WO2022241200A1 - Cross-reactive coronavirus antibodies - Google Patents

Cross-reactive coronavirus antibodies Download PDF

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Publication number
WO2022241200A1
WO2022241200A1 PCT/US2022/029160 US2022029160W WO2022241200A1 WO 2022241200 A1 WO2022241200 A1 WO 2022241200A1 US 2022029160 W US2022029160 W US 2022029160W WO 2022241200 A1 WO2022241200 A1 WO 2022241200A1
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seq
antibody
cov
cdrh3
cdrl3
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PCT/US2022/029160
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French (fr)
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Ivelin Stefanov Georgiev
Andrea R. SHIAKOLAS
Kevin J. Kramer
James E. Crowe
Robert Carnahan
Jason MCLELLAN
Nicole Johnson
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Vanderbilt University
Board Of Regents, The University Of Texas System
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Publication of WO2022241200A1 publication Critical patent/WO2022241200A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—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
    • C07K2317/70—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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Definitions

  • the present disclosure relates to antibodies and uses thereof for treating, preventing, and detecting coronavirus infection.
  • BACKGROUND SARS-CoV-2 or the 2019 novel coronavirus (COVID-19)
  • COVID-19 2019 novel coronavirus
  • BACKGROUND SARS-CoV-2 or the 2019 novel coronavirus (COVID-19)
  • COVID-19 2019 novel coronavirus
  • BACKGROUND SARS-CoV-2 or the 2019 novel coronavirus (COVID-19)
  • COVID-19 2019 novel coronavirus
  • a recombinant antibody comprising a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and/or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH3 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11224-11232. In some embodiments, CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196.
  • CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232.
  • CDRH1 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11170-11178; and/or CDRL1 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11206-11214.
  • CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178.
  • CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214.
  • CDRH2 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11179-11187; and/or CDRL2 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11215-11223. In some embodiments, CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187. In some embodiments, CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223. In some embodiments, VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169. In some embodiments, VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205.
  • the recombinant antibody is selected from Table 1. In some embodiments, the recombinant antibody is selected from Table 2. In one aspect, disclosed herein is a nucleic acid encoding a recombinant antibody as disclosed herein. In one aspect, disclosed herein is a recombinant expression cassette or plasmid comprising a sequence to express a recombinant antibody as disclosed herein. In one aspect, disclosed herein is a host cell comprising an expression cassette or a plasmid as disclosed herein. In one aspect, disclosed herein is a method of producing an antibody, comprising cultivating or maintaining a host cell under conditions to produce the antibody.
  • a method of treating a coronavirus infection in a subject comprising administering to the subject a therapeutically effective amount of a recombinant antibody as disclosed herein.
  • the coronavirus is SARS-CoV-2.
  • a method for detecting a coronavirus infection in a subject comprising: providing a biological sample from the subject, and detecting a coronavirus antigen in the biological sample with an antibody that specifically binds to the coronavirus antigen, wherein the antibody is from any aspect as disclosed herein, and wherein the presence of the coronavirus antigen in the biological sample indicates the subject is infected with a coronavirus.
  • the coronavirus is SARS-CoV-2.
  • FIGS.1A-1C show identification and characterization of SARS-CoV-2 antibodies isolated using LIBRA-seq.
  • FIG.1A Variable heavy gene usage (x-axis) as a function of IgG + B cells with a SARS-CoV-2 spike LIBRA-seq score (>1) (y-axis). The nine lead antibodies are highlighted in purple.
  • FIG. 1B RTCA VSV-SARS-CoV-2 neutralization by lead antibodies.
  • IC 50 values are calculated by non-linear regression analysis by GraphPad Prism software.
  • FIG. 1C Sequence characteristics and antigen specificity of nine lead antibodies from a recovered COVID-19 donor. Percent identity is calculated at the nucleotide level, and CDR length and sequences are noted at the amino acid level.
  • LIBRA-seq scores for each antigen are displayed as a heatmap with a LIBRA-seq score of -2 displayed as light yellow, 0 as white, and 2 in purple; in this heatmap scores lower or higher than that range are shown as -2 and 2, respectively.
  • ELISA binding data are displayed as a heatmap of the AUC analysis calculated from ( Figure 7A) with AUC of 0 displayed as light yellow, 50% maximum as white, and maximum AUC as purple.
  • FIG. 1B The sequences in FIG. 1B are SEQ ID NO: 6197, SEQ ID NO: 5528, SEQ ID NO: 5893, SEQ ID NO: 5720, SEQ ID NO: 5308, SEQ ID NO: 5509, SEQ ID NO: 6161, SEQ ID NO: 5039, SEQ ID NO: 6187, SEQ ID NO: 11157, SEQ ID NO: 10488, SEQ ID NO: 10853, SEQ ID NO: 10680, SEQ ID NO: 10268, SEQ ID NO: 10469, SEQ ID NO: 11121, SEQ ID NO: 9999, and SEQ ID NO: 11147.
  • FIGS. 2A-2D show antigenic characterization of antibody 54042-4. (FIG.
  • FIG.2A A biolayer interferometry sensogram that shows binding to recombinant SARS-CoV-2 RBD-SD1. Binding data are depicted by the black lines and the best fit line of the data to a 1:1 binding model is shown in red.
  • FIGS.3A-3D show atomic resolution of 54042-4 binding mode to SARS-CoV-2 S.
  • FIG. 3A Side and top views of Fab 54042-4 bound to SARS-CoV-2 spike, shown as cryo-EM density.
  • FIG.3B Focused refinement density showing the 54042-4 epitope at the inner edge of the RBM (left). Top-down view of the 54042-4 epitope showing heavy and light chain contacts, as well as residues outside of the binding interface that are mutated in circulating VOCs (right).
  • FIG. 3C The 54042-4 heavy chain binds to RBD residues 443-447 primarily through a network of hydrogen bonds involving CDRH2 and CDRH3 and noncovalent contacts involving Ile32 of CRDH1.
  • FIGS.4A-4E show sequence and structural comparison of 54042-4 to known SARS-CoV- 2 antibodies.
  • FIG.4A Amino acid CDRH3 identity to 54042-4 (x-axis) is plotted against CDRL3 identity to 54042-4 (y-axis) for paired heavy and light chain sequences obtained from the CoV- AbDab database.
  • Antibodies using the same heavy and light chain germline gene as 54042- 4 (IGHV2-5 and IGKV1-39) are shown in light blue.
  • Antibodies using the IGHV2-5 heavy chain gene and a non-IGKV1-39 light chain gene are shown in orange. Additionally, antibodies using a non-IGHV2-5 heavy chain gene and the IGKV1-39 light chain gene, with CDRH3 or CDRL3 identity to 54042-4 of at least 50%, are highlighted in purple. Finally, antibodies that do not use IGHV2-5 or IGKV1-39, but that have at least 50% identity to CDRH3 or CDRL3 of 54042-4, are shown in grey.
  • FIG. 4B Pearson correlation of epitopes of known SARS-CoV-2 antibodies (Table 3) in comparison to 54042-4 antibody, with the six antibodies showing a statistically significant (p ⁇ 0.05) positive correlation highlighted in red.
  • FIG.4D Distinct angles of approach of antibodies 54042-4 (heavy chain: orange, light chain: white), REGN10987 (heavy chain: blue, light chain: white) (PDB id: 6XDG), 2-7 (heavy chain: pink, light chain: white) (PDB id: 7LSS), and LY- CoV1404 (heavy chain: purple, light chain: white) (PDB id:7MMO) to the SARS-CoV-2 RBD (green).
  • FIG. 4E Structural comparison of CDRH1, 2, and 3 of antibodies 54042-4 and 2-7. CDRH1 of 2-7 extends further than 54042-4, forming additional contacts with Thr345 and Arg346 of the RBD (left).
  • FIGS.5A-5E Functional characterization of antibody 54042-4.
  • FIG.5A Binding data of 54042-4 antibody to a shotgun alanine mutagenesis screening library of the SARS-CoV-2 RBD (Wuhan-Hu-1 strain). Residues displayed are the alanine substitutions that resulted in the biggest loss of binding to 54042-4 yet still retained signal with the RBD antibody control.
  • FIG.5B RTCA Neutralization of VSV SARS-CoV-2 chimera variants harboring specific substitutions.
  • Cell sensograms are shown in boxes corresponding to mutations indicated in each row. Columns (from left to right) are each chimera treated with COV2-2381, 54042-4 and virus only control. Neutralization of 54042-4 of USA-WA1 strain and cells only are indicated on the right.
  • COV2- 2381 was chosen as a positive control due to its distinct epitope footprint from the selected mutations.
  • 54042-4 epitope residues (non-zero buried surface area on SARS-CoV-2 RBD) with their associated % conservation (the percentage of deposited sequences containing the highest-frequency amino acid at that position) in the GISAID database. The only 54042-4 epitope residue with a % conservation of less than 99%, N439, is highlighted in red.
  • FIG. 5D ELISA AUC of 54042-4, CR3022, and an influenza HA-specific negative control antibody 3602-1707. AUC is displayed as a heatmap with a value of 0 corresponding to white, 50% maximum as light- purple, and maximum AUC as purple.
  • FIGS. 6A-6E Authentic SARS-CoV-2 % neutralization of USA-WA1, Alpha, Beta, Delta, and Gamma strains (y-axis) is depicted as a function of antibody concentration (x-axis). Also shown are the respective IC50 and IC80 values for 54042-4 neutralization against each variant.
  • FIG. 6A VSV-SARS-CoV-2 capacity of serum is displayed from time points at day 18, day 28, day 56, and days 80-90 post-COVID-19 infection.
  • FIG. 6B Gating scheme for fluorescent-activated cell sorting of recovered COVID-19 individual.
  • Cells were stained with Ghost Red 780, CD14-APC-Cy7, CD3-FITC, CD19-BV711, and IgG-PE-Cy5 along with a DNA-barcoded antigen screening library.
  • To detect antigen-positive B cells cells were washed and treated with a streptavidin-PE secondary stain. Gates as drawn are based on gates used during the sort, and percentages from the sort are listed.
  • FIG.6C LIBRA-seq scores for SARS- CoV-2 S, SARS-CoV-2 S D614G, SARS-CoV S, MERS-CoV S, HCoV-OC43 S, HCoV-229E S, HCoV-NL63 S, SARS-CoV-2 RBD, SARS-CoV RBD, and MERS-CoV RBD, as well as negative-control antigens ZM197 Env and hemagglutinin (HA) NC99 are shown.
  • LIBRA-seq scores for each antigen are displayed as a heatmap with a LIBRA-seq score of -2 displayed as light yellow, 0 as white, and 2 in purple; in this heatmap, scores lower or higher than that range are shown as -2 and 2, respectively.
  • FIG.6D ELISA binding data of antibodies identified by LIBRA- seq against SARS-CoV-2 S HP. The optical density at 450 nm (y-axis) is depicted as a function of antibody concentration (x-axis).
  • FIG.6E ELISA binding data of the antibodies that displayed neutralization in the high-throughput VSV SARS-CoV-2 RTCA ( Figure 1B) for the antigens SARS-CoV-2 S D614G, SARS-CoV S, MERS-CoV S, HCoV-OC43 S, HCoV-HKU1 S, HCoV- NL63 S, and HCoV-229E S.
  • the optical density at 450 nm (y-axis) is depicted as a function of antibody concentration (x-axis).
  • FIGS. 7A-7B FIGS. 7A-7B.
  • FIG. 7A ELISA binding data of antibodies identified by LIBRA-seq against SARS-CoV-2 spike HP.
  • FIG.7B ELISA binding data against SARS-CoV-2 subdomains RBD, NTD, S1, and S2 are shown.
  • CR3022 was used as a positive control RBD-directed antibody whereas 46472-4 and 46472-6 antibodies were used as positive controls for the S2 and NTD, respectively.
  • the HA-specific 3602-1707 antibody was used as a negative control.
  • FIGS. 8A-8B Amino acids comprising the epitope of 54042-4 are shown with their associated buried surface area ( ⁇ 2 ) are shown.
  • FIG. 8B 54042-4 amino acids comprising the paratope to SARS-CoV-2 spike and their associated buried surface area values ( ⁇ 2 ) are shown.
  • FIGS. 9A-9C are shown.
  • FIG. 9A ELISA binding data against SARS-CoV-2 Wuhan-1 RBD and RBDs with substitutions E484K, N501Y, N439K, K417N, E484Q, or L452R.
  • CR3022 was used as a positive control and 3602-1707, an HA-specific antibody, was used as a negative control.
  • FIG. 9B ELISA binding data against SARS-CoV-2 S HP, SARS-CoV S, and SARS-CoV-2 S HP constructs with substitutions in the S1 domain for the Beta, and Alpha variants of concern.
  • CR3022 was used as a positive control and 3602-1707 was used as a negative control antibody.
  • FIG.9C The substitutions and deletions present in the Alpha and Beta SARS-CoV-2 S constructs used in the ELISAs depicted in Figure 9B.
  • FIG. 10 shows Cryo-EM data processing workflow. Flowchart outlining cryo-EM data processing of Fab 54042-4 Fab bound to SARS-CoV-2 S. Additional information can be found in the Methods section under “Cryogenic electron microscopy” (cryo-EM).
  • FIGS. 11A-11D Cryo-EM structure validation.
  • FIG. 11A FSC curve and distribution plot for the C3 S-ECD/54042-4 structure, generated in cryoSPARC v3.2.0.
  • FIG.11B FSC curve and viewing distribution plot for focused refinement of the S-RBD bound to 54042-4 Fab.
  • FIG. 11C Local resolution shown by color of the C3 S-ECD/54042-4 (left) and focused S-RBD/54042- 4 (right) reconstructions.
  • FIG.11D Map resulting from focused refinement of the RBD (green) (left), 54042-4 heavy chain (orange), and 54042-4 light chain (white). Detailed views of the binding interface and corresponding map (center, right). Oxygen atoms are colored red, nitrogen blue, and sulfur yellow.
  • recombinant antibodies that specifically bind a viral protein of a coronavirus and uses thereof for treating, preventing, inhibiting, reducing, and detecting coronavirus infection, wherein the coronavirus is SARS-CoV-2.
  • administering includes any route of introducing or delivering to a subject an agent. Administration can be carried out by any suitable route, including oral, intravenous, intraperitoneal, intranasal, inhalation and the like. Administration includes self- administration and the administration by another.
  • the terms “may,” “optionally,” and “may optionally” are used interchangeably and are meant to include cases in which the condition occurs as well as cases in which the condition does not occur.
  • a formulation “may include an excipient” is meant to include cases in which the formulation includes an excipient as well as cases in which the formulation does not include an excipient.
  • the term “subject” or “host” can refer to living organisms such as mammals, including, but not limited to humans, livestock, dogs, cats, and other mammals. Administration of the therapeutic agents can be carried out at dosages and for periods of time effective for treatment of a subject. In some embodiments, the subject is a human.
  • the term “antigen” refers to a molecule that is capable of binding to an antibody. In some embodiments, the antigen stimulates an immune response such as by production of antibodies specific for the antigen.
  • antibodies in a broad sense and includes both polyclonal and monoclonal antibodies. In addition to intact immunoglobulin molecules, also included in the term “antibodies” are fragments or polymers of those immunoglobulin molecules, and human or humanized versions of immunoglobulin molecules or fragments thereof.
  • the antibodies can be tested for their desired activity using the in vitro assays described herein, or by analogous methods, after which their in vivo therapeutic and/or prophylactic activities are tested according to known clinical testing methods.
  • Native antibodies are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at one end (VL) and a constant domain at its other end.
  • VH variable domain
  • VL variable domain
  • IgA, IgD, IgE, IgG and IgM There are five major classes of human immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG-1, IgG-2, IgG-3, and IgG-4; IgA-1 and IgA-2.
  • IgG-1, IgG-2, IgG-3, and IgG-4 subclasses
  • the heavy chain constant domains that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu, respectively.
  • Each antibody molecule is made up of the protein products of two genes: heavy-chain gene and light-chain gene.
  • the heavy-chain gene is constructed through somatic recombination of V, D, and J gene segments. In human, there are 51 VH, 27 DH, 6 JH, 9 CH gene segments on human chromosome 14.
  • the light-chain gene is constructed through somatic recombination of V and J gene segments. There are 40 V ⁇ , 31 V ⁇ , 5 J ⁇ , 4 J ⁇ gene segments on human chromosome 14 (80 VJ).
  • the heavy-chain constant domains that correspond to the different classes of immunoglobulins are called ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • the “light chains” of antibodies from any vertebrate species can be assigned to one of two clearly distinct types, called kappa ( ⁇ ) and lambda ( ⁇ ), based on the amino acid sequences of their constant domains.
  • ⁇ kappa
  • ⁇ lambda
  • the term “monoclonal antibody” as used herein refers to an antibody obtained from a substantially homogeneous population of antibodies, i.e., the individual antibodies within the population are identical except for possible naturally occurring mutations that may be present in a small subset of the antibody molecules.
  • the monoclonal antibodies herein specifically include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, as long as they exhibit the desired antagonistic activity.
  • the disclosed monoclonal antibodies can be made using any procedure which produces monoclonal antibodies. For example, disclosed monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975).
  • a mouse or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
  • the lymphocytes may be immunized in vitro.
  • the monoclonal antibodies may also be made by recombinant DNA methods. DNA encoding the disclosed monoclonal antibodies can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). Libraries of antibodies or active antibody fragments can also be generated and screened using phage display techniques, e.g., as described in U.S. Patent No.
  • antibody or antigen binding fragment thereof encompasses chimeric antibodies and hybrid antibodies, with dual or multiple antigen or epitope specificities, and fragments, such as F(ab’)2, Fab’, Fab, Fv, sFv, scFv, nanoantibody and the like, including hybrid fragments.
  • fragments of the antibodies that retain the ability to bind their specific antigens are provided.
  • Such antibodies and fragments can be made by techniques known in the art and can be screened for specificity and activity according to the methods set forth in the Examples and in general methods for producing antibodies and screening antibodies for specificity and activity (See Harlow and Lane. Antibodies, A Laboratory Manual.
  • the fragments can also include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the antibody or antibody fragment is not significantly altered or impaired compared to the non-modified antibody or antibody fragment. These modifications can provide for some additional property, such as to remove/add amino acids capable of disulfide bonding, to increase its bio-longevity, to alter its secretory characteristics, etc. In any case, the antibody or antibody fragment must possess a bioactive property, such as specific binding to its cognate antigen.
  • antibody or antibody fragment may be identified by mutagenesis of a specific region of the protein, followed by expression and testing of the expressed polypeptide. Such methods are readily apparent to a skilled practitioner in the art and can include site-specific mutagenesis of the nucleic acid encoding the antibody or antibody fragment. (Zoller, M.J. Curr. Opin. Biotechnol.3:348-354, 1992).
  • antibody or “antibodies” can also refer to a human antibody and/or a humanized antibody. Many non-human antibodies (e.g., those derived from mice, rats, or rabbits) are naturally antigenic in humans, and thus can give rise to undesirable immune responses when administered to humans.
  • antibody heavy chain refers to the larger of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations.
  • antibody light chain refers to the smaller of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations, ⁇ and ⁇ light chains refer to the two major antibody light chain isotypes.
  • CDR refers to the “complementarity determining regions” of the antibody which consist of the antigen binding loops.
  • Each of the two variable domains of an antibody Fv fragment contain, for example, three CDRs.
  • native four-chain antibodies comprise six HVRs; three in the VH (H1, H2, H3), and three in the VL (L1, L2, L3).
  • HVRs generally comprise amino acid residues from the hypervariable loops and/or from the complementarity determining regions (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. With the exception of CDR1 in VH, CDRs generally comprise the amino acid residues that form the hypervariable loops.
  • CDRs complementarity determining regions
  • Hypervariable regions (HVRs) are also referred to as “complementarity determining regions” (CDRs), and these terms are used herein interchangeably in reference to portions of the variable region that form the antigen-binding regions.
  • the amino acid sequence boundaries of a CDR can be determined by one of skill in the art using any of a number of known numbering schemes, including those described by Kabat et al., supra (“Kabat” numbering scheme): Al-Lazikani et al., 1997. J. Mol. Biol., 273:927-948 (“Chothia” numbering scheme); MacCallum et al., 1996, J. Mol. Biol, 262:732-745 (“Contact” numbering scheme); Lefranc et al., Dev. Comp. Immunol., 2003, 27:55-77 (“IMGT” numbering scheme); and Honegge and Plückthun, J. Mol.
  • Effective amount encompasses, without limitation, an amount that can ameliorate, reverse, mitigate, prevent, or diagnose a symptom or sign of a medical condition or disorder. Unless dictated otherwise, explicitly or by context, an “effective amount” is not limited to a minimal amount sufficient to ameliorate a condition.
  • the severity of a disease or disorder, as well as the ability of a treatment to prevent, treat, or mitigate, the disease or disorder can be measured, without implying any limitation, by a biomarker or by a clinical parameter.
  • the term “effective amount of a recombinant antibody” refers to an amount of a recombinant antibody sufficient to prevent, treat, or mitigate a coronavirus infection (e.g., SARS-CoV-2 infection).
  • the “fragments” or “functional fragments,” whether attached to other sequences or not, can include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the fragment is not significantly altered or impaired compared to the nonmodified peptide or protein. These modifications can provide for some additional property, such as to remove or add amino acids capable of disulfide bonding, to increase its bio-longevity, to alter its secretory characteristics, etc.
  • the functional fragment must possess a bioactive property, such as binding to a coronavirus antigen (e.g., SARS- CoV-2 antigen), and/or ameliorating the viral infection.
  • a coronavirus antigen e.g., SARS- CoV-2 antigen
  • identity shall be construed to mean the percentage of nucleotide bases or amino acid residues in the candidate sequence that are identical with the bases or residues of a corresponding sequence to which it is compared, after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent identity for the entire sequence, and not considering any conservative substitutions as part of the sequence identity.
  • a polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) that has a certain percentage (for example, 80%, 85%, 90%, or 95%) of "sequence identity" to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences.
  • This alignment and the percent homology or sequence identity can be determined using software programs known in the art. Such alignment can be provided using, for instance, the method of Needleman et al. (1970) J. Mol. Biol. 48: 443-453, implemented conveniently by computer programs such as the Align program (DNAstar, Inc.).
  • “increased” or “increase” as used herein generally means an increase by a statically significant amount; for example, “increased” means an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3- fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level.
  • the terms “nanobody”, “VHH”, “VHH antibody fragment” and “single domain antibody” are used indifferently and designate a variable domain of a single heavy chain of an antibody of the type found in Camelidae, which are without any light chains, such as those derived from Camelids as described in PCT Publication No. WO 94/04678, which is incorporated by reference in its entirety.
