.g., analytical biochemical methods such as NMR, spectrophotometry, radiography, electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), and hyperdiffusion chromatography, various immunological methods, such as fluid or gel precipition reactions, immunodiffusion (single or double), immunoelectrophoresis, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, Southern analysis, Northern analysis, dot-blot analysis, gel electrophoresis (e.g., SDS-PAGE), RT-PCR, quantitative PCR, other nucleic acid or target or signal amplification methods, radiolabeling, scintillation counting, and affinity chromatography.
  • analytical biochemical methods such as NMR, spect
  • nucleic acid compositions of the present invention while often in a native sequence (except for modified restriction sites and the like), from either cDNA, genomic or mixtures may be mutated, thereof in accordance with standard techniques to provide gene sequences. For coding sequences, these mutations, may affect amino acid sequence as desired.
  • DNA sequences substantially homologous to or derived from such sequences described herein are contemplated (where "derived" indicates that a sequence is identical or modified from another sequence).
  • EXAMPLE 1 Identification and characterization of anti-SARS-CoV-2 antibodies from convalescent COVID-19 patients
  • Table 1 overview of RBD-binding titers and neutralizing antibody titers in serum, and percentage RBD-positive B cells in PBMCs from 26 convalescent COVID-19 patients
  • Patient K-COV19-901 having both a high titer of neutralizing antibodies and a high number of RBD-specific B cells, was selected for the isolation of individual RBD- specific B cells via fluorescence-activated cell sorting (FACS), using biotinylated RBD (Wuhan isolate) combined with streptavidin-PE as bait (Figure 7).
  • FACS fluorescence-activated cell sorting
  • VSV vesicular stomatitis virus
  • D614G SARS-CoV-2 spike protein
  • IC50 half-maximal 50% inhibitory concentration
  • Table 2 Overview of antigen binding, affinity and neutralizing capacity of 20 selected antibodies.
  • RBD antigens bearing the single mutations E484K, E484Q, N501Y and L452R present - alone or combined - in multiple SARS-CoV-2 variants (i.e. alpha, beta, gamma, delta and others), as well as RBD antigens bearing the double mutation E484Q, L452R or triple mutation K417N, E484K, N501Y, as present in SARS-CoV-2 variants kappa and beta respectively [CDC. SARS-CoV-2 Variant Classifications and Definitions.
  • RBD mutations N439K described as an antibody evasion mutant [Thomson et al. Cell 184, 1171-1187. e20 (2021); Chen et al. J. Mol. Biol. 433, (2021); Sanyaolu et al. Ther. Adv. Vaccines 8, 1-10 (2021)], and RBD Y453F, originating from Danish mink farms and a potential neutralization resistance mutation [Lassauniere et al. Front. Microbiol. 12, 1-9 (2021); Baum et al. Science 369, 1014-1018 (2020)], were evaluated (an overview of the analyzed RBD single mutations and their presence in SARS-CoV-2 variants is given in Table 3).
  • Table 3 overview of single RBD mutants used in this study and their presence in different SARS-CoV-2 variants of concern, variants of interest, variants under monitoring or de-escalated variants. Information retrieved from European Centre for Disease Prevention and Control (https://www.ecdc.europa.eu/en/covid-19/variants- concern)
  • SARS-CoV-2 variants were evaluated in a cytopathic effect neutralization test (CPENT) using live SARS-CoV-2 Wuhan, alpha, beta and gamma virus strains and Vero E6 cells, as well as in a plaque reduction neutralization test (PRNT) using live SARS-CoV-2 delta strain with the same cell line.
  • CPENT cytopathic effect neutralization test
  • PRNT plaque reduction neutralization test
  • Infection with SARS-CoV-2 Wuhan and alpha was best neutralized by antibodies 3B8 and 2B2 (IC50 ⁇ 0.63 and ⁇ 0.16 nM respectively), while SARS-CoV- 2 beta infection was best neutralized by antibodies 3B8 and 3E6 (IC50 ⁇ 0.32 nM).
  • SARS-CoV-2 gamma (IC50 ⁇ 0.37 nM for 3B8 and 3E6), although the high standard deviations hinder drawing strong conclusions.
  • antibodies 2B11 and 1C11 lost their neutralizing activity against SARS-CoV-2 delta (IC50 > 67 nM).
  • antibody 3B8 was the most potent neutralizing mAb towards all variants, with IC50 values ranging from 0.37 nM to 0.01 nM for neutralization of SARS-CoV-2 gamma and delta strain respectively ( Figure 2 and Table 5).
  • Table 5 Overview of in vitro neutralizing activity (IC50) towards SARS-CoV- 2 Wuhan, alpha, beta, gamma and delta for top 8 mAbs.
  • Neutralizing activity (IC50; in nM) was determined via CPE assay for SARS-CoV-2 Wuhan, alpha, beta and gamma and via PRNT assay for SARS-CoV-2 delta.
  • the eight selected neutralizing antibodies were also tested for their ability to cross- neutralize other human coronavirus strains using VSV pseudotypes expressing the spike protein from SARS-CoV, Middle East respiratory stress (MERS)-CoV or 229E- CoV on their surface.
  • MERS Middle East respiratory stress
  • none of the selected antibodies was able to cross- neutralize one of these coronavirus species when used at a concentration of 16.67 nM (or 2.5 pg/ml) (data not shown).
  • the selected mAbs were classified in different categories based on their epitope specificity using an ELISA cross-competition assay where the antibodies were pairwise tested against one another. Two groups could be distinguished consisting of antibodies 1A10, 1C1 and 2D6 on the one hand and antibodies 2B2, 2B11 and 1C11 on the other hand. Antibodies 3B8 and 3E6 could not be classified in one of these groups ( Figure 3). This suggests that the 8 selected mAbs bind to 4 different regions of the RBD antigen.
  • Example 4 Potent in vivo efficacy on different SARS-CoV-2 variants in the Syrian golden hamster model
  • Antibodies, 3B8, 3E6, 2B2 and 1C1 were selected for in vivo evaluation based on their in vitro neutralizing activity combined with their variability in epitope binding.
  • 30 hamsters were divided into 5 groups (6 animals/group) and infected intranasally with 50 pl of SARS-CoV-2 Wuhan virus suspension (containing approximately 2xl0 6 tissue culture infective dose (TCIDso))- After 24h, antibodies 3B8, 3E6, 2B2, 1C1 or an IgGl isotype control were injected intraperitoneally at a dose of 5 mg/kg.
  • SARS-CoV-2 variants of concern beta and delta are more resistant to neutralization by vaccine-induced antibodies or currently available mAb treatments, and given that SARS-CoV-2 delta is the most dominant variant worldwide, we decided to evaluate in vivo treatment efficacy of our antibodies against both variants as well.
  • Viral RNA load in lung tissue was significantly reduced by treatment with antibody 3B8, 3E6 and REGN-CoV- 2 compared to isotype control (p ⁇ 0.05 for 3B8 and 3E6; p ⁇ 0.01 for REGN-CoV- 2), while the reduction observed for 2B2 was not statistically significant (Figure 5b).
  • No infectious viral titer in lung tissue (TCID50) could be detected upon treatment with 3B8, 3E6 or REGN-CoV-2 (p ⁇ 0.01 compared to isotype control), while a viral titer was still detectable in four out of five animals treated with 2B2 (Figure 5c).
  • Antibodies 3B8 and 3E6 both completely abrogated infectious viral titers after infection with SARS-CoV-2 Wuhan, beta and delta when administered 24h post infection at 5mg/kg. As 3B8 was superior to 3E6 in in vitro neutralization experiments, this antibody was used in an in vivo dose-response experiment. Hamsters were intranasally infected with SARS-CoV-2 delta (IxlO 4 TCIDso). At 24h post infection, isotype control (5 mg/kg) or antibody 3B8 (5 mg/kg; 1 mg/kg, 0.2 mg/kg or 0.04 mg/kg) was administered intraperitoneally. Animals were sacrificed at day 4 post infection.
  • EXAMPLE 6 DNA based vaccination.
  • 3B8 was delivered encoded in plasmid DNA (pDNA) in vivo, as an equimolar mixture of the 3B8 heavy and light chain.
  • Hamsters received an intramuscular pDNA injection in their right & left tibialis anterior and gastrocnemius muscle (pretreated with hyaluronidase), followed by electroporation. This allows for intramuscular production and systemic circulation of 3B8. A series of electrical pulses were thereby delivered at 120V, using a plate electrode.
  • Total pDNA amount delivered per hamster was 600 pg (75 pl pDNA, at 2 pg/pl per muscle).
  • Intramuscular pDNA administration was performed either on day -10, day -7 or day -5 infection (6 animals per timepoint).
  • EXAMPLE 7 Neutralizing capacity of anti-SARS-CoV-2 human mAbs against SARS-CoV-2 delta and omicron
  • PBMCs peripheral blood mononuclear cells
  • PBMCs were resuspended in freezing medium consisting of 10% (v/v) dimethyl sulfoxide (DMSO; Merck) and 90% fetal bovine serum (FBS; GIBCO) for cryopreservation at -80°C or in liquid nitrogen for long term storage.
  • DMSO dimethyl sulfoxide
  • FBS fetal bovine serum
  • Human B cells were enriched from cryopreserved PBMCs using the EasySepTM Human B Cell Enrichment Kit (STEMCELL Technologies) according to the manufacturer's instructions. After purification, B cells were stained with Zombie AquaTM Fixable Viability Kit (Biolegend) and blocked with FcR Blocking Reagent (Miltenyi Biotec) for 15 minutes on ice. Following the 15 minutes incubation, B cells were washed with FACS buffer (phosphate-buffered saline (PBS) + 2% FBS + 2 mM EDTA) and incubated with biotinylated SARS-CoV-2 RBD protein for 60 minutes at on ice.
  • FACS buffer phosphate-buffered saline (PBS) + 2% FBS + 2 mM EDTA
  • SARS-CoV-2 RBD The Native Antigen Company
  • EZ-Link Sulfo-NHS-LC-Biotin kit Thermofisher Scientific
  • B cells were washed with FACS buffer and stained with PerCP-cy5.5 anti-human CD19 antibody (Biolegend, 363016), FITC anti-human CD3 antibody (Biolegend, 300306) and PE streptavidin (Biolegend, 405203) for 25 minutes on ice.
  • the stained cells were washed twice with FACS buffer and single-cell sorted by BD InfluxTM Cell Sorter (BD Biosciences). UltraComp eBeadsTM Compensation Beads and tosylactivated M-280 Dynabeads (Invitrogen) coupled with SARS-CoV-2 RBD protein according to the manufacturer's instructions were used for compensation.
  • Selection of RBD-specific B cells was performed using the following gating strategy: lymphocytes were selected using FSC and SSC, followed by selection of single cells based on width versus area of FSC and SSC signals. Next, live cells were selected as Zombia Aqua negative cells.
  • B cells were selected as CD19+ CD3- cells and evaluated for RBD surface staining.
  • Transcripts of lysed single B cells were denatured and hybridized with a mix of 1 pL 10 mM each nucleotide dNTP-Mix (Invitrogen) and 1 pL 10 pM oligo-dT primerat 72°C for 3 minutes. Subsequently, cDNA synthesis and pre-amplification was performed according to Picelli et al 43 . cDNA was stored at -20°C. cDNA was purified with Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer's protocol and quantified on the BioAnalyzer 2100 instrument (Agilent) and on a QubitTM fluorometer (Thermofisher Scientific).
  • the sequences encoding the immunoglobulin (Ig) heavy- and light-chain variable regions (V H and V L ) of IgM and IgG were amplified using reverse primers described in Ozawa et al. Biotechniques 40, 469-478 (2006) and forward primer described by Picelli et al. Nat. Protoc. 9, 171-181 (2014).
  • the PCR reaction was performed with KAPA HiFi HotStart ReadyMix (Roche) at 95°C for 3 min, followed by 30 cycles at 98°C for 20 seconds, 60°C for 45 seconds and 72°C for 60 seconds and terminated at 72°C for 5 minutes. All PCR products were checked on a 1% agarose gel and purified using the Agencourt AMPure XP beads. Concentrations were measured on a QubitTM fluorometer for Sanger sequencing.
  • the Ig V H and V L sequences were cloned into a pcDNA3.4 expression vector containing human IgGl constant regions.
  • the plasmid DNA (pDNA) was amplified by transformation in DH5o E. coli and subsequent purification using the NucleoBond Xtra Maxi EF kit (Machery - Nagel) according to the manufacturer's instructions. Plasmid purity and integrity was checked on a 1% agarose gel.
  • Recombinant antibodies were transiently transfected and produced in vitro in 293F Freestyle suspension cells (Thermofisher Scientific). Briefly, equal amounts of heavy- and light chain pDNA were mixed with X-tremeGENE HP DNA Transfection Reagent (Roche) in FreestyleTM 293 Expression Medium (Thermofisher Scientific) according to the manufacturer's protocol and incubated for at least 15 minutes to allow the pDNA to enter the liposomes. The transfection reagent mixture was added in a dropwise manner to 293F Freestyle suspension cells.
  • the cells were cultured in T175 flasks (Sarstedt, Germany) on an orbital shaker (Thermofischer Scientific) at 135 rpm and 8% CO2 in a 37°C humidified incubator for 5 days. At day 5, supernatant containing the recombinant antibodies was collected by centrifugation (1,400 x g for 10 minutes at room temperature), filtered through a 0.2 pm filter unit (VWR) and stored at - 20°C.
  • the recombinant antibodies were eluted from the column with 100 mM sodium acetate, pH 3.5 and the collected fractions were immediately neutralized with IM Tris, pH 9. The fractions were pooled and dialyzed against sterile-filtered PBS. The AKTAprime plus system and all glasswork was treated with 30% hydrogen peroxide (VWR) to reduce the presence of endotoxin.
  • VWR hydrogen peroxide
  • Purified recombinant antibodies were assessed by SDS-PAGE under nonreducing conditions using the Amersham PhastsystemTM (GE Healthcare) according to the manufacturer's instructions. Endotoxin levels were measured on Endosafe®-PTSTM (Charles River) according to the manufacturer's instructions.
  • SARS-CoV-2 antigens The binding of the purified recombinant antibodies to the following SARS-CoV-2 antigens was assessed via ELISA: spike glycoprotein (SI) RBD-His (REC31849-500, The Native Antigen Company), RBD(N439K)-His (40592-V08H14, Sino Biological), RBD(N501Y)-His (40592-V08H82, Sino Biological), RBD(E484K)-His (40592-
  • Polystyrene 96-well flat-bottom microtiter plates were coated with 4 pg/mL purified recombinant capture antibody in PBS (100 pL/well) and incubated at 4°C. After an overnight incubation, plates were blocked with 200 pL/well blocking buffer for 2 hours at room temperature. The plates were washed six times with washing buffer and 10 ng/mL SARS-CoV-2 RBD protein diluted in PTA buffer (100 pL/well) was added to the plates for a 2-hour incubation at room temperature. After the incubation, the plates were washed and captured antigen was detected with 100 pL/well of 1/100 biotin- conjugated purified recombinant antibodies diluted in PTA buffer.
  • Biotinylation of the purified recombinant mAbs was performed with the EZ-Link Sulfo-NHS-LC-Biotin kit according to the manufacturer's protocol. After a 1-hour incubation at room temperature and washing, biotinylated recombinant antibodies that were able to bind the antigen were detected with 1/10,000 poly-HRP-conjugated streptavidin (Sanquin) diluted in PTA buffer (100 pL/well) and incubated for an additional 30 minutes at room temperature. After a final washing step, 100 pL/well substrate was added to the plate and incubated at room temperature for 30 minutes in the dark at room. The color reaction was stopped with 50 pL/well 4 M H2SO4.
  • Optical density (OD) was measured at 492 nm with an ELx808 ELISA reader (BioTek). Very low OD values indicate the detection antibody was not able to bind, suggesting similar epitopes of both coating and detection antibodies, while high OD values indicate both antibodies have a different epitope.
  • Epitope binning graphs were made in Microsoft Excel and clustering was done with ClustVis web tool (htt iit.cs.ut.ee/clustvis/).
  • SPR Surface Plasmon Resonance
  • Monoclonal Abs were then captured between 30 and 100 RU. Increasing concentrations of analyte were sequentially injected in one single cycle at a flow rate of 30 pl/min. The dissociation was monitored for 30 min. The chip was finally regenerated with 3M MgCI2 before a new mAb was captured. A reference flow was used as a control for non-specific binding and refractive index changes. Several buffer blanks were used for double referencing. Binding affinities (KD) were derived after fitting the experimental data to the 1 : 1 binding model in the Biacore T200 Evaluation Software 3.1 using the single cycle kinetic procedure. Each interaction was repeated a least three times.
  • SARS2, SARS1, MERS, 229E Production of S-pseudotyped virus and serum neutralization test (SARS2, SARS1, MERS, 229E)
  • the percentage of GFP expressing cells was quantified on a Cell Insight CX5/7 High Content Screening platform (Thermo Fischer Scientific) with Thermo Fisher Scientific HCS Studio (v.6.6.0) software.
  • Neutralization IC50 values were determined by normalizing the serum neutralization dilution curve to a virus (100%) and cell control (0%) and fitting in Graphpad Prism (GraphPad Software, Inc.).