  • the term “reduced”, “reduce”, “reduction”, or “decrease” as used herein generally means a decrease by a statistically significant amount.
  • “reduced” means a decrease by at least 10% as compared to a reference level, for example a decrease by at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% decrease (i.e. absent level as compared to a reference sample), or any decrease between 10- 100% as compared to a reference level.
  • Nucleotide can mean a deoxyribonucleotide, ribonucleotide residue, or another similar nucleoside analogue.
  • a nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage.
  • the base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T).
  • the sugar moiety of a nucleotide is a ribose or a deoxyribose.
  • the phosphate moiety of a nucleotide is pentavalent phosphate.
  • a non-limiting example of a nucleotide would be 3'-AMP (3'-adenosine monophosphate) or 5'-GMP (5'-guanosine monophosphate). There are many varieties of these types of molecules available in the art and available herein.
  • primers which are capable of interacting with the disclosed nucleic acids, such as the antigen barcode as disclosed herein.
  • the primers are used to support DNA amplification reactions.
  • the primers will be capable of being extended in a sequence specific manner.
  • Extension of a primer in a sequence specific manner includes any methods wherein the sequence and/or composition of the nucleic acid molecule to which the primer is hybridized or otherwise associated directs or influences the composition or sequence of the product produced by the extension of the primer.
  • Extension of the primer in a sequence specific manner therefore includes, but is not limited to, PCR, DNA sequencing, DNA extension, DNA polymerization, RNA transcription, or reverse transcription.
  • the primers are used for the DNA amplification reactions, such as PCR or direct sequencing. It is understood that in certain embodiments the primers can also be extended using non-enzymatic techniques, where for example, the nucleotides or oligonucleotides used to extend the primer are modified such that they will chemically react to extend the primer in a sequence specific manner.
  • the disclosed primers hybridize with the disclosed nucleic acids or region of the nucleic acids or they hybridize with the complement of the nucleic acids or complement of a region of the nucleic acids.
  • amplification refers to the production of one or more copies of a genetic fragment or target sequence, specifically the “amplicon”. As it refers to the product of an amplification reaction, amplicon is used interchangeably with common laboratory terms, such as "PCR product.”
  • polypeptide refers to a compound made up of a single chain of D- or L-amino acids or a mixture of D- and L-amino acids joined by peptide bonds.
  • Encoding refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom.
  • a gene encodes a protein if transcription and translation of mRNA.
  • An “expression cassette” refers to a DNA coding sequence or segment of DNA that code for an expression product that can be inserted into a vector at defined restriction sites. The cassette restriction sites are designed to ensure insertion of the cassette in the proper reading frame.
  • expression vectors comprise the expression cassette and additionally usually comprise an origin for autonomous replication in the host cells or a genome integration site, one or more selectable markers (e.g. an amino acid synthesis gene or a gene conferring resistance to antibiotics such as zeocin, kanamycin, G418 or hygromycin), a number of restriction enzyme cleavage sites, a suitable promoter sequence and a transcription terminator, which components are operably linked together.
  • selectable markers e.g. an amino acid synthesis gene or a gene conferring resistance to antibiotics such as zeocin, kanamycin, G418 or hygromycin
  • vector includes autonomously replicating nucleotide sequences as well as genome integrating nucleotide sequences.
  • a common type of vector is a “plasmid”, which generally is a self-contained molecule of double-stranded DNA that can readily accept additional (foreign) DNA and which can readily be introduced into a suitable host cell.
  • a plasmid vector often contains coding DNA and promoter DNA and has one or more restriction sites suitable for inserting foreign DNA.
  • vector or plasmid refers to a vehicle by which a DNA or RNA sequence (e.g. a foreign gene) can be introduced into a host cell, so as to transform the host and promote expression (e.g. transcription and translation) of the introduced sequence.
  • host cell shall refer to primary subject cells trans-formed to produce a particular recombinant protein, such as an antibody as described herein, and any progeny thereof. It should be understood that not all progeny are exactly identical to the parental cell (due to deliberate or inadvertent mutations or differences in environment), however, such altered progeny are included in these terms, so long as the progeny retain the same functionality as that of the originally transformed cell.
  • host cell line refers to a cell line of host cells as used for expressing a recombinant gene to produce recombinant polypeptides such as recombinant antibodies.
  • cell line refers to an established clone of a particular cell type that has acquired the ability to proliferate over a prolonged period of time. Such host cell or host cell line may be maintained in cell culture and/or cultivated to produce a recombinant polypeptide.
  • the term "gene” or “gene sequence” refers to the coding sequence or control sequence, or fragments thereof. A gene may include any combination of coding sequence and control sequence, or fragments thereof. Thus, a "gene” as referred to herein may be all or part of a native gene.
  • a polynucleotide sequence as referred to herein may be used interchangeably with the term “gene”, or may include any coding sequence, non-coding sequence or control sequence, fragments thereof, and combinations thereof.
  • the term “gene” or “gene sequence” includes, for example, control sequences upstream of the coding sequence.
  • “Pharmaceutically acceptable carrier” (sometimes referred to as a “carrier”) means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non-toxic, and includes a carrier that is acceptable for veterinary and/or human pharmaceutical or therapeutic use.
  • carrier or “pharmaceutically acceptable carrier” can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil/water or water/oil emulsion) and/or various types of wetting agents.
  • carrier encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in pharmaceutical formulations.
  • the choice of a carrier for use in a composition will depend upon the intended route of administration for the composition.
  • physiologically acceptable carriers include saline, glycerol, DMSO, buffers such as phosphate buffers, citrate buffer, and buffers with other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such
  • compositions disclosed herein can advantageously comprise between about 0.1% and 99% by weight of the total of one or more of the subject compounds based on the weight of the total composition including carrier or diluent.
  • specificity refers to the number of different types of antigens or antigenic determinants to which a particular antigen-binding molecule (such as the recombinant antibody of the invention) can bind.
  • the term “specifically binds,” as used herein with respect to a recombinant antibody refers to the recombinant antibody’s preferential binding to one or more epitopes as compared with other epitopes.
  • Specific binding can depend upon binding affinity and the stringency of the conditions under which the binding is conducted.
  • an antibody specifically binds an epitope when there is high affinity binding under stringent conditions. It should be understood that the specificity of an antigen-binding molecule (e.g., the recombinant antibodies of the present invention) can be determined based on affinity and/or avidity.
  • the affinity represented by the equilibrium constant for the dissociation of an antigen with an antigen-binding molecule (KD), is a measure for the binding strength between an antigenic determinant and an antigen-binding site on the antigen-binding molecule: the lesser the value of the KD, the stronger the binding strength between an antigenic determinant and the antigen-binding molecule (alternatively, the affinity can also be expressed as the affinity constant (KA), which is 1/ KD).
  • affinity can be determined in a manner known per se, depending on the specific antigen of interest.
  • Avidity is the measure of the strength of binding between an antigen-binding molecule (such as the recombinant antibodies of the present invention) and the pertinent antigen. Avidity is related to both the affinity between an antigenic determinant and its antigen binding site on the antigen-binding molecule and the number of pertinent binding sites present on the antigen-binding molecule.
  • antigen-binding proteins such as the recombinant antibodies of the invention
  • KD dissociation constant
  • “Therapeutically effective amount” refers to the amount of a composition such as recombinant antibody that will elicit the biological or medical response of a tissue, system, animal, or human that is being sought by the researcher, veterinarian, medical doctor or other clinician over a generalized period of time.
  • a desired response is reduction of coronaviral titers in a subject.
  • the desired response is mitigation of coronavirus infection and/or related symptoms.
  • a desired biological or medical response is achieved following administration of multiple dosages of the composition to the subject over a period of days, weeks, or years.
  • the therapeutically effective amount will vary depending on the composition, the disorder or conditions and its severity, the route of administration, time of administration, rate of excretion, drug combination, judgment of the treating physician, dosage form, and the age, weight, general health, sex and/or diet of the subject to be treated.
  • the therapeutically effective amount of recombinant antibodies as described herein can be determined by one of ordinary skill in the art.
  • a therapeutically significant reduction in a symptom is, e.g.
  • Measured or measurable parameters include clinically detectable markers of disease, for example, elevated or depressed levels of a biological marker, such as decreased viral titers, decreased viral RNA levels, increase in CD4 T lymphocyte counts, and/or prolonged survival of a subject. It will be understood, that the total daily usage of the compositions and formulations as disclosed herein will be decided by the attending physician within the scope of sound medical judgment.
  • Treatments according to the invention include partially or completely delaying, alleviating, mitigating or reducing the intensity of one or more attendant symptoms.
  • Treatments according to the invention may be applied preventively, prophylactically, palliatively or remedially.
  • Prophylactic treatments are administered to a subject prior to onset (e.g., before obvious signs of an infection), during early onset (e.g., upon initial signs and symptoms of an infection), after an established development of an infection, or during chronic infection. Prophylactic administration can occur for several minutes to months prior to the manifestation of an infection.
  • preventing a disorder or unwanted physiological event in a subject refers specifically to the prevention of the occurrence of symptoms and/or their underlying cause, wherein the subject may or may not exhibit heightened susceptibility to the disorder or event.
  • Antibodies and Compositions in some aspects, disclosed herein is a recombinant antibody, said antibody comprising a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least
  • a recombinant antibody comprising a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical
  • the CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11224. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11225. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11226. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11227.
  • the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11228. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11229. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11230. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11231. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11232.
  • the CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11188. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11189. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11190. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11191.
  • the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11192. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11193. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11194. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11195. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11196.
  • the CDRH1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11170-11178; and CDRL1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11206- 11214.
  • the CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRH1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214. In some embodiments, the CDRL1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11206-11214.
  • the CDRH2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11179-11187; and CDRL2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11215- 11223.
  • the CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRH2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223. In some embodiments, the CDRL2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11215-11223.
  • VH comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11161- 11169.
  • VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169.
  • VL comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11197- 11205.
  • VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205.
  • a CDR sequence (for example CDRL1, CDRL2, CDRL3, CDRH1, CDRH2, or CDRH3) comprises one amino acid mutation, two amino acid mutations, three amino acid mutations, four amino acid mutations, five amino acid mutations, etc.
  • the recombinant antibody when compared to a CDR sequence as disclosed herein.
  • the recombinant antibody is a monoclonal antibody.
  • the recombinant antibody is an isolated antibody.
  • the recombinant antibody is a non-naturally occurring antibody.
  • the recombinant antibody is an antibody or antigen binding fragment thereof.
  • combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating coronavirus infection.
  • combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating SARS-CoV-2 infection.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11170, CDRH2 is SEQ ID NO:11179, CDRH3 is SEQ ID NO:11188, CDRL1 is SEQ ID NO:11206, CDRL2 is SEQ ID NO:11215, and CDRL3 is SEQ ID NO:11224.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11171, CDRH2 is SEQ ID NO:11180, CDRH3 is SEQ ID NO:11189, CDRL1 is SEQ ID NO:11207, CDRL2 is SEQ ID NO:11216, and CDRL3 is SEQ ID NO:11225.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • CDRL1 is SEQ ID NO:11207
  • CDRL2 is SEQ ID NO:11216
  • CDRL3 is SEQ ID NO:11225.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11172, CDRH2 is SEQ ID NO:11181, CDRH3 is SEQ ID NO:11190, CDRL1 is SEQ ID NO:11208, CDRL2 is SEQ ID NO:11217, and CDRL3 is SEQ ID NO:11226.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11173, CDRH2 is SEQ ID NO:11182, CDRH3 is SEQ ID NO:11191, CDRL1 is SEQ ID NO:11209, CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • CDRL1 is SEQ ID NO:11209
  • CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11174, CDRH2 is SEQ ID NO:11183, CDRH3 is SEQ ID NO:11192, CDRL1 is SEQ ID NO:11210, CDRL2 is SEQ ID NO:11219, and CDRL3 is SEQ ID NO:11228.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11175, CDRH2 is SEQ ID NO:11184, CDRH3 is SEQ ID NO:11193, CDRL1 is SEQ ID NO:11211, CDRL2 is SEQ ID NO:11220, and CDRL3 is SEQ ID NO:11229.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • CDRL1 is SEQ ID NO:11211
  • CDRL2 is SEQ ID NO:11220
  • CDRL3 is SEQ ID NO:11229.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11176, CDRH2 is SEQ ID NO:11185, CDRH3 is SEQ ID NO:11194, CDRL1 is SEQ ID NO:11212, CDRL2 is SEQ ID NO:11221, and CDRL3 is SEQ ID NO:11230.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11177, CDRH2 is SEQ ID NO:11186, CDRH3 is SEQ ID NO:11195, CDRL1 is SEQ ID NO:11213, CDRL2 is SEQ ID NO:11222, and CDRL3 is SEQ ID NO:11231.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11178, CDRH2 is SEQ ID NO:11187, CDRH3 is SEQ ID NO:11196, CDRL1 is SEQ ID NO:11214, CDRL2 is SEQ ID NO:11223, and CDRL3 is SEQ ID NO:11232.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11161, and VL is SEQ ID NO: 11197.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11162, and VL is SEQ ID NO: 11198.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11163, and VL is SEQ ID NO: 11199.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11164, and VL is SEQ ID NO: 11200.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11165, and VL is SEQ ID NO: 11201.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11166, and VL is SEQ ID NO: 11202.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11167, and VL is SEQ ID NO: 11203.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11168, and VL is SEQ ID NO: 11204.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11169, and VL is SEQ ID NO: 11205.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VH comprising an amino acid sequence selected from SEQ ID NOs: 1241-2480. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VL comprising an amino acid sequence selected from SEQ ID NOs: 6201-7440. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH1 comprising an amino acid sequence selected from SEQ ID NOs: 2481-3720. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH2 comprising an amino acid sequence selected from SEQ ID NOs: 3721-4960.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH3 comprising an amino acid sequence selected from SEQ ID NOs: 4961-6200.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL1 comprising an amino acid sequence selected from SEQ ID NOs: 7441-8680.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL2 comprising an amino acid sequence selected from SEQ ID NOs: 8681-9920.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL3 comprising an amino acid sequence selected from SEQ ID NOs: 9921-11160.
  • Methods Disclosed herein are methods for preventing, treating, inhibiting, reducing, or detecting coronavirus infection.
  • a method of producing a recombinant antibody comprising cultivating or maintaining the host cell of any preceding aspect under conditions to produce a recombinant antibody as described herein.
  • a method of treating, preventing, reducing, and/or inhibiting coronavirus infection comprising administering to a subject a therapeutically effective amount of a recombinant antibody, wherein the recombinant antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at
  • a method of treating, preventing, reducing, and/or inhibiting coronavirus infection comprising administering to a subject a therapeutically effective amount of a recombinant antibody, wherein the recombinant antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at
  • the CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11224. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11225. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11226. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11227.
  • the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11228. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11229. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11230. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11231. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11232.
  • the CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11188. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11189. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11190. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11191.
  • the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11192. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11193. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11194. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11195. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11196.
  • the CDRH1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11170-11178; and CDRL1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11206- 11214.
  • the CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRH1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214. In some embodiments, the CDRL1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11206-11214.
  • the CDRH2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11179-11187; and CDRL2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11215- 11223.
  • the CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRH2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223. In some embodiments, the CDRL2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11215-11223.
  • VH comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11161- 11169.
  • VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169.
  • VL comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11197- 11205.
  • VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205.
  • a CDR sequence (for example CDRL1, CDRL2, CDRL3, CDRH1, CDRH2, or CDRH3) comprises one amino acid mutation, two amino acid mutations, three amino acid mutations, four amino acid mutations, five amino acid mutations, etc.
  • the recombinant antibody when compared to a CDR sequence as disclosed herein.
  • the recombinant antibody is a monoclonal antibody.
  • the recombinant antibody is an isolated antibody.
  • the recombinant antibody is an antibody or antigen binding fragment thereof.
  • combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating coronavirus infection.
  • combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating SARS-CoV-2 infection.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11170, CDRH2 is SEQ ID NO:11179, CDRH3 is SEQ ID NO:11188, CDRL1 is SEQ ID NO:11206, CDRL2 is SEQ ID NO:11215, and CDRL3 is SEQ ID NO:11224.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11171, CDRH2 is SEQ ID NO:11180, CDRH3 is SEQ ID NO:11189, CDRL1 is SEQ ID NO:11207, CDRL2 is SEQ ID NO:11216, and CDRL3 is SEQ ID NO:11225.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • CDRL1 is SEQ ID NO:11207
  • CDRL2 is SEQ ID NO:11216
  • CDRL3 is SEQ ID NO:11225.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11172, CDRH2 is SEQ ID NO:11181, CDRH3 is SEQ ID NO:11190, CDRL1 is SEQ ID NO:11208, CDRL2 is SEQ ID NO:11217, and CDRL3 is SEQ ID NO:11226.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11173, CDRH2 is SEQ ID NO:11182, CDRH3 is SEQ ID NO:11191, CDRL1 is SEQ ID NO:11209, CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • CDRL1 is SEQ ID NO:11209
  • CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11174, CDRH2 is SEQ ID NO:11183, CDRH3 is SEQ ID NO:11192, CDRL1 is SEQ ID NO:11210, CDRL2 is SEQ ID NO:11219, and CDRL3 is SEQ ID NO:11228.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11175, CDRH2 is SEQ ID NO:11184, CDRH3 is SEQ ID NO:11193, CDRL1 is SEQ ID NO:11211, CDRL2 is SEQ ID NO:11220, and CDRL3 is SEQ ID NO:11229.
  • VL light chain variable region
  • CDRL light chain complementarity determining region
  • CDRL3 heavy chain complementarity determining region
  • CDRL1 is SEQ ID NO:11211
  • CDRL2 is SEQ ID NO:11220
  • CDRL3 is SEQ ID NO:11229.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11176, CDRH2 is SEQ ID NO:11185, CDRH3 is SEQ ID NO:11194, CDRL1 is SEQ ID NO:11212, CDRL2 is SEQ ID NO:11221, and CDRL3 is SEQ ID NO:11230.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11177, CDRH2 is SEQ ID NO:11186, CDRH3 is SEQ ID NO:11195, CDRL1 is SEQ ID NO:11213, CDRL2 is SEQ ID NO:11222, and CDRL3 is SEQ ID NO:11231.
  • the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11178, CDRH2 is SEQ ID NO:11187, CDRH3 is SEQ ID NO:11196, CDRL1 is SEQ ID NO:11214, CDRL2 is SEQ ID NO:11223, and CDRL3 is SEQ ID NO:11232.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11161, and VL is SEQ ID NO: 11197.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11162, and VL is SEQ ID NO: 11198.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11163, and VL is SEQ ID NO: 11199.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11164, and VL is SEQ ID NO: 11200.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11165, and VL is SEQ ID NO: 11201.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11166, and VL is SEQ ID NO: 11202.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11167, and VL is SEQ ID NO: 11203.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11168, and VL is SEQ ID NO: 11204.
  • the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11169, and VL is SEQ ID NO: 11205.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VH comprising an amino acid sequence selected from SEQ ID NOs: 1241-2480. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VL comprising an amino acid sequence selected from SEQ ID NOs: 6201-7440. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH1 comprising an amino acid sequence selected from SEQ ID NOs: 2481-3720. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH2 comprising an amino acid sequence selected from SEQ ID NOs: 3721-4960.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH3 comprising an amino acid sequence selected from SEQ ID NOs: 4961-6200.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL1 comprising an amino acid sequence selected from SEQ ID NOs: 7441-8680.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL2 comprising an amino acid sequence selected from SEQ ID NOs: 8681-9920.
  • the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL3 comprising an amino acid sequence selected from SEQ ID NOs: 9921-11160.
  • the recombinant antibody binds to at least one coronavirus antigen.
  • the recombinant antibody binds to at least one SARS-CoV-2 antigen.
  • the target protein comprises a viral protein.
  • the viral protein is a coronavirus protein.
  • Coronaviruses constitute the subfamily Orthocoronavirinae, in the family Coronaviridae, order Nidovirales, and realm Riboviria.
  • coronavirus are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry.
  • the genome size of coronaviruses ranges from approximately 27 to 34 kilobases.
  • the structure of coronavirus generally consists of the following: spike protein, hemagglutinin-esterase dimer (HE), a membrane glycoprotein (M), an envelope protein (E) a nucleoclapid protein (N) and RNA.
  • the coronavirus family comprises genera including, for example, alphacoronavirus (e.g., Human coronavirus 229E, Human coronavirus NL63, Miniopterus bat coronavirus 1, Miniopterus bat coronavirus HKU8, Porcine epidemic diarrhea virus, Rhinolophus bat coronavirus HKU2, Scotophilus bat coronavirus 512), betacoronavirus (e.g., SARS-CoV-2, Betacoronavirus 1, Human coronavirus HKU1, Murine coronavirus, Pipistrellus bat coronavirus HKU5, Rousettus bat coronavirus HKU9, Severe acute respiratory syndrome-related coronavirus, Tylonycteris bat coronavirus HKU4, Middle East respiratory syndrome-related coronavirus (MERS), Human coronavirus OC43, Hedgehog coronavirus 1 (EriCoV)), gammacoronavirus (e.g., Beluga whale coronavirus SW1, Infectious bronchit
  • the viral protein is a protein of severe acute respiratory syndrome-related coronavirus. In some embodiments, the viral protein is a protein of MERS coronavirus. In some embodiments, the viral protein is a SARS-CoV-2 protein, including, for example, SARS-CoV-2 spike protein, SARS-CoV-2 envelope protein, SARS-CoV-2 membrane protein, or SARS-CoV-2 nucleocapsid protein, or a fragment thereof. In some embodiments, the viral protein is a receptor binding domain of a SARS-CoV-2 spike protein. In some aspects, disclosed herein is a method of producing a recombinant antibody comprising cultivating or maintaining the host cell of any preceding aspect under conditions to produce said recombinant antibody.
  • a method of treating, preventing, reducing, and/or inhibiting coronavirus infection comprising administering to a subject a therapeutically effective amount of the recombinant antibody of any preceding aspect.
  • the antibody repertoire characterization done herein is also readily generalizable to other pathogens, and as such, have a broad and lasting impact on the development of countermeasures for established and emerging infectious diseases.
  • Methods for determining antibody sequences and antigen-antibody specificities are known in the art. See, e.g., International Publication Number: WO 2020/033164, incorporated by reference.
  • a method for detecting a coronavirus infection in a subject comprising: providing a biological sample from the subject, and detecting a coronavirus antigen in the biological sample with an antibody that specifically binds to the coronavirus antigen, wherein the antibody is from any aspect as disclosed herein, and wherein the presence of the coronavirus antigen in the biological sample indicates the subject is infected with a coronavirus.
  • the biological sample can be from, for example, a throat swab, a nasal swab, a nasopharyngeal swab, an oropharyngeal swab, cells, blood, serum, plasma, saliva, urine, stool, sputum, or nasopharyngeal aspirates.
  • the coronavirus infection is caused by SARS-CoV-2.
  • the method comprises contacting the biological sample with a SARS-CoV-2 antigen.
  • the SARS-CoV-2 antigen is directly immobilized on a substrate and is detected by an antibody disclosed herein directly or indirectly by a labeled heterologous anti-isotype antibody, wherein the bound antibody can be detected by a detection assay.
  • the SARS-CoV-2 antigen can be selected from the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, or a fragment thereof.
  • the term “labeled”, with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled.
  • Examples of indirect labeling include detection of a primary antibody using a secondary antibody that is labeled a fluorescent probe or with biotin for detection.
  • In vitro techniques for detection of the antibodies of SARS-CoV-2 include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence, IgM antibody capture enzyme immunoassay (MAC-ELISA), indirect IgG ELISA, indirect fluorescent antibody assay (IFAT), hemagglutination inhibition (HIT), and serum dilution cross-species plaque reduction neutralization tests (PRNTs).
  • ELISAs enzyme linked immunosorbent assays
  • Western blots Western blots, immunoprecipitations and immunofluorescence
  • IgM antibody capture enzyme immunoassay MAC-ELISA
  • indirect IgG ELISA indirect fluorescent antibody assay
  • IFAT indirect fluorescent antibody assay
  • HIT hemagglutination inhibition
  • PRNTs serum dilution cross-species plaque reduction
  • in vitro techniques for detection of an antigen of SARS-CoV-2 include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence.
  • in vivo techniques for detection of SARS-CoV-2 include introducing into a subject a labeled antibody directed against the polypeptide.
  • the antibody can be labeled with a radioactive marker whose presence and location can be detected by standard imaging techniques, including autoradiography.
  • the levels of the antibodies are determined by immunoassay comprising Enzyme linked immunospot (ELISPOT), Enzyme-linked immunosorbent assay (ELISA), western blot, or a multiplex ELISA assay.
  • ELISPOT Enzyme linked immunospot
  • ELISA Enzyme-linked immunosorbent assay
  • western blot or a multiplex ELISA assay.
  • the multiplex ELISA assay is selected from the group consisting of Luminex, Veriplex, LEGENDplex, Bio-Plex, Milliplex MAP, and FirePlex.
  • the steps of various useful immunodetection methods have been described in the scientific literature, such as, e.g., Maggio et al., Enzyme-Immunoassay, (1987) and Nakamura, et al., Enzyme Immunoassays: Heterogeneous and Homogeneous Systems, Handbook of Experimental Immunology, Vol.1: Immunochemistry, 27.1-27.20 (1986), each of which is incorporated herein by reference in its entirety and specifically for its teaching regarding immunodetection methods.
  • Immunoassays in their most simple and direct sense, are binding assays involving binding between antibodies and antigen. Many types and formats of immunoassays are known and all are suitable for detecting the disclosed biomarkers. Examples of immunoassays are enzyme linked immunosorbent assays (ELISAs), radioimmunoassays (RIA), radioimmune precipitation assays (RIPA), immunobead capture assays, Western blotting, dot blotting, gel-shift assays, Flow cytometry, protein arrays, multiplexed bead arrays, magnetic capture, in vivo imaging, fluorescence resonance energy transfer (FRET), and fluorescence recovery/localization after photobleaching (FRAP/ FLAP).
  • ELISAs enzyme linked immunosorbent assays
  • RIA radioimmunoassays
  • RIPA radioimmune precipitation assays
  • immunobead capture assays Western blotting, dot blotting, gel-shift assays
  • kits for detecting the presence of SARS-CoV-2 or a polypeptide/antigen thereof in a biological sample can comprise, for example: (1) a first antibody (e.g., attached to a solid support) which binds to a coronavirus antigen; and, optionally, (2) a second, different antibody which binds to either the coronavirus antigen or the first antibody and is conjugated to a detectable agent.
  • a first antibody e.g., attached to a solid support
  • a second, different antibody which binds to either the coronavirus antigen or the first antibody and is conjugated to a detectable agent.
  • Example 1 Ultra-potent neutralization of SARS-CoV-2 variants of concern by an antibody with a unique genetic signature and structural mode of spike recognition.
  • a panel of SARS-CoV-2 antibodies isolated from an individual who recovered from COVID-19 using LIBRA-seq technology are reported.
  • 54042-4 showed ultra-potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs).
  • VOCs variants of concern
  • a 2.7 ⁇ cryo-EM structure of 54042-4 in complex with SARS-CoV-2 spike revealed an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages.
  • 54042-4 possesses unique genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings identify 54042-4 for clinical development to counteract current and potential SARS-CoV-2 VOCs.
  • SARS-CoV-2 SARS-CoV-2 spike
  • S SARS-CoV-2 spike
  • SARS-CoV-2 spike is a class I viral fusion protein that is a trimer of heterodimers composed of S1 and S2 subunits.
  • S1 which includes both the receptor-binding domain (RBD) and the N-terminal domain (NTD)
  • RBD receptor-binding domain
  • NTD N-terminal domain
  • S2 drives membrane fusion by refolding from a prefusion to postfusion conformation.
  • the primary contact of ACE2 and spike is in the receptor-binding domain (RBD) of the S1 subunit which is composed of a receptor binding motif (RBM) and RBD core.
  • RBD receptor-binding domain
  • the three RBDs within each spike can adopt an ACE2-accessible “up” conformation and an ACE2- inaccessible “down” conformation via a hinge-like motion.
  • the RBD serves as the dominant target of neutralizing antibodies via antagonism of ACE2 binding, although other neutralizing epitopes have been identified.
  • Neutralizing antibodies targeting the RBD have been characterized extensively and partition into different classes based on binding mode, ACE2 interface overlap, and cross- reactivity with other Sarbecoviruses.
  • neutralizing antibodies predominantly encoded by IGHV3-53 and IGHV3-66 have epitopes directly covering the ACE2 interaction footprint in the RBM.
  • this class of antibodies are clinical EUA candidates REGN10933 and COV2-2196.
  • Antibodies that bind the RBM but are more distal to the ACE2 interface form another distinct class that includes REGN10987 and COV2-2130.
  • cross reactive antibodies such as S309, CR3022 and ADG-2 that cross-react with other coronaviruses comprise a more diverse group yet targeting residues in the RBD-core, as a result of high sequence conservation at this site.
  • VOCs viral variants of concern
  • the L452R substitution, detected in both the B.1.429 (Epsilon) and B.1.617.2 (Delta) variants also permits escape to monoclonal antibodies and a reduction in neutralization titer in comparison to USA- WA1 in vaccinees as well as individuals recovered from COVID-19 infection.
  • the Epsilon lineage also contains substitutions (S13I and W152C) that disrupt the conformation of the NTD, resulting in the loss of numerous published NTD-directed SARS-CoV-2 neutralizing antibodies.
  • N501Y can increase affinity for ACE2, resulting in increased infectivity, whereas E484K disrupts the antigenic landscape of the RBD that can lead to substantial decreases in neutralization titers.
  • SARS-CoV-2 VOCs also escape neutralization by polyclonal antibodies in the serum from vaccine recipients and individuals previously infected with SARS- CoV-2.
  • These observations highlight the critical need for a wide range of potently neutralizing antibodies that are not sensitive to substitutions arising in VOCs.
  • LIBRA-seq a recently developed antibody discovery technology, was applied to interrogate the B cell repertoire of an individual who had recovered from COVID-19.
  • Antibody 54042-4 therefore can be used for further prophylactic or therapeutic development for protection against a broad range of SARS-CoV-2 variants.
  • Results Identification of SARS-CoV-2-neutralizing antibodies by LIBRA-seq To identify SARS-CoV-2 S-directed antibodies, LIBRA-seq (Linking B Cell receptor to antigen specificity through sequencing) was used, a technology that enables a high-throughput simultaneous determination of B cell receptor sequence and antigen reactivity at the single-cell level, expediting the process of lead antibody selection and characterization.
  • the LIBRA-seq antigen screening library included SARS-CoV-2 and SARS-CoV-2 D614G spikes stabilized in a prefusion conformation, along with antigens from other coronaviruses including SARS-CoV S, MERS-CoV S, , HCoV-OC43 S, HCoV-229E S, HCoV-NL63 S, SARS-CoV-2 RBD, SARS-CoV RBD, and MERS-CoV RBD, as well as negative control antigens.
  • Antigen-specific B cells were isolated from a donor with potently neutralizing antibodies in serum (1:258 NT 50 ) three months after infection confirmed by nasal swab RT-PCR testing for SARS-CoV-2 ( Figures 6A and 6B). Of the 73 IgG + B cells were observed with high LIBRA-seq scores ( ⁇ 1) for SARS-CoV-2 S ( Figure 1A), nine lead antibodies were chosen with diverse sequence characteristics, CDRH3 length, and germline V gene usage for characterization as recombinant monoclonal antibodies ( Figure 1B and Figure 6C).
  • COV2-2196 and COV2-2130 which form the basis of AZD7442, an antibody cocktail currently under investigation in clinical trials for COVID-19 treatment and prevention (ClinicalTrials.gov Identifiers: NCT04625725, NCT04723394, NCT04518410, and NCT04501978) and CR3022.
  • the competition experiment showed that 54042-4 competed for binding to SARS-CoV-2 S protein with COV2-2130, but not COV2-2196 or CR3022 (Figure 2D). Together, these results indicate that 54042-4 targets an epitope on SARS-CoV-2 RBD that at least partially overlaps with the binding sites for both ACE2 and other potently neutralizing RBD- directed antibodies.
  • 54042-4 binds the apex of the SARS-CoV-2 RBD in the down conformation
  • a 2.7 ⁇ resolution cryo-EM structure was determined of the 54042-4 antigen-binding fragments (Fabs) bound to the SARS-CoV-2 S extracellular domain (ECD) modified so that all three RBDs were disulfide-locked in the down conformation.
  • Figure 3A Local refinement of one RBD bound to a 54042-4 Fab was performed to improve the interpretability of the map at the binding interface, resulting in a local 3D reconstruction with a resolution of 2.8 ⁇
  • CDRH2 From CDRH2, Asp56 forms a hydrogen bond and salt bridge with Lys444, whereas Arg58 forms hydrogen bonds with mainchain atoms from Gly446 and Gly447.
  • the CDRH1 contributes a lone residue, Ile32, to the binding interface, forming minor contacts near Leu441.
  • the 54042-4 light chain surrounds the opposite side of this RBD region, mediating interactions primarily through hydrophobic contacts formed by CDRL1 and CDRL3 near RBD residue Val445 ( Figure 3D). Additional light chain contacts are made with residues 498 to 500 of the RBD, including a hydrogen bond between His92 of CDRL3 and Thr500, and hydrophobic interactions involving CDRL1 Phe30 and Tyr32.
  • 54042-4 binds all three RBDs locked in the down position, the epitope region is equally accessible when the RBD is in the up position. Additionally, the epitope lies outside the RBD hinge region, makes no additional contacts with the spike trimer, and partially overlaps the ACE2 binding site. Therefore, the mechanism of neutralization likely involves inhibition of ACE2 binding rather than locking the RBDs in the down conformation. Notably, the complex structure indicated that 54042-4 does not make substantial contact with a number of spike substitutions associated with current VOCs.
  • RBD residue Asn501 (present as Tyr501 in several VOCs, including Alpha, Beta, and Gamma) lies just outside of the 54042-4 epitope
  • C ⁇ atoms of Glu484 (present as Lys484 or Gln484 in, e.g., Beta, Gamma, and B.1.617 (Kappa)
  • Leu452 (present as Arg452 in Epsilon and Delta) are approximately 18 and 14 ⁇ away from the C ⁇ atoms of the nearest 54042-4 residue, respectively ( Figure 3B).
  • the substitution Gly614, which is found in all current VOCs is outside of the RBD is approximately 75 ⁇ from the nearest 54042-4 residue.
  • Antibody 54042-4 has un uncommon genetic signature and distinct structural mode of RBD recognition Public clonotype sequence signatures (those shared by multiple individuals recovered from COVID-19 infection) have been identified for potently neutralizing SARS-CoV-2 antibodies, including antibodies currently in clinical trials or approved for emergency use, have been identified. To investigate whether antibody sequences that are closely related to 54042-4 can be identified among known SARS-CoV-2 antibodies, this study searched the CoV-AbDab database that contains paired heavy-light chain sequences of coronavirus antibodies. Notably, only 0.5% of antibodies in the database used the same combination of IGHV2-5 heavy chain and IGKV1-39 light chain germline V genes as 54042-4.
  • both C119 and COVOX-75, as well as COV2-2130 have substantial buried surface area ( ⁇ 2 ) interactions with a number of additional residues compared to those in the epitope of 54042-4 ( Figure 4C), indicating that these three antibodies can be susceptible to additional potential spike substitutions that would not directly affect antigen interactions with 54042-4. It was also observed that while the epitopes of antibodies 2-7, LY-CoV1404, and REGN10987 correlate well with that of 54042-4, these antibodies have distinct angles of antigen approach (Figure 4D). To quantify this observation, the RBDs from the 2-7, LY-CoV1404, and REGN10987 complex structures were aligned with the RBD from the 54042-4 structure.
  • RMSD root mean square deviations
  • antibody 54042-4 utilizes an uncommon genetic signature and a distinct structural mode of antigen recognition compared to other known SARS-CoV-2 antibodies.
  • Antibody 54042-4 is not affected by current SARS-CoV-2 VOC substitutions
  • shotgun alanine-scanning mutagenesis of the SARS-CoV-2 RBD was performed. The only tested substitutions that substantially affected binding in comparison to an RBD antibody control were K444A, V445A, G446A, and P499A (Figure 5A), which all fall within the 54042-4 epitope ( Figure 3C, 3D, and Figure 8A).
  • SARS-CoV-2 neutralizing antibody discovery efforts have produced an extensive panel of antibodies that show a wide range of functional effects, and most antibodies discovered to date cluster into several classes based on RBD-binding orientation, ACE2 antagonism, and cross- reactivity to related SARS-like coronaviruses.
  • this study reports the identification of 54042- 4, an antibody that exhibited potent SARS-CoV-2 neutralization against USA-WA1 as well as the currently circulating Alpha, Beta, Delta, and Gamma VOCs.
  • Antibody 54042-4 neutralized virus at comparable IC 50 s to the clinical candidates LY-CoV1404 and REGN10987, despite having ⁇ 10- fold lower affinity for the RBD. While the epitope of antibody 54042-4 showed partial overlap with that of several other known RBD-directed antibodies, these findings revealed a distinct mode of SARS-CoV-2 spike recognition, paired with an uncommon genetic signature that distinguishes 54042-4 from other SARS-CoV-2 antibodies. Notably, important differences were observed even for the six antibodies with the highest epitope correlations to 54042-4, with all six of these antibodies exhibiting substantially greater contacts with one or more known residues associated with currently circulating VOCs, as well as with other spike residues (Figure 4C).
  • Variants that encode the E484K substitution appear to pose a significantly higher risk of neutralization escape in vaccine recipients and individuals who have recovered from COVID-19. Indeed, the rise of cases associated with the P.1 variant that harbors the E484K substitution (among others) in Manaus, Brazil is on a dangerous trajectory, despite having a 76% population seropositivity rate dating back to March 2020. In the context of vaccination, early vaccine trial data for Novavax against the Beta lineage in South Africa (also encoding the E484K substitution) demonstrated a significant decrease in efficacy. The enhanced transmission profile and recent rise in new infection cases as a result of the Delta variant is another demonstration of the need for SARS-CoV-2 therapeutics.
  • Beta variant or any lineage harboring the Glu484 substitution has yet to propagate in the United States, the nearly complete abrogation of neutralization activity of LY- CoV555 (Bamlinivimab) and REGN10933 against the Beta variant poses a significant risk for the currently available EUA clinical candidates. Further, the rise in cases with the L452R substitution (Epsilon and Delta variants) and the corresponding reduction in neutralization potency associated with the Eli Lilly cocktail (Bamlinivimab and Etesivimab), as well as Regdanivimab (approved for use in Europe), further motivates the continued investigation into antibodies insensitive to currently circulating VOCs.
  • SARS-CoV-2 S HP For all antigens with the exception of SARS-CoV-2 S HP, transfections were treated with 1 ⁇ M kifunensine to ensure uniform glycosylation three hours post-transfection. Transfected supernatants were harvested after 6 days of expression. SARS-CoV- 2 RBD-SD1, SARS-CoV RBD-SD1, and MERS-CoV RBD were purified using Protein A resin (Pierce). SARS-CoV-2 S HP, MERS-CoV S-2P Avi, and HCoV-OC43 S-2P were purified using StrepTrap HP columns (Cytiva Life Sciences).
  • SARS-CoV-2 RBD-SD1, SARS- CoV RBD-SD1, and MERS-CoV RBD were further purified over a Superdex200 column (GE Life Sciences).
  • SARS-CoV-2 S HP, SARS-CoV-2 S HP Beta, SARS-CoV-2 S HP Alpha, SARS- CoV S-2P, MERS-CoV S-2P, and HCoV-OC43 S-2P were purified over a Superose6 Increase column (GE Life Sciences).
  • HCoV-NL63 and HCoV-229E alpha coronavirus spike proteins as well as the SARS-CoV-2 S1, SARS-CoV-2 S2, and SARS-CoV-2 NTD truncated proteins were purchased from the commercial vendor, Sino Biological.
  • Avitagged antigens were biotinylated using BirA biotin ligase (Avidity LLC).
  • Recombinant NC99 HA protein contains the HA ectodomain with a point mutation at the sialic acid-binding site (Y98F), T4 fibritin foldon trimerization domain, AviTag, and hexahistidine-tag, and were expressed in Expi 293F mammalian cells using Expifectamine 293 transfection reagent (Thermo Fisher Scientific) cultured for 4-5 days. Culture supernatant was harvested and cleared as above, and then adjusted pH and NaCl concentration by adding 1M Tris- HCl (pH 7.5) and 5M NaCl to 50 mM and 500 mM, respectively.
  • Ni Sepharose excel resin (GE Healthcare) was added to the supernatant to capture hexahistidine tag. Resin was separated on a column by gravity and captured HA protein was eluted by a Tris-NaCl (pH 7.5) buffer containing 300 mM imidazole. The eluate was further purified by a size exclusion chromatography with a HiLoad 16/60 Superdex 200 column (GE Healthcare). Fractions containing HA were concentrated, analyzed by SDS-PAGE and tested for antigenicity by ELISA with known antibodies.
  • Spike protein used for cryo-EM was expressed by transiently transfecting plasmid encoding the HexaPro spike variant containing additional S383C and D985C substitutions with a C-terminal TwinStrep tag into FreeStyle 293-F cells (Thermo Fisher) using polyethyleneimine.5 ⁇ M kifunensine was added 3h post-transfection. The cell culture was harvested four days after transfection and the spike-containing medium was separated from the cells by centrifugation. Supernatants were passed through a 0.22 ⁇ m filter and passaged over StrepTactin resin (IBA).
  • IBA StrepTactin resin
  • DNA-barcoding of Antigens Oligos were used that possess 15 bp antigen barcode, a sequence capable of annealing to the template switch oligo that is part of the 10X bead-delivered oligos, and contain truncated TruSeq small RNA read 1 sequences in the following structure: 5’- CCTTGGCACCCGAGAATTCCANNNNNNNNNNNCCCATATAAGA*A*A-3’ (SEQ ID NO: 11233), where Ns represent the antigen barcode, and * represents a phosphorothioate bond.
  • GCAGCGTATAAGTCA SARS-CoV-2 S
  • AACCCACCGTTGTTA SARS-CoV-2 S D614G
  • GCTCCTTTACACGTA SARS-CoV S
  • GGTAGCCCTAGAGTA MERS-CoV S
  • AGACTAATAGCTGAC HCAGCGTATAAGTCA
  • TCATTTCCTCCGATT H NC99
  • SEQ ID NO: 11242 TCATTTCCTCCGATT
  • a unique DNA barcode was directly conjugated to the antigen itself.
  • 5’amino-oligonucleotides were conjugated directly to each antigen using the Solulink Protein-Oligonucleotide Conjugation Kit (TriLink cat no. S-9011) according to manufacturer’s instructions. Briefly, the oligo and protein were desalted, and then the amino-oligo was modified with the 4FB crosslinker, and the biotinylated antigen protein was modified with S-HyNic. Then, the 4FB-oligo and the HyNic-antigen were mixed together. This causes a stable bond to form between the protein and the oligonucleotide.
  • the concentration of the antigen-oligo conjugates was determined by a BCA assay, and the HyNic molar substitution ratio of the antigen-oligo conjugates was analyzed using the NanoDrop according to the Solulink protocol guidelines.
  • AKTA FPLC was used to remove excess oligonucleotide from the protein-oligo conjugates, which were also verified using SDS-PAGE with a silver stain.
  • Antigen-oligo conjugates were also used in flow cytometry titration experiments.
  • Antigen-specific B cell sorting Cells were stained and mixed with DNA-barcoded antigens and other antibodies, and then sorted using fluorescence activated cell sorting (FACS). First, cells were counted and viability was assessed using Trypan Blue.
  • Antibody 54042-2 was natively an IGHG2, but was cloned into an IGHG1 Fc backbone vector for monoclonal antibody characterization. Antibodies were expressed in Expi293F mammalian cells (Thermo Fisher Scientific) by co-transfecting heavy chain and light chain expressing plasmids using polyethylenimine transfection reagent and cultured for 5-7 days. Cells were maintained in FreeStyle F17 expression medium supplemented at final concentrations of 0.1% Pluronic Acid F- 68 and 20% 4mM L-Glutamine. These cells were cultured at 37°C with 8% CO 2 saturation and shaking.
  • microscale transfection were performed ( ⁇ 1 ml per antibody) of CHO cell cultures using the Gibco ExpiCHO Expression System and a protocol for deep 96-well blocks (Thermo Fisher Scientific).
  • synthesized antibody-encoding DNA ( ⁇ 2 ⁇ g per transfection) was added to OptiPro serum free medium (OptiPro SFM), incubated with ExpiFectamine CHO Reagent and added to 800 ⁇ l of ExpiCHO cell cultures into 96-deep-well blocks using a ViaFlo 384 liquid handler (Integra Biosciences).