  • CPE Cell-based cytopathic (CPE) assay and CPE-based virus neutralization test (CPENT) (SARS-CoV-2 Wuhan, alpha, beta, gamma)
  • the titers of the virus stocks (TCID50) and 50% neutralizing titers (log CPENTso) were determined using cytopathic effect (CPE)-based cell assays and CPE-based virus neutralization tests (CPENT), respectively, on VeroE6 cells with some modifications. Shortly, 10 4 VeroE6 cells/well were seeded in 96-well plates one day prior to the titration and inoculated with 10-fold serial dilutions of virus solutions and cultured for 3 days at 37°C. Later, assays first visually scored for CPE and then stained with MTS/Phenazine methosulphate (PMS; Sigma- Aldrich) solution for 1.5 h at 37 °C in the dark.
  • CPE cytopathic effect
  • CPENT CPE-based virus neutralization tests
  • Post MTS/PMS staining absorbance was measured at 498 nm for each well. All assays were performed in six replicates and TCIDso/ml was determined using Reed and Muench method. CPENT was measured in a similar way as the CPE assays for viral titration with some modifications.
  • serial dilutions of antibodies were mixed separately with live SARS-CoV-2 Wuhan, alpha, beta and gamma virus strains, incubated at 37 °C for Ih, and added to the monolayer of Vero E6 cells. All distinct antibodies were assayed in triplicate in serial dilutions.
  • the PRNT experiments were performed with a SARS-CoV-2 isolate from the B.1.617.2 lineage. This virus was isolated from oropharyngeal swabs taken from a patient in Belgium (EPI_ISL_2425097; 2021-04-20). Virus stocks were prepared by 2x passaging on Vero E6 cells.
  • Dose-dependent neutralization of distinct antibodies was assessed by mixing the antibodies at different concentrations, with 100 PFU SARS-CoV-2 in DMEM supplemented with 2% FBS and incubating the mixture at 37°C for Ih. Antibodyvirus complexes were then added to VeroE6 cell monolayers in 12-well plates and incubated at 37°C for Ih. Subsequently, the inoculum mixture was replaced with 0.8% (w/v) methylcellulose in DMEM supplemented with 2% FBS. After 3 days incubation at 37°C, the overlays were removed, the cells were fixed with 3.7% PFA, and stained with 0.5% crystal violet.
  • Half-maximum neutralization titers PRNT50 were defined as the antibody concentration that resulted in a plaque reduction of 50%.
  • BetaCov/Belgium/GHB- 03021/2020 (EPI ISL 109 407976
  • a close relation with the prototypic Wuhan-Hu-1 2019-nCoV (GenBank accession 112 number MN908947.3) strain was confirmed by phylogenetic analysis. Infectious virus was isolated by serial passaging on Huh7 and Vero E6 cells [Kaptein et al. Proc. Natl. Acad. Sci.
  • Beta variant B.1.351 (hCoV-19/Belgium/rega-1920/2021; EPI_ISL_896474, 2021-01-11) was isolated from nasopharyngeal swabs taken from a traveler returning to Belgium in January 2021 who became a patient with respiratory symptoms.
  • the Delta variant, B.1.617.2 (hCoV-19/Belgium/rega- 7214/2021; EPI_ISL_2425097; 2021-04-20) was isolated from nasopharyngeal swabs in April 2021 in Belgium through active surveillance.
  • Vero E6 cells African green monkey kidney, ATCC CRL-1586 were cultured in minimal essential medium (MEM, Gibco) supplemented with 10% fetal bovine serum (Integra), 1% non-essential amino acids (NEAA, Gibco), 1% L- glutamine (Gibco) and 1% bicarbonate (Gibco). End-point titrations on Vero E6 cells were performed with medium containing 2% fetal bovine serum instead of 10%.
  • Huh7 cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (Integra), 1% bicarbonate (Gibco), 2% HEPES buffer (Gibco). Both cells were kept in a humidified 5% CO2 incubator at 37°C.
  • Lungs were collected and viral RNA and infectious virus were quantified by RT-qPCR and end-point virus titration, respectively. Blood samples were collected at end-point for pharmacokinetic analysis. No randomization methods were used and confounders were not controlled, though all caretakers and technicians were blinded to group allocation in the animal facility and to sample numbers for analysis (qPCR, titration, and histology).
  • RT-qPCR was performed on a LightCycler96 platform (Roche) using the iTaq Universal Probes One-Step RT-qPCR kit (BioRad) with N2 primers and probes targeting the nucleocapsid.
  • Standards of SARS-CoV-2 cDNA (IDT) were used to express viral genome copies per mg tissue. End-point virus titrations
  • Lung tissues were homogenized using bead disruption (Precellys) in 350 pL minimal essential medium and centrifuged (10,000 rpm, 5min, 4°C) to pellet the cell debris.
  • Precellys bead disruption
  • endpoint titrations were performed on confluent Vero E6 cells in 96- well plates.
  • Viral titers were calculated by the Reed and Muench method 46 using the Lindenbach calculator and were expressed as 50% tissue culture infectious dose (TCID50) per mg tissue.
  • the RBD binding region of antibodies 1C1, 2B2, 3B8 and 3E6 was evaluated in an epitope binning experiment by the Coronavirus Immunotherapeutic Consortium (CoVIC).
  • CoVIC Coronavirus Immunotherapeutic Consortium
  • H-SPR high-throughput surface plasmon resonance
  • COVIC To understand the position of each community relative to the others, COVIC next mapped the footprints by negative-stain electron microscopy (NS-EM) for 25 example RBD-reactive mAbs chosen to span the range of communities and key clusters (Hastie et al., Science 374, 472-478 (2021)). This allowed to assign different structural regions of the RBD antigen to different epitope communities (figure 10, figurell).
  • Antibodies 1C1, 2B2, 3B8 and 3E6 were included in epitope binning experiments of the COVIC consortium and assigned to epitope communities RBD-7b, RBD-4b, RBD- 3 and RBD-2a, respectively.
  • RBD-2 and RBD-3 are part of the receptor binding motive (RBM) of the RBD antigen, while RBD-4 is part of the RBD "outer face” and RBD-7 lies outside the RBM in the RBD "inner face” (Fig 2).
  • RBM and RBD-7 are part of the receptor binding motive (RBM) of the RBD antigen, while RBD-4 is part of the RBD "outer face” and RBD-7 lies outside the RBM in the RBD "inner face” (Fig 2).
  • Epitope binning was performed with a classical sandwich assay format on a Carterra LSA® HT-SPR instrument equipped with a CMDP sensor chip at 25 °C and in a HBSTE-BSA running buffer (10 mM HEPES pH 7.4, 150 mM NaCI, 3 mM EDTA, 0.05% Tween-20, supplemented with 0.5 mg/ml BSA).
  • Surface preparation was performed with 25 mM MES pH 5.5 with 0.05% Tween-20 as a running buffer.
  • the chip was activated with a freshly prepared solution of 130 mM l-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) + 33 mM N-hydroxysulfosuccinimide (Sulfo-NHS) in 0.1 M MES pH 5.5 using the SFC.
  • Antibodies were immobilized using the 96PH for 10 minutes at 10 pg/mL diluted into 10 mM sodium acetate (pH 4.25). Unreactive esters were quenched with a 7-minute injection of 1 M ethanolamine-HCI (pH 8.5) using the SFC.
  • the binning analysis was performed over this array with the HBSTE-BSA buffer as the running buffer and sample diluent.
  • the RBD antigen was injected in each cycle for 4 minutes at 50 nM (1.8 pg/mL) and followed immediately by a 4-minute injection of the analyte antibody at 30 pg/mL (200 nM for IgG constructs).
  • the surface was regenerated each cycle with double pulses (17 seconds per pulse) of 10 mM Glycine pH 2.0.
  • Data was processed and analyzed with Epitope® software (Carterra). Briefly, data was referenced using unprinted locations on the array and each binding cycle was normalized to the RBD capture level.
  • the binding level of the analyte antibody just after the end of the injection was compared to that of a buffer alone injection. Signals that were significantly increased relative to the buffer controls are described as sandwiches and represent non-blocking behavior. Competition results were visualized as a heat map that depicts blocking relationships of analyte/ligand pairs. Clones having similar patterns of competition are clustered together in a dendrogram and can be assigned to shared communities.
  • Plasmid preps of two independently generated deep mutational SARS-CoV2 RBD libraries in the pETcon vector (Starr et al. (2020), Cell 182, 1295-1310. e20). Ten ng of these preps were transformed to E. coli TOP10 strain via electroporation, and allowed to recover for one hour in SOC medium at 37°C. The transformation mixture was divided and plated on ten 24.5 cm x 24.5 cm large bio-assay dishes containing low salt LB medium supplemented with carbenicillin, at an expected density of 100.000 clones per plate. After growing overnight, all colonies were scraped from the plates and resuspended into 300 ml low salt LB supplemented with carbenicillin.
  • the cultures were grown for 2 hours and a half before pelleting.
  • the cell pellet was washed once with sterile MQ, and plasmid was extracted via the QIAfilter plasmid Giga prep kit (Qiagen) according to the manufacturer's instructions.
  • the CDS of the RBD of SARS-CoV2 (N331-T531) was ordered as a yeast codon- optimized gBIock and cloned into the pETcon vector by Gibson assembly.
  • the cloning mixture was similarly electroporated into E. coli TOPIO cells, and plasmid was extracted via a Miniprep kit (Promega) according to the manufacturer's instructions.
  • the plasmid was Sanger sequenced with primers covering the entire RBD CDS.
  • the plasmid was transformed to Saccharomyces cerevisiae strain EBY100, according to the small-scale protocol by (Gietz et al. Nature Protocols (2007) 2, 31- 34). Transformants were selected via a yeast colony PCR.
  • the cells pellets were washed thrice with washing buffer (IX PBS + 1 mM EDTA, pH 7.2 + 1 Complete Inhibitor EDTA-free tablet (Roche) per 50ml buffer), and stained at an ODeoo of 8/ml with 9.09 nM hACE2-muFc (Sino Biological) in staining buffer (washing buffer + 0.5 mg/ml of Bovine Serum Albumin) for one hour at 4°C on a rotating wheel.
  • washing buffer IX PBS + 1 mM EDTA, pH 7.2 + 1 Complete Inhibitor EDTA-free tablet (Roche) per 50ml buffer
  • staining buffer washing buffer + 0.5 mg/ml of Bovine Serum Albumin
  • Cells were washed thrice with staining buffer and stained with 1 : 100 anti-cmyc-FITC (Immunology Consultants Lab), 1 : 1000 anti-mouse-IgG-AF568 (Molecular Probes) and 1:2000 L/D eFluor506 (Thermo Fischer Scientific) for one hour at 4°C on a rotating wheel. Cells were washed thrice with staining buffer, and filtered over 35 pm cell strainers before sorting on a FACS Melody (BD Biosciences). A selection gate was drawn that captures the ACE2+ cells, such that, after compensation, max. 0.1% of cells of unstained and single stained controls appeared above the background.
  • ACE2+ cells were collected per library, each in 5 ml polypropylene tubes coated with 2X YPAD + 1% BSA. Sorted cells were recovered by growth in liquid SD -trp -ura medium with 100 U/ml penicillin and 100 pg/ml streptomycin (Thermo Fisher Scientific) for 72 hours at 28°C, and flash frozen at -80°C in 9 ODeoo unit aliquots in 15% glycerol.
  • the cells pellets were washed thrice with washing buffer (IX PBS + 1 mM EDTA, pH 7.2 + 1 Complete Inhibitor EDTA-free tablet (Roche) per 50ml buffer, freshly made and filter sterile) and stained at an ODeoo of 8/ml with a specific concentration per stained antibody in staining buffer (washing buffer + 0.5 mg/ml of Bovine Serum Albumin) for one hour at 4°C on a rotating wheel.
  • washing buffer IX PBS + 1 mM EDTA, pH 7.2 + 1 Complete Inhibitor EDTA-free tablet (Roche) per 50ml buffer, freshly made and filter sterile
  • staining buffer washing buffer + 0.5 mg/ml of Bovine Serum Albumin
  • Cells were washed thrice with staining buffer and stained with 1 : 100 anti-c-myc-FITC (Immunology Consultants Lab), 1: 1000 anti-human IgG AF594 (Molecular Probes) and 1:2000 L/D eFluor506 (Thermo Fischer Scientific) for one hour at 4°C on a rotating wheel. Cells were washed thrice with staining buffer, and filtered over 35 pm cell strainers before sorting on a FACS Melody (BD Biosciences). Gating was chosen as such that, after compensation, max. 0.1% of cells of the fully stained WT RBD control appeared in the selection gate. Between 150.000 and 300.000 escaped cells were collected per library, each in 5 ml polypropylene tubes coated with 2X YPAD + 1% BSA.
  • Sorted cells were recovered by growth in liquid SD -trp -ura medium supplemented with 100 U/ml penicillin and 100 pg/ml streptomycin (Thermo Fisher Scientific) for 16 hours at 28°C.
  • Plasmids were extracted from sorted cells using the Zymoprep yeast plasmid miniprep II kit (Zymo Research) according to the manufacturer's instructions, but with the exception of a longer (2 hour) incubation with the Zymolyase enzyme, and with the addition of a freeze-thaw cycle in liquid nitrogen after Zymolyase incubation.
  • a PCR was performed on the extracted plasmids using KAPA HiFi HotStart ReadyMix to add sample indices and remaining Illumina adaptor sequences using NEBNext UDI primers (20 cycles). PCR samples were purified once using CleanNGS magnetic beads (CleanNA), and once using AMPure magnetic beads (Beckman Coulter).
  • Fragments were eluted in 15 pl O.lx TE buffer. Size distributions were assessed using the High Sensitivity NGS kit (DNF-474, Advanced Analytical) on a 12-capillary Fragment Analyzer (Advanced Analytical). Hundred bp single-end sequencing was performed on a NovaSeq 6000.
  • the resulting variants were filtered to remove unreliably low counts and keep variants with sufficient RBD expression and ACE2 binding (based on published data (Starr et al., 2020, Celll82, 1295-1310. e20)).
  • the effects of individual mutations were estimated with global epistasis models, excluding mutations not observed in at least one single mutant variant and two variants overall.
  • the resulting escape measurements correlated well between the duplicate experiments and the average across libraries was thus used for further analysis.
  • RBD positions were identified where the total site escape was > lOx the median across all sites, and was also at least 10% of the maximum total site escape across all positions for a given antibody.

Abstract

The invention relates to antibodies or antigen binding fragments thereof, specifically binding to the trimeric spike protein of Wuhan Covid-SARS-2 and specifically binding to the RBD domain of all of Wuhan, alpha, beta, gamma, delta and omicron variant of Covid-SARS-2 spike protein, characterized in that said antibody or antigen binding fragment thereof has an IC50 in a SARS-CoV-2 pseudovirus infection lower than 1 nm in a SARS-CoV-2 pseudovirus infection, and in that said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 500 pM, and in that said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM.

Description

NEUTRALIZING ANTI-SARS-COV-2 HUMAN ANTIBODIES
FIELD OF THE INVENTION
The invention relates to antibodies which are particularly suitable in the treatment of beta, delta, and omicron variant of COVID 19.
BACKGROUND OF THE INVENTION
The COVID-19 pandemic, caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in an unprecedented global health and economic crisis and has already caused more than 4,8 million deaths worldwide. The spike protein of SARS-CoV-2 consists of an SI subunit that recognizes host cell receptors and an S2 subunit that promotes membrane fusion of virus and host cells. Within the SI subunit, the receptor binding domain (RBD) is responsible for interaction with receptor angiotensin-converting enzyme 2 (ACE2) on host cells to mediate viral entry. Consequently, SARS-CoV-2 spike protein is the major target of neutralizing antibodies (Ab).
Antibodies can be elicited by natural infection and vaccination, or can be administered as recombinant monoclonal antibodies (mAbs) in a passive immunization strategy. Although vaccines are essential tools to fight this pandemic, therapeutic mAbs play a crucial role as well, especially for (immune-compromised) individuals who may not generate a robust response to their vaccine, cannot be vaccinated, are at high risk for severe illness or are still awaiting their vaccine.
Until now, four mAb treatments have received emergency use authorization: three in the United States (REGN-COV2 (i.e. REGN10933 + REGN10987) from Regeneron, LY-CoV555 with/without LY-C0VOI6 from AbCellera/Eli Lilly and VIR-7831 from Vir Biotechnology/GlaxoSmithKline) and one in South Korea (CT-P59 from Celltrion) [The Antibody Society: COVID-19 Biologies Tracker, https:// www.antibodysociety.org/ covid-19-biologics-tracker/ (2021)].
Unfortunately, SARS-CoV-2 variants beta, gamma and delta escape from some of the currently available therapeutic mAbs. REGN10933 (i.e. one of the antibodies from the REGN-COV2 antibody cocktail) showed reduced activity against SARS-CoV-2 beta and gamma, and activity of CT-P59 was reduced against beta, gamma and delta. LY- CoV555 completely lost its activity against beta, gamma and delta. This demonstrates that several of the commercially available therapeutic mAbs lose their activity against the current SARS-CoV-2 variant. The latest SARS-CoV-2 variant of concern (VoC) B.1.1.529, designated omicron, was first reported to WHO from South Africa at the end of November 2021 and is rapidly spreading across many countries, replacing the already highly transmissible SARS- CoV-2 delta (B.1.617.2) VoC. SARS-CoV-2 omicron has a large number of mutations compared to the pandemic founder, many of which are predicted to result in resistance towards the currently available neutralizing (therapeutic) antibodies, including those induced upon vaccination. The majority of currently available antibodies, by the end of December 2021, show a strongly reduced or no activity against the omicron variant. GSK reported that their therapeutic monoclonal antibody (mAb) Sotrovimab retains activity against the omicron variant (IC50 of 0.27 pg/ml ), while mAbs REGN 10933 and REGN 10987 from Regeneron, and Ly-CoV016 and Ly- CoV555 from Abcellera/Eli Lilly, all failed to neutralize omicron at the highest concentration tested (10 pg/ml) in a pseudovirus neutralization assay. In addition, also the lead mAb from Adagio Therapeutics, which was specifically designed to be highly potent and broadly neutralizing against coronavirus variants, showed a more than 300-fold reduction in neutralizing capacity against omicron when tested in both an authentic and pseudovirus assay.