  • the plates were incubated on an orbital shaker at 1,000 r.p.m. with an orbital diameter of 3 mm at 37 °C in 8% CO 2 .
  • the next day after transfection ExpiFectamine CHO Enhancer and ExpiCHO Feed reagents (Thermo Fisher Scientific) were added to the cells, followed by 4 d incubation for a total of 5 d at 37 °C in 8% CO 2 .
  • Culture supernatants were collected after centrifuging the blocks at 450g for 5 min and were stored at 4°C until use.
  • fritted deep-well plates were used containing 25 ⁇ l of settled protein G resin (GE Healthcare Life Sciences) per well.
  • Clarified culture supernatants were incubated with protein G resin for antibody capturing, washed with PBS using a 96-well plate manifold base (Qiagen) connected to the vacuum and eluted into 96-well PCR plates using 86 ⁇ l of 0.1 M glycine-HCL buffer pH 2.7. After neutralization with 14 ⁇ l of 1 M Tris-HCl pH 8.0, purified antibodies were buffer-exchanged into PBS using Zeba Spin Desalting Plates (Thermo Fisher Scientific) and stored at 4°C until use. ELISA To assess antibody binding, soluble protein was plated at 2 ⁇ g/ml overnight at 4°C.
  • biotinylated antibodies diluted in blocking buffer were added directly to each well in a volume of 5 ⁇ L per well (such that the final concentrations of each biotinylated mAb were equal to the respective EC 90 of each mAb), and then incubated for 30 min at ambient temperature. Plates were then washed with PBS-T and incubated for 1 h with HRP- conjugated avidin (Sigma, 25 ⁇ L of a 1:3,500 dilution in blocking buffer). Plates were washed with PBS-T and 25 ⁇ L TMB substrate was added to each well. After sufficient development, the reactions were quenched by addition 25 ⁇ L 1M HCl and absorbance at 450 nm was quantified using a plate reader.
  • the signal obtained for binding of the biotin-labeled reference mAb in the presence of the unlabeled tested mAb was expressed as a percentage of the binding of the reference antibody in the presence of 10 ⁇ g/mL of the anti-dengue mAb DENV 2D22, which served as a no-competition control.
  • Tested antibodies were considered competing if their presence reduced the reference mAb binding to less than 60% of its maximal binding and non-competing if the signal was greater than 30%.
  • RTCA Real-time Cell Analysis
  • Vero-furin cells Six thousand (6,000) Vero-furin cells in 20 ⁇ l of cell culture medium were seeded per well, and the plate was placed on the analyzer. Sensograms were visualized using RTCA HT software version 1.0.1 (ACEA Biosciences).
  • RTCA HT software version 1.0.1 (ACEA Biosciences).
  • a screening neutralization assay equal amounts of virus were mixed with micro-scale purified antibodies in a total volume of 40 ⁇ L using DMEM supplemented with 2% FBS as a diluent and incubated for 1 h at 37 °C in 5% CO 2 . At ⁇ 17–20 h after seeding the cells, the virus–antibody mixtures were added to the cells in 384-well E-plates.
  • Wells containing virus only (in the absence of antibody) and wells containing only Vero cells in medium were included as controls. Plates were measured every 8– 12 h for 48–72 h to assess virus neutralization. Micro-scale antibodies were assessed in four 5- fold dilutions (starting from a 1:20 sample dilution), and their concentrations were not normalized. Neutralization was calculated as the percent of maximal cell index in control wells without virus minus cell index in control (virus-only) wells that exhibited maximal CPE at 40–48 h after applying virus–antibody mixture to the cells.
  • RTCA Potency Neutralization Screening Assay To determine neutralizing activity of IgG and convalescent serum, real-time cell analysis (RTCA) assay was used on an xCELLigence RTCA MP Analyzer (ACEA Biosciences Inc.) that measures virus-induced cytopathic effect (CPE) (Surytowna N et al., 2021).
  • DMEM fetal bovine serum
  • ViaFlo384 liquid handler Integra Biosciences
  • a suspension of 18,000 Vero-E6 cells in 50 ⁇ L of cell culture medium was seeded in each well, and the plate was placed on the analyzer. Measurements were taken automatically every 15 min, and the sensograms were visualized using RTCA software version 2.1.0 (ACEA Biosciences Inc).
  • VSV-SARS-CoV-2 (0.01 MOI, ⁇ 120 PFU per well) was mixed 1:1 with a dilution of antibody in a total volume of 100 ⁇ L using DMEM supplemented with 2% FBS as a diluent and incubated for 1 h at 37°C in 5% CO 2 .
  • the virus-antibody mixtures were added in replicates to the cells in 96-well E-plates.
  • CI Normalized cellular index
  • Epitope mapping was performed essentially as described previously using a SARS-CoV-2 (strain Wuhan-Hu-1) spike protein RBD shotgun mutagenesis mutation library, made using an expression construct for full-length spike protein. 184 residues of the RBD (between spike residues 335 and 526) were mutated individually to alanine, and alanine residues to serine and clones arrayed in 384-well plates, one mutant per well. Antibody binding to each mutant clone was determined, in duplicate, by high-throughput flow cytometry. Each spike protein mutant was transfected into HEK- 293T cells and allowed to express for 22 hrs.
  • Plaque reduction neutralization test The virus neutralization with live authentic SARS-CoV-2 virus was performed in the BSL- 3 facility of the Galveston National Laboratory using Vero E6 cells (ATCC CRL-1586) following the standard procedure. Briefly, Vero E6 cells were cultured in 96-well plates (10 4 cells/well). Next day, 4-fold serial dilutions of antibodies were made using MEM-2% FBS, as to get an initial concentration of 100 ⁇ g/ml. Equal volume of diluted antibodies (60 ⁇ l) were mixed gently with authentic virus (60 ⁇ l containing 200 pfu) and incubated for 1 h at 37°C/5% CO 2 atmosphere.
  • virus-serum mixture (100 ⁇ l) was added to cell monolayer in duplicates and incubated for 1 at h 37°C/5% CO 2 atmosphere. Later, virus-serum mixture was discarded gently, and cell monolayer was overlaid with 0.6% methylcellulose and incubated for 2 days. The overlay was removed, and the plates were fixed in 4% paraformaldehyde twice following BSL-3 protocol. The plates were stained with 1% crystal violet and virus-induced plaques were counted. The percent neutralization and/or NT50 of antibody was calculated by dividing the plaques counted at each dilution with plaques of virus-only control.
  • the inhibitory concentration at 50% (IC50) values were calculated in GraphPad Prism software by plotting the midway point between the upper and lower plateaus of the neutralization curve among dilutions.
  • the Alpha variant virus incorporates the following substitutions: Del 69-70, 144 Del, E484K, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H.
  • the Beta variant incorporates the following substitutions: 24 Del, 242-243 Del, D80A, D215G, K417N, E484K, N501Y, D614G, H665Y, T1027I.
  • the Delta variant incorporates the following substitutions: T19R, G142D, Del 156-157, R158G, L452R, T478K, D614G, P681R, Del 689-691, D950N; the deletion at positions 689-691 has not been observed in nature, and was identified upon one passage of the virus.
  • the Gamma variant incorporates the following substitutions: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I.
  • BioLayer Interferometry (BLI) Purified 54042-4 IgG was immobilized to AHC sensortips (FortéBio) to a response level of approximately 1.4 nm in a buffer composed of 10 mM HEPES pH 7.5, 150 mM NaCl, 3 mM EDTA, 0.05% Tween 20 and 0.1% (w/v) BSA. Immobilized IgG was then dipped into wells containing four-fold dilutions of SARS-CoV-2 RBD-SD1 ranging in concentration from 100- 1.5625 nM, to measure association. Dissociation was measured by dipping sensortips into wells containing only running buffer.
  • ACE2 Binding Inhibition Assay 96-well plates were coated with 2 ⁇ g/mL purified recombinant SARS-CoV-2 at 4°C overnight. The next day, plates were washed three times with PBS supplemented with 0.05% Tween-20 (PBS-T) and coated with 5% milk powder in PBS-T. Plates were incubated for one hour at room temperature and then washed three times with PBS-T. Purified antibodies were diluted in blocking buffer at 10 ⁇ g/mL in triplicate, added to the wells, and incubated at room temperature.
  • recombinant human ACE2 protein with a mouse Fc tag was added to wells for a final 0.4 ⁇ g/mL concentration of ACE2 and incubated for 40 minutes at room temperature. Plates were washed three times with PBS-T, and bound ACE2 was detected using HRP-conjugated anti- mouse Fc antibody and TMB substrate. The plates were incubated at room temperature for ten minutes, and then 1N sulfuric acid was added to stop the reaction. Plates were read at 450 nm. ACE2 binding without antibody served as a control. Experiment was done in biological replicate and technical triplicates.
  • RTCA Neutralization Assay with Known Antibody Escape Mutants A real-time cell analysis assay (RTCA) and xCELLigence RTCA MP Analyzer (ACEA Biosciences Inc.) were used with modification of previously described assays (Gilchuk et al., 2020a; Weisblum et al., 2020, SuryJea et al.,2021). Fifty (50) ⁇ L of cell culture medium (DMEM supplemented with 2% FBS) was added to each well of a 96-well E-plate to obtain a background reading. Eighteen thousand (18,000) Vero E6 cells in 50 ⁇ L of cell culture medium were seeded per each well, and plates were placed on the analyzer.
  • DMEM fetal bovine serum
  • VSV-SARS-CoV-2 or wild-type VSV-SARS- CoV-2 virus (5e3 plaque forming units [PFU] per well, ⁇ 0.3 MOI) was mixed with a saturating neutralizing concentration of individual antibody (5 ⁇ g/mL) in a total volume of 100 ⁇ L and incubated for 1 h at 37°C. At 16-20 h after seeding the cells, the virus-antibody mixtures were added into 8 to 96 replicate wells of 96-well E-plates with cell monolayers.
  • the complex was incubated on ice for 30 min before 3 ⁇ L of the sample was deposited on Au-3001.2/1.3 grids (UltrAuFoil) that had been plasma cleaned in a Solarus 950 plasma cleaner (Gatan) for 4 minutes using a 4:1 ratio of O2:H2.
  • a force of -4 was used to blot excess liquid for 3 s using a Vitrobot Mark IV (Thermo Fisher) followed by plunge-freezing with liquid ethane.
  • 3,762 micrographs were collected from a single grid using a Titan Krios (Thermo Fisher) equipped with a K3 detector (Gatan) with the stage set at a 30° tilt.
  • SerialEM was used to collect movies at 29,000X nominal magnification with a calibrated pixel size of 0.81 ⁇ /pixel. Additional details about data collection parameters can be found in Table 4.
  • Cryogenic electron microscopy (Cryo-EM) Motion correction, CTF estimation, particle picking, and preliminary 2D classification were performed using cryoSPARC v3.2.0 live processing. The final iteration of 2D class averaging distributed 374,669 particles into 60 classes using an uncertainty factor of 2. From that, 241,732 particles were used to perform an ab inito reconstruction with four classes followed by heterogeneous refinement of those four classes. Particles from the two highest quality classes were used for homogenous refinement of the best volume with applied C3 symmetry.
  • Non-uniform refinement was performed on the resulting volume using per-particle defocus and per-group CTF optimizations applied.
  • C3 symmetry expansion was performed followed by local refinement using a mask created in ChimeraX that encompassed the entire 54042-4 Fab and RBD.
  • Local refinement was performed using a pose/shift gaussian prior during alignment, 3° standard deviation of prior over rotation and 1 ⁇ standard deviation of prior over shifts. Additionally, maximum alignment resolution was limited to 2.8 ⁇ resolution to avoid over-refining.
  • the focused refinement volumes were processed using the DeepEMhancer tool via COSMIC science gateway, which included the use of a refinement mask to help define noise while sharpening.
  • the spike glycoprotein sequences were extracted and translated, and pairwise sequence alignment with the reference sequence hCoV-19/Wuhan/WIV04/2019 was then performed. After removing incomplete sequences and sequences with alignment errors, the pairwise alignments for the remaining 1,148,887 spike protein sequences were combined to compute the conservation of each residue position using in-house perl scripts.
  • RMSD Calculation Differences in Angle of Antigen Approach for Different Antibodies
  • the SARS-CoV-2 spike receptor binding domain coordinates present in each antibody- antigen complex were aligned in PyMOL (The PyMOL Molecular Graphics System, Version 2.3.5, Schrödinger, LLC.) using an all-atom alignment with 5 cycles of outlier rejection of atom pairs having an RMSD greater than 2.
  • the alignment was performed for RBD residues 329-529 in antibody 54042-4 (PDB ID: TBD chain A), 329-529 in antibody 2-7 (PDB ID: 7LSS chain B), 333-526 in antibody REGN10987 (PDB ID: 6XDG chain A), and 334-527 in antibody LY- COV1404 (PDB ID: 7MMO chain C).
  • alpha carbon root mean square deviation between antibodies was calculated over this region in the heavy and light chains using residue pairs from the sequence alignment.
  • RMSD values were calculated from 183, 183, and 180 alpha carbon pairs for the 54042-4 vs REGN1087, REGN1087 vs 2-7, and 54042-4 vs 2-7 comparisons respectively.
  • large numbers of antibody sequences were determined (see sequences provided below).
  • the following paired heavy chain and light chain sequences are used herein for methods of treating, preventing, or detecting coronavirus infections. Table 1. Paired heavy and light chains and the CDRs thereof Table 2. Additional paired heavy and light chains and the CDRs thereof Table 3. PDB files Used for Epitope Comparisons Table 4.

Abstract

The present disclosure relates to antibodies and uses thereof for treating, preventing, and detecting coronavirus infection.

Description

CROSS-REACTIVE CORONAVIRUS ANTIBODIES CROSS REFERENCE TO RELATED APPLICATIONS This application claims the priority benefit of U.S. Provisional Application No. 63/188,720, filed May 14, 2021, and U.S. Provisional Application No. 63/232,394, filed August 12, 2021, which are expressly incorporated herein by reference in their entireties. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH This invention was made with government support under Grant Nos. 3 R01 AI131722- 04S1 and R01-AI127521 awarded by the National Institutes of Health. The government has certain rights in the invention. FIELD The present disclosure relates to antibodies and uses thereof for treating, preventing, and detecting coronavirus infection. BACKGROUND SARS-CoV-2, or the 2019 novel coronavirus (COVID-19), is a significant pandemic threat that has resulted in over 126,000,000 diagnosed cases including 2,760,000 deaths as of March 26, 2021. Initially detected in Wuhan, China, human-human transmission has resulted in confirmed cases all over the world. On January 30, 2020, the World Health Organization declared a Public Health of International Concern due to the COVID-19 outbreak and pronounced it a global pandemic on March 12, 2020. The development of preventive and therapeutic measures that can counteract the ongoing, and any future, coronavirus pandemics is therefore of utmost significance for public health worldwide. What is needed are novel compositions and methods for treating and diagnosing SARS-CoV-2 infection. SUMMARY Disclosed herein are recombinant antibodies and uses thereof for preventing, treating, and detecting coronavirus infection. Antibody sequences were obtained from an individual previously infected with a SARS-CoV-2 infection. In some aspects, disclosed herein is a recombinant antibody, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and/or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH3 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11224-11232. In some embodiments, CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196. In some embodiments, CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232. In some embodiments, CDRH1 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11170-11178; and/or CDRL1 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11206-11214. In some embodiments, CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178. In some embodiments, CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214. In some embodiments, CDRH2 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11179-11187; and/or CDRL2 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11215-11223. In some embodiments, CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187. In some embodiments, CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223. In some embodiments, VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169. In some embodiments, VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205. In some embodiments, the recombinant antibody is selected from Table 1. In some embodiments, the recombinant antibody is selected from Table 2. In one aspect, disclosed herein is a nucleic acid encoding a recombinant antibody as disclosed herein. In one aspect, disclosed herein is a recombinant expression cassette or plasmid comprising a sequence to express a recombinant antibody as disclosed herein. In one aspect, disclosed herein is a host cell comprising an expression cassette or a plasmid as disclosed herein. In one aspect, disclosed herein is a method of producing an antibody, comprising cultivating or maintaining a host cell under conditions to produce the antibody. In one aspect, disclosed herein is a method of treating a coronavirus infection in a subject, comprising administering to the subject a therapeutically effective amount of a recombinant antibody as disclosed herein. In some embodiments, the coronavirus is SARS-CoV-2. In some aspects, disclosed herein is a method for detecting a coronavirus infection in a subject, comprising: providing a biological sample from the subject, and detecting a coronavirus antigen in the biological sample with an antibody that specifically binds to the coronavirus antigen, wherein the antibody is from any aspect as disclosed herein, and wherein the presence of the coronavirus antigen in the biological sample indicates the subject is infected with a coronavirus. In some embodiments, the coronavirus is SARS-CoV-2. BRIEF DESCRIPTION OF DRAWINGS The accompanying figures, which are incorporated in and constitute a part of this specification, illustrate aspects described below. FIGS.1A-1C show identification and characterization of SARS-CoV-2 antibodies isolated using LIBRA-seq. (FIG.1A) Variable heavy gene usage (x-axis) as a function of IgG+ B cells with a SARS-CoV-2 spike LIBRA-seq score (>1) (y-axis). The nine lead antibodies are highlighted in purple. (FIG. 1B) RTCA VSV-SARS-CoV-2 neutralization by lead antibodies. IC50 values are calculated by non-linear regression analysis by GraphPad Prism software. (FIG. 1C) Sequence characteristics and antigen specificity of nine lead antibodies from a recovered COVID-19 donor. Percent identity is calculated at the nucleotide level, and CDR length and sequences are noted at the amino acid level. LIBRA-seq scores for each antigen are displayed as a heatmap with a LIBRA-seq score of -2 displayed as light yellow, 0 as white, and 2 in purple; in this heatmap scores lower or higher than that range are shown as -2 and 2, respectively. ELISA binding data are displayed as a heatmap of the AUC analysis calculated from (Figure 7A) with AUC of 0 displayed as light yellow, 50% maximum as white, and maximum AUC as purple. The sequences in FIG. 1B are SEQ ID NO: 6197, SEQ ID NO: 5528, SEQ ID NO: 5893, SEQ ID NO: 5720, SEQ ID NO: 5308, SEQ ID NO: 5509, SEQ ID NO: 6161, SEQ ID NO: 5039, SEQ ID NO: 6187, SEQ ID NO: 11157, SEQ ID NO: 10488, SEQ ID NO: 10853, SEQ ID NO: 10680, SEQ ID NO: 10268, SEQ ID NO: 10469, SEQ ID NO: 11121, SEQ ID NO: 9999, and SEQ ID NO: 11147. FIGS. 2A-2D show antigenic characterization of antibody 54042-4. (FIG. 2A) ELISA binding values against SARS-CoV-2 subdomains are displayed as a heatmap of AUC values calculated from the data in (Figure 7B). Antibodies CR3022, 46472-6, 46472-4 were used as positive controls for the RBD, NTD, and S2 antigens, respectively.3602-1707 was included as a HA-specific negative control antibody. (FIG.2B) A biolayer interferometry sensogram that shows binding to recombinant SARS-CoV-2 RBD-SD1. Binding data are depicted by the black lines and the best fit line of the data to a 1:1 binding model is shown in red. (FIG. 2C) SARS-CoV-2 spike/ACE2 inhibition ELISA is shown with SARS-CoV-2 antibody CR3022 and negative control HA-specific antibody 3602-1707. (FIG.2D) Competition ELISA of 54042-4 with antibodies with published epitopes, COV2-2196, COV2-2130, and CR3022. Values in white indicate no competition (presence of competing mAb reduced reference mAb binding by less than 71%) and values in dark grey indicate competition (presence of competing mAb reduced the reference mAb to less than 41% of its maximal binding). FIGS.3A-3D show atomic resolution of 54042-4 binding mode to SARS-CoV-2 S. (FIG. 3A) Side and top views of Fab 54042-4 bound to SARS-CoV-2 spike, shown as cryo-EM density. (FIG.3B) Focused refinement density showing the 54042-4 epitope at the inner edge of the RBM (left). Top-down view of the 54042-4 epitope showing heavy and light chain contacts, as well as residues outside of the binding interface that are mutated in circulating VOCs (right). (FIG. 3C) The 54042-4 heavy chain binds to RBD residues 443-447 primarily through a network of hydrogen bonds involving CDRH2 and CDRH3 and noncovalent contacts involving Ile32 of CRDH1. (FIG. 3D) The 54042-4 light chain contacts RBD residues 498-500 through a hydrogen bond between Thr500 and His92 of CDRL3 and hydrophobic contacts involving Phe30 and Tyr32 of CDRL1. FIGS.4A-4E show sequence and structural comparison of 54042-4 to known SARS-CoV- 2 antibodies. (FIG.4A) Amino acid CDRH3 identity to 54042-4 (x-axis) is plotted against CDRL3 identity to 54042-4 (y-axis) for paired heavy and light chain sequences obtained from the CoV- AbDab database. Antibodies using the same heavy and light chain germline gene as 54042- 4 (IGHV2-5 and IGKV1-39) are shown in light blue. Antibodies using the IGHV2-5 heavy chain gene and a non-IGKV1-39 light chain gene are shown in orange. Additionally, antibodies using a non-IGHV2-5 heavy chain gene and the IGKV1-39 light chain gene, with CDRH3 or CDRL3 identity to 54042-4 of at least 50%, are highlighted in purple. Finally, antibodies that do not use IGHV2-5 or IGKV1-39, but that have at least 50% identity to CDRH3 or CDRL3 of 54042-4, are shown in grey. (FIG. 4B) Pearson correlation of epitopes of known SARS-CoV-2 antibodies (Table 3) in comparison to 54042-4 antibody, with the six antibodies showing a statistically significant (p<0.05) positive correlation highlighted in red. (FIG. 4C) Heatmap (top) depicting buried surface area (Å2) at the SARS-CoV-2 RBD interface for the six antibodies with highest epitope correlations with 54042-4. Bar graph (bottom) showing the frequency (%) of substitutions at each given residue position in log scale, with a dashed line at 1% and residue positions with a frequency greater than 1% highlighted in red. (FIG.4D) Distinct angles of approach of antibodies 54042-4 (heavy chain: orange, light chain: white), REGN10987 (heavy chain: blue, light chain: white) (PDB id: 6XDG), 2-7 (heavy chain: pink, light chain: white) (PDB id: 7LSS), and LY- CoV1404 (heavy chain: purple, light chain: white) (PDB id:7MMO) to the SARS-CoV-2 RBD (green). (FIG. 4E) Structural comparison of CDRH1, 2, and 3 of antibodies 54042-4 and 2-7. CDRH1 of 2-7 extends further than 54042-4, forming additional contacts with Thr345 and Arg346 of the RBD (left). The CDRH2 region of 2-7 approaches at a different angle, but maintains RBD contacts via Asp56 and Arg58 (center). The CDRH3 contacts of 2-7 and 54042-4 are divergent, with unique CDRH3 residues and RBD interactions (right). FIGS.5A-5E. Functional characterization of antibody 54042-4. (FIG.5A) Binding data of 54042-4 antibody to a shotgun alanine mutagenesis screening library of the SARS-CoV-2 RBD (Wuhan-Hu-1 strain). Residues displayed are the alanine substitutions that resulted in the biggest loss of binding to 54042-4 yet still retained signal with the RBD antibody control. (FIG.5B) RTCA Neutralization of VSV SARS-CoV-2 chimera variants harboring specific substitutions. Cell sensograms are shown in boxes corresponding to mutations indicated in each row. Columns (from left to right) are each chimera treated with COV2-2381, 54042-4 and virus only control. Neutralization of 54042-4 of USA-WA1 strain and cells only are indicated on the right. COV2- 2381 was chosen as a positive control due to its distinct epitope footprint from the selected mutations. (FIG. 5C) 54042-4 epitope residues (non-zero buried surface area on SARS-CoV-2 RBD) with their associated % conservation (the percentage of deposited sequences containing the highest-frequency amino acid at that position) in the GISAID database. The only 54042-4 epitope residue with a % conservation of less than 99%, N439, is highlighted in red. (FIG. 5D) ELISA AUC of 54042-4, CR3022, and an influenza HA-specific negative control antibody 3602-1707. AUC is displayed as a heatmap with a value of 0 corresponding to white, 50% maximum as light- purple, and maximum AUC as purple. (FIG. 5E) Authentic SARS-CoV-2 % neutralization of USA-WA1, Alpha, Beta, Delta, and Gamma strains (y-axis) is depicted as a function of antibody concentration (x-axis). Also shown are the respective IC50 and IC80 values for 54042-4 neutralization against each variant. FIGS. 6A-6E. (FIG. 6A) VSV-SARS-CoV-2 capacity of serum is displayed from time points at day 18, day 28, day 56, and days 80-90 post-COVID-19 infection. (FIG. 6B) Gating scheme for fluorescent-activated cell sorting of recovered COVID-19 individual. Cells were stained with Ghost Red 780, CD14-APC-Cy7, CD3-FITC, CD19-BV711, and IgG-PE-Cy5 along with a DNA-barcoded antigen screening library. To detect antigen-positive B cells, cells were washed and treated with a streptavidin-PE secondary stain. Gates as drawn are based on gates used during the sort, and percentages from the sort are listed. (FIG.6C) LIBRA-seq scores for SARS- CoV-2 S, SARS-CoV-2 S D614G, SARS-CoV S, MERS-CoV S, HCoV-OC43 S, HCoV-229E S, HCoV-NL63 S, SARS-CoV-2 RBD, SARS-CoV RBD, and MERS-CoV RBD, as well as negative-control antigens ZM197 Env and hemagglutinin (HA) NC99 are shown. LIBRA-seq scores for each antigen are displayed as a heatmap with a LIBRA-seq score of -2 displayed as light yellow, 0 as white, and 2 in purple; in this heatmap, scores lower or higher than that range are shown as -2 and 2, respectively. (FIG.6D) ELISA binding data of antibodies identified by LIBRA- seq against SARS-CoV-2 S HP. The optical density at 450 nm (y-axis) is depicted as a function of antibody concentration (x-axis). (FIG.6E) ELISA binding data of the antibodies that displayed neutralization in the high-throughput VSV SARS-CoV-2 RTCA (Figure 1B) for the antigens SARS-CoV-2 S D614G, SARS-CoV S, MERS-CoV S, HCoV-OC43 S, HCoV-HKU1 S, HCoV- NL63 S, and HCoV-229E S. The optical density at 450 nm (y-axis) is depicted as a function of antibody concentration (x-axis). FIGS. 7A-7B. (FIG. 7A) ELISA binding data of antibodies identified by LIBRA-seq against SARS-CoV-2 spike HP. (FIG.7B) ELISA binding data against SARS-CoV-2 subdomains RBD, NTD, S1, and S2 are shown. CR3022 was used as a positive control RBD-directed antibody whereas 46472-4 and 46472-6 antibodies were used as positive controls for the S2 and NTD, respectively. The HA-specific 3602-1707 antibody was used as a negative control. FIGS. 8A-8B. (FIG.8A) Amino acids comprising the epitope of 54042-4 are shown with their associated buried surface area (Å2) are shown. (FIG. 8B) 54042-4 amino acids comprising the paratope to SARS-CoV-2 spike and their associated buried surface area values (Å2) are shown. FIGS. 9A-9C. (FIG. 9A) ELISA binding data against SARS-CoV-2 Wuhan-1 RBD and RBDs with substitutions E484K, N501Y, N439K, K417N, E484Q, or L452R. CR3022 was used as a positive control and 3602-1707, an HA-specific antibody, was used as a negative control. (FIG. 9B) ELISA binding data against SARS-CoV-2 S HP, SARS-CoV S, and SARS-CoV-2 S HP constructs with substitutions in the S1 domain for the Beta, and Alpha variants of concern. CR3022 was used as a positive control and 3602-1707 was used as a negative control antibody. (FIG.9C) The substitutions and deletions present in the Alpha and Beta SARS-CoV-2 S constructs used in the ELISAs depicted in Figure 9B. FIG. 10 shows Cryo-EM data processing workflow. Flowchart outlining cryo-EM data processing of Fab 54042-4 Fab bound to SARS-CoV-2 S. Additional information can be found in the Methods section under “Cryogenic electron microscopy” (cryo-EM). FIGS. 11A-11D. Cryo-EM structure validation. (FIG. 11A) FSC curve and distribution plot for the C3 S-ECD/54042-4 structure, generated in cryoSPARC v3.2.0. (FIG.11B) FSC curve and viewing distribution plot for focused refinement of the S-RBD bound to 54042-4 Fab. (FIG. 11C) Local resolution shown by color of the C3 S-ECD/54042-4 (left) and focused S-RBD/54042- 4 (right) reconstructions. (FIG.11D) Map resulting from focused refinement of the RBD (green) (left), 54042-4 heavy chain (orange), and 54042-4 light chain (white). Detailed views of the binding interface and corresponding map (center, right). Oxygen atoms are colored red, nitrogen blue, and sulfur yellow. DETAILED DESCRIPTION Therefore, in some aspects, disclosed herein are recombinant antibodies that specifically bind a viral protein of a coronavirus and uses thereof for treating, preventing, inhibiting, reducing, and detecting coronavirus infection, wherein the coronavirus is SARS-CoV-2. Reference will now be made in detail to the embodiments of the invention, examples of which are illustrated in the drawings and the examples. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. The term “comprising” and variations thereof as used herein is used synonymously with the term “including” and variations thereof and are open, non-limiting terms. Although the terms “comprising” and “including” have been used herein to describe various embodiments, the terms “consisting essentially of” and “consisting of” can be used in place of “comprising” and “including” to provide for more specific embodiments and are also disclosed. As used in this disclosure and in the appended claims, the singular forms “a”, “an”, “the”, include plural referents unless the context clearly dictates otherwise. The following definitions are provided for the full understanding of terms used in this specification. Terminology The term “about” as used herein when referring to a measurable value such as an amount, a percentage, and the like, is meant to encompass variations of ±20%, ±10%, ±5%, or ±1% from the measurable value. “Administration” to a subject or “administering” includes any route of introducing or delivering to a subject an agent. Administration can be carried out by any suitable route, including oral, intravenous, intraperitoneal, intranasal, inhalation and the like. Administration includes self- administration and the administration by another. As used herein, the terms “may,” “optionally,” and “may optionally” are used interchangeably and are meant to include cases in which the condition occurs as well as cases in which the condition does not occur. Thus, for example, the statement that a formulation “may include an excipient” is meant to include cases in which the formulation includes an excipient as well as cases in which the formulation does not include an excipient. As used herein, the term “subject” or “host” can refer to living organisms such as mammals, including, but not limited to humans, livestock, dogs, cats, and other mammals. Administration of the therapeutic agents can be carried out at dosages and for periods of time effective for treatment of a subject. In some embodiments, the subject is a human. As used herein, the term “antigen” refers to a molecule that is capable of binding to an antibody. In some embodiments, the antigen stimulates an immune response such as by production of antibodies specific for the antigen. In the present invention, “specific for” and “specificity” means a condition where one of the molecules is involved in selective binding. Accordingly, an antibody that is specific for one antigen selectively binds that antigen and not other antigens. The term “antibodies” is used herein in a broad sense and includes both polyclonal and monoclonal antibodies. In addition to intact immunoglobulin molecules, also included in the term “antibodies” are fragments or polymers of those immunoglobulin molecules, and human or humanized versions of immunoglobulin molecules or fragments thereof. The antibodies can be tested for their desired activity using the in vitro assays described herein, or by analogous methods, after which their in vivo therapeutic and/or prophylactic activities are tested according to known clinical testing methods. Native antibodies are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at one end (VL) and a constant domain at its other end. There are five major classes of human immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG-1, IgG-2, IgG-3, and IgG-4; IgA-1 and IgA-2. One skilled in the art would recognize the comparable classes for mouse. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu, respectively. Each antibody molecule is made up of the protein products of two genes: heavy-chain gene and light-chain gene. The heavy-chain gene is constructed through somatic recombination of V, D, and J gene segments. In human, there are 51 VH, 27 DH, 6 JH, 9 CH gene segments on human chromosome 14. The light-chain gene is constructed through somatic recombination of V and J gene segments. There are 40 Vκ , 31 Vλ , 5 Jκ , 4 Jλ gene segments on human chromosome 14 (80 VJ). The heavy-chain constant domains that correspond to the different classes of immunoglobulins are called α, δ, ε, γ, and μ, respectively. The “light chains” of antibodies from any vertebrate species can be assigned to one of two clearly distinct types, called kappa (κ) and lambda (λ), based on the amino acid sequences of their constant domains. The term “monoclonal antibody” as used herein refers to an antibody obtained from a substantially homogeneous population of antibodies, i.e., the individual antibodies within the population are identical except for possible naturally occurring mutations that may be present in a small subset of the antibody molecules. The monoclonal antibodies herein specifically include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, as long as they exhibit the desired antagonistic activity. The disclosed monoclonal antibodies can be made using any procedure which produces monoclonal antibodies. For example, disclosed monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro. The monoclonal antibodies may also be made by recombinant DNA methods. DNA encoding the disclosed monoclonal antibodies can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). Libraries of antibodies or active antibody fragments can also be generated and screened using phage display techniques, e.g., as described in U.S. Patent No. 5,804,440 to Burton et al. and U.S. Patent No. 6,096,441 to Barbas et al. In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. For instance, digestion can be performed using papain. Examples of papain digestion are described in WO 94/29348 published Dec. 22, 1994 and U.S. Pat. No.4,342,566. Papain digestion of antibodies typically produces two identical antigen binding fragments, called Fab fragments, each with a single antigen binding site, and a residual Fc fragment. Pepsin treatment yields a fragment that has two antigen combining sites and is still capable of cross-linking antigen. As used herein, the term “antibody or antigen binding fragment thereof” or “antibody or fragments thereof” encompasses chimeric antibodies and hybrid antibodies, with dual or multiple antigen or epitope specificities, and fragments, such as F(ab’)2, Fab’, Fab, Fv, sFv, scFv, nanoantibody and the like, including hybrid fragments. Thus, fragments of the antibodies that retain the ability to bind their specific antigens are provided. Such antibodies and fragments can be made by techniques known in the art and can be screened for specificity and activity according to the methods set forth in the Examples and in general methods for producing antibodies and screening antibodies for specificity and activity (See Harlow and Lane. Antibodies, A Laboratory Manual. Cold Spring Harbor Publications, New York, (1988)). The fragments, whether attached to other sequences or not, can also include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the antibody or antibody fragment is not significantly altered or impaired compared to the non-modified antibody or antibody fragment. These modifications can provide for some additional property, such as to remove/add amino acids capable of disulfide bonding, to increase its bio-longevity, to alter its secretory characteristics, etc. In any case, the antibody or antibody fragment must possess a bioactive property, such as specific binding to its cognate antigen. Functional or active regions of the antibody or antibody fragment may be identified by mutagenesis of a specific region of the protein, followed by expression and testing of the expressed polypeptide. Such methods are readily apparent to a skilled practitioner in the art and can include site-specific mutagenesis of the nucleic acid encoding the antibody or antibody fragment. (Zoller, M.J. Curr. Opin. Biotechnol.3:348-354, 1992). As used herein, the term “antibody” or “antibodies” can also refer to a human antibody and/or a humanized antibody. Many non-human antibodies (e.g., those derived from mice, rats, or rabbits) are naturally antigenic in humans, and thus can give rise to undesirable immune responses when administered to humans. Therefore, the use of human or humanized antibodies in the methods serves to lessen the chance that an antibody administered to a human will evoke an undesirable immune response. The terms “antigen binding site”, “binding site” and “binding domain” refer to the specific elements, parts or amino acid residues of a polypeptide, such as an antibody, that bind the antigenic determinant or epitope. An "antibody heavy chain," as used herein, refers to the larger of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations. An "antibody light chain," as used herein, refers to the smaller of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations, κ and λ light chains refer to the two major antibody light chain isotypes. The term "CDR" as used herein refers to the “complementarity determining regions” of the antibody which consist of the antigen binding loops. (Kabat E.A. et al., (1991) Sequences of proteins of immunological interest. NIH Publication 91-3242). Each of the two variable domains of an antibody Fv fragment contain, for example, three CDRs. The term “hypervariable region” or “HVR”, as used herein, refers to each of the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops (“hypervariable loops”). Generally, native four-chain antibodies comprise six HVRs; three in the VH (H1, H2, H3), and three in the VL (L1, L2, L3). HVRs generally comprise amino acid residues from the hypervariable loops and/or from the complementarity determining regions (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. With the exception of CDR1 in VH, CDRs generally comprise the amino acid residues that form the hypervariable loops. Hypervariable regions (HVRs) are also referred to as “complementarity determining regions” (CDRs), and these terms are used herein interchangeably in reference to portions of the variable region that form the antigen-binding regions. The amino acid sequence boundaries of a CDR can be determined by one of skill in the art using any of a number of known numbering schemes, including those described by Kabat et al., supra (“Kabat” numbering scheme): Al-Lazikani et al., 1997. J. Mol. Biol., 273:927-948 (“Chothia” numbering scheme); MacCallum et al., 1996, J. Mol. Biol, 262:732-745 (“Contact” numbering scheme); Lefranc et al., Dev. Comp. Immunol., 2003, 27:55-77 (“IMGT” numbering scheme); and Honegge and Plückthun, J. Mol. Biol., 2001, 309:657-70 (“AHo” numbering scheme); each of which is incorporated by reference in its entirety. “Effective amount” encompasses, without limitation, an amount that can ameliorate, reverse, mitigate, prevent, or diagnose a symptom or sign of a medical condition or disorder. Unless dictated otherwise, explicitly or by context, an “effective amount” is not limited to a minimal amount sufficient to ameliorate a condition. The severity of a disease or disorder, as well as the ability of a treatment to prevent, treat, or mitigate, the disease or disorder can be measured, without implying any limitation, by a biomarker or by a clinical parameter. In some embodiments, the term “effective amount of a recombinant antibody” refers to an amount of a recombinant antibody sufficient to prevent, treat, or mitigate a coronavirus infection (e.g., SARS-CoV-2 infection). The “fragments” or “functional fragments,” whether attached to other sequences or not, can include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the fragment is not significantly altered or impaired compared to the nonmodified peptide or protein. These modifications can provide for some additional property, such as to remove or add amino acids capable of disulfide bonding, to increase its bio-longevity, to alter its secretory characteristics, etc. In any case, the functional fragment must possess a bioactive property, such as binding to a coronavirus antigen (e.g., SARS- CoV-2 antigen), and/or ameliorating the viral infection. The term "identity" or "homology" shall be construed to mean the percentage of nucleotide bases or amino acid residues in the candidate sequence that are identical with the bases or residues of a corresponding sequence to which it is compared, after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent identity for the entire sequence, and not considering any conservative substitutions as part of the sequence identity. A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) that has a certain percentage (for example, 80%, 85%, 90%, or 95%) of "sequence identity" to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art. Such alignment can be provided using, for instance, the method of Needleman et al. (1970) J. Mol. Biol. 48: 443-453, implemented conveniently by computer programs such as the Align program (DNAstar, Inc.). The term “increased” or “increase” as used herein generally means an increase by a statically significant amount; for example, “increased” means an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3- fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level. As used herein, the terms “nanobody”, “VHH”, “VHH antibody fragment” and “single domain antibody” are used indifferently and designate a variable domain of a single heavy chain of an antibody of the type found in Camelidae, which are without any light chains, such as those derived from Camelids as described in PCT Publication No. WO 94/04678, which is incorporated by reference in its entirety. The term “reduced”, “reduce”, “reduction”, or “decrease” as used herein generally means a decrease by a statistically significant amount. However, for avoidance of doubt, “reduced” means a decrease by at least 10% as compared to a reference level, for example a decrease by at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% decrease (i.e. absent level as compared to a reference sample), or any decrease between 10- 100% as compared to a reference level. “Nucleotide,” “nucleoside,” “nucleotide residue,” and “nucleoside residue,” as used herein, can mean a deoxyribonucleotide, ribonucleotide residue, or another similar nucleoside analogue. A nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage. The base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T). The sugar moiety of a nucleotide is a ribose or a deoxyribose. The phosphate moiety of a nucleotide is pentavalent phosphate. A non-limiting example of a nucleotide would be 3'-AMP (3'-adenosine monophosphate) or 5'-GMP (5'-guanosine monophosphate). There are many varieties of these types of molecules available in the art and available herein. The method and the system disclosed here including the use of primers, which are capable of interacting with the disclosed nucleic acids, such as the antigen barcode as disclosed herein. In certain embodiments the primers are used to support DNA amplification reactions. Typically, the primers will be capable of being extended in a sequence specific manner. Extension of a primer in a sequence specific manner includes any methods wherein the sequence and/or composition of the nucleic acid molecule to which the primer is hybridized or otherwise associated directs or influences the composition or sequence of the product produced by the extension of the primer. Extension of the primer in a sequence specific manner therefore includes, but is not limited to, PCR, DNA sequencing, DNA extension, DNA polymerization, RNA transcription, or reverse transcription. Techniques and conditions that amplify the primer in a sequence specific manner are preferred. In certain embodiments the primers are used for the DNA amplification reactions, such as PCR or direct sequencing. It is understood that in certain embodiments the primers can also be extended using non-enzymatic techniques, where for example, the nucleotides or oligonucleotides used to extend the primer are modified such that they will chemically react to extend the primer in a sequence specific manner. Typically, the disclosed primers hybridize with the disclosed nucleic acids or region of the nucleic acids or they hybridize with the complement of the nucleic acids or complement of a region of the nucleic acids. The term “amplification” refers to the production of one or more copies of a genetic fragment or target sequence, specifically the “amplicon”. As it refers to the product of an amplification reaction, amplicon is used interchangeably with common laboratory terms, such as "PCR product." The term “polypeptide” refers to a compound made up of a single chain of D- or L-amino acids or a mixture of D- and L-amino acids joined by peptide bonds. "Encoding" refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA. An “expression cassette” refers to a DNA coding sequence or segment of DNA that code for an expression product that can be inserted into a vector at defined restriction sites. The cassette restriction sites are designed to ensure insertion of the cassette in the proper reading frame. Generally, foreign DNA is inserted at one or more restriction sites of the vector DNA, and then is carried by the vector into a host cell along with the transmissible vector DNA. A segment or sequence of DNA having inserted or added DNA, such as an expression vector, can also be called a “DNA construct”. Expression vectors comprise the expression cassette and additionally usually comprise an origin for autonomous replication in the host cells or a genome integration site, one or more selectable markers (e.g. an amino acid synthesis gene or a gene conferring resistance to antibiotics such as zeocin, kanamycin, G418 or hygromycin), a number of restriction enzyme cleavage sites, a suitable promoter sequence and a transcription terminator, which components are operably linked together. The term “vector” as used herein includes autonomously replicating nucleotide sequences as well as genome integrating nucleotide sequences. A common type of vector is a “plasmid”, which generally is a self-contained molecule of double-stranded DNA that can readily accept additional (foreign) DNA and which can readily be introduced into a suitable host cell. A plasmid vector often contains coding DNA and promoter DNA and has one or more restriction sites suitable for inserting foreign DNA. Specifically, the term “vector” or “plasmid” refers to a vehicle by which a DNA or RNA sequence (e.g. a foreign gene) can be introduced into a host cell, so as to transform the host and promote expression (e.g. transcription and translation) of the introduced sequence. The term “host cell” as used herein shall refer to primary subject cells trans-formed to produce a particular recombinant protein, such as an antibody as described herein, and any progeny thereof. It should be understood that not all progeny are exactly identical to the parental cell (due to deliberate or inadvertent mutations or differences in environment), however, such altered progeny are included in these terms, so long as the progeny retain the same functionality as that of the originally transformed cell. The term “host cell line” refers to a cell line of host cells as used for expressing a recombinant gene to produce recombinant polypeptides such as recombinant antibodies. The term “cell line” as used herein refers to an established clone of a particular cell type that has acquired the ability to proliferate over a prolonged period of time. Such host cell or host cell line may be maintained in cell culture and/or cultivated to produce a recombinant polypeptide. The term "gene" or "gene sequence" refers to the coding sequence or control sequence, or fragments thereof. A gene may include any combination of coding sequence and control sequence, or fragments thereof. Thus, a "gene" as referred to herein may be all or part of a native gene. A polynucleotide sequence as referred to herein may be used interchangeably with the term "gene”, or may include any coding sequence, non-coding sequence or control sequence, fragments thereof, and combinations thereof. The term "gene" or "gene sequence" includes, for example, control sequences upstream of the coding sequence. "Pharmaceutically acceptable carrier" (sometimes referred to as a “carrier”) means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non-toxic, and includes a carrier that is acceptable for veterinary and/or human pharmaceutical or therapeutic use. The terms "carrier" or "pharmaceutically acceptable carrier" can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil/water or water/oil emulsion) and/or various types of wetting agents. As used herein, the term “carrier” encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in pharmaceutical formulations. The choice of a carrier for use in a composition will depend upon the intended route of administration for the composition. The preparation