There is a need for additional potent mAbs that recognize a broad range of different SARS-CoV-2 variants, such as delta and omicron.
SUMMARY OF THE INVENTION
In this work, we therefore sought to identify potent human mAbs reactive to all current SARS-CoV-2 variants both in vitro and in vivo. We were able to generate highly potent and broadly neutralizing mAbs that are capable of treating SARS-CoV- 2 Wuhan, beta, delta and omicron infection in Golden Syrian hamsters.
Therapeutic monoclonal antibodies (mAbs) are an essential tool to combat COVID- 19 morbidity and mortality, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Four mAbs have already received emergency use authorization either in the United States or South Korea. Unfortunately, several SARS-CoV-2 variants escape some of these therapeutic mAbs. Using PBMCs from convalescent patients and B cell receptor cloning, we identified six mAbs, classified in four different epitope groups, that potently neutralize live SARS-CoV-2 Wuhan, alpha, beta, gamma and delta infection in vitro. In addition, antibodies 3E6 and 3B8 potently cure infection with SARS-CoV-2 Wuhan, beta and delta in an in vivo hamster model when administered therapeutically at 5 mg/kg. Interestingly, antibody 3B8 still reduced infectious viral titers after therapeutic administration at only 0.2 mg/kg, highlighting its superior potency. Combined with its reactivity against all tested SARS-CoV-2 variants, our data mark 3B8 as a promising candidate to help fight COVID-19. The 3B8 antibody binds to a novel yet unidentified specific epitope. This has unprecedented advantages in combination therapies whereby competition of different antibodies for the same antibody is avoided.
The invention is further summarized in the following statements:
1. An antibody or antigen binding fragment thereof, specifically binding to the trimeric spike protein of Wuhan Covid-SARS-2 and specifically binding to the RBD domain of all of Wuhan, alpha, beta, gamma, delta and omicron variant of Covid- SARS-2 spike protein, characterized in that: said antibody or antigen binding fragment thereof has an IC50 in a SARS-CoV-2 pseudovirus infection lower than 1 nm, lower than 0,8 nm, lower than 0,6 nm, lower than 0,4 nm or lower than 0,2 nm in a SARS-CoV-2 pseudovirus infection, and in that said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 500 pM, less than 400 pM, less than 300 pM, less than 200 pM, less than 100 pM or less than 50 pM, and in that said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM, less than 200 pM, less than 100 pM or less than 50 pM.
2. The antibody or antigen binding fragment thereof according to statement 1, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,4, and said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 400 pM, and, said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM.
3. The antibody or antigen binding fragment thereof according to statement 1 or 2, wherein, said antibody or antigen binding fragment thereof has an IC50, lower than 0,05 and said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 250 pM, and said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 100 pM. 4. The antibody or antigen binding fragment thereof according to any one of statements 1 to 3, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
5. The antibody or antigen binding fragment thereof according to statement 4, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 24.
6. The antibody or antigen binding fragment thereof according to statement 1 or 2, which is an antibody or antibody fragment comprising :
-a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GVIVSRNY [SEQ ID NO: 6], IYSGGST [SEQ ID NO: 7] and ARWGPNYYGSGSDHYNSYGMDV [SEQ ID NO: 8] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGVSSSS [SEQ ID NO: 9], GAS and QQSGSSPQYT[SEQ ID NO: 10].
7. The antibody or antigen binding fragment thereof according to statement 6, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 26 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 28.
8. The antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising :
-a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GFTFDDYA[SEQ ID NO: 11], VSWNSGTI [SEQ ID NO: 12] and AKDVSVYRFREQSYGMDV [SEQ ID NO: 13] and comprising - a variable light chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence SSDIGGYNF [SEQ ID NO: 14], EVT, and SSYTSSSLVV [SEQ ID NO: 15].
9. The antibody or antigen binding fragment thereof according to statement 8, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 30 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 32.
10. The antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GFSLDDYG [SEQ ID NO: 16], ISWNSGDR [SEQ ID NO: 17], and AKGSGAHYDIMTGARLDY [SEQ ID NO: 18] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSITNY [SEQ ID NO: 19], AAS, CDR 3: QQSYSTPWT [SEQ ID NO: 20].
11. The antibody or antigen binding fragment thereof according to statement 10, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 34 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 36.
12. The antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYSFTSHW [SEQ ID. NO: 37], IFPGDSKT [SEQ ID. NO: 38], and ARPNRYYDDSGNYDGSYYFDY [SEQ ID. NO: 39], a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSVNTN [SEQ ID. NO: 40], GAF, and QQYNNWPPAWT [SEQ ID. NO: 41].
13. The antibody or antigen binding fragment thereof according to statement 12, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 58 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 60.
14. The antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTTYY [SEQ ID. NO: 42], INSSGGST[SEQ ID. NO: 43], and ATSGWYRGAFDY [SEQ ID. NO: 44] a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SGSIDNNY [SEQ ID. NO: 45], EDN, and QSIDSNSWV [SEQ ID. NO: 46].
15. The antibody or antigen binding fragment thereof according to statement 14, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 62 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 64.
16. The antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGSLSVYY [SEQ ID. NO: 47], INHSGST [SEQ ID. NO: 48], and ARTSLHTWNPFDY [SEQ ID. NO: 49], and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGISSY [SEQ ID. NO: 50], AAS, and QQLNNYPLT [SEQ ID. NO: 51].
17. The antibody or antigen binding fragment thereof according to statement 16, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 66 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 68.
18. The antibody or antigen binding fragment thereof according to statement 1, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGTFSNYA [SEQ ID. NO: 52], IIAIFGTP [SEQ ID. NO: 53], and ARRSTILERLPRHYYGMDV [SEQ ID. NO: 54], and a variable light chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence QSLLHSNGNIY [SEQ ID. NO: 55], LGS and MQTLQTLRAT [SEQ ID. NO: 56].
19. The antibody or antigen binding fragment thereof according to statement 18, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 70 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 72.
20. The antibody or antigen binding fragment thereof according to any one of statements 1 to 19, wherein the antibody is a human antibody.
21. A polynucleotide encoding the antibody or antigen binding fragment thereof in accordance with any one of statements 1 to 20.
22. The antibody or antigen binding fragment thereof according to any one of statements 1 to 20, for use in the treatment and prevention of COVID 19 in an individual.
23. The antibody antigen binding fragment thereof according to any one of statements 22, for use in the treatment or prevention of COVID 19 in an individual, wherein only one antibody is administered to said individual.
24. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to statement 22 or 23, wherein said antibody is administered intravenous or intramuscularly, in an amount from between 100 mg, 500 mg, or 1000 mg Ab per individual up to 2000, 4000, 6000 or 10000 mg per individual [all ranges with one of the mentioned lower and upper concentrations are herewith explicitly disclosed].
25. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 24, wherein COVID 19 is the beta, delta or omicron variant of COVID 19.
26. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the antibody or antibody fragment comprises:
-a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising a variable light chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
27. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 24.
28. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, comprising a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GVIVSRNY [SEQ ID NO: 6], IYSGGST [SEQ ID NO: 7] and ARWGPNYYGSGSDHYNSYGMDV [SEQ ID NO: 8] and comprising a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGVSSSS [SEQ ID NO: 9], GAS and QQSGSSPQYT[SEQ ID NO: 10]
29. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 26 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 28.
30. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYSFTSHW [SEQ ID. NO: 37], IFPGDSKT [SEQ ID. NO: 38], and ARPNRYYDDSGNYDGSYYFDY [SEQ ID. NO: 39], a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSVNTN [SEQ ID. NO: 40], GAF, and QQYNNWPPAWT [SEQ ID. NO: 41]. 31. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 58 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 60.
32. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTTYY [SEQ ID. NO: 42], INSSGGST[SEQ ID. NO: 43], and ATSGWYRGAFDY [SEQ ID. NO: 44] a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SGSIDNNY [SEQ ID. NO: 45], EDN, and QSIDSNSWV [SEQ ID. NO: 46].
33. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 62 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 64.
34. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising : a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGSLSVYY [SEQ ID. NO: 47], INHSGST [SEQ ID. NO: 48], and ARTSLHTWNPFDY [SEQ ID. NO: 49], and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QGISSY [SEQ ID. NO: 50], AAS, and QQLNNYPLT [SEQ ID. NO: 51].
35. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 66 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 68.
36. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, which is an antibody or antibody fragment comprising: a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GGTFSNYA [SEQ ID. NO: 52], IIAIFGTP [SEQ ID. NO: 53], and ARRSTILERLPRHYYGMDV [SEQ ID. NO: 54], and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence QSLLHSNGNIY [SEQ ID. NO: 55], LGS and MQTLQTLRAT [SEQ ID. NO: 56].
37. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to any one of statements 22 to 25, wherein the variable domain comprises a VH region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity with the amino acid sequence of SEQ ID NO: 70 and a VL region that has outside the CDR regions at least 80%, at least 90%, at least 95%, at least 97 %, or at least 99 % sequence identity to the amino acid sequence of SEQ ID NO: 72.
38. A polynucleotide comprising a sequence encoding the antibody or antigen binding fragment thereof according to any one of statements 1 to 20, for use in the treatment and prevention of COVID 19. herein "a" polynucleotide can be a single polynucleotide strand comprising both the sequences encoding the light and heavy chain or fragments of these.
Alternatively two polynucleotide strands (e.g. plasmids)are administered, wherein one polynucleotide expresses the light chain or fragments thereof, and a second polynucleotide expresses the heavy chain or fragments thereof.
39. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statement 38, wherein COVID 19 is the beta delta, or omicronvariant of COVID 19.
40. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 21 and SEQ ID NO: 23. 41. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO:
25 and SEQ ID NO: 27.
42. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 29 and SEQ ID NO: 31.
43. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 33 and SEQ ID NO: 35.
44. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 57 and SEQ ID NO: 59.
45. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 61 and SEQ ID NO: 63.
46. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 65 and SEQ ID NO: 67.
47. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statements 38 or 39, comprising the sequence of SEQ ID NO: 69 and SEQ ID NO: 71.
48. An antibody or antigen binding fragment thereof, specifically binding to the trimeric spike protein of Wuhan Covid-SARS-2 and specifically binding to a confirmational epitope of the Receptor Binding Domain of all of Wuhan, alpha, beta, gamma, delta and omicron variants of Covid-SARS-2 spike protein.
49. The antibody or antigen binding fragment thereof according to statement 48, wherein said antibody or antigen binding fragment thereof has an IC50 in a SARS- CoV-2 pseudovirus infection lower than 1 nm, and wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 500 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM.
50. The antibody or antigen binding fragment thereof according to statement 48 or 49, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,4, wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 400 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM.
51. The antibody or antigen binding fragment thereof according to any one of statements 48 to 50, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,05 and wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 250 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 100 pM.
52. The antibody or antigen binding fragment thereof according to any one of statements 48 to 51, wherein the confirmational epitope resides in the receptor binding motif with SEQ ID NO: 77 which is a fragment of the RBD with SEQ ID NO: 74.
53. The antibody or antigen binding fragment thereof according to any one of statements 48 to 52, wherein the confirmational epitope in the receptor binding motif of the RBD is defined by amino acids Vai 445, Gly446, Pro499 and Thr500 of the spike protein of Wuhan Covid-SARS-2 [SEQ ID NO: 73].
54. The antibody or antigen binding fragment thereof according to any one of statements 48 to 53, which is an antibody or antigen binding fragment there of comprising:
-a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising
- a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
55. The antibody or antigen binding fragment thereof according to any one of statements 48 to 54, wherein the variable domain comprises a VH region that has outside the CDR regions at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 24.
56. The antibody or antigen binding fragment thereof according to any one of statements 48 to 55, wherein the antibody is a human antibody.
57. A polynucleotide encoding the antibody or antigen binding fragment thereof in accordance with any one of statements 48 to 56.
58. The antibody or antigen binding fragment thereof according to any one of statements 48 to 56, for use in the treatment and prevention of the beta, delta or omicron variant of COVID 19 in an individual.
59. The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to statement 58, wherein the antibody or antibody fragment comprises:
-a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
60. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to statement 58 or 59, wherein the variable domain comprises a VH region that has outside the CDR regions at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 24.
61. A polynucleotide comprising a sequence encoding the antibody or antigen binding fragment thereof according to statement 57, for use in the treatment and prevention of the beta, delta or omicron variant COVID 19.
62. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to statement 61, comprising the sequence of SEQ ID NO: 21 and SEQ ID NO: 23.
DETAILED DESCRIPTION
Figure legends
Figure 1: Neutralizing activity of top 8 most potent antibodies. Percentage neutralizing activity, measured via a SARS-CoV-2 D614G VSV pseudotyped assay, is given at different concentrations for the top 8 antibodies. Symbols show mean and standard deviation of 3 replicates, graph is representative for 2 independent experiments.
Figure 2: in vitro neutralization of infection with live SARS-CoV-2 variants. Concentration-dependent neutralizing activity (% neutralization) was measured via CPENT assay using SARS-CoV-2 Wuhan, alpha, beta and gamma (A-D) or via PRNT assay using SARS-CoV-2 delta (E) for the 8 selected antibodies. Symbols show mean and standard deviation (only upper bar is shown for clarity) of 3 (A-D) or 2 (E) replicates.
Figure 3: Epitope specificity of top 8 mAbs. A) Visual representation of the crosscompetition ELISA. All antibodies were pairwise tested against one another as coating or detection antibody. Signal strength is visualized by color intensity, with a white color indicating no binding of the detection antibody could occur, and dark red indicating strong binding of the detection antibody. B) Principal component analysis of the results obtained in the cross-competition ELISA to enable classification of the antibodies in different epitope groups. Data are representative for 2 independent experiments.
Figure 4: Treatment of SARS-CoV-2 Wuhan infection by antibodies 3B8, 3E6, 2B2 and 1C1 (5 mg/kg) in hamsters. A) Study design. Hamsters were intranasally infected with SARS-CoV-2 on day 0 and received antibody treatment (5 mg/kg) 24h post infection. Animals were sacrificed at day 4 for analysis of lung and blood samples. B) Concentration (pg/ml) of the administered antibodies in serum at day 4 post infection. Animals without detectable antibody serum levels were excluded from the graphs in panel C and D. C) Viral RNA levels, expressed as logic RNA copies per mg of lung tissue, on day 4 post infection. D) Infectious viral loads, expressed as log TCID50 per mg lung tissue, at day 4 post infection. Individual data with median values are shown. Dotted line represents the detection limit. * = p < 0.05; ** = p < 0.01 as determined via Mann-Whitney U test.
Figure 5: Treatment of SARS-CoV-2 beta and delta infection by antibodies 3B8, 3E6, 2B2 and REGN-COV-2 (5 mg/kg) in hamsters. Concentration (pg/ml) of the administered antibodies at day 4 post infection in serum from hamsters infected with SARS-CoV-2 beta (A) or delta (D). Viral RNA levels in the lungs of hamsters infected with SARS-CoV-2 beta (B) or delta (E), on day 4 post infection. Infectious viral loads, in lungs of hamsters infected with SARS-CoV-2 beta (C) or delta (F), on day 4 post infection. Animals without detectable antibody serum levels were excluded from the graphs in panel B-C-E-F. Individual data and median values are shown. Dotted line represents the detection limit, ns = p > 0.05; * = p < 0.05; ** = p < 0.01 as determined via Mann-Whitney U test.
Figure 6: Dose-response experiment for treatment of SARS-CoV-2 delta infection with antibody 3B8 (5, 1, 0.2 or 0.04 mg/kg) in hamsters. A)
Concentration (pg/ml) of the administered antibodies in serum at day 4 post infection. B) Viral RIMA levels, expressed as logw RNA copies per mg of lung tissue, on day 4 post infection. C) Infectious viral loads, expressed as log TCID50 per mg lung tissue, at day 4 post infection. Individual data and median values are shown. Dotted line represents the detection limit, ns = p > 0.05; ** = p < 0.01 as determined via Mann-Whitney U test.
Figure 7: gating strategy for selection of RBD-specific B cells from PBMCs of patients K-COV19-901.
Lymphocytes were selected based on FSC and SSC, followed by selection of single cells and live cells (Zombia Aqua negative). Here, B cells were selected as CD19+ CD3- cells and evaluated for RBD surface staining using PE as fluorophore. Fully stained sample is shown in panel A, fluorescence minus one (FMO) control for RBD fluorescence is shown in panel B.
Figure 8: DNA base vaccination
Analysis of viral RNA levels (left panel) and infectious viral titers (right panel) upon injection of hamsters with 3B8 pDNA. Individual data with median values are shown. Dotted line represents the detection limit. ** = p < 0.01 as determined via Mann- Whitney U test.