of pharmaceutically acceptable carriers and formulations containing these materials is described in, e.g., Remington's Pharmaceutical Sciences, 21st Edition, ed. University of the Sciences in Philadelphia, Lippincott, Williams & Wilkins, Philadelphia, PA, 2005. Examples of physiologically acceptable carriers include saline, glycerol, DMSO, buffers such as phosphate buffers, citrate buffer, and buffers with other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEENTM (ICI, Inc.; Bridgewater, New Jersey), polyethylene glycol (PEG), and PLURONICSTM (BASF; Florham Park, NJ). To provide for the administration of such dosages for the desired therapeutic treatment, compositions disclosed herein can advantageously comprise between about 0.1% and 99% by weight of the total of one or more of the subject compounds based on the weight of the total composition including carrier or diluent. The term “specificity” refers to the number of different types of antigens or antigenic determinants to which a particular antigen-binding molecule (such as the recombinant antibody of the invention) can bind. As used herein, the term "specifically binds," as used herein with respect to a recombinant antibody refers to the recombinant antibody’s preferential binding to one or more epitopes as compared with other epitopes. Specific binding can depend upon binding affinity and the stringency of the conditions under which the binding is conducted. In one example, an antibody specifically binds an epitope when there is high affinity binding under stringent conditions. It should be understood that the specificity of an antigen-binding molecule (e.g., the recombinant antibodies of the present invention) can be determined based on affinity and/or avidity. The affinity, represented by the equilibrium constant for the dissociation of an antigen with an antigen-binding molecule (KD), is a measure for the binding strength between an antigenic determinant and an antigen-binding site on the antigen-binding molecule: the lesser the value of the KD, the stronger the binding strength between an antigenic determinant and the antigen-binding molecule (alternatively, the affinity can also be expressed as the affinity constant (KA), which is 1/ KD). As will be clear to the skilled person (for example on the basis of the further disclosure herein), affinity can be determined in a manner known per se, depending on the specific antigen of interest. Avidity is the measure of the strength of binding between an antigen-binding molecule (such as the recombinant antibodies of the present invention) and the pertinent antigen. Avidity is related to both the affinity between an antigenic determinant and its antigen binding site on the antigen-binding molecule and the number of pertinent binding sites present on the antigen-binding molecule. Typically, antigen-binding proteins (such as the recombinant antibodies of the invention) will bind to their antigen with a dissociation constant (KD) of 10−5 to 10−12 moles/liter or less, and preferably 10−7 to 10−12 moles/liter or less, and more preferably 10−8 to 10−12 moles/liter. “Therapeutically effective amount” refers to the amount of a composition such as recombinant antibody that will elicit the biological or medical response of a tissue, system, animal, or human that is being sought by the researcher, veterinarian, medical doctor or other clinician over a generalized period of time. In some embodiments, a desired response is reduction of coronaviral titers in a subject. In some embodiments, the desired response is mitigation of coronavirus infection and/or related symptoms. In some instances, a desired biological or medical response is achieved following administration of multiple dosages of the composition to the subject over a period of days, weeks, or years. The therapeutically effective amount will vary depending on the composition, the disorder or conditions and its severity, the route of administration, time of administration, rate of excretion, drug combination, judgment of the treating physician, dosage form, and the age, weight, general health, sex and/or diet of the subject to be treated. The therapeutically effective amount of recombinant antibodies as described herein can be determined by one of ordinary skill in the art. A therapeutically significant reduction in a symptom is, e.g. at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 125%, at least about 150% or more in a measured parameter as compared to a control or non-treated subject. Measured or measurable parameters include clinically detectable markers of disease, for example, elevated or depressed levels of a biological marker, such as decreased viral titers, decreased viral RNA levels, increase in CD4 T lymphocyte counts, and/or prolonged survival of a subject. It will be understood, that the total daily usage of the compositions and formulations as disclosed herein will be decided by the attending physician within the scope of sound medical judgment. The exact amount required will vary depending on factors such as the type of disease being treated. The terms “treat,” “treating,” “treatment,” and grammatical variations thereof as used herein, include partially or completely delaying, alleviating, mitigating or reducing the intensity of one or more attendant symptoms. Treatments according to the invention may be applied preventively, prophylactically, palliatively or remedially. Prophylactic treatments are administered to a subject prior to onset (e.g., before obvious signs of an infection), during early onset (e.g., upon initial signs and symptoms of an infection), after an established development of an infection, or during chronic infection. Prophylactic administration can occur for several minutes to months prior to the manifestation of an infection. As used herein, the term “preventing” a disorder or unwanted physiological event in a subject refers specifically to the prevention of the occurrence of symptoms and/or their underlying cause, wherein the subject may or may not exhibit heightened susceptibility to the disorder or event. Antibodies and Compositions In some aspects, disclosed herein is a recombinant antibody, said antibody comprising a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11224-11232. In some aspects, disclosed herein is a recombinant antibody, said antibody comprising a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11224-11232. In some embodiments, the CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11224. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11225. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11226. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11227. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11228. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11229. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11230. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11231. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11232. In some embodiments, the CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11188. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11189. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11190. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11191. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11192. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11193. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11194. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11195. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11196. In some embodiments, the CDRH1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11170-11178; and CDRL1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11206- 11214. In some embodiments, the CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRH1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214. In some embodiments, the CDRL1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11206-11214. In some embodiments, the CDRH2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11179-11187; and CDRL2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11215- 11223. In some embodiments, the CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRH2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223. In some embodiments, the CDRL2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11215-11223. In some embodiments, VH comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11161- 11169. In some embodiments, VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169. In some embodiments, VL comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11197- 11205. In some embodiments, VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205. In some embodiments, a CDR sequence (for example CDRL1, CDRL2, CDRL3, CDRH1, CDRH2, or CDRH3) comprises one amino acid mutation, two amino acid mutations, three amino acid mutations, four amino acid mutations, five amino acid mutations, etc. when compared to a CDR sequence as disclosed herein. In some embodiments, the recombinant antibody is a monoclonal antibody. In some embodiments, the recombinant antibody is an isolated antibody. In some embodiments, the recombinant antibody is a non-naturally occurring antibody. In some embodiments, the recombinant antibody is an antibody or antigen binding fragment thereof. In some embodiments, combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating coronavirus infection. In some embodiments, combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating SARS-CoV-2 infection. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11170, CDRH2 is SEQ ID NO:11179, CDRH3 is SEQ ID NO:11188, CDRL1 is SEQ ID NO:11206, CDRL2 is SEQ ID NO:11215, and CDRL3 is SEQ ID NO:11224. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11171, CDRH2 is SEQ ID NO:11180, CDRH3 is SEQ ID NO:11189, CDRL1 is SEQ ID NO:11207, CDRL2 is SEQ ID NO:11216, and CDRL3 is SEQ ID NO:11225. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11172, CDRH2 is SEQ ID NO:11181, CDRH3 is SEQ ID NO:11190, CDRL1 is SEQ ID NO:11208, CDRL2 is SEQ ID NO:11217, and CDRL3 is SEQ ID NO:11226. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11173, CDRH2 is SEQ ID NO:11182, CDRH3 is SEQ ID NO:11191, CDRL1 is SEQ ID NO:11209, CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11174, CDRH2 is SEQ ID NO:11183, CDRH3 is SEQ ID NO:11192, CDRL1 is SEQ ID NO:11210, CDRL2 is SEQ ID NO:11219, and CDRL3 is SEQ ID NO:11228. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11175, CDRH2 is SEQ ID NO:11184, CDRH3 is SEQ ID NO:11193, CDRL1 is SEQ ID NO:11211, CDRL2 is SEQ ID NO:11220, and CDRL3 is SEQ ID NO:11229. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11176, CDRH2 is SEQ ID NO:11185, CDRH3 is SEQ ID NO:11194, CDRL1 is SEQ ID NO:11212, CDRL2 is SEQ ID NO:11221, and CDRL3 is SEQ ID NO:11230. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11177, CDRH2 is SEQ ID NO:11186, CDRH3 is SEQ ID NO:11195, CDRL1 is SEQ ID NO:11213, CDRL2 is SEQ ID NO:11222, and CDRL3 is SEQ ID NO:11231. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11178, CDRH2 is SEQ ID NO:11187, CDRH3 is SEQ ID NO:11196, CDRL1 is SEQ ID NO:11214, CDRL2 is SEQ ID NO:11223, and CDRL3 is SEQ ID NO:11232. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11161, and VL is SEQ ID NO: 11197. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11162, and VL is SEQ ID NO: 11198. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11163, and VL is SEQ ID NO: 11199. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11164, and VL is SEQ ID NO: 11200. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11165, and VL is SEQ ID NO: 11201. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11166, and VL is SEQ ID NO: 11202. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11167, and VL is SEQ ID NO: 11203. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11168, and VL is SEQ ID NO: 11204. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11169, and VL is SEQ ID NO: 11205. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VH comprising an amino acid sequence selected from SEQ ID NOs: 1241-2480. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VL comprising an amino acid sequence selected from SEQ ID NOs: 6201-7440. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH1 comprising an amino acid sequence selected from SEQ ID NOs: 2481-3720. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH2 comprising an amino acid sequence selected from SEQ ID NOs: 3721-4960. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH3 comprising an amino acid sequence selected from SEQ ID NOs: 4961-6200. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL1 comprising an amino acid sequence selected from SEQ ID NOs: 7441-8680. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL2 comprising an amino acid sequence selected from SEQ ID NOs: 8681-9920. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL3 comprising an amino acid sequence selected from SEQ ID NOs: 9921-11160. Methods Disclosed herein are methods for preventing, treating, inhibiting, reducing, or detecting coronavirus infection. In some aspects, disclosed herein is a method of producing a recombinant antibody comprising cultivating or maintaining the host cell of any preceding aspect under conditions to produce a recombinant antibody as described herein. In some aspects, disclosed herein is a method of treating, preventing, reducing, and/or inhibiting coronavirus infection, comprising administering to a subject a therapeutically effective amount of a recombinant antibody, wherein the recombinant antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11224-11232. In some aspects, disclosed herein is a method of treating, preventing, reducing, and/or inhibiting coronavirus infection, comprising administering to a subject a therapeutically effective amount of a recombinant antibody, wherein the recombinant antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein CDRH3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11224-11232. In some embodiments, the CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11224. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11225. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11226. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11227. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11228. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11229. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11230. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11231. In some embodiments, the CDRL3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11232. In some embodiments, the CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11188. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11189. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11190. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11191. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11192. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11193. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11194. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11195. In some embodiments, the CDRH3 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NO: 11196. In some embodiments, the CDRH1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11170-11178; and CDRL1 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11206- 11214. In some embodiments, the CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRH1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11170-11178. In some embodiments, the CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214. In some embodiments, the CDRL1 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11206-11214. In some embodiments, the CDRH2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11179-11187; and CDRL2 comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11215- 11223. In some embodiments, the CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRH2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11179-11187. In some embodiments, the CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223. In some embodiments, the CDRL2 comprises at least 1, 2, 3, 4, 5, or 6 substitutions when compared to SEQ ID NOs: 11215-11223. In some embodiments, VH comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11161- 11169. In some embodiments, VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169. In some embodiments, VL comprises an amino acid sequence at least 60% (for example, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%) identical to SEQ ID NOs: 11197- 11205. In some embodiments, VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205. In some embodiments, a CDR sequence (for example CDRL1, CDRL2, CDRL3, CDRH1, CDRH2, or CDRH3) comprises one amino acid mutation, two amino acid mutations, three amino acid mutations, four amino acid mutations, five amino acid mutations, etc. when compared to a CDR sequence as disclosed herein. In some embodiments, the recombinant antibody is a monoclonal antibody. In some embodiments, the recombinant antibody is an isolated antibody. In some embodiments, the recombinant antibody is an antibody or antigen binding fragment thereof. In some embodiments, combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating coronavirus infection. In some embodiments, combinations of antibodies or antigen binding fragments thereof disclosed herein are used for treating SARS-CoV-2 infection. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11170, CDRH2 is SEQ ID NO:11179, CDRH3 is SEQ ID NO:11188, CDRL1 is SEQ ID NO:11206, CDRL2 is SEQ ID NO:11215, and CDRL3 is SEQ ID NO:11224. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11171, CDRH2 is SEQ ID NO:11180, CDRH3 is SEQ ID NO:11189, CDRL1 is SEQ ID NO:11207, CDRL2 is SEQ ID NO:11216, and CDRL3 is SEQ ID NO:11225. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11172, CDRH2 is SEQ ID NO:11181, CDRH3 is SEQ ID NO:11190, CDRL1 is SEQ ID NO:11208, CDRL2 is SEQ ID NO:11217, and CDRL3 is SEQ ID NO:11226. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11173, CDRH2 is SEQ ID NO:11182, CDRH3 is SEQ ID NO:11191, CDRL1 is SEQ ID NO:11209, CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11174, CDRH2 is SEQ ID NO:11183, CDRH3 is SEQ ID NO:11192, CDRL1 is SEQ ID NO:11210, CDRL2 is SEQ ID NO:11219, and CDRL3 is SEQ ID NO:11228. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11175, CDRH2 is SEQ ID NO:11184, CDRH3 is SEQ ID NO:11193, CDRL1 is SEQ ID NO:11211, CDRL2 is SEQ ID NO:11220, and CDRL3 is SEQ ID NO:11229. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11176, CDRH2 is SEQ ID NO:11185, CDRH3 is SEQ ID NO:11194, CDRL1 is SEQ ID NO:11212, CDRL2 is SEQ ID NO:11221, and CDRL3 is SEQ ID NO:11230. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11177, CDRH2 is SEQ ID NO:11186, CDRH3 is SEQ ID NO:11195, CDRL1 is SEQ ID NO:11213, CDRL2 is SEQ ID NO:11222, and CDRL3 is SEQ ID NO:11231. In some embodiments, the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11178, CDRH2 is SEQ ID NO:11187, CDRH3 is SEQ ID NO:11196, CDRL1 is SEQ ID NO:11214, CDRL2 is SEQ ID NO:11223, and CDRL3 is SEQ ID NO:11232. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11161, and VL is SEQ ID NO: 11197. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11162, and VL is SEQ ID NO: 11198. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11163, and VL is SEQ ID NO: 11199. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11164, and VL is SEQ ID NO: 11200. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11165, and VL is SEQ ID NO: 11201. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11166, and VL is SEQ ID NO: 11202. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11167, and VL is SEQ ID NO: 11203. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11168, and VL is SEQ ID NO: 11204. In some embodiments, the antibody or antigen binding fragment thereof comprises a light chain variable region (VL) and/or a heavy chain variable region (VH), wherein: VH is SEQ ID NO: 11169, and VL is SEQ ID NO: 11205. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VH comprising an amino acid sequence selected from SEQ ID NOs: 1241-2480. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a VL comprising an amino acid sequence selected from SEQ ID NOs: 6201-7440. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH1 comprising an amino acid sequence selected from SEQ ID NOs: 2481-3720. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH2 comprising an amino acid sequence selected from SEQ ID NOs: 3721-4960. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRH3 comprising an amino acid sequence selected from SEQ ID NOs: 4961-6200. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL1 comprising an amino acid sequence selected from SEQ ID NOs: 7441-8680. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL2 comprising an amino acid sequence selected from SEQ ID NOs: 8681-9920. In some embodiments, the recombinant antibody or antigen binding fragment thereof of any preceding aspect comprises a CDRL3 comprising an amino acid sequence selected from SEQ ID NOs: 9921-11160. In some embodiments, the recombinant antibody binds to at least one coronavirus antigen. In some embodiments, the recombinant antibody binds to at least one SARS-CoV-2 antigen. In some embodiments, the target protein comprises a viral protein. In some embodiments, the viral protein is a coronavirus protein. Coronaviruses constitute the subfamily Orthocoronavirinae, in the family Coronaviridae, order Nidovirales, and realm Riboviria. They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses ranges from approximately 27 to 34 kilobases. The structure of coronavirus generally consists of the following: spike protein, hemagglutinin-esterase dimer (HE), a membrane glycoprotein (M), an envelope protein (E) a nucleoclapid protein (N) and RNA. The coronavirus family comprises genera including, for example, alphacoronavirus (e.g., Human coronavirus 229E, Human coronavirus NL63, Miniopterus bat coronavirus 1, Miniopterus bat coronavirus HKU8, Porcine epidemic diarrhea virus, Rhinolophus bat coronavirus HKU2, Scotophilus bat coronavirus 512), betacoronavirus (e.g., SARS-CoV-2, Betacoronavirus 1, Human coronavirus HKU1, Murine coronavirus, Pipistrellus bat coronavirus HKU5, Rousettus bat coronavirus HKU9, Severe acute respiratory syndrome-related coronavirus, Tylonycteris bat coronavirus HKU4, Middle East respiratory syndrome-related coronavirus (MERS), Human coronavirus OC43, Hedgehog coronavirus 1 (EriCoV)), gammacoronavirus (e.g., Beluga whale coronavirus SW1, Infectious bronchitis virus), and deltacoronavirus (e.g., Bulbul coronavirus HKU11, Porcine coronavirus HKU15). In some embodiments, the viral protein is a protein of severe acute respiratory syndrome-related coronavirus. In some embodiments, the viral protein is a protein of MERS coronavirus. In some embodiments, the viral protein is a SARS-CoV-2 protein, including, for example, SARS-CoV-2 spike protein, SARS-CoV-2 envelope protein, SARS-CoV-2 membrane protein, or SARS-CoV-2 nucleocapsid protein, or a fragment thereof. In some embodiments, the viral protein is a receptor binding domain of a SARS-CoV-2 spike protein. In some aspects, disclosed herein is a method of producing a recombinant antibody comprising cultivating or maintaining the host cell of any preceding aspect under conditions to produce said recombinant antibody. In some aspects, disclosed herein is a method of treating, preventing, reducing, and/or inhibiting coronavirus infection comprising administering to a subject a therapeutically effective amount of the recombinant antibody of any preceding aspect. The antibody repertoire characterization done herein is also readily generalizable to other pathogens, and as such, have a broad and lasting impact on the development of countermeasures for established and emerging infectious diseases. Methods for determining antibody sequences and antigen-antibody specificities are known in the art. See, e.g., International Publication Number: WO 2020/033164, incorporated by reference. In some aspects, disclosed herein is a method for detecting a coronavirus infection in a subject, comprising: providing a biological sample from the subject, and detecting a coronavirus antigen in the biological sample with an antibody that specifically binds to the coronavirus antigen, wherein the antibody is from any aspect as disclosed herein, and wherein the presence of the coronavirus antigen in the biological sample indicates the subject is infected with a coronavirus. The biological sample can be from, for example, a throat swab, a nasal swab, a nasopharyngeal swab, an oropharyngeal swab, cells, blood, serum, plasma, saliva, urine, stool, sputum, or nasopharyngeal aspirates. In some embodiments, the coronavirus infection is caused by SARS-CoV-2. In some embodiments, the method comprises contacting the biological sample with a SARS-CoV-2 antigen. In some embodiments, the SARS-CoV-2 antigen is directly immobilized on a substrate and is detected by an antibody disclosed herein directly or indirectly by a labeled heterologous anti-isotype antibody, wherein the bound antibody can be detected by a detection assay. The SARS-CoV-2 antigen can be selected from the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, or a fragment thereof. The term “labeled”, with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a secondary antibody that is labeled a fluorescent probe or with biotin for detection. In vitro techniques for detection of the antibodies of SARS-CoV-2 include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence, IgM antibody capture enzyme immunoassay (MAC-ELISA), indirect IgG ELISA, indirect fluorescent antibody assay (IFAT), hemagglutination inhibition (HIT), and serum dilution cross-species plaque reduction neutralization tests (PRNTs). In some embodiments, in vitro techniques for detection of an antigen of SARS-CoV-2 include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence. Furthermore, in vivo techniques for detection of SARS-CoV-2 include introducing into a subject a labeled antibody directed against the polypeptide. For example, the antibody can be labeled with a radioactive marker whose presence and location can be detected by standard imaging techniques, including autoradiography. In some embodiments, the levels of the antibodies are determined by immunoassay comprising Enzyme linked immunospot (ELISPOT), Enzyme-linked immunosorbent assay (ELISA), western blot, or a multiplex ELISA assay. In some embodiments, the multiplex ELISA assay is selected from the group consisting of Luminex, Veriplex, LEGENDplex, Bio-Plex, Milliplex MAP, and FirePlex. The steps of various useful immunodetection methods have been described in the scientific literature, such as, e.g., Maggio et al., Enzyme-Immunoassay, (1987) and Nakamura, et al., Enzyme Immunoassays: Heterogeneous and Homogeneous Systems, Handbook of Experimental Immunology, Vol.1: Immunochemistry, 27.1-27.20 (1986), each of which is incorporated herein by reference in its entirety and specifically for its teaching regarding immunodetection methods. Immunoassays, in their most simple and direct sense, are binding assays involving binding between antibodies and antigen. Many types and formats of immunoassays are known and all are suitable for detecting the disclosed biomarkers. Examples of immunoassays are enzyme linked immunosorbent assays (ELISAs), radioimmunoassays (RIA), radioimmune precipitation assays (RIPA), immunobead capture assays, Western blotting, dot blotting, gel-shift assays, Flow cytometry, protein arrays, multiplexed bead arrays, magnetic capture, in vivo imaging, fluorescence resonance energy transfer (FRET), and fluorescence recovery/localization after photobleaching (FRAP/ FLAP). The invention also encompasses kits for detecting the presence of SARS-CoV-2 or a polypeptide/antigen thereof in a biological sample. For antibody-based kits, the kit can comprise, for example: (1) a first antibody (e.g., attached to a solid support) which binds to a coronavirus antigen; and, optionally, (2) a second, different antibody which binds to either the coronavirus antigen or the first antibody and is conjugated to a detectable agent. EXAMPLES The following examples are set forth below to illustrate the antibodies, methods, and results according to the disclosed subject matter. These examples are not intended to be inclusive of all aspects of the subject matter disclosed herein, but rather to illustrate representative methods and results. These examples are not intended to exclude equivalents and variations of the present invention which are apparent to one skilled in the art. Example 1. Ultra-potent neutralization of SARS-CoV-2 variants of concern by an antibody with a unique genetic signature and structural mode of spike recognition. The emergence of novel SARS-CoV-2 lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable challenge to the clinical treatment of COVID-19. Therefore, the need for ongoing discovery efforts to identify broadly reactive monoclonal antibodies to SARS-CoV-2 is of utmost importance. Here, a panel of SARS-CoV-2 antibodies isolated from an individual who recovered from COVID-19 using LIBRA-seq technology are reported. Of these antibodies, 54042-4 showed ultra-potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs). A 2.7 Å cryo-EM structure of 54042-4 in complex with SARS-CoV-2 spike revealed an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages. Further, 54042-4 possesses unique genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings identify 54042-4 for clinical development to counteract current and potential SARS-CoV-2 VOCs. Introduction The COVID-19 pandemic caused by a novel coronavirus in the Sarbecovirus genus, SARS-CoV-2, spawned an unprecedented global research effort dedicated to therapeutic countermeasure development resulting in rapid US FDA Emergency Use Authorization (EUA) for vaccines and monoclonal antibodies. The primary target for vaccine and antibody therapeutic development is the SARS-CoV-2 spike (S) protein, which facilitates host-cell attachment and entry. The emergence of distinct viral lineages that accumulate mutations in the S protein, however, pose a significant threat to the countermeasures currently approved for clinical use. Continued genomic surveillance and persistent efforts to identify novel antibodies with distinct binding modes and mechanisms of action are crucial to maintain availability of therapeutics in the event of further neutralization-escape by SARS-CoV-2 variants of concerns (VOCs). SARS-CoV-2 spike is a class I viral fusion protein that is a trimer of heterodimers composed of S1 and S2 subunits. S1, which includes both the receptor-binding domain (RBD) and the N-terminal domain (NTD), initiates attachment to the receptor angiotensin-converting enzyme 2 (ACE2) whereas S2 drives membrane fusion by refolding from a prefusion to postfusion conformation. The primary contact of ACE2 and spike is in the receptor-binding domain (RBD) of the S1 subunit which is composed of a receptor binding motif (RBM) and RBD core. The three RBDs within each spike can adopt an ACE2-accessible “up” conformation and an ACE2- inaccessible “down” conformation via a hinge-like motion. As a result, the RBD serves as the dominant target of neutralizing antibodies via antagonism of ACE2 binding, although other neutralizing epitopes have been identified. Neutralizing antibodies targeting the RBD have been characterized extensively and partition into different classes based on binding mode, ACE2 interface overlap, and cross- reactivity with other Sarbecoviruses. For example, neutralizing antibodies predominantly encoded by IGHV3-53 and IGHV3-66 have epitopes directly covering the ACE2 interaction footprint in the RBM. Examples of this class of antibodies are clinical EUA candidates REGN10933 and COV2-2196. Antibodies that bind the RBM but are more distal to the ACE2 interface form another distinct class that includes REGN10987 and COV2-2130. On the other hand, cross reactive antibodies such as S309, CR3022 and ADG-2 that cross-react with other coronaviruses comprise a more diverse group yet targeting residues in the RBD-core, as a result of high sequence conservation at this site. The continued transmission of SARS-CoV-2 in the human population has led to the evolution of viral variants of concern (VOCs) with increased transmissibility and resistance to available medical countermeasures, including to some RBD-directed monoclonal antibodies. Some of the most consequential amino acid substitutions observed so far have occurred in the RBD, particularly N501Y in the B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma) lineages, and the additional combination of K417N/T and E484K in the Gamma and Beta lineages. The L452R substitution, detected in both the B.1.429 (Epsilon) and B.1.617.2 (Delta) variants also permits escape to monoclonal antibodies and a reduction in neutralization titer in comparison to USA- WA1 in vaccinees as well as individuals recovered from COVID-19 infection. Notably, the Epsilon lineage also contains substitutions (S13I and W152C) that disrupt the conformation of the NTD, resulting in the loss of numerous published NTD-directed SARS-CoV-2 neutralizing antibodies. N501Y can increase affinity for ACE2, resulting in increased infectivity, whereas E484K disrupts the antigenic landscape of the RBD that can lead to substantial decreases in neutralization titers. In some cases, SARS-CoV-2 VOCs also escape neutralization by polyclonal antibodies in the serum from vaccine recipients and individuals previously infected with SARS- CoV-2. These observations highlight the critical need for a wide range of potently neutralizing antibodies that are not sensitive to substitutions arising in VOCs. To address this challenge, LIBRA-seq, a recently developed antibody discovery technology, was applied to interrogate the B cell repertoire of an individual who had recovered from COVID-19. These efforts led to the discovery of a potently neutralizing antibody, designated 54042-4, which uses an uncommon genetic signature and distinct structural mode of SARS-CoV- 2 RBD recognition to neutralization maintain potency to known VOCs. Antibody 54042-4, therefore can be used for further prophylactic or therapeutic development for protection against a broad range of SARS-CoV-2 variants. Results Identification of SARS-CoV-2-neutralizing antibodies by LIBRA-seq To identify SARS-CoV-2 S-directed antibodies, LIBRA-seq (Linking B Cell receptor to antigen specificity through sequencing) was used, a technology that enables a high-throughput simultaneous determination of B cell receptor sequence and antigen reactivity at the single-cell level, expediting the process of lead antibody selection and characterization. The LIBRA-seq antigen screening library included SARS-CoV-2 and SARS-CoV-2 D614G spikes stabilized in a prefusion conformation, along with antigens from other coronaviruses including SARS-CoV S, MERS-CoV S, , HCoV-OC43 S, HCoV-229E S, HCoV-NL63 S, SARS-CoV-2 RBD, SARS-CoV RBD, and MERS-CoV RBD, as well as negative control antigens. Antigen-specific B cells were isolated from a donor with potently neutralizing antibodies in serum (1:258 NT50) three months after infection confirmed by nasal swab RT-PCR testing for SARS-CoV-2 (Figures 6A and 6B). Of the 73 IgG+ B cells were observed with high LIBRA-seq scores (≥1) for SARS-CoV-2 S (Figure 1A), nine lead antibodies were chosen with diverse sequence characteristics, CDRH3 length, and germline V gene usage for characterization as recombinant monoclonal antibodies (Figure 1B and Figure 6C). Binding to SARS-CoV-2 S by ELISA was confirmed for eight of these antibodies, with the only exception being antibody 54042-2, in agreement with its lower LIBRA-seq score (Figure 1B and Figures 6C and 6D). Five of these antibodies showed SARS- CoV-2 neutralization activity in a high-throughput neutralization screen using a live chimeric VSV displaying SARS-CoV-2 spike protein (Figure 1B). None of the antibodies showed neutralization against VSV SARS-CoV. Further, the five neutralizing antibodies did not show binding cross- reactivity to other coronavirus antigens in the screening panel, with the exception of SARS-CoV (Figure 6E). Full dose-response neutralization curves in the chimeric VSV assay were obtained for four of these five antibodies, with antibody 54042-4 showing the best potency, at a half- maximal inhibitory concentration (IC50) of 9 ng/mL (Figure 1C). Antibody 54054-2 targets the SARS-CoV-2 receptor binding domain Because of the potent (≤ 10 ng/mL) virus neutralization observed for 54042-4, this antibody was selected for further characterization. ELISAs performed with purified RBD, NTD, S1, and S2 protein constructs revealed 54042-4 IgG bound to the SARS-CoV-2 S1 subunit as well as the RBD (Figure 2A, Figure 7). To determine the affinity of the antibody-antigen binding interaction, biolayer interferometry experiments were performed by measuring the association and dissociation kinetics of immobilized 54042-4 IgG binding to a soluble protein comprising the RBD and subdomain-1 (SD1) of the SARS-CoV-2 S protein, and curve-fitting resulted in a calculated KD of 21.8 nM (Figure 2B). Given the neutralization potency of 9 ng/mL (60 pM, these data suggest that the IgG avidly binds to the S protein on the virus surface. To assess whether 54042-4 neutralizes viral infection by directly competing with ACE2, a receptor blocking assay was performed by testing competition of 54042-4 with soluble ACE2 for binding to SARS-CoV-2 S. The results demonstrated that 54042-4 inhibits interaction of ACE2 to SARS-CoV-2 S protein, unlike the control antibody CR3022, an extensively characterized SARS-CoV antibody that binds a cryptic epitope in the RBD of both SARS-CoV and SARS-CoV-2, and the influenza HA-specific 3602-1707 antibody (Figure 2C). Next, competition ELISA was performed to determine if 54042- 4 competes for binding with three other RBD-directed antibodies with distinct epitopes. These antibodies included COV2-2196 and COV2-2130, which form the basis of AZD7442, an antibody cocktail currently under investigation in clinical trials for COVID-19 treatment and prevention (ClinicalTrials.gov Identifiers: NCT04625725, NCT04723394, NCT04518410, and NCT04501978) and CR3022. The competition experiment showed that 54042-4 competed for binding to SARS-CoV-2 S protein with COV2-2130, but not COV2-2196 or CR3022 (Figure 2D). Together, these results indicate that 54042-4 targets an epitope on SARS-CoV-2 RBD that at least partially overlaps with the binding sites for both ACE2 and other potently neutralizing RBD- directed antibodies. 54042-4 binds the apex of the SARS-CoV-2 RBD in the down conformation To gain a better understanding of the recognition of SARS-CoV-2 S by antibody 54042-4, a 2.7 Å resolution cryo-EM structure was determined of the 54042-4 antigen-binding fragments (Fabs) bound to the SARS-CoV-2 S extracellular domain (ECD) modified so that all three RBDs were disulfide-locked in the down conformation. (Figure 3A). Local refinement of one RBD bound to a 54042-4 Fab was performed to improve the interpretability of the map at the binding interface, resulting in a local 3D reconstruction with a resolution of 2.8 Å (Figure 3B). The structure revealed that 54042-4 forms an extensive interface with the RBD, making contacts through the complementarity determining regions (CDRs) CDRL1, CDRL3, and all three CDRs of the heavy chain, to form a clamp around the apex of the RBM saddle (Figures 3C, 3D, Figure 8). The primary interactions involve RBD residues 439-450, with a network of hydrogen bonds between the 54042-4 heavy chain and RBD residues 443-447 (Figure 3C). From CDRH3, Ser99 forms a hydrogen bond with RBD residue Ser443, and a hydrogen bond is formed between the mainchain atoms of Phe97 and Val445. From CDRH2, Asp56 forms a hydrogen bond and salt bridge with Lys444, whereas Arg58 forms hydrogen bonds with mainchain atoms from Gly446 and Gly447. The CDRH1 contributes a lone residue, Ile32, to the binding interface, forming minor contacts near Leu441. The 54042-4 light chain surrounds the opposite side of this RBD region, mediating interactions primarily through hydrophobic contacts formed by CDRL1 and CDRL3 near RBD residue Val445 (Figure 3D). Additional light chain contacts are made with residues 498 to 500 of the RBD, including a hydrogen bond between His92 of CDRL3 and Thr500, and hydrophobic interactions involving CDRL1 Phe30 and Tyr32. Although 54042-4 binds all three RBDs locked in the down position, the epitope region is equally accessible when the RBD is in the up position. Additionally, the epitope lies outside the RBD hinge region, makes no additional contacts with the spike trimer, and partially overlaps the ACE2 binding site. Therefore, the mechanism of neutralization likely involves inhibition of ACE2 binding rather than locking the RBDs in the down conformation. Notably, the complex structure indicated that 54042-4 does not make substantial contact with a number of spike substitutions associated with current VOCs. For example, RBD residue Asn501 (present as Tyr501 in several VOCs, including Alpha, Beta, and Gamma) lies just outside of the 54042-4 epitope, whereas the Cα atoms of Glu484 (present as Lys484 or Gln484 in, e.g., Beta, Gamma, and B.1.617 (Kappa)) and Leu452 (present as Arg452 in Epsilon and Delta) are approximately 18 and 14 Å away from the Cα atoms of the nearest 54042-4 residue, respectively (Figure 3B). Furthermore, the substitution Gly614, which is found in all current VOCs is outside of the RBD, is approximately 75 Å from the nearest 54042-4 residue. Antibody 54042-4 has un uncommon genetic signature and distinct structural mode of RBD recognition Public clonotype sequence signatures (those shared by multiple individuals recovered from COVID-19 infection) have been identified for potently neutralizing SARS-CoV-2 antibodies, including antibodies currently in clinical trials or approved for emergency use, have been identified. To investigate whether antibody sequences that are closely related to 54042-4 can be identified among known SARS-CoV-2 antibodies, this study searched the CoV-AbDab database that contains paired heavy-light chain sequences of coronavirus antibodies. Notably, only 0.5% of antibodies in the database used the same combination of IGHV2-5 heavy chain and IGKV1-39 light chain germline V genes as 54042-4. Further, antibodies with high sequence identity to the 54042-4 CDRH3 and CDRL3 were not identified, whether or not the search was restricted to the IGHV2-5 heavy chain and IGKV1-39 light chain genes (Figure 4A). Next, the 54042-4 epitope was compared to the epitopes of other known SARS-CoV-2 antibodies by computing pairwise correlations between the antibody-antigen buried surface areas for 54042-4 against a set of 99 publicly available SARS-CoV-2 antibody-antigen structures from the Protein Data Bank, as well as the structure of antibody COV2-2130 in complex with the SARS- CoV-2 RBD (Table 3). The results revealed significant positive correlations with only six other antibodies: REGN10987, 2-7, C119, COVOX-75, COV2-2130 (in agreement with the observed binding competition with 54042-4, Figure 2D), and LY-CoV1404 (Figure 4B). However, of these six antibodies, C119 makes substantial contact with residues Glu484 and Asn501, indicating potential susceptibility of this antibody to substitutions at those positions that are currently associated with relatively high substitution rates (Figure 4C) and are present in several circulating SARS-CoV-2 VOCs. Further, both C119 and COVOX-75, as well as COV2-2130, have substantial buried surface area (Å2) interactions with a number of additional residues compared to those in the epitope of 54042-4 (Figure 4C), indicating that these three antibodies can be susceptible to additional potential spike substitutions that would not directly affect antigen interactions with 54042-4. It was also observed that while the epitopes of antibodies 2-7, LY-CoV1404, and REGN10987 correlate well with that of 54042-4, these antibodies have distinct angles of antigen approach (Figure 4D). To quantify this observation, the RBDs from the 2-7, LY-CoV1404, and REGN10987 complex structures were aligned with the RBD from the 54042-4 structure. Using the antibody coordinates when the respective RBDs were aligned, this study computed the root mean square deviations (RMSD) between the Cα atoms in the FWR1-FWR3 regions of the antibody heavy and light chains. This resulted in RMSDs of 16.4 Å, 16.5Å, and 22 Å between 54042-4 versus 2-7, LY-CoV1404, and REGN10987, respectively, confirming the substantial differences in the structural mode of antigen recognition by 54042-4 compared to 2-7, LY- CoV1404, and REGN10987. Although 54042-4 and 2-7 both originate from the same IGHV2-5 germline gene and share analogous RBD contacts in the CDRH2 region, these antibodies exhibit different CDRH1 and CDRH3 interactions (Figure 4E) and use a different light chain germline gene (VK1-39 for 54042-4, and VL2-14 for 2-7). Antibodies 2-7 and LY-CoV1404 use identical heavy and light chain germline genes, and have virtually indistinguishable structural mode of antigen recognition (RMSD, computed as above, of 1.7Å). Notably, all of 2-7, LY-CoV1404, and REGN10987 have greater interactions with RBD residues 439–441 compared to 54042-4, with buried surface areas of 172, 164, 127, and 60 Å2 for 2-7, LY-CoV1404, REGN10987, and 54042- 4, respectively (Figure 4C), indicating 2-7, LY-CoV1404, and REGN10987 can be more prone to viral escape in that region. Indeed, the N439K substitution is present in several independent SARS- CoV-2 lineages and has been found to affect binding and neutralization by REGN10987. Together, these data show that antibody 54042-4 utilizes an uncommon genetic signature and a distinct structural mode of antigen recognition compared to other known SARS-CoV-2 antibodies. Antibody 54042-4 is not affected by current SARS-CoV-2 VOC substitutions To identify substitutions capable of disrupting binding to antibody 54042-4, shotgun alanine-scanning mutagenesis of the SARS-CoV-2 RBD was performed. The only tested substitutions that substantially affected binding in comparison to an RBD antibody control were K444A, V445A, G446A, and P499A (Figure 5A), which all fall within the 54042-4 epitope (Figure 3C, 3D, and Figure 8A). Next, to assess the functional effect of substitutions within the 54042-4 epitope, neutralization was tested against VSV-SARS-CoV-2 chimeras containing single substitutions at K444R/T/E/N, G446D, or Q498R. These mutants were generated from neutralization escape experiments using saturating concentrations of either COV2-2130 antibody (a 54042-4 competitor, Figure 2D) or COV2-2499 (a COV2-2130 competitor). These experiments revealed that the chimeric VSVs with mutations at Lys444, Gly446, and Gln498 were resistant to neutralization by 54042-4 (Figure 5B). Together, the alanine-scanning and neutralization experiments indicated that 54042-4 may be sensitive to substitutions at spike residues K444, V445, G446, Q498, and P499. However, analysis of currently circulating SARS-CoV-2 isolates from the GISAID database as of May 6, 2021 revealed that substitutions at these five residue positions are only present at low levels (Figure 5C). Further, virtually all of the 54042-4 epitope residues (Figure 8A) are also highly conserved in circulating SARS-CoV-2 lineages (Figure 5C). The only exception IS residue N439, which has a substitution frequency of 2.1% (Figure 5C); however, this residue makes only minimal contacts with antibody 54042-4 (Figure 8A), suggesting that residue N439 may not be critical for 54042-4 recognition of the SARS-CoV-2 spike. To investigate the ability of antibody 54042-4 to recognize current SARS-CoV-2 VOCs, this study performed ELISAs to test binding of 54042-4 to RBD proteins containing substitutions found in one or more VOCs. These substitutions included K417N found in many isolates in the Beta lineage, as well as E484K (Beta, Gamma), N501Y (Alpha, Beta, Gamma, Delta, Kappa), L452R (Delta, Epsilon) and N439K found in lineages B.1.141 and B.1.258. Notably, antibody 54042-4 bound to these RBD variants at a similar level compared to the binding to the RBD from the Wuhan-1 isolate (Figure 5D, Figure 9A). These results are consistent with the structural observations that 54042-4 makes only minimal contacts with residue N439, and that none of the other RBD substitutions were at residues in the 54042-4 epitope (Figure 8A). Binding of antibody 54042-4 also was not affected in the context of SARS-CoV-2 S ECD proteins that included deletions and substitutions in the S1 domain of the Beta and Alpha VOCs (Figure 5D, Figures 9B and 9C). Finally, the study tested the ability of 54042-4 to neutralize authentic SARS-CoV-2 USA-WA1, Alpha, and Beta, Delta, and Gamma SARS-CoV-2 variants. Consistent with the ELISA data, 54042-4 neutralized each virus potently with IC50 values of 3.2, 5.5, 9.7, 1.5, and 3.7, and IC80 values of 10, 48, 49, 3.9, and 11.4 ng/mL, respectively (Figure 5E). Together, these data indicate that 54042-4 can be an effective countermeasure against currently circulating SARS-CoV-2 variants. SARS-CoV-2 neutralizing antibody discovery efforts have produced an extensive panel of antibodies that show a wide range of functional effects, and most antibodies discovered to date cluster into several classes based on RBD-binding orientation, ACE2 antagonism, and cross- reactivity to related SARS-like coronaviruses. Here, this study reports the identification of 54042- 4, an antibody that exhibited potent SARS-CoV-2 neutralization against USA-WA1 as well as the currently circulating Alpha, Beta, Delta, and Gamma VOCs. Antibody 54042-4 neutralized virus at comparable IC50s to the clinical candidates LY-CoV1404 and REGN10987, despite having ~10- fold lower affinity for the RBD. While the epitope of antibody 54042-4 showed partial overlap with that of several other known RBD-directed antibodies, these findings revealed a distinct mode of SARS-CoV-2 spike recognition, paired with an uncommon genetic signature that distinguishes 54042-4 from other SARS-CoV-2 antibodies. Notably, important differences were observed even for the six antibodies with the highest epitope correlations to 54042-4, with all six of these antibodies exhibiting substantially greater contacts with one or more known residues associated with currently circulating VOCs, as well as with other spike residues (Figure 4C). While it is not possible to predict what SARS-CoV-2 variants will emerge in the future, having access