Figure 9: Neutralizing activity of mAbs against SARS-CoV-2 delta and omicron VoC.
Percentage neutralizing activity, measured via a SARS-CoV-2 delta (A) or omicron (B) VSV pseudotyped assay, at different concentrations of the respective mAbs tested. Symbols show mean and standard deviation of 3 replicates, measured in one experiment.
Figure 10: Escape plot for 3B8 ("stacked logo") with the positions V445, G446, P499 and T500 identified as crucial residues for 3B8 binding.
Figure 11: Summary of the 7 RBD-directed communities based on antibody competition profiles and interpreted by previous epitope studies adapted from Hastie et al 2021 ).
Figure 12: The antigenic landscape of the SARS-CoV-2 RBD can be divided into seven binding communities. Figure 13: Escape plot for 3B8 ("stacked logo") with the positions V445, G446, P499 and T500 identified as crucial residues for 3B8 binding.
Figure 14: DNA and protein sequence of heavy and light chain variable regions.
Despite vaccination rates steadily increasing, less than 40% of individuals has been fully vaccinated worldwide and the number of SARS-CoV-2 related deaths continues to increase1. In addition, vaccine-breakthrough infections have been reported and may be explained by the emergence of several SARS-CoV-2 variants showing a reduced sensitivity to vaccine-elicited antibody neutralization6,7'24-31. Monoclonal antibodies may therefore play a crucial role to treat individuals that cannot be vaccinated, to treat vaccinated individuals still suffering from serious COVID-19 caused by infection with current or future SARS-CoV-2 variants of concern and to prevent rapid dissemination of viral infection in specific settings, such as elderly care homes.
In this study, 8 highly potent neutralizing antibodies (IC50 < 1 nM) were identified from a convalescent COVID-19 patient and evaluated for their efficacy against different SARS-CoV-2 variants. Six out of eight antibodies bound all analyzed recombinant SARS-CoV-2 RBD antigens bearing single or multiple mutations. Affinities were evaluated for RBD antigens with single mutations and shown to be in the picomolar range. Corresponding to the antigen binding data, in vitro neutralization assays using live SARS-CoV-2 Wuhan, alpha, beta, gamma and delta strains showed that these antibodies potently cross-neutralized all variants with IC50 values ranging from 0.01 to 3.97 nM. Interestingly, data from the cross-competition ELISA showed that these antibodies were not all targeting the same epitope, but could be divided into 4 epitope groups.
The most potent antibody of each of these epitope classes was tested for therapeutic activity in vivo in the Syrian golden hamster model. This model has been widely used to assess the efficacy of vaccines and therapeutics against SARS-CoV-2 infection as it closely mimics the clinical disease observed in humans32-34. Using this model, we designed three different therapeutic studies to evaluate the efficacy of our antibodies as a treatment for SARS-CoV-2 Wuhan, beta, delta and omicron infection. We showed that antibodies 3B8 and 3E6 reduced median viral RNA titers with a factor 50 - 5000 or 10 - 330 respectively when used as a treatment (5 mg/kg) for all tested SARS- CoV-2 strains. In addition, treatment with these antibodies resulted in undetectable levels of infectious virus in the lungs of almost all animals. Our in vitro and in vivo data suggest that 3B8 and 3E6 target an epitope conserved between the different variants, abolishing the need for combination therapy for the current SARS-CoV-2 variants. In addition, since we identified potent neutralizing antibodies from different epitope groups, combination therapy remains an option in the future if additional variants of concern appear.
Importantly, we also showed that antibody 3B8 is an ultrapotent therapeutic antibody, with treatment at a dose of 1 mg/kg resulting in undetectable infectious viral titers. Even when administered at 0.2 mg/kg, viral replication was reduced, with median infectious viral titers of the treatment group being 67 times lower compared to the isotype control group. This further highlights the potency of antibody 3B8 in a therapeutic setting [Andreano et al. Cell 184, 1821-1835. el6 (2021)]. High potencies are crucial to decrease cost of goods, enable sustainable manufacturability and increase the number of doses produced annually, and may therefore also facilitate the availability of therapeutic mAbs to low- and middle-income countries.
When comparing the antibodies generated in this study with the commercially available ones, we noticed that KD values observed for our antibodies were consistently between 3- and 200-fold lower than values reported for marketed antibodies of Vir Biotechnology, Regeneron Pharmaceuticals or Eli Lilly. However, when analyzing KD values of REGN-COV2 antibodies 10933 and 10987 in our own experiments for benchmarking purposes, KD values were similar to values observed for our mAbs (data not shown). In addition, it should be noted that antibodies 3B8 and 3E6 each performed equally well as monotherapy (when administered at 5 mg/kg) to treat SARS-CoV-2 infection beta and delta in hamsters when compared to the marketed REGN-COV2 antibody cocktail, which consists of two different antibodies [FDA Fact Sheet for Health Care Providers Emergency Use Authorization Of REGEN-COV. (2021).]. Moreover, we could observe therapeutic efficacy of antibody 3B8 in vivo at a dose of only 0.2 mg/kg. Interestingly, to the best of our knowledge, no in vivo therapeutic mAb efficacy data have been published yet for SARS-CoV-2 delta infection in hamsters. In addition, only for REGN-COV2 some therapeutic efficacy was reported in hamsters at such low mAb doses, although after infection of hamsters with SARS-CoV-2 Wuhan and using different readouts32.
Although no clear evidence for antibody-dependent disease enhancement (ADE) in COVID-19 patients has been reported until now, it has been suggested that its potential risk should be continuously monitored. In this light, it should be emphasized that the high potency of 3B8 could be obtained without the contribution of Fc- mediated effector functions, as fully human IgGl antibodies were not species- matched before administration to hamsters. This suggests that antibody 3B8 will tolerate the future introduction of Fc-effector silence mutations to avoid any potential risk of ADE, favoring its further evaluation as a future antibody treatment.
The high therapeutic potency of antibody 3B8 in vivo against SARS-CoV-2 delta, which is currently the most dominant variant worldwide, combined with its broad cross-reactivity against all other tested SARS-CoV-2 variants, make 3B8 a very interesting candidate to help fight the COVID pandemic, also for yet to come coronavirus variants.
The present invention discloses the in vitro neutralizing activity against SARS-CoV-2 delta and omicron. Three mAbs that retain neutralizing activity against both delta and omicron, with mAb 3B8 showing a very high potency with complete neutralization at a concentration of 0.02 pg/ml for both variants. The results reported here for neutralization of SARS-CoV-2 delta are in line with those previously described using another assay format (VSV pseudotyped assay versus plaque reduction assay respectively), thereby indicating a high reliability of the current data. Of note, as our mAb panel was isolated from a convalescent COVID-19 patient who got infected in March 2020 with one of the first SARS-CoV-2 strains, our data also show that at least some of the neutralizing antibodies elicited upon infection (or vaccination) with the original virus strain potently cross-react with SARS-CoV-2 omicron. Considering the broad cross-reactivity and high potency of mAb 3B8 reported previously , together with its strong neutralizing capacity towards SARS-CoV-2 omicron in vitro described here, in combination with the fact that multiple currently available therapeutic mAbs lose their activity against omicron, in particular the Ab 3B8 might be a game-changer to help fight the continuously evolving COVID-19 pandemic.
The phrase "specifically bind(s)" or "bind(s) specifically" when referring to a peptide, refers to a peptide molecule which has intermediate or high binding affinity, exclusively or predominately, to a target molecule. The phrases "specifically binds to" refers to a binding reaction which is determinative of the presence of a target protein in the presence of a heterogeneous population of proteins and other biologies. Thus, under designated assay conditions, the specified binding moieties bind preferentially to a particular target protein and do not bind in a significant amount to other components present in a test sample. Specific binding to a target protein under such conditions may require a binding moiety that is selected for its specificity for a particular target antigen. A variety of assay formats may be used to select ligands that are specifically reactive with a particular protein, for example, solid-phase ELISA immunoassays, or immunoprecipitation. Typically, a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 times background. For instance, antibodies and antibody fragments of the invention preferentially bind to the RBD domain of the spike protein SI subunit of Sars-Cov-2, whereby by "preferentially binding", "preferentially recognizing" or "preferentially reacting with" is meant that the antibodies or antibody fragments show greater binding capacity for RBD domain of the spike protein SI subunit of Sars-Cov-2 as compared to any other antigen. The binding capacity of an antibody or antibody fragment to an antigen is reflective of its affinity and/or avidity for that antigen.
Binding specificity can be expressed by association and dissociation constants as determined by ELISA or BIACORE.
The terms "antibody" and "antibodies" are recognized in the art and refer to proteins also known as immunoglobulins that bind to antigens. It is to be understood that these terms encompass conventional vertebrate antibodies like IgA, IgD, IgE, IgG, IgM, IgT, IgX and IgY, composed of at least two heavy and two light chains, as well as antibodies only composed of two heavy chains (VHH antibodies, IgNAR, heavychain antibodies, single-domain antibodies or nanobodies), and single-chain antibodies. In the case of conventional antibodies, the antigen binding sites are contributed to by the variable domains of both the heavy and light chains (VH and VL). The term "variable domain" refers to the part or domain of an antibody which is partially or fully responsible for antigen binding. Generally, variable domains will be amino acid sequences that essentially consist of 4 framework regions (FRI to FR4 respectively) and 3 complementarity determining regions (CDR1 to CDR3 respectively), or any suitable fragment of such an amino acid sequence which usually contains at least some of the amino acid residues that form at least one of the CDR's. Such variable domains and fragments are most preferably such that they comprise an immunoglobulin fold or are capable for forming, under suitable conditions, an immunoglobulin fold. Each CDR may contribute to a greater or lesser extent to antigen binding by the antibody. Single domain antibodies or heavy-chain antibodies can be found in camelids and sharks, and each of the antigen-binding sites of these antibodies is formed by a single heavy chain variable domain (VHH) only. Therefore, only three CDRs contribute to a greater or lesser extent to each antigen-binding site. Single chain antibodies (scFv) are derived from conventional antibodies by translational fusion of the VH and VL domains, separated by a flexible linker, into a single antigen-binding domain. Framework sequences of an antibody may be altered without altering the antigenic specificity of the antibody, or in order to change the binding affinity of the antibody. Furthermore, conventional antibodies may switch classes or isotypes without substantially affecting antigen-binding characteristics.
The term "complementarity determining region" or "CDR" refers to variable regions of either H (heavy) or L (light) chains (abbreviated as VH and VL, respectively) and contains the amino acid sequences capable of specifically binding to antigenic targets. These CDR regions account for the specificity of the antibody for a particular antigenic determinant structure. Such regions are also referred to as "hypervariable regions." The CDRs represent non-contiguous stretches of amino acids within the variable regions but, regardless of species, the positional locations of these critical amino acid sequences within the variable heavy and light chain regions have been found to have similar locations within the amino acid sequences of the variable chains. The accepted CDR regions and variable domains of an antibody are known to the skilled person and have been described by Padlan et al. (1995) FASEB J. 9, 133-139.
The skilled person is familiar with the concept that, upon alignment of corresponding CDRs of different antibodies with similar antigen specificity, the positions in the alignment which are conserved, i.e. identical in all sequences in the alignment, are critical for the antigen specificity of the antibodies. The residues of a particular CDR at these critical positions are known as "specificity-determining residues" or "SDRs". As a consequence, positions which are not conserved contribute less to the specificity of the antibodies and can be substituted without substantially affecting the antigen specificity of an antibody. Therefore, the skilled person is able to determine which residues could be substituted without substantially affecting antigen specificity of the antibody or antibody fragment. In the same way, the skilled person is able to determine the minimum sequence identity between a particular CDR of an antibody and the corresponding CDR of an antibody of the present invention, which is required for the particular CDR to have a similar antigen specificity as the corresponding CDR of an antibody of the present invention. The same holds true for the variable regions.
By the term "antibody fragment" is meant a fragment of an antibody that largely retains antigen-binding capacity of the antibody from which it is derived. Therefore, an antibody fragment of the invention is capable of preferentially binding to RBD domain of the spike protein SI subunit of Sars-Cov-2. Antigen-binding capacity is determined by the variable domain or domains, more particularly by 1, 2, 3, 4, 5 or 6 CDRs located in the VH and/or VL domains in the case of conventional and singlechain antibodies, and 1, 2 or 3 CDRs in the case of single-domain antibodies. Preferred antibody fragments of the invention therefore comprise antigen-binding sites comprising 1, 2, 3, 4, 5 or 6 CDRs. Two or more CDRs may be physically separated from each other by connecting regions to provide a framework structure for the CDRs. More preferred antibody fragments of the invention comprise antigenbinding sites comprising 1 or 2 variable domains. Examples of antibody fragments are well-known to the skilled person and include the monovalent antigen-binding fragments (Fab), bivalent F(ab')2 fragments, Fv fragments (e.g. single chain antibodies scFv), miniaturized antibodies, single-domain antibody fragments like nanobodies (Nelson (2010) mAbs 2, 77-83). Antibody fragments of the invention may be obtained by enzymatic or chemical proteolysis, or by recombinant DNA technology techniques well known to the skilled person.
Antibodies and antibody fragments of the invention may be further chemically conjugated, non-covalently bound, or translationally fused to other proteins. Single chain antibodies scFv are an example of translational fusion between a VH and a VL domain. Further examples are albumin-conjugated antibodies or antibody fragments, bivalent diabodies, and monospecific and bispecific tandem svFcs (Nelson et al. cited above).
A single-chain antibody (also referred to as "scFv") can be prepared by linking a heavy chain V region and a light chain V region of an antibody. Methods for preparing single-chain antibodies are known in the art (US5,455,030). In such scFvs, the heavy chain V region and the light chain V region are linked together via a linker, preferably, a polypeptide linker. The heavy chain V region and the light chain V region in a scFv may be derived from the same antibody, or from different antibodies.
An "Fv" fragment is the smallest antibody fragment, and contains a complete antigen recognition site and a binding site. This region is a dimer (VH-VL dimer) wherein the variable regions of each of the heavy chain and light chain are strongly connected by a noncovalent bond. The three CDRs of each of the variable regions interact with each other to form an antigen binding site on the surface of the VH-VL dimer. In other words, a total of six CDRs from the heavy and light chains function together as an antibody's antigen-binding site. However, a variable region (or a half Fv, which contains only three antigen-specific CDRs) alone is also known to be able to recognize and bind to an antigen, although its affinity is lower than the affinity of the entire binding site. Thus, a preferred antibody fragment of the present invention is an Fv fragment, but is not limited thereto.
Such an antibody fragment may be a polypeptide which comprises an antibody fragment of heavy or light chain CDRs which are conserved, and which can recognize and bind its antigen.
A Fab fragment (also referred to as F(ab)) also contains a light chain constant region and heavy chain constant region (CHI). For example, papain digestion of an antibody produces the two kinds of fragments: an antigen-binding fragment, called a Fab fragment, containing the variable regions of a heavy chain and light chain, which serve as a single antigen-binding domain; and the remaining portion, which is called an "Fc" because it is readily crystallized. A Fab' fragment is different from a Fab fragment in that a Fab' fragment also has several residues derived from the carboxyl terminus of a heavy chain CHI region, which contains one or more cysteine residues from the hinge region of an antibody.
A Fab' fragment is, however, structurally equivalent to Fab in that both are antigenbinding fragments which comprise the variable regions of a heavy chain and light chain, which serve as a single antigen-binding domain. Herein, an antigen-binding fragment comprising the variable regions of a heavy chain and light chain which serve as a single antigen-binding domain, and which is equivalent to that obtained by papain digestion, is referred to as a "Fab-like antibody", even when it is not identical to an antibody fragment produced by protease digestion. Fab'-SH is Fab' with one or more cysteine residues having free thiol groups in its constant region. A F(ab') fragment is produced by cleaving the disulfide bond between the cysteine residues in the hinge region of F(ab')2. Other chemically crosslinked antibody fragments are also known to those skilled in the art.
Pepsin digestion of an antibody yields two fragments; one is a F(ab')2 fragment which comprises two antigen-binding domains and can cross-react with antigens, and the other is the remaining fragment (referred to as pFc'). Herein, an antibody fragment equivalent to that obtained by pepsin digestion is referred to as a "F(ab')2-like antibody" when it comprises two antigen-binding domains and can cross-react with antigens. Such antibody fragments can also be produced, for example, by genetic engineering. Such antibody fragments can also be isolated, for example, from the antibody phage library described above. Alternatively, F(ab')2-SH fragments can be recovered directly from hosts, such as E. coli, and then allowed to form F(ab')2 fragments by chemical crosslinking.
Antibodies and antibody fragments of the invention may be further modified. Examples of such modifications include the addition of detectable enzymatic, fluorescent, luminescent, or radioactive marker groups or molecules that act in detection such as streptavidin. Other examples include the chemical modification to alter the half-life of antibodies and antibody fragments, such as PEGylation. Still other examples add effector moieties to antibodies and antibody fragments, such as toxins, radioisotopes, enzymes, cytokines, and antigens (Nelson (2010) mAbs 2, 77-83). Antibodies or antibody fragments may be further modified into an antibody-derived scaffold or antibody-like scaffolds that largely retains antigen-binding capacity of the antibody or antibody fragments from which it is derived. Examples of antibody- derived scaffolds or antibody-like scaffolds are domain antibodies (dAb) that selectively or preferentially bind the same epitope as a natural antibody, for instance dAb with fully human frameworks, for instance dAb fused to a human Fc domain or for instance nanobodies engineered in a molecule that has an IgG-like circulating half-life in humans or antibody fragments with retained antigen-binding capacity or domain antibody with active scaffolds for controlled and cell delivery.
Single domain antibodies can be engineered into antibody like fragments. Single domain antibodies are antibodies whose complementary determining regions are part of a single domain polypeptide. Examples include, but are not limited to, heavy chain antibodies, antibodies naturally devoid of light chains, single domain antibodies derived from conventional 4-chain antibodies, engineered antibodies and single domain scaffolds other than those derived from antibodies. Single domain antibodies may be any of the art, or any future single domain antibodies. Single domain antibodies may be derived from any species including, but not limited to mouse, human, camel, llama, goat, rabbit, bovine. According to one aspect of the invention, a single domain antibody as used herein is a naturally occurring single domain antibody known as heavy chain antibody devoid of light chains. Such single domain antibodies are disclosed in WO9404678 for example. For clarity reasons, this variable domain derived from a heavy chain antibody naturally devoid of light chain is known herein as a VHH or nanobody to distinguish it from the conventional VH of four chain immunoglobulins. Such a VHH molecule can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, alpaca and guanaco or Elasmobranchii species for instance skates, rays (batoidea), and sharks (selachii). Other species besides Camelidae may produce heavy chain antibodies naturally devoid of light chain; such VHHs are within the scope of the invention. The singlechain polypeptide may be produced by various methods well known in the art such as genetic engineering technique and chemical synthesis. The genetic engineering technique includes constructing a replicable cloning vector or expression vector, transforming the host cell with the vector, culturing the transformed host cell to express the nucleic acid in it, collecting and purifying the single-chain polypeptide. The vector usually comprises the nucleic acid encoding one of the two single-chain polypeptides constituting the diabody-type bispecific antibody according to the present invention. In such case, the resulting two kinds of the vectors are preferably introduced into the same host cell.
Alternatively, the two kinds of nucleic acid encoding the different single-chain polypeptides from each other may be comprised in the same vector. The term "replicable expression vector" or "expression vector" as used herein refers to a piece of DNA (usually double-stranded) that may comprise a fragment of a foreign DNA fragment inserted therein. The foreign DNA is also defined as a "heterologous DNA", which cannot be found naturally in a host cell in interest. The vector is used to carry or convey the foreign or heterologous DNA into an appropriate host cell. Once the vector is introduced into the host cell, it may be replicated independently from a chromosomal DNA of the host cell to produce copies of the vector and foreign DNA inserted therein. The vector also comprises elements essential for translating the foreign DNA into a polypeptide so that the polypeptide molecules encoded by the foreign DNA will be synthesized very quickly.
The above vector means a DNA construct comprising an appropriate control sequence and DNA sequence that are operably linked together (i.e., linked together so that the foreign DNA can be expressed). The control sequence includes a promoter for transcription, an optional operator sequence to regulate the transcription, a sequence encoding an appropriate mRNA ribosome-biding site, an enhancer, a polyadenylation sequence, and a sequence controlling the termination of transcription and translation. The vector may further comprise various sequences known in the art, such as a restriction enzyme cleaving site, a marker gene (selection gene) such as a drugresistant gene, a signal sequence, and a leader sequence. These sequences and elements may be optionally selected by those skilled in the art depending on the kinds of the foreign DNA and host cell, and conditions of culture medium.
The vector may be in any form such as a plasmid, phage particle, or just simply genomic insert. Once the appropriate host cell is transformed with the vector, the vector will be replicated or function independently from the genome of the host cell, or the vector will alternatively be integrated into the genome of the cell. Any cell known in the art may be used as the host cell, for example, there may be mentioned procaryotic cells such as including E. coli, eucaryotic cells such as mammalian cells such Chinese hamster ovary (CHO) cell and human cells, yeast, and insect cells.
Although the single-chain polypeptide obtained by the expression in the host cell is usually secreted and collected from the culture medium, it may be also collected from cell lysate when it is directly expressed without a secretion signal. In case the singlechain polypeptide has a membrane-binding property, it may be released from the membrane with an appropriate surfactant such as Triton-XIOO.
Purification of the polypeptide may be carried out by any method known to those skilled in the art such as centrifugation, hydroxyapatite chromatography, gel electrophoresis, dialysis, separation on ion-exchange chromatography, ethanol precipitation, reverse phase HPLC, silica chromatography, heparin-sepharose chromatography, anion-or cation-resin chromatography such as polyaspartic acid column, chromato-focusing, SDS-PAGE, precipitation with ammonium sulfate, and affinity chromatography. The affinity chromatography, which utilizes affinity with a peptide tag of the single-chain polypeptide, is one of the preferred purification techniques with a high efficiency.
Since the collected single-chain polypeptide may be often included in an insoluble fraction, the polypeptide is preferably purified after being solubilized and denatured. The solubilization treatment may be carried out with the use of any agent known in the art, including alcohol such ethanol, a dissolving agent such as guanidine hydrochloride and urea.
The antibody-like fragments according to the present invention are produced by assembling the single-chain polypeptides, eventually on a scaffold, and separating and collecting the thus formed antibody-like fragments.
Assembling treatment brings the single-chain polypeptides back in an appropriate spatial arrangement in which a desired biological activity is shown. Thus, since this treatment brings the polypeptides or domains back into an assembling state, it may be considered "re-assembling." It may be also called "re-constitution" or "refolding" in view of gaining the desired biological activity.
The assembling treatment may be carried out by any method known in the art preferably by gradually lowering the concentration of a denaturing agent such as guanidine hydrochloride in a solution comprising the single-chain polypeptide by means of dialysis. During these processes, an anti-coagulant or oxidizing agent may be optionally added in a reaction system in order to promote the oxidation. The separation and collection of the formed antibody-like fragment may be done by any method known in the art as well.
VHHs, according to the present invention, and as known to the skilled addressee, are heavy chain variable domains derived from immunoglobulins naturally devoid of light chains such as those derived from Camelidae as described in WO9404678 (and referred to hereinafter as VHH domains or nanobodies). VHH molecules are about lOx smaller than IgG molecules. They are single polypeptides and very stable, resisting extreme pH and temperature conditions. Moreover, they are resistant to the action of proteases which is not the case for conventional antibodies. Furthermore, in vitro expression of VHHs produces high yield, properly folded functional VHHs. In addition, antibodies generated in Camelids will recognize epitopes other than those recognised by antibodies generated in vitro through the use of antibody libraries or via immunization of mammals other than Camelids or Elasmobranchii species (WO 9749805). As such, anti-albumin VHH's may interact in a more efficient way with serum albumin which is known to be a carrier protein. As a carrier protein some of the epitopes of serum albumin may be inaccessible by bound proteins, peptides and small chemical compounds. Since VHH's are known to bind into 'unusual' or non- conventional epitopes such as cavities (WO9749805), the affinity of such VHH's to circulating albumin may be increased.
In one embodiment, the antibodies and antibody fragments of the invention are humanized. Antibody fragments derived from an antibody of the invention can be fused to the Fc region of a human antibody, in order to obtain humanized antibodies and antibody fragments. Humanized antibodies or antibody fragments can also be obtained by grafting of one or more CDRs or only their specificity-determining residues (SDRs), optionally together with one or more framework residues important for optimal CDR functionality, of a non-human antibody having the desired antigenbinding specificity, into framework polypeptide sequences of a human antibody or 1 antibody fragment, or even into a universal humanized nanobody scaffold. Methods to humanize antibodies are well known to those skilled in the art [see e.g. De Pascalis et al. J Immunol. 169, 3076-3084 (2002)].
The term "humanized antibody" as used herein means a human immunoglobulin (a recipient antibody) in which at least part of the residues of complementary- determining region (CDR) is replaced with residues derived from the CDR of a nonhuman animal antibody (a donor antibody) that has a desired specificity, affinity and capability, such as those of mouse, rat, and rabbit. In some cases, the residue(s) of a Fv framework (FR) in the human immunoglobulin is replaced with residue(s) of the corresponding non-human antibody. The humanized antibody may further comprise a residue that is not found in the recipient antibody or the introduced CDR or framework. These changes are made in order to optimize or improve the properties of the resulting antibody. More detailed information on these changes are referred to Presta Curr. Op. Struct. Biol, 2, 593-596 (1992).
The antibody fragments of the present invention can also be generated using various phage display methods known in the art. In phage display methods, functional antibody domains are displayed on the surface of phage particles which carry the polynucleotide sequences encoding them. In particular, such phage can be utilized to display epitope-binding domains expressed from a repertoire or combinatorial antibody library (e.g., human or murine). Phage expressing an epitope-binding domain that binds the antigen of interest can be selected or identified with antigen, e.g., using labeled antigen bound or captured to a solid surface or bead. Phages used in these methods are typically filamentous phage including fd and M13 binding domains expressed from phage with antigen-binding antibody domains recombinantly fused to either the phage gene III or gene VIII protein. Examples of phage display methods that can be used to make the antibodies or antibody fragments of the present invention include those disclosed in Persic et al. Gene 187, 9-18 (1997).
After phage selection, the regions of the phage encoding the fragments can be isolated and used to generate the epitope-binding fragments through expression in a chosen host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, using recombinant DNA technology. For example, techniques to recombinantly produce antigen-binding fragments can also be employed using methods known in the art such as those disclosed in Sawai et al. AJRI, 34, 2634 (1995). Examples of techniques which can be used to produce single-chain Fvs and antibodies include those described in Shu et al. PNAS 90, 7995-7999 (1993).
Changes may be made to the residues that comprise the CDRs without interfering with the ability of the antibody to recognize and bind its cognate epitope. For example, changes that do not affect epitope recognition, yet increase the binding affinity of the antibody for the epitope may be made. Several studies have surveyed the effects of introducing one or more amino acid changes at various positions in the sequence of an antibody, based on the knowledge of the primary antibody sequence, on its properties such as binding and level of expression [Rader et al., Proc Natl Acad Sci U.S.A. 95, 8910-8915 (1998)]. In these studies (so called affinity maturation techniques), altered versions of the antibody have been generated by changing the sequences of the encoding genes in the CDR1, CDR2, CDR3, or framework regions, using methods such as oligonucleotide-mediated site-directed mutagenesis, cassette mutagenesis, error-prone PCR, DNA shuffling, or mutator-strains of E. coli (Vaughan et al. Nat Biotechnol. 16, 535-539 (1998)). These methods of changing the sequence of the antibody have resulted in improved affinities of the resulting antibodies [e.g. Short et al. J Biol Chem. 277, 16365-16370 (2002)].
In a preferred embodiment of the invention, the antibody of the invention is monoclonal. The term "monoclonal antibody" is well recognized in the art and refers to an antibody or a homogenous population of antibodies that is derived from a single clone. Individual antibodies from a monoclonal antibody population are essentially identical, in that minor naturally occurring mutations may be present. Antibodies from a monoclonal antibody population show a homogenous binding specificity and affinity for a particular epitope.
As used herein, "percentage identity" or"% sequence identity" between two or more amino acid sequences or two or more nucleotide sequences refers to the ratio, expressed in %, of : the number of amino acids or nucleotides in an optimal alignment of the amino acid sequences or nucleotide sequences that are identical in both sequences (i.e. match), to the length of the alignment, i.e. the number of aligned positions, including gaps if any.
The term "nucleic acid" is intended to include DNA molecules and RNA molecules. A nucleic acid can be single-stranded or double-stranded. The nucleic acids of the invention are present in whole cells, in a cell lysate, or in a partially purified or substantially pure form. A nucleic acid is "isolated" or "rendered substantially pure" when purified away from other cellular components or other contaminants, e.g., other cellular nucleic acids or proteins, by standard techniques, including alkaline/SDS treatment, CsCI banding, column chromatography, agarose gel electrophoresis and others well known in the art. see, e.g., Sambrook, Tijssen and Ausubel. The nucleic acid sequences of the invention and other nucleic acids used to practice this invention, whether RIMA, cDNA, genomic DNA, or hybrids thereof, may be isolated from a variety of sources, genetically engineered, amplified, and/or expressed recombinantly. Any recombinant expression system can be used, including, in addition to bacterial, e.g., yeast, insect or mammalian systems. Alternatively, these nucleic acids can be chemically synthesized in vitro. Techniques for the manipulation of nucleic acids, such as, e.g., subcloning into expression vectors, labeling probes, sequencing, and hybridization are well described in the scientific and patent literature, see, e.g., Sambrook, Tijssen and Ausubel. Nucleic acids can be analyzed and quantified by any of a number of general means well known to those of skill in the art. These include, e.g., analytical biochemical methods such as NMR, spectrophotometry, radiography, electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), and hyperdiffusion chromatography, various immunological methods, such as fluid or gel precipition reactions, immunodiffusion (single or double), immunoelectrophoresis, radioimmunoassays (RIAs), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, Southern analysis, Northern analysis, dot-blot analysis, gel electrophoresis (e.g., SDS-PAGE), RT-PCR, quantitative PCR, other nucleic acid or target or signal amplification methods, radiolabeling, scintillation counting, and affinity chromatography.
The nucleic acid compositions of the present invention, while often in a native sequence (except for modified restriction sites and the like), from either cDNA, genomic or mixtures may be mutated, thereof in accordance with standard techniques to provide gene sequences. For coding sequences, these mutations, may affect amino acid sequence as desired. In particular, DNA sequences substantially homologous to or derived from such sequences described herein are contemplated (where "derived" indicates that a sequence is identical or modified from another sequence).
EXAMPLES EXAMPLE 1. Identification and characterization of anti-SARS-CoV-2 antibodies from convalescent COVID-19 patients
To identify fully human SARS-CoV-2 neutralizing antibodies, we first analyzed RBD- binding titers and neutralizing antibody titers in serum, as well as the percentage RBD-positive B cells in PBMCs from 26 convalescent COVID-19 patients (see Table 1).
Table 1: overview of RBD-binding titers and neutralizing antibody titers in serum, and percentage RBD-positive B cells in PBMCs from 26 convalescent COVID-19 patients
Figure imgf000032_0001
Patient K-COV19-901, having both a high titer of neutralizing antibodies and a high number of RBD-specific B cells, was selected for the isolation of individual RBD- specific B cells via fluorescence-activated cell sorting (FACS), using biotinylated RBD (Wuhan isolate) combined with streptavidin-PE as bait (Figure 7). Next, these single B cells were used as starting material for our single B cell cloning strategy, where we amplified the coding sequence of the IgG antibody heavy and light chain variable domains and combined them with the human IgGl constant domain in a vector for recombinant antibody production. A panel of 20 unique antibody sequences (labelled K-COV-901-X, further mentioned as "X") was selected for in vitro production and subsequent characterization. All 20 antibodies retained RBD and trimeric spike antigen (Wuhan) binding in vitro when analyzed via ELISA or surface plasmon resonance (SPR) assays. In addition, antibodies showed picomolar affinities to the RBD antigen and tri meric spike antigen with equilibrium constants (KD values) ranging from 31 to 443 pM and 32 to 243 pM, respectively (Table 2).
Next, we evaluated the functional activity of these antibodies in vitro. To this end, we used a pseudovirus assay with vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike protein (D614G) on its surface and evaluated pseudovirus infection of Vero E6 cells in the presence and absence of each of the antibodies. Out of 20 mAbs, 16 could neutralize SARS-CoV-2 pseudovirus infection, with 8 very potent mAbs having a half-maximal 50% inhibitory concentration (IC50) lower than 1 nM and antibody 3B8 having an IC50 of only 0.017 nM (Figure 1 8<. Table 2). Given their potent neutralizing capacity, these 8 mAbs were selected for further characterization.
Table 2: Overview of antigen binding, affinity and neutralizing capacity of 20 selected antibodies.
Figure imgf000033_0001
Figure imgf000034_0001
Antigen binding was evaluated for RBD and trimeric spike protein (Wuhan) via ELISA (in duplicate) and SPR (min. triplicate). Affinity (KD ; in pM; average ± standard deviation of at least 3 replicates) was determined via SPR. Neutralizing capacity is given in 50% inhibitory concentration (IC50; in nM) and was measured in triplicate via a SARS-CoV-2 D614G VSV pseudovirus assay. Bold and italic = 8 best neutralizing antibodies; + = potent antigen binding (OD > 2) at antibody concentration of 1 pg/ml or lower; / - no neutralizing activity when tested at a concentration of 5 pg/ml or 33.34 nM.
Example 2. Evaluation of in vitro efficacy against SARS-CoV-2 variants and other coronavirus species
With the continuous emergence of new SARS-CoV-2 variants, it was crucial to evaluate antigen binding and neutralizing capacity of the selected antibodies against these variants as well. RBD antigens bearing the single mutations E484K, E484Q, N501Y and L452R, present - alone or combined - in multiple SARS-CoV-2 variants (i.e. alpha, beta, gamma, delta and others), as well as RBD antigens bearing the double mutation E484Q, L452R or triple mutation K417N, E484K, N501Y, as present in SARS-CoV-2 variants kappa and beta respectively [CDC. SARS-CoV-2 Variant Classifications and Definitions. Sep 23 https://www.cdc.gov/coronavirus/2019- ncov/variants/variant-info.html#Interest (2021)], were used to assess binding and affinity of the 8 most potent antibodies via both ELISA and SPR. In addition, RBD mutations N439K, described as an antibody evasion mutant [Thomson et al. Cell 184, 1171-1187. e20 (2021); Chen et al. J. Mol. Biol. 433, (2021); Sanyaolu et al. Ther. Adv. Vaccines 8, 1-10 (2021)], and RBD Y453F, originating from Danish mink farms and a potential neutralization resistance mutation [Lassauniere et al. Front. Microbiol. 12, 1-9 (2021); Baum et al. Science 369, 1014-1018 (2020)], were evaluated (an overview of the analyzed RBD single mutations and their presence in SARS-CoV-2 variants is given in Table 3).
Table 3: overview of single RBD mutants used in this study and their presence in different SARS-CoV-2 variants of concern, variants of interest, variants under monitoring or de-escalated variants. Information retrieved from European Centre for Disease Prevention and Control (https://www.ecdc.europa.eu/en/covid-19/variants- concern)
Figure imgf000035_0001
*These variants of SARS-CoV-2 have been de-escalated based on at least one the following criteria: (1) the variant is no longer circulating, (2) the variant has been circulating for a long time without any impact on the overall epidemiological situation, (3) scientific evidence demonstrates that the variant is not associated with any concerning properties (https://www.ecdc.europa.eu/en/covid-19/variants-concern).
Interestingly, 7 out of 8 antibodies retained their binding capacity against all analyzed RBD single mutant antigens. One antibody, 2B11, showed reduced binding to RBD L452R and did not bind RBD E484K. This antibody did neither bind the antigens with multiple mutations that included L452R or E484K. Antibody 1C11, although binding with all single mutant antigens, lost its activity against RBD L452R, E484Q double mutant antigen (Table 4 top part). All antibodies that bound the single mutant RBD antigens, still showed high affinities to these antigens, as evident from the equilibrium constants (KD) ranging from 9 - 647 pM. Only antibodies 1C11 and 2B11 showed an increased KD value for RBD L452R (2940 pM and 3146 pM respectively) (Table 4 bottom part). able 4: Overview of binding and affinity of top 8 mAbs with
RBD mutant antigens
Figure imgf000036_0001
Antigen binding was evaluated for RBD mutant antigens via ELISA and SPR. Affinity (Ko ; in pM) was determined via SPR, mean ± standard deviation of minimum 3 replicates is given. + = maximal signal obtained at antibody concentration of 1 pg/ml or lower; ± = ± 50% of the maximal signal was obtained at 1 pg/ml; / - no signal was obtained at antibody concentration of 1 pg/ml; - = no binding at RBD antigen concentration of 80 nM
In addition to antigen binding, functional activity against SARS-CoV-2 variants was evaluated in a cytopathic effect neutralization test (CPENT) using live SARS-CoV-2 Wuhan, alpha, beta and gamma virus strains and Vero E6 cells, as well as in a plaque reduction neutralization test (PRNT) using live SARS-CoV-2 delta strain with the same cell line. Infection with SARS-CoV-2 Wuhan and alpha was best neutralized by antibodies 3B8 and 2B2 (IC50 < 0.63 and < 0.16 nM respectively), while SARS-CoV- 2 beta infection was best neutralized by antibodies 3B8 and 3E6 (IC50 < 0.32 nM). The same was true for SARS-CoV-2 gamma (IC50 < 0.37 nM for 3B8 and 3E6), although the high standard deviations hinder drawing strong conclusions. SARS-CoV- 2 delta was most potently neutralized by 3B8 (IC50 = 0.01 nM), with next in line antibodies 1C1, 2D6, 3E6 (IC50 values between 0.98 - 1.08 nM). On the other hand, antibodies 2B11 and 1C11 lost their neutralizing activity against SARS-CoV-2 delta (IC50 > 67 nM). Overall, antibody 3B8 was the most potent neutralizing mAb towards all variants, with IC50 values ranging from 0.37 nM to 0.01 nM for neutralization of SARS-CoV-2 gamma and delta strain respectively (Figure 2 and Table 5).
Table 5: Overview of in vitro neutralizing activity (IC50) towards SARS-CoV- 2 Wuhan, alpha, beta, gamma and delta for top 8 mAbs.
Figure imgf000037_0001
Neutralizing activity (IC50; in nM) was determined via CPE assay for SARS-CoV-2 Wuhan, alpha, beta and gamma and via PRNT assay for SARS-CoV-2 delta.
The eight selected neutralizing antibodies were also tested for their ability to cross- neutralize other human coronavirus strains using VSV pseudotypes expressing the spike protein from SARS-CoV, Middle East respiratory stress (MERS)-CoV or 229E- CoV on their surface. However, none of the selected antibodies was able to cross- neutralize one of these coronavirus species when used at a concentration of 16.67 nM (or 2.5 pg/ml) (data not shown).
Example 3. Classification of antibody epitopes
The selected mAbs were classified in different categories based on their epitope specificity using an ELISA cross-competition assay where the antibodies were pairwise tested against one another. Two groups could be distinguished consisting of antibodies 1A10, 1C1 and 2D6 on the one hand and antibodies 2B2, 2B11 and 1C11 on the other hand. Antibodies 3B8 and 3E6 could not be classified in one of these groups (Figure 3). This suggests that the 8 selected mAbs bind to 4 different regions of the RBD antigen. Example 4. Potent in vivo efficacy on different SARS-CoV-2 variants in the Syrian golden hamster model
Antibodies, 3B8, 3E6, 2B2 and 1C1, were selected for in vivo evaluation based on their in vitro neutralizing activity combined with their variability in epitope binding. In a first study, 30 hamsters were divided into 5 groups (6 animals/group) and infected intranasally with 50 pl of SARS-CoV-2 Wuhan virus suspension (containing approximately 2xl06 tissue culture infective dose (TCIDso))- After 24h, antibodies 3B8, 3E6, 2B2, 1C1 or an IgGl isotype control were injected intraperitoneally at a dose of 5 mg/kg. All animals were sacrificed at 4 days post infection for analysis of viral RIMA and viral infectious titer in the lungs, as well as antibody concentration in serum (Figure 4a). The presence of therapeutic RBD-specific human antibodies circulating in the blood of the treated hamsters was verified through ELISA. This revealed that 5 animals (1 out of 6 for clone 3E6 and 2 out of 6 for clones 2B2 and 1C1) were not successfully injected (Figure 4b). We therefore excluded all animals without detectable serum levels from further analysis. In all groups, antibody treatment reduced viral RNA load in lung tissue as compared to the isotype control group with statistical significance (p < 0.05 for 2B2; p < 0.01 for 3B8, 3E6, 1C1) (Figure 4c). No infectious virus in the lung tissue could be detected in any of the animals treated with antibody 3B8. In animals treated with antibodies 3E6 and 2B2, a low infectious titer was detected in 1 animal, while three out of four animals treated with antibody 1C1 had a low detectable titer. In all groups, the difference was statistically significant (p < 0.01) compared to the isotype control group, thus showing good in vivo efficacy for the treatment of SARS-CoV-2 (Wuhan) infection (Figure 4d).
As it was shown previously that SARS-CoV-2 variants of concern beta and delta are more resistant to neutralization by vaccine-induced antibodies or currently available mAb treatments, and given that SARS-CoV-2 delta is the most dominant variant worldwide, we decided to evaluate in vivo treatment efficacy of our antibodies against both variants as well. A study design similar to the first study was used, with 30 hamsters divided in 5 groups and intranasally infected with 50 pl of SARS-CoV-2 beta or SARS-CoV-2 delta suspension (both containing approximately IxlO4 TCIDso)- Animals were injected intraperitoneally with IgGl isotype control or antibodies 3B8, 3E6, 2B2 and REGN-COV-2 at 5 mg/kg 24h post infection and were sacrificed 4 days post infection, with REGN-COV-2 antibody cocktail being included for benchmarking purposes. In the study using SARS-CoV-2 beta, one animal from groups 3B8, 2B2, 1C1 and REGN-CoV-2 as well as two animals from group 3E6 were excluded from analysis because of the absence of detectable antibody serum levels (Figure 5a). In addition, it should be noted that two animals, one from group 3B8 and one from group 2B2, showed very low antibody serum titers, but were not excluded from analysis (indicated by open symbols in the respective groups). Viral RNA load in lung tissue was significantly reduced by treatment with antibody 3B8, 3E6 and REGN-CoV- 2 compared to isotype control (p < 0.05 for 3B8 and 3E6; p < 0.01 for REGN-CoV- 2), while the reduction observed for 2B2 was not statistically significant (Figure 5b). No infectious viral titer in lung tissue (TCID50) could be detected upon treatment with 3B8, 3E6 or REGN-CoV-2 (p < 0.01 compared to isotype control), while a viral titer was still detectable in four out of five animals treated with 2B2 (Figure 5c). When analyzing the efficacy of our antibodies against SARS-CoV-2 delta infection, a similar picture was observed. Here, only one animal from group 2B2 was excluded because of a lack of detectable serum concentrations (Figure 5d). All treatments resulted in a significant reduction (p < 0.01) of both viral load and infectious viral titers in lung tissue (Figure 5 e and f), with no detectable viral titers in animals treated with antibodies 3B8, 3E6 and REGN-CoV-2. In conclusion, treatment with antibodies 3B8 and 3E6 at 24h post infection resulted in a statistically significant reduction of virus in lung tissue of animals infected with SARS-CoV-2 beta or delta. Although significantly reducing infectious viral titers in lung tissue of animals infected with SARS-CoV-2 delta, antibody 2B2 seems to be less potent as treatment for SARS- CoV-2 beta and delta infection compared to antibodies 3B8 and 3E6.
Example 5. Dose-dependent therapeutic efficacy of 3B8
Antibodies 3B8 and 3E6 both completely abrogated infectious viral titers after infection with SARS-CoV-2 Wuhan, beta and delta when administered 24h post infection at 5mg/kg. As 3B8 was superior to 3E6 in in vitro neutralization experiments, this antibody was used in an in vivo dose-response experiment. Hamsters were intranasally infected with SARS-CoV-2 delta (IxlO4 TCIDso). At 24h post infection, isotype control (5 mg/kg) or antibody 3B8 (5 mg/kg; 1 mg/kg, 0.2 mg/kg or 0.04 mg/kg) was administered intraperitoneally. Animals were sacrificed at day 4 post infection. No animals were excluded from analysis based on a lack of detectable antibody serum levels, although one animal from group 0.2 mg/kg had serum levels 3 times lower compared to its group members (animal indicated by open symbol) (Figure 6a). Treatment with a dose of 5 mg/kg and 1 mg/kg of 3B8 significantly reduced the amount of viral RIMA detected in lung tissue, and resulted in undetectable levels of infectious virus. When dosing at 0.2 mg/kg, no decrease in viral RNA was seen, but infectious virus was undetectable in lung tissue of 3 out of 6 animals, and was decreased (more than 4 times lower than lower limit of 95% confidence interval from isotype control group) in a fourth animal. In the animal having reduced antibody titers (open symbol), no reduction in viral titer could be observed. Also, at the lowest dose of 0.04 mg/kg, no effect could be observed on viral RNA or infectious viral titer (Figure 6b and c).
EXAMPLE 6. DNA based vaccination.
3B8 was delivered encoded in plasmid DNA (pDNA) in vivo, as an equimolar mixture of the 3B8 heavy and light chain. Hamsters received an intramuscular pDNA injection in their right & left tibialis anterior and gastrocnemius muscle (pretreated with hyaluronidase), followed by electroporation. This allows for intramuscular production and systemic circulation of 3B8. A series of electrical pulses were thereby delivered at 120V, using a plate electrode. Total pDNA amount delivered per hamster was 600 pg (75 pl pDNA, at 2 pg/pl per muscle). Intramuscular pDNA administration was performed either on day -10, day -7 or day -5 infection (6 animals per timepoint). On day 0, all animals were infected intranasally with SARS-CoV-2 delta (B.1.617.2). Animals of the negative control group were left untreated. Animals were sacrificed at day 4 for analysis of viral RNA levels (left panel) and infectious viral titers (right panel) in their lungs. Injection of hamsters with 3B8 pDNA resulted in a 5-fold log reduction of viral RNA in the lungs, and undetectable infectious viral titers in all animals except for 1, pointing to a successful neutralization of SARS-CoV-2 delta in all groups. In the figure, individual data with median values are shown. Dotted line represents the detection limit. ** = p < 0.01 as determined via Mann-Whitney U test.
EXAMPLE 7. Neutralizing capacity of anti-SARS-CoV-2 human mAbs against SARS-CoV-2 delta and omicron
We evaluated the neutralizing capacity of our eight anti-SARS-CoV-2 human mAbs against SARS-CoV-2 delta and omicron, using a pseudovirus assay with vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike protein from the delta or omicron variant. As shown in Figure 9A, six out of eight mAbs neutralized SARS-CoV- 2 delta, with mAb 3B8 still resulting in complete neutralization at a concentration of 0.02 pg/ml, corresponding to our previously reported data using a plaque reduction neutralization assay. In addition, three of the eight mAbs also retained neutralizing activity towards SARS-CoV-2 omicron (Figure 9B), with mAbs 2B2 and 1A10 showing 50% neutralization of omicron (IC50) at a concentration of 1.1 and 1.7 pg/ml respectively. Highly interesting, mAb 3B8 completely neutralized SARS-CoV-2 omicron at the lowest concentration tested (0.02 pg/ml).
EXAMPLE 8. Materials and methods
Isolation of PBMCs from convalescent COVID-19 patients
Patients with a PCR-confirmed SARS-CoV-2 infection (>18 years old; recovered from disease) were recruited from the University Hospital Leuven or AZ Groeninge Kortrijk for peripheral blood collection. The study and corresponding experiments were approved by the local ethics committee (S64089) and all patients gave their written informed consent. Immediately after blood sample collection, peripheral blood mononuclear cells (PBMCs) were isolated from EDTA-treated blood by density centrifugation (Lymphoprep, STEMCELL Technologies Inc). After washing, the collected PBMCs were resuspended in freezing medium consisting of 10% (v/v) dimethyl sulfoxide (DMSO; Merck) and 90% fetal bovine serum (FBS; GIBCO) for cryopreservation at -80°C or in liquid nitrogen for long term storage.
Single-cell sorting of antigen-specific B cells
Human B cells were enriched from cryopreserved PBMCs using the EasySep™ Human B Cell Enrichment Kit (STEMCELL Technologies) according to the manufacturer's instructions. After purification, B cells were stained with Zombie Aqua™ Fixable Viability Kit (Biolegend) and blocked with FcR Blocking Reagent (Miltenyi Biotec) for 15 minutes on ice. Following the 15 minutes incubation, B cells were washed with FACS buffer (phosphate-buffered saline (PBS) + 2% FBS + 2 mM EDTA) and incubated with biotinylated SARS-CoV-2 RBD protein for 60 minutes at on ice. His- tag labeled SARS-CoV-2 RBD (The Native Antigen Company) was biotinylated with the EZ-Link Sulfo-NHS-LC-Biotin kit (Thermofisher Scientific) according to the manufacturer's protocol, corresponding to 1-3 biotin groups per antibody molecule. After the 60 minutes incubation, B cells were washed with FACS buffer and stained with PerCP-cy5.5 anti-human CD19 antibody (Biolegend, 363016), FITC anti-human CD3 antibody (Biolegend, 300306) and PE streptavidin (Biolegend, 405203) for 25 minutes on ice. Subsequently, the stained cells were washed twice with FACS buffer and single-cell sorted by BD Influx™ Cell Sorter (BD Biosciences). UltraComp eBeads™ Compensation Beads and tosylactivated M-280 Dynabeads (Invitrogen) coupled with SARS-CoV-2 RBD protein according to the manufacturer's instructions were used for compensation. Selection of RBD-specific B cells was performed using the following gating strategy: lymphocytes were selected using FSC and SSC, followed by selection of single cells based on width versus area of FSC and SSC signals. Next, live cells were selected as Zombia Aqua negative cells. Here, B cells were selected as CD19+ CD3- cells and evaluated for RBD surface staining. To allow proper gating of RBD-positive cells, a fluorescence minus one (FMO) control was included (figure 7). Individual B cells were sorted into 96-wells PCR plates (Bioke) containing 2 pL lysis buffer (0.2% (v/v) Triton X-100 + 2U/pL RNaseOUT™ Recombinant Ribonuclease (Invitrogen) in UltraPure™ DNAse/RNase free distilled water (Invitrogen)) per well. The plates were sealed with a Microseal® 'F' Film (BioRad) and immediately frozen on dry ice before storage at -80°C for further use.
Amplification of antibody variable domains
Transcripts of lysed single B cells were denatured and hybridized with a mix of 1 pL 10 mM each nucleotide dNTP-Mix (Invitrogen) and 1 pL 10 pM oligo-dT primerat 72°C for 3 minutes. Subsequently, cDNA synthesis and pre-amplification was performed according to Picelli et al43. cDNA was stored at -20°C. cDNA was purified with Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer's protocol and quantified on the BioAnalyzer 2100 instrument (Agilent) and on a Qubit™ fluorometer (Thermofisher Scientific). The sequences encoding the immunoglobulin (Ig) heavy- and light-chain variable regions (VH and VL) of IgM and IgG were amplified using reverse primers described in Ozawa et al. Biotechniques 40, 469-478 (2006) and forward primer described by Picelli et al. Nat. Protoc. 9, 171-181 (2014). The PCR reaction was performed with KAPA HiFi HotStart ReadyMix (Roche) at 95°C for 3 min, followed by 30 cycles at 98°C for 20 seconds, 60°C for 45 seconds and 72°C for 60 seconds and terminated at 72°C for 5 minutes. All PCR products were checked on a 1% agarose gel and purified using the Agencourt AMPure XP beads. Concentrations were measured on a Qubit™ fluorometer for Sanger sequencing.
Recombinant antibody production and purification
Generation and amplification of expression vectors containing the selected heavy- and light chain sequences
Generation of antibody expression vectors was outsourced (Genscript). The Ig VH and VL sequences were cloned into a pcDNA3.4 expression vector containing human IgGl constant regions. The plasmid DNA (pDNA) was amplified by transformation in DH5o E. coli and subsequent purification using the NucleoBond Xtra Maxi EF kit (Machery - Nagel) according to the manufacturer's instructions. Plasmid purity and integrity was checked on a 1% agarose gel.
Production of recombinant antibody in HEK93F cells
Recombinant antibodies were transiently transfected and produced in vitro in 293F Freestyle suspension cells (Thermofisher Scientific). Briefly, equal amounts of heavy- and light chain pDNA were mixed with X-tremeGENE HP DNA Transfection Reagent (Roche) in Freestyle™ 293 Expression Medium (Thermofisher Scientific) according to the manufacturer's protocol and incubated for at least 15 minutes to allow the pDNA to enter the liposomes. The transfection reagent mixture was added in a dropwise manner to 293F Freestyle suspension cells. The cells were cultured in T175 flasks (Sarstedt, Germany) on an orbital shaker (Thermofischer Scientific) at 135 rpm and 8% CO2 in a 37°C humidified incubator for 5 days. At day 5, supernatant containing the recombinant antibodies was collected by centrifugation (1,400 x g for 10 minutes at room temperature), filtered through a 0.2 pm filter unit (VWR) and stored at - 20°C.
Purification of recombinant antibody
Purification of the recombinant antibodies was conducted on a AKTAprime plus system (GE Healthcare Life Sciences) at 4°C using a 1 mL HiTrap® Protein A HP prepacked Protein A Sepharose® column (Cytiva). Briefly, the column was first equilibrated in buffer A (20 mM sodium phosphate, 150mM NaCI, pH 7.5) before the sample was loaded on the column. The flow rate for all steps was 1 mL/min. The column was washed with buffer A and buffer B (20mM Sodium Phosphate, 500 mM NaCI, pH 7.5). The recombinant antibodies were eluted from the column with 100 mM sodium acetate, pH 3.5 and the collected fractions were immediately neutralized with IM Tris, pH 9. The fractions were pooled and dialyzed against sterile-filtered PBS. The AKTAprime plus system and all glasswork was treated with 30% hydrogen peroxide (VWR) to reduce the presence of endotoxin.
Quality control using SDS-PAGE and endotoxin measurements
Purified recombinant antibodies were assessed by SDS-PAGE under nonreducing conditions using the Amersham Phastsystem™ (GE Healthcare) according to the manufacturer's instructions. Endotoxin levels were measured on Endosafe®-PTS™ (Charles River) according to the manufacturer's instructions.
ELISA
Antigen binding
The binding of the purified recombinant antibodies to the following SARS-CoV-2 antigens was assessed via ELISA: spike glycoprotein (SI) RBD-His (REC31849-500, The Native Antigen Company), RBD(N439K)-His (40592-V08H14, Sino Biological), RBD(N501Y)-His (40592-V08H82, Sino Biological), RBD(E484K)-His (40592-
V08H84, Sino Biological), RBD(Y453F)-His (40592-V08H80, Sino Biological), RBD(E484Q)-His (40592-V08H81, Sino Biological), RBD(L425R)-His (40592-
V08H28, Sino Biological), RBD(L425R,E484Q)-His (40592-V08H88, Sino Biological), RBD(K417N, E484K, N501Y)-His (40592-V08H85, Sino Biological), Spike Glycoprotein (Full-Length)-His (REC31868-500, The Native Antigen Company). Briefly, polystyrene 96-well flat-bottom microtiter plates (Corning costar) were coated with 100 pL/well of 2 pg/mL antigen diluted in PBS and incubated overnight at 4°C. The next day, plates were blocked with 200 pL/well blocking buffer containing 1% (w/v) Bovine Serum Albumin (BSA, Sigma Aldrich) in PBS for 2 hours at room temperature. The plates were then washed six times with wash buffer (0.002% (v/v) Tween-80 (Sigma Aldrich) in PBS). After washing, 100 pL/well of the samples, calibrators and/or controls were added. As a positive and negative control, an anti- SARS-CoV-2 RBD mAb (40150-D004, Sino Biological) and anti-SARS-CoV-2 nucleocapsid antibody (MBS2563841, MyBioSource) were used, respectively. All samples and controls were diluted in PBS + 0.1% (w/v) BSA + 0.002% (v/v) Tween 80 with or without 1,86 g/L EDTA (PTA(E) buffer). After incubation, the plates were washed six times and incubated with 100 pL/well horseradish peroxidase (HRP)- conjugated goat anti-human IgG (Fc-specific, Sigma Aldrich) diluted 1/5000 in PTA buffer. After 1 hour incubation at room temperature, the plate was again washed six times and 100 pL/well substrate (200 pL 40 mg/mL o-Phenylenediamine dihydrochloride 99+% (OPD, Acros Organics BVBA) + 2 pL H2O2 (Merck) in 20 mL citrate buffer, pH 5 (0.1 M citric acid monohydrate from Sigma and 0.2 M disodium phosphate dihydrate from Merck)) was added to the plate and incubated for 30 minutes in the dark. The color reaction was stopped with 50 pL/well 4 M H2SO4 (Thermofisher Scientific). Optical density (OD) was measured at 492 nm with an ELx808 ELISA reader (BioTek). Analysis was performed using Graphpad Prism 9.0 (Graph pad Software). Competition assay
Polystyrene 96-well flat-bottom microtiter plates were coated with 4 pg/mL purified recombinant capture antibody in PBS (100 pL/well) and incubated at 4°C. After an overnight incubation, plates were blocked with 200 pL/well blocking buffer for 2 hours at room temperature. The plates were washed six times with washing buffer and 10 ng/mL SARS-CoV-2 RBD protein diluted in PTA buffer (100 pL/well) was added to the plates for a 2-hour incubation at room temperature. After the incubation, the plates were washed and captured antigen was detected with 100 pL/well of 1/100 biotin- conjugated purified recombinant antibodies diluted in PTA buffer. Biotinylation of the purified recombinant mAbs was performed with the EZ-Link Sulfo-NHS-LC-Biotin kit according to the manufacturer's protocol. After a 1-hour incubation at room temperature and washing, biotinylated recombinant antibodies that were able to bind the antigen were detected with 1/10,000 poly-HRP-conjugated streptavidin (Sanquin) diluted in PTA buffer (100 pL/well) and incubated for an additional 30 minutes at room temperature. After a final washing step, 100 pL/well substrate was added to the plate and incubated at room temperature for 30 minutes in the dark at room. The color reaction was stopped with 50 pL/well 4 M H2SO4. Optical density (OD) was measured at 492 nm with an ELx808 ELISA reader (BioTek). Very low OD values indicate the detection antibody was not able to bind, suggesting similar epitopes of both coating and detection antibodies, while high OD values indicate both antibodies have a different epitope. Epitope binning graphs were made in Microsoft Excel and clustering was done with ClustVis web tool (htt
Figure imgf000045_0001
iit.cs.ut.ee/clustvis/).
Surface plasmon resonance
Surface Plasmon Resonance (SPR) was used to evaluate the interaction between monoclonal Abs and SARS-CoV-2 antigens (i.e. full-length spike protein, RBD and RBD mutants; see catalog numbers under Methods section "ELISA"). The binding experiments were performed at 25°C on a Biacore T200 instrument (GE Healthcare, Uppsala, Sweden) in HBS-EP+ buffer (10 mM HEPES, 150 mM NaCI, 3 mM EDTA and 0.05% v/v Surfactant P20). First, mouse anti-human IgG (Fc) antibody (Human Antibody Capture Kit, Cytiva) was immobilized on a CM5 chip according to manufacturer instructions. Monoclonal Abs were then captured between 30 and 100 RU. Increasing concentrations of analyte were sequentially injected in one single cycle at a flow rate of 30 pl/min. The dissociation was monitored for 30 min. The chip was finally regenerated with 3M MgCI2 before a new mAb was captured. A reference flow was used as a control for non-specific binding and refractive index changes. Several buffer blanks were used for double referencing. Binding affinities (KD) were derived after fitting the experimental data to the 1 : 1 binding model in the Biacore T200 Evaluation Software 3.1 using the single cycle kinetic procedure. Each interaction was repeated a least three times.
Monoclonal antibody neutralization assays
Production of S-pseudotyped virus and serum neutralization test (SARS2, SARS1, MERS, 229E)
VSV S-pseudotypes were generated as described in Sanchez-Felipe et al. Nature 590, 320-325 (2021). Briefly, HEK-293T cells (SARS-CoV, SARS-CoV-2 and MERS-S) or BHK-21J cells (229E) were transfected with the respective S protein expression plasmids, and one day later infected (MOI = 2) with GFP-encoding VSVAG backbone virus (purchased from Kerafast).
Production of S-pseudotyped virus and serum neutralization test:
HEK-293T cells were transfected with the respective S protein expression plasmids for the Delta variant (Cat. No. plv-spike-v8, Invivogen) and the Omicron variant (A67V, A69-70, T95I, G142D, A143-145, A211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F as based on the information available on the ECDC website on November 29th, 20212) and one day later infected (MOI = 2) with GFP- encoding VSVAG backbone virus (purchased from Kerafast). Two hours later, the medium was replaced by medium containing anti-VSV-G antibody (Il-hybridoma, ATCC CRL-2700) to neutralize residual VSV-G input. After 24 h incubation at 32 0, the supernatants were harvested. To quantify nAbs, serial dilutions of serum samples were incubated for 1 hour at 37 °C with an equal volume of S pseudotyped VSV particles and inoculated on Vero E6 cells.
Two hours later, the medium was replaced by medium containing anti-VSV-G antibody (Il-hybridoma, ATCC CRL-2700) to neutralize residual VSV-G input. After 24 h incubation at 320, the supernatants were harvested. To quantify nAbs, serial dilutions of serum samples were incubated for 1 hour at 37 °C with an equal volume of S pseudotyped VSV particles and inoculated on Vero E6 cells (SARS-CoV and SARS- CoV-2) or Huh-7 cells (229E and MERS-S) for 18 hours. The percentage of GFP expressing cells was quantified on a Cell Insight CX5/7 High Content Screening platform (Thermo Fischer Scientific) with Thermo Fisher Scientific HCS Studio (v.6.6.0) software. Neutralization IC50 values were determined by normalizing the serum neutralization dilution curve to a virus (100%) and cell control (0%) and fitting in Graphpad Prism (GraphPad Software, Inc.).
Cell-based cytopathic (CPE) assay and CPE-based virus neutralization test (CPENT) (SARS-CoV-2 Wuhan, alpha, beta, gamma)
The titers of the virus stocks (TCID50) and 50% neutralizing titers (log CPENTso) were determined using cytopathic effect (CPE)-based cell assays and CPE-based virus neutralization tests (CPENT), respectively, on VeroE6 cells with some modifications. Shortly, 104 VeroE6 cells/well were seeded in 96-well plates one day prior to the titration and inoculated with 10-fold serial dilutions of virus solutions and cultured for 3 days at 37°C. Later, assays first visually scored for CPE and then stained with MTS/Phenazine methosulphate (PMS; Sigma- Aldrich) solution for 1.5 h at 37 °C in the dark. Post MTS/PMS staining absorbance was measured at 498 nm for each well. All assays were performed in six replicates and TCIDso/ml was determined using Reed and Muench method. CPENT was measured in a similar way as the CPE assays for viral titration with some modifications. In brief, serial dilutions of antibodies were mixed separately with live SARS-CoV-2 Wuhan, alpha, beta and gamma virus strains, incubated at 37 °C for Ih, and added to the monolayer of Vero E6 cells. All distinct antibodies were assayed in triplicate in serial dilutions. CPE neutralization was calculated with the following formula: % neutralization activity = % CPE reduction = (OD Virus + antibody OD vc) I (OD cc - OD vc) *100 and 50% neutralization titers (CPENT50) were calculated with non-linear regression. Cells either unexposed to the virus or mixed with TCID50 SARS-CoV-2 were used as negative (uninfected) and positive (infected) controls, respectively.
SARS-Co\/-2 plague reduction neutralization test (PRNT) (SARS-CoV-2 delta)
The PRNT experiments were performed with a SARS-CoV-2 isolate from the B.1.617.2 lineage. This virus was isolated from oropharyngeal swabs taken from a patient in Belgium (EPI_ISL_2425097; 2021-04-20). Virus stocks were prepared by 2x passaging on Vero E6 cells.
Dose-dependent neutralization of distinct antibodies was assessed by mixing the antibodies at different concentrations, with 100 PFU SARS-CoV-2 in DMEM supplemented with 2% FBS and incubating the mixture at 37°C for Ih. Antibodyvirus complexes were then added to VeroE6 cell monolayers in 12-well plates and incubated at 37°C for Ih. Subsequently, the inoculum mixture was replaced with 0.8% (w/v) methylcellulose in DMEM supplemented with 2% FBS. After 3 days incubation at 37°C, the overlays were removed, the cells were fixed with 3.7% PFA, and stained with 0.5% crystal violet. Half-maximum neutralization titers (PRNT50) were defined as the antibody concentration that resulted in a plaque reduction of 50%.
Golden Syrian hamster studies
SARS-CoV-2
Three SARS-CoV-2 strains were used in this study. BetaCov/Belgium/GHB- 03021/2020 (EPI ISL 109 407976|2020-02-03), was recovered from a nasopharyngeal swab taken from an RT-qPCR confirmed asymptomatic patient who returned from Wuhan, China in the beginning of February 2020. A close relation with the prototypic Wuhan-Hu-1 2019-nCoV (GenBank accession 112 number MN908947.3) strain was confirmed by phylogenetic analysis. Infectious virus was isolated by serial passaging on Huh7 and Vero E6 cells [Kaptein et al. Proc. Natl. Acad. Sci. USA 117, 26955-26965 (2020)]; passage 6 virus was used for the study described here. The Beta variant B.1.351 (hCoV-19/Belgium/rega-1920/2021; EPI_ISL_896474, 2021-01-11) was isolated from nasopharyngeal swabs taken from a traveler returning to Belgium in January 2021 who became a patient with respiratory symptoms. The Delta variant, B.1.617.2 (hCoV-19/Belgium/rega- 7214/2021; EPI_ISL_2425097; 2021-04-20) was isolated from nasopharyngeal swabs in April 2021 in Belgium through active surveillance. Both strains were subjected to sequencing on a MinlON platform (Oxford pore) directly from the nasopharyngeal swabs. Infectious virus was isolated by passaging on VeroE6 cells [Abdelnabi et al. EBioMedicine 68, 103403 (2021)]; passage 2 was used for the study described here. Live virus-related work was conducted in the high-containment A3 and BSL3+ facilities of the KU Leuven Rega Institute (3CAPS) under licenses AMV 30112018 SBB 219 2018 0892 and AMV 23102017 SBB 219 20170589 according to institutional guidelines.
Cells
Vero E6 cells (African green monkey kidney, ATCC CRL-1586) were cultured in minimal essential medium (MEM, Gibco) supplemented with 10% fetal bovine serum (Integra), 1% non-essential amino acids (NEAA, Gibco), 1% L- glutamine (Gibco) and 1% bicarbonate (Gibco). End-point titrations on Vero E6 cells were performed with medium containing 2% fetal bovine serum instead of 10%. Huh7 cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (Integra), 1% bicarbonate (Gibco), 2% HEPES buffer (Gibco). Both cells were kept in a humidified 5% CO2 incubator at 37°C.
SARS-CoV-2 infection model in hamsters
The hamster infection model of SARS-CoV-2 has been described before [Kaptein, et al. Proc. Natl. Acad. Sci. USA. 117, 26955-26965 (2020); Boudewijns et al. Nat. Commun. 11, 1-10 (2020)]. Female Syrian hamsters Mesocricetus auratus) were purchased from Janvier Laboratories and kept per two in individually ventilated isolator cages (IsoCage N Bio-containment System, Tecniplast) at 21°C, 55% humidity and 12: 12 day/night cycles. Housing conditions and experimental procedures were approved by the ethics committee of animal experimentation of KU Leuven (license P065-2020). For infection, female hamsters of 6-8 weeks old were anesthetized with ketamine/xylazine/atropine and inoculated intranasally with 50 pL containing either 2x l06 TCID50 SARS-CoV-2 (ancestral Wuhan strain), IxlO4 TCID50 (Beta B.1.351), or Ix lO4 TCID50 (Delta B.1.617.2). Antibody treatments were initiated 24 hours post infection by intraperitoneal injection. Hamsters were monitored for appearance, behavior, and weight. At day 4 post-infection, animals were euthanized by intraperitoneal injection of 500 pL Dolethal (200 mg/mL sodium pentobarbital, Vetoquinol SA). Lungs were collected and viral RNA and infectious virus were quantified by RT-qPCR and end-point virus titration, respectively. Blood samples were collected at end-point for pharmacokinetic analysis. No randomization methods were used and confounders were not controlled, though all caretakers and technicians were blinded to group allocation in the animal facility and to sample numbers for analysis (qPCR, titration, and histology).
SARS-CoV-2 RT-qPCR
Hamster lung tissues were collected after sacrifice and were homogenized using bead disruption (Precellys) in 350 pL TRK lysis buffer (E.Z.N.A.® Total RNA Kit, Omega Bio-tek) and centrifuged (10.000 rpm, 5 min) to pellet the cell debris. RNA was extracted according to the manufacturer's instructions. RT-qPCR was performed on a LightCycler96 platform (Roche) using the iTaq Universal Probes One-Step RT-qPCR kit (BioRad) with N2 primers and probes targeting the nucleocapsid. Standards of SARS-CoV-2 cDNA (IDT) were used to express viral genome copies per mg tissue. End-point virus titrations
Lung tissues were homogenized using bead disruption (Precellys) in 350 pL minimal essential medium and centrifuged (10,000 rpm, 5min, 4°C) to pellet the cell debris. To quantify infectious SARS-CoV-2 particles, endpoint titrations were performed on confluent Vero E6 cells in 96- well plates. Viral titers were calculated by the Reed and Muench method46 using the Lindenbach calculator and were expressed as 50% tissue culture infectious dose (TCID50) per mg tissue.
Sample size justification
For antiviral efficacy, we want to detect at least 1 logic reduction in viral RNA levels in treated subjects compared to the untreated, infected control group. Group size was calculated based on the independent t-test with an effect size of 2.0 and a power of 80% (effect size = delta mean/SD = 1 logic decrease in viral RNA/0.5 logic), resulting in 5-6 animals/group. Sample sizes maximized considering limits in BSL3 housing capacity, numbers of animals that can be handled under BSL3 conditions, and availability of compounds.
Ethics
Housing conditions and experimental procedures were done with the approval and under the guidelines of the ethics committee of animal experimentation of KU Leuven (license P065-2020).
Statistics
All statistical analyses were performed using GraphPad Prism 9 software (GraphPad, San Diego, CA, USA), unless indicated otherwise in the respective methods sections. Statistical significance was determined using the non-parametric Mann Whitney U- test. P-values of <0.05 were considered significant.
Example 9 Epitope mapping
The RBD binding region of antibodies 1C1, 2B2, 3B8 and 3E6 was evaluated in an epitope binning experiment by the Coronavirus Immunotherapeutic Consortium (CoVIC). Herein, antibodies were analyzed via high-throughput surface plasmon resonance (HT-SPR) by COVIC, resulting in the distinction of seven core "communities" of RBD-binding antibodies that are broadly defined by the competition profile of each antibody relative to the others. (Figure 10) To understand the position of each community relative to the others, COVIC next mapped the footprints by negative-stain electron microscopy (NS-EM) for 25 example RBD-reactive mAbs chosen to span the range of communities and key clusters (Hastie et al., Science 374, 472-478 (2021)). This allowed to assign different structural regions of the RBD antigen to different epitope communities (figure 10, figurell).
Antibodies 1C1, 2B2, 3B8 and 3E6 were included in epitope binning experiments of the COVIC consortium and assigned to epitope communities RBD-7b, RBD-4b, RBD- 3 and RBD-2a, respectively.
Table 5:
Figure imgf000051_0001
Epitope communities RBD-2 and RBD-3 are part of the receptor binding motive (RBM) of the RBD antigen, while RBD-4 is part of the RBD "outer face" and RBD-7 lies outside the RBM in the RBD "inner face" (Fig 2). The RBM and RBD-7
For antibody 3B8, additional epitope mapping was performed via deep mutational scanning. In this assay, a library of RBD mutants was expressed on yeast cells and escape mutants (i.e. abolishing 3B8 binding) were identified. The four amino acid residues V445, G446, P499, T500, form a conformational epitope and were determined as being crucial for the binding of 3B8 with RBD (Figure 12).
Materials and methods
Epitope binning was performed with a classical sandwich assay format on a Carterra LSA® HT-SPR instrument equipped with a CMDP sensor chip at 25 °C and in a HBSTE-BSA running buffer (10 mM HEPES pH 7.4, 150 mM NaCI, 3 mM EDTA, 0.05% Tween-20, supplemented with 0.5 mg/ml BSA). Two microfluidic modules, a 96- channel print-head (96PH) and a single flow cell (SFC), were used to deliver samples onto the sensor chip. Surface preparation was performed with 25 mM MES pH 5.5 with 0.05% Tween-20 as a running buffer. The chip was activated with a freshly prepared solution of 130 mM l-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) + 33 mM N-hydroxysulfosuccinimide (Sulfo-NHS) in 0.1 M MES pH 5.5 using the SFC. Antibodies were immobilized using the 96PH for 10 minutes at 10 pg/mL diluted into 10 mM sodium acetate (pH 4.25). Unreactive esters were quenched with a 7-minute injection of 1 M ethanolamine-HCI (pH 8.5) using the SFC. The binning analysis was performed over this array with the HBSTE-BSA buffer as the running buffer and sample diluent. The RBD antigen was injected in each cycle for 4 minutes at 50 nM (1.8 pg/mL) and followed immediately by a 4-minute injection of the analyte antibody at 30 pg/mL (200 nM for IgG constructs). The surface was regenerated each cycle with double pulses (17 seconds per pulse) of 10 mM Glycine pH 2.0. Data was processed and analyzed with Epitope® software (Carterra). Briefly, data was referenced using unprinted locations on the array and each binding cycle was normalized to the RBD capture level. The binding level of the analyte antibody just after the end of the injection was compared to that of a buffer alone injection. Signals that were significantly increased relative to the buffer controls are described as sandwiches and represent non-blocking behavior. Competition results were visualized as a heat map that depicts blocking relationships of analyte/ligand pairs. Clones having similar patterns of competition are clustered together in a dendrogram and can be assigned to shared communities.
Deep mutational scanning
Transformation of deep mutational SARS-CoV2 RBD libraries to E. coli
Plasmid preps of two independently generated deep mutational SARS-CoV2 RBD libraries in the pETcon vector (Starr et al. (2020), Cell 182, 1295-1310. e20). Ten ng of these preps were transformed to E. coli TOP10 strain via electroporation, and allowed to recover for one hour in SOC medium at 37°C. The transformation mixture was divided and plated on ten 24.5 cm x 24.5 cm large bio-assay dishes containing low salt LB medium supplemented with carbenicillin, at an expected density of 100.000 clones per plate. After growing overnight, all colonies were scraped from the plates and resuspended into 300 ml low salt LB supplemented with carbenicillin. The cultures were grown for 2 hours and a half before pelleting. The cell pellet was washed once with sterile MQ, and plasmid was extracted via the QIAfilter plasmid Giga prep kit (Qiagen) according to the manufacturer's instructions.
Transformation of deep mutational SARS-CoV2 RBD libraries to S. cerevisiae
Ten pg of the resulting plasmid preps were transformed to Saccharomyces cerevisiae strain EBY100, according to the large-scale protocol by (Gietz et al. Nature Protocols 2007, 2, 31-345). Transformants were selected in 100 ml liquid yeast drop-out medium (SD -trp -ura) for 16 hours. Then the cultures were back-diluted into lOOmL fresh SD -trp -ura at 1 ODeoo for an additional 9 hours passage. Afterwards, the cultures were flash frozen in le8 cells aliquots in 15% glycerol and stored at -80°C.
Cloning and transformation of WT RBD of SARS-CoV2
The CDS of the RBD of SARS-CoV2 (N331-T531) was ordered as a yeast codon- optimized gBIock and cloned into the pETcon vector by Gibson assembly. The cloning mixture was similarly electroporated into E. coli TOPIO cells, and plasmid was extracted via a Miniprep kit (Promega) according to the manufacturer's instructions. The plasmid was Sanger sequenced with primers covering the entire RBD CDS. Finally, the plasmid was transformed to Saccharomyces cerevisiae strain EBY100, according to the small-scale protocol by (Gietz et al. Nature Protocols (2007) 2, 31- 34). Transformants were selected via a yeast colony PCR.
Presorting of deep mutational SARS-CoV2 RBD libraries on ACE2
One aliquot of each library was thawed and grown overnight in 10 ml liquid repressive medium (SRaf -ura -trp) at 28°C. Additionally, the control EBY100 strain containing the pETcon plasmid expressing WT RBD from SARS-CoV2 was inoculated in 10 ml liquid repressive medium and grown overnight at 28°C. These precultures were then back-diluted to 50 ml liquid inducing medium (SRaf/Gal -ura -trp) at an OD600 of 0.67/ml and grown for 16 hours before harvest.
The cells pellets were washed thrice with washing buffer (IX PBS + 1 mM EDTA, pH 7.2 + 1 Complete Inhibitor EDTA-free tablet (Roche) per 50ml buffer), and stained at an ODeoo of 8/ml with 9.09 nM hACE2-muFc (Sino Biological) in staining buffer (washing buffer + 0.5 mg/ml of Bovine Serum Albumin) for one hour at 4°C on a rotating wheel. Cells were washed thrice with staining buffer and stained with 1 : 100 anti-cmyc-FITC (Immunology Consultants Lab), 1 : 1000 anti-mouse-IgG-AF568 (Molecular Probes) and 1:2000 L/D eFluor506 (Thermo Fischer Scientific) for one hour at 4°C on a rotating wheel. Cells were washed thrice with staining buffer, and filtered over 35 pm cell strainers before sorting on a FACS Melody (BD Biosciences). A selection gate was drawn that captures the ACE2+ cells, such that, after compensation, max. 0.1% of cells of unstained and single stained controls appeared above the background. Approximately 1 million ACE2+ cells were collected per library, each in 5 ml polypropylene tubes coated with 2X YPAD + 1% BSA. Sorted cells were recovered by growth in liquid SD -trp -ura medium with 100 U/ml penicillin and 100 pg/ml streptomycin (Thermo Fisher Scientific) for 72 hours at 28°C, and flash frozen at -80°C in 9 ODeoo unit aliquots in 15% glycerol.
Antibody escape mutant sorting on ACE2-sorted deep mutational SARS-CoV2 RBD libraries
One ACE2-sorted aliquot of each library was thawed and grown overnight in 10 ml liquid repressive medium (SRaf -ura -trp) at 28°C. Additionally, the control EBY100 strain containing the pETcon plasmid expressing WT RBD from SARS-CoV2 was inoculated in 10 ml liquid repressive medium and grown overnight at 28°C. These precultures were then back-diluted to 50 ml liquid inducing medium (SRaf/Gal —ura -trp) at an OD600 of 0.67/ml and grown for 16 hours before harvest.
The cells pellets were washed thrice with washing buffer (IX PBS + 1 mM EDTA, pH 7.2 + 1 Complete Inhibitor EDTA-free tablet (Roche) per 50ml buffer, freshly made and filter sterile) and stained at an ODeoo of 8/ml with a specific concentration per stained antibody in staining buffer (washing buffer + 0.5 mg/ml of Bovine Serum Albumin) for one hour at 4°C on a rotating wheel. Cells were washed thrice with staining buffer and stained with 1 : 100 anti-c-myc-FITC (Immunology Consultants Lab), 1: 1000 anti-human IgG AF594 (Molecular Probes) and 1:2000 L/D eFluor506 (Thermo Fischer Scientific) for one hour at 4°C on a rotating wheel. Cells were washed thrice with staining buffer, and filtered over 35 pm cell strainers before sorting on a FACS Melody (BD Biosciences). Gating was chosen as such that, after compensation, max. 0.1% of cells of the fully stained WT RBD control appeared in the selection gate. Between 150.000 and 300.000 escaped cells were collected per library, each in 5 ml polypropylene tubes coated with 2X YPAD + 1% BSA.
Sorted cells were recovered by growth in liquid SD -trp -ura medium supplemented with 100 U/ml penicillin and 100 pg/ml streptomycin (Thermo Fisher Scientific) for 16 hours at 28°C.
DNA extraction and Illumina sequencing of antibody escape sorted deep mutational SARS-CoV2 RBD libraries
Plasmids were extracted from sorted cells using the Zymoprep yeast plasmid miniprep II kit (Zymo Research) according to the manufacturer's instructions, but with the exception of a longer (2 hour) incubation with the Zymolyase enzyme, and with the addition of a freeze-thaw cycle in liquid nitrogen after Zymolyase incubation. A PCR was performed on the extracted plasmids using KAPA HiFi HotStart ReadyMix to add sample indices and remaining Illumina adaptor sequences using NEBNext UDI primers (20 cycles). PCR samples were purified once using CleanNGS magnetic beads (CleanNA), and once using AMPure magnetic beads (Beckman Coulter). Fragments were eluted in 15 pl O.lx TE buffer. Size distributions were assessed using the High Sensitivity NGS kit (DNF-474, Advanced Analytical) on a 12-capillary Fragment Analyzer (Advanced Analytical). Hundred bp single-end sequencing was performed on a NovaSeq 6000.
Analysis of sequencing data and epitope calculation using mutation escape profiles Deep sequencing reads were processed as described by Greaney et al. (Greaney et al., 2021, Cell Host Microbe) using the code available at https://qithub.com/ibloomlab/SARS-CoV-2-RBD MAP Crowe antibodies, with adjustments. Briefly, nucleotide barcodes and their corresponding mutations were counted using the dms_variants package (0.8.6). Escape fraction for each barcode was defined as the fraction of reads after enrichment divided by the fraction of reads before enrichment of escape variants. The resulting variants were filtered to remove unreliably low counts and keep variants with sufficient RBD expression and ACE2 binding (based on published data (Starr et al., 2020, Celll82, 1295-1310. e20)). For variants with several mutations, the effects of individual mutations were estimated with global epistasis models, excluding mutations not observed in at least one single mutant variant and two variants overall. The resulting escape measurements correlated well between the duplicate experiments and the average across libraries was thus used for further analysis. To determine the most prominent escape sites for each antibody, RBD positions were identified where the total site escape was > lOx the median across all sites, and was also at least 10% of the maximum total site escape across all positions for a given antibody.

Claims

54 CLAIMS
1. An antibody or antigen binding fragment thereof, specifically binding to the trimeric spike protein of Wuhan Covid-SARS-2 and specifically binding to a confirmational epitope of the Receptor Binding Domain of all of Wuhan, alpha, beta, gamma, delta and omicron variants of Covid-SARS-2 spike protein.
2. The antibody or antigen binding fragment thereof according to claim 1, wherein said antibody or antigen binding fragment thereof has an IC50 in a SARS-CoV-2 pseudovirus infection lower than 1 nm, and wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 500 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM.
3. The antibody or antigen binding fragment thereof according to claim 1 or 2, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,4, wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 400 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 300 pM.
4. The antibody or antigen binding fragment thereof according to any one of claims 1 to 3, wherein said antibody or antigen binding fragment thereof has an IC50, lower than 0,05 and wherein said antibody or antigen binding fragment thereof has an affinity for RBD domain Wuhan Covid-SARS-2 spike protein with a KD of less than 250 pM, and wherein said antibody or antigen binding fragment thereof has an affinity for trimeric spike protein of Wuhan Covid-SARS-2 with a KD of less than 100 pM.
5. The antibody or antigen binding fragment thereof according to any one of claims 1 to 4, wherein the confirmational epitope resides in the receptor 55 binding motif with SEQ ID NO: 77 which is a fragment of the RBD with SEQ ID NO: 74.
6. The antibody or antigen binding fragment thereof according to any one of claims 1 to 5, wherein the confirmational epitope in the receptor binding motif of the RBD is defined by amino acids Vai 445, Gly446, Pro499 and Thr500 of the spike protein of Wuhan Covid-SARS-2 [SEQ ID NO: 73].
7. The antibody or antigen binding fragment thereof according to any one of claims 1 to 6, which is an antibody or antigen binding fragment there of comprising:
-a variable heavy chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and comprising
- a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5].
8. The antibody or antigen binding fragment thereof according to any one of claims 1 to 7, wherein the variable domain comprises a VH region that has outside the CDR regions at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 24.
9. The antibody or antigen binding fragment thereof according to any one of claims 1 to 8, wherein the antibody is a human antibody.
10. A polynucleotide encoding the antibody or antigen binding fragment thereof in accordance with any one of claims 1 to 9.
11. The antibody or antigen binding fragment thereof according to any one of claims 1 to 9, for use in the treatment and prevention of the beta, delta or omicron variant of COVID 19 in an individual. 56 The antibody or antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to claim 11, wherein the antibody or antibody fragment comprises:
-a variable heavy chain wherein the sequence of the CDR1, CDR.2 and CDR.3 region consist respectively of the sequence of GYTFTSHY [SEQ ID NO: 1], IDSSGGGA [SEQ ID NO: 2], and AKAHSTNWYGWFDP [SEQ ID NO: 3] and a variable light chain wherein the sequence of the CDR1, CDR2 and CDR3 region consist respectively of the sequence SSNIGSNT [SEQ ID NO: 4], NNN and AAWDDGLNGSGWV [SEQ ID NO: 5]. The antibody antigen binding fragment thereof for use in the treatment or prevention of COVID 19 in an individual according to claim 11 or 12, wherein the variable domain comprises a VH region that has outside the CDR regions at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 22 and a VL region that has outside the CDR regions at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 24. A polynucleotide comprising a sequence encoding the antibody or antigen binding fragment thereof according to any one of claims 10, for use in the treatment and prevention of the beta, delta or omicron variant COVID 19. The polynucleotide for use in the treatment or prevention of COVID 19 in an individual according to claim 14, comprising the sequence of SEQ ID NO: 21 and SEQ ID NO: 23.
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