to antibodies with differences in epitope interactions is critical to broadening the portfolio of countermeasures, should virus variants emerge that are resistant to current therapies. The discovery of antibody 54042-4 is therefore a promising addition to the limited set of antibodies with a high potential for effectively counteracting current SARS-CoV-2 VOCs. The increased spread of several SARS-CoV-2 VOCs over the past few months has emphasized the need for continued surveillance of vaccine efficacy against the evolving virus targets. The increased transmission rates of the Alpha lineage are likely a product of enhanced ACE2 affinity for the SARS-CoV-2 RBD, and not a result of escape from pre-existing antibodies in convalescent or vaccinated individuals. Variants that encode the E484K substitution appear to pose a significantly higher risk of neutralization escape in vaccine recipients and individuals who have recovered from COVID-19. Indeed, the rise of cases associated with the P.1 variant that harbors the E484K substitution (among others) in Manaus, Brazil is on a dangerous trajectory, despite having a 76% population seropositivity rate dating back to March 2020. In the context of vaccination, early vaccine trial data for Novavax against the Beta lineage in South Africa (also encoding the E484K substitution) demonstrated a significant decrease in efficacy. The enhanced transmission profile and recent rise in new infection cases as a result of the Delta variant is another demonstration of the need for SARS-CoV-2 therapeutics. These observations underscore the ongoing need for genomic surveillance to monitor the emergence and spread of new SARS-CoV- 2 variants and their effects on population immunity. In addition to vaccines, antibody therapeutics can play an important role for treating SARS- CoV-2 infections. Given the unknown future trajectory of the pandemic and the potential for emergence of VOCs that may escape neutralization by vaccine-elicited immunity, the development of a wide array of antibody therapeutics that are insensitive to substitutions found in major VOCs may prove critical in the fight against COVID-19. However, current VOCs have already shown an ability to escape neutralization by a number of antibodies in clinical development. Although the Beta variant or any lineage harboring the Glu484 substitution has yet to propagate in the United States, the nearly complete abrogation of neutralization activity of LY- CoV555 (Bamlinivimab) and REGN10933 against the Beta variant poses a significant risk for the currently available EUA clinical candidates. Further, the rise in cases with the L452R substitution (Epsilon and Delta variants) and the corresponding reduction in neutralization potency associated with the Eli Lilly cocktail (Bamlinivimab and Etesivimab), as well as Regdanivimab (approved for use in Europe), further motivates the continued investigation into antibodies insensitive to currently circulating VOCs. In contrast to these clinical candidates, the binding, neutralization, and structural data indicate that antibody 54042-4 maintains functional activity independent of the current major substitutions in circulating VOCs. As SARS-CoV-2 virus evolution continues due to various factors, such as a lack of vaccine access and the associated delayed vaccine rollout to underserved parts of the world, new VOCs are likely to keep emerging, with the potential to decrease or even abrogate protection induced by current vaccines. Antibody therapeutic development, especially focusing on broad protection against diverse SARS-CoV-2 variants, is therefore of continued significance. Methods Donor Information The donor had previous laboratory-confirmed COVID-19, 3 months prior to blood collection. The studies were reviewed and approved by the Institutional Review Board of Vanderbilt University Medical Center. The sample was obtained after written informed consent was obtained. Antigen Purification A variety of recombinant soluble protein antigens were used in the LIBRA-seq experiment and other experimental assays. Plasmids encoding residues 1–1208 of the SARS-CoV-2 spike with a mutated S1/S2 cleavage site, proline substitutions at positions 817, 892, 899, 942, 986 and 987, and a C-terminal T4-fibritin trimerization motif, an 8x HisTag, and a TwinStrepTag (SARS-CoV-2 spike HP); 1– 1208 of the SARS-CoV-2 spike with a mutated S1/S2 cleavage site, proline substitutions at positions 817, 892, 899, 942, 986 and 987, a glycine mutation at 614, and a C-terminal T4-fibritin trimerization motif, an 8x HisTag, and a TwinStrepTag (SARS-CoV-2 spike HP D614G) 1–1208 of the SARS-CoV-2 spike with a mutated S1/S2 cleavage site, proline substitutions at positions 817, 892, 899, 942, 986 and 987, as well as mutations L18F, D80A, L242-244L del, R246I, K417N, E484K, N501Y, and a C-terminal T4-fibritin trimerization motif, an 8x HisTag, and a TwinStrepTag (SARS-CoV-2 spike HP Beta); 1–1208 of the SARS-CoV-2 spike with a mutated S1/S2 cleavage site, proline substitutions at positions 817, 892, 899, 942, 986 and 987, as well as mutations 69-70del, Y144del, N501Y, A570D, P681H, and a C-terminal T4-fibritin trimerization motif, an 8x HisTag, and a TwinStrepTag (SARS-CoV-2 spike HP Alpha); residues 1-1190 of the SARS-CoV spike with proline substitutions at positions 968 and 969, and a C-terminal T4- fibritin trimerization motif, an 8x HisTag, and a TwinStrepTag (SARS-CoV S-2P); residues 1- 1291 of the MERS-CoV spike with a mutated S1/S2 cleavage site, proline substitutions at positions 1060 and 1061, and a C-terminal T4-fibritin trimerization motif, an AviTag, an 8x HisTag, and a TwinStrepTag (MERS-CoV S-2P Avi); residues 1-1278 of the HCoV-OC43 spike with proline substitutions at positions 1070 and 1071, and a C-terminal T4-fibritin trimerization motif, an 8x HisTag, and a TwinStrepTag (HCoV-OC43 S-2P); residues 319–591 of SARS-CoV-2 S with a C- terminal monomeric human IgG Fc-tag and an 8x HisTag (SARS-CoV-2 RBD-SD1); residues 306−577 of SARS-CoV S (Tor2 strain) were cloned upstream of a C-terminal HRV3C protease cleavage site, a monomeric Fc tag and an 8x HisTag (SARS-CoV RBD-SD1); residues 367–589 of MERS-CoV S with a C-terminal monomeric human IgG Fc-tag and an 8x HisTag (MERS-CoV RBD); residues 306–577 of MERS-CoV S with a C-terminal monomeric human IgG Fc-tag and an 8x HisTag (SARS-CoV RBD-SD1) were transiently transfected into FreeStyle293F cells (Thermo Fisher) using polyethylenimine. For all antigens with the exception of SARS-CoV-2 S HP, transfections were treated with 1 µM kifunensine to ensure uniform glycosylation three hours post-transfection. Transfected supernatants were harvested after 6 days of expression. SARS-CoV- 2 RBD-SD1, SARS-CoV RBD-SD1, and MERS-CoV RBD were purified using Protein A resin (Pierce). SARS-CoV-2 S HP, MERS-CoV S-2P Avi, and HCoV-OC43 S-2P were purified using StrepTrap HP columns (Cytiva Life Sciences). Affinity-purified SARS-CoV-2 RBD-SD1, SARS- CoV RBD-SD1, and MERS-CoV RBD were further purified over a Superdex200 column (GE Life Sciences). SARS-CoV-2 S HP, SARS-CoV-2 S HP Beta, SARS-CoV-2 S HP Alpha, SARS- CoV S-2P, MERS-CoV S-2P, and HCoV-OC43 S-2P were purified over a Superose6 Increase column (GE Life Sciences). HCoV-NL63 and HCoV-229E alpha coronavirus spike proteins as well as the SARS-CoV-2 S1, SARS-CoV-2 S2, and SARS-CoV-2 NTD truncated proteins were purchased from the commercial vendor, Sino Biological. Recombinant, soluble HIV-1 gp140 SOSIP trimer from strain ZM197 (clade) containing an AviTag and recombinant NC99 HA protein consisting of the HA ectodomain with a point mutation at the sialic acid-binding site (Y98F) to abolish non-specific interactions, a T4 fibritin foldon trimerization domain, AviTag, and hexahistidine-tag, were expressed in Expi 293F cells using polyethylenimine transfection reagent and cultured. FreeStyle F17 expression medium supplemented with pluronic acid and glutamine was used. The cells were cultured at 37°C with 8% CO2 saturation and shaking. After 5-7 days, cultures were centrifuged and supernatant was filtered and run over an affinity column of agarose bound Galanthus nivalis lectin. The column was washed with PBS and antigens were eluted with 30 mL of 1M methyl-a-D-mannopyranoside. Protein elutions were buffer exchanged into PBS, concentrated, and run on a Superdex 200 Increase 10/300 GL Sizing column on the AKTA FPLC system. Fractions corresponding to correctly folded protein were collected, analyzed by SDS-PAGE and antigenicity was characterized by ELISA using known monoclonal antibodies specific to each antigen. Avitagged antigens were biotinylated using BirA biotin ligase (Avidity LLC). Recombinant NC99 HA protein contains the HA ectodomain with a point mutation at the sialic acid-binding site (Y98F), T4 fibritin foldon trimerization domain, AviTag, and hexahistidine-tag, and were expressed in Expi 293F mammalian cells using Expifectamine 293 transfection reagent (Thermo Fisher Scientific) cultured for 4-5 days. Culture supernatant was harvested and cleared as above, and then adjusted pH and NaCl concentration by adding 1M Tris- HCl (pH 7.5) and 5M NaCl to 50 mM and 500 mM, respectively. Ni Sepharose excel resin (GE Healthcare) was added to the supernatant to capture hexahistidine tag. Resin was separated on a column by gravity and captured HA protein was eluted by a Tris-NaCl (pH 7.5) buffer containing 300 mM imidazole. The eluate was further purified by a size exclusion chromatography with a HiLoad 16/60 Superdex 200 column (GE Healthcare). Fractions containing HA were concentrated, analyzed by SDS-PAGE and tested for antigenicity by ELISA with known antibodies. Spike protein used for cryo-EM was expressed by transiently transfecting plasmid encoding the HexaPro spike variant containing additional S383C and D985C substitutions with a C-terminal TwinStrep tag into FreeStyle 293-F cells (Thermo Fisher) using polyethyleneimine.5 μM kifunensine was added 3h post-transfection. The cell culture was harvested four days after transfection and the spike-containing medium was separated from the cells by centrifugation. Supernatants were passed through a 0.22 µm filter and passaged over StrepTactin resin (IBA). Further purification was achieved by size-exclusion chromatography using a Superose 610/300 column (GE Healthcare) in buffer containing 2 mM Tris pH 8.0, 200 mM NaCl and 0.02% NaN3. DNA-barcoding of Antigens Oligos were used that possess 15 bp antigen barcode, a sequence capable of annealing to the template switch oligo that is part of the 10X bead-delivered oligos, and contain truncated TruSeq small RNA read 1 sequences in the following structure: 5’- CCTTGGCACCCGAGAATTCCANNNNNNNNNNNNNCCCATATAAGA*A*A-3’ (SEQ ID NO: 11233), where Ns represent the antigen barcode, and * represents a phosphorothioate bond. The following antigen barcodes were used: GCAGCGTATAAGTCA (SARS-CoV-2 S) (SEQ ID NO: 11234), AACCCACCGTTGTTA (SARS-CoV-2 S D614G) (SEQ ID NO: 11235), GCTCCTTTACACGTA (SARS-CoV S) (SEQ ID NO: 11236), GGTAGCCCTAGAGTA (MERS-CoV S) (SEQ ID NO: 11237), AGACTAATAGCTGAC (HCoV-OC43 S) (SEQ ID NO: 11238), GACAAGTGATCTGCA (HCoV-NL63 S) (SEQ ID NO: 11239), GTGTGTTGTCCTATG (HCoV-229E S) (SEQ ID NO: 11240), TACGCCTATAACTTG (ZM197 HIV EnV) (SEQ ID NO: 11241), TCATTTCCTCCGATT (HA NC99) (SEQ ID NO: 11242), TGGTAACGACAGTCC (SARS-CoV RBD-SD1) (SEQ ID NO: 11243), TTTCAACGCCCTTTC (SARS-CoV-2 RBD-SD1) (SEQ ID NO: 11244), GTAAGACGCCTATGC (MERS-CoV RBD) (SEQ ID NO: 11245), CAGTAAGTTCGGGAC (SARS-CoV-2 NTD) (SEQ ID NO: 11246), Oligos were ordered from IDT with a 5’ amino modification and HPLC purified. For each antigen, a unique DNA barcode was directly conjugated to the antigen itself. In particular, 5’amino-oligonucleotides were conjugated directly to each antigen using the Solulink Protein-Oligonucleotide Conjugation Kit (TriLink cat no. S-9011) according to manufacturer’s instructions. Briefly, the oligo and protein were desalted, and then the amino-oligo was modified with the 4FB crosslinker, and the biotinylated antigen protein was modified with S-HyNic. Then, the 4FB-oligo and the HyNic-antigen were mixed together. This causes a stable bond to form between the protein and the oligonucleotide. The concentration of the antigen-oligo conjugates was determined by a BCA assay, and the HyNic molar substitution ratio of the antigen-oligo conjugates was analyzed using the NanoDrop according to the Solulink protocol guidelines. AKTA FPLC was used to remove excess oligonucleotide from the protein-oligo conjugates, which were also verified using SDS-PAGE with a silver stain. Antigen-oligo conjugates were also used in flow cytometry titration experiments. Antigen-specific B cell sorting Cells were stained and mixed with DNA-barcoded antigens and other antibodies, and then sorted using fluorescence activated cell sorting (FACS). First, cells were counted and viability was assessed using Trypan Blue. Then, cells were washed three times with DPBS supplemented with 0.1% Bovine serum albumin (BSA). Cells were resuspended in DPBS-BSA and stained with cell markers including viability dye (Ghost Red 780), CD14-APC-Cy7, CD3-FITC, CD19-BV711, and IgG-PE-Cy5. Additionally, antigen-oligo conjugates were added to the stain. After staining in the dark for 30 minutes at room temperature, cells were washed three times with DPBS-BSA at 300g for five minutes. Cells were then incubated for 15 minutes at room temperature with Streptavidin-PE to label cells with bound antigen. Cells were washed three times with DPBS-BSA, resuspended in DPBS, and sorted by FACS. Antigen positive cells were bulk sorted and delivered to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) sequencing core at an appropriate target concentration for 10X Genomics library preparation and subsequent sequencing. FACS data were analyzed using FlowJo. Sample preparation, library preparation, and sequencing Single-cell suspensions were loaded onto the Chromium Controller microfluidics device (10X Genomics) and processed using the B-cell Single Cell V(D)J solution according to manufacturer’s suggestions for a target capture of 10,000 B cells per 1/810X cassette, with minor modifications in order to intercept, amplify and purify the antigen barcode libraries as previously described. Sequence processing and bioinformatic analysis The previously described pipeline was utilized and modified to use paired-end FASTQ files of oligo libraries as input, process and annotate reads for cell barcode, unique molecular identifier (UMI), and antigen barcode, and generate a cell barcode - antigen barcode UMI count matrix. BCR contigs were processed using Cell Ranger (10X Genomics) using GRCh38 as reference. Antigen barcode libraries were also processed using Cell Ranger (10X Genomics). The overlapping cell barcodes between the two libraries were used as the basis of the subsequent analysis. Cell barcodes were removed that had only non-functional heavy chain sequences as well as cells with multiple functional heavy chain sequences and/or multiple functional light chain sequences, reasoning that these may be multiplets. Additionally, the BCR contigs were aligned (filtered_contigs.fasta file output by Cell Ranger, 10X Genomics) to IMGT reference genes using HighV-Quest. The output of HighV-Quest was parsed using ChangeO and merged with an antigen barcode UMI count matrix. Finally, this study determined the LIBRA-seq score for each antigen in the library for every cell as previously described. Antibody Expression and Purification For each antibody, variable genes were inserted into custom plasmids encoding the constant region for the IgG1 heavy chain as well as respective lambda and kappa light chains (pTwist CMV BetaGlobin WPRE Neo vector, Twist Bioscience). Antibody 54042-2 was natively an IGHG2, but was cloned into an IGHG1 Fc backbone vector for monoclonal antibody characterization. Antibodies were expressed in Expi293F mammalian cells (Thermo Fisher Scientific) by co-transfecting heavy chain and light chain expressing plasmids using polyethylenimine transfection reagent and cultured for 5-7 days. Cells were maintained in FreeStyle F17 expression medium supplemented at final concentrations of 0.1% Pluronic Acid F- 68 and 20% 4mM L-Glutamine. These cells were cultured at 37°C with 8% CO2 saturation and shaking. After transfection and 5-7 days of culture, cell cultures were centrifuged and supernatant was 0.45 μm filtered with Nalgene Rapid Flow Disposable Filter Units with PES membrane. Filtered supernatant was run over a column containing Protein A agarose resin equilibrated with PBS. The column was washed with PBS, and then antibodies were eluted with 100 mM Glycine HCl at 2.7 pH directly into a 1:10 volume of 1M Tris-HCl pH 8.0. Eluted antibodies were buffer exchanged into PBS 3 times using Amicon Ultra centrifugal filter units and concentrated. Antibodies were analyzed by SDS-PAGE. High-throughput Antibody Expression For high-throughput production of recombinant antibodies, approaches were used that are designated as microscale. For antibody expression, microscale transfection were performed (~1 ml per antibody) of CHO cell cultures using the Gibco ExpiCHO Expression System and a protocol for deep 96-well blocks (Thermo Fisher Scientific). In brief, synthesized antibody-encoding DNA (~2 μg per transfection) was added to OptiPro serum free medium (OptiPro SFM), incubated with ExpiFectamine CHO Reagent and added to 800 µl of ExpiCHO cell cultures into 96-deep-well blocks using a ViaFlo 384 liquid handler (Integra Biosciences). The plates were incubated on an orbital shaker at 1,000 r.p.m. with an orbital diameter of 3 mm at 37 °C in 8% CO2. The next day after transfection, ExpiFectamine CHO Enhancer and ExpiCHO Feed reagents (Thermo Fisher Scientific) were added to the cells, followed by 4 d incubation for a total of 5 d at 37 °C in 8% CO2. Culture supernatants were collected after centrifuging the blocks at 450g for 5 min and were stored at 4°C until use. For high-throughput microscale antibody purification, fritted deep-well plates were used containing 25 μl of settled protein G resin (GE Healthcare Life Sciences) per well. Clarified culture supernatants were incubated with protein G resin for antibody capturing, washed with PBS using a 96-well plate manifold base (Qiagen) connected to the vacuum and eluted into 96-well PCR plates using 86 μl of 0.1 M glycine-HCL buffer pH 2.7. After neutralization with 14 μl of 1 M Tris-HCl pH 8.0, purified antibodies were buffer-exchanged into PBS using Zeba Spin Desalting Plates (Thermo Fisher Scientific) and stored at 4°C until use. ELISA To assess antibody binding, soluble protein was plated at 2 μg/ml overnight at 4°C. The next day, plates were washed three times with PBS supplemented with 0.05% Tween-20 (PBS-T) and coated with 5% milk powder in PBS-T. Plates were incubated for one hour at room temperature and then washed three times with PBS-T. Primary antibodies were diluted in 1% milk in PBS-T, starting at 10 μg/ml with a serial 1:5 dilution and then added to the plate. The plates were incubated at room temperature for one hour and then washed three times in PBS-T. The secondary antibody, goat anti-human IgG conjugated to peroxidase, was added at 1:10,000 dilution in 1% milk in PBS-T to the plates, which were incubated for one hour at room temperature. Plates were washed three times with PBS-T and then developed by adding 3,3′,5,5′-tetramethylbenzidine (TMB) substrate to each well. The plates were incubated at room temperature for ten minutes, and then 1N sulfuric acid was added to stop the reaction. Plates were read at 450 nm. The area under the curve (AUC) was calculated using GraphPad Prism 8.0.0. Competition ELISA Competition ELISA was performed as done previously. Briefly, antibodies were biotinylated using NHS-PEG4-biotin (Thermo Fisher Scientific, cat# A39259) according to manufacturer protocol. Following biotinylation, specific binding of biotinylated antibodies was confirmed using ELISA. Wells of 384-well microtiter plates were coated with 1 µg/mL SARS- CoV-2 S HP protein at 4ºC overnight. Plates were washed with PBS-T and blocked for 1 h with blocking buffer (1% BSA in PBS-T). Plates were then washed with PBS-T and unlabeled antibodies were added at a concentration of 10 µg/mL in a total volume of 25 µL blocking buffer and incubated 1 h. Without washing, biotinylated antibodies diluted in blocking buffer were added directly to each well in a volume of 5 µL per well (such that the final concentrations of each biotinylated mAb were equal to the respective EC90 of each mAb), and then incubated for 30 min at ambient temperature. Plates were then washed with PBS-T and incubated for 1 h with HRP- conjugated avidin (Sigma, 25 µL of a 1:3,500 dilution in blocking buffer). Plates were washed with PBS-T and 25 µL TMB substrate was added to each well. After sufficient development, the reactions were quenched by addition 25 µL 1M HCl and absorbance at 450 nm was quantified using a plate reader. After subtracting the background signal, the signal obtained for binding of the biotin-labeled reference mAb in the presence of the unlabeled tested mAb was expressed as a percentage of the binding of the reference antibody in the presence of 10 µg/mL of the anti-dengue mAb DENV 2D22, which served as a no-competition control. Tested antibodies were considered competing if their presence reduced the reference mAb binding to less than 60% of its maximal binding and non-competing if the signal was greater than 30%. Real-time Cell Analysis (RTCA) HT Neutralization Assay Screen To screen for neutralizing activity in the panel of recombinantly expressed antibodies, a high-throughput and quantitative RTCA assay and xCelligence RTCA HT Analyzer (ACEA Biosciences) were used that assesses kinetic changes in cell physiology, including virus-induced cytopathic effect (CPE). Twenty µl of cell culture medium (DMEM supplemented with 2% FBS) was added to each well of a 384-well E-plate using a ViaFlo384 liquid handler (Integra Biosciences) to obtain background reading. Six thousand (6,000) Vero-furin cells in 20 μl of cell culture medium were seeded per well, and the plate was placed on the analyzer. Sensograms were visualized using RTCA HT software version 1.0.1 (ACEA Biosciences). For a screening neutralization assay, equal amounts of virus were mixed with micro-scale purified antibodies in a total volume of 40 μL using DMEM supplemented with 2% FBS as a diluent and incubated for 1 h at 37 °C in 5% CO2. At ∼17–20 h after seeding the cells, the virus–antibody mixtures were added to the cells in 384-well E-plates. Wells containing virus only (in the absence of antibody) and wells containing only Vero cells in medium were included as controls. Plates were measured every 8– 12 h for 48–72 h to assess virus neutralization. Micro-scale antibodies were assessed in four 5- fold dilutions (starting from a 1:20 sample dilution), and their concentrations were not normalized. Neutralization was calculated as the percent of maximal cell index in control wells without virus minus cell index in control (virus-only) wells that exhibited maximal CPE at 40–48 h after applying virus–antibody mixture to the cells. An antibody was classified as fully neutralizing if it completely inhibited SARS-CoV-2-induced CPE at the highest tested concentration, while an antibody was classified as partially neutralizing if it delayed but did not fully prevent CPE at the highest tested concentration. Further, if the CPE curve lies between partial and the virus-only control, those mAbs were designated weak. RTCA Potency Neutralization Screening Assay To determine neutralizing activity of IgG and convalescent serum, real-time cell analysis (RTCA) assay was used on an xCELLigence RTCA MP Analyzer (ACEA Biosciences Inc.) that measures virus-induced cytopathic effect (CPE) (Suryadevara N et al., 2021). Briefly, 50 μL of cell culture medium (DMEM supplemented with 2% FBS) was added to each well of a 96-well E- plate using a ViaFlo384 liquid handler (Integra Biosciences) to obtain background reading. A suspension of 18,000 Vero-E6 cells in 50 μL of cell culture medium was seeded in each well, and the plate was placed on the analyzer. Measurements were taken automatically every 15 min, and the sensograms were visualized using RTCA software version 2.1.0 (ACEA Biosciences Inc). VSV-SARS-CoV-2 (0.01 MOI, ~120 PFU per well) was mixed 1:1 with a dilution of antibody in a total volume of 100 μL using DMEM supplemented with 2% FBS as a diluent and incubated for 1 h at 37°C in 5% CO2. At 16 h after seeding the cells, the virus-antibody mixtures were added in replicates to the cells in 96-well E-plates. Triplicate wells containing virus only (maximal CPE in the absence of antibody) and wells containing only Vero cells in medium (no-CPE wells) were included as controls. Plates were measured continuously (every 15 min) for 48 h to assess virus neutralization. Normalized cellular index (CI) values at the endpoint (48 h after incubation with the virus) were determined using the RTCA software version 2.1.0 (ACEA Biosciences Inc.). Results are expressed as percent neutralization in a presence of respective antibody relative to control wells with no CPE minus CI values from control wells with maximum CPE. RTCA IC50 and NT50 values were determined by nonlinear regression analysis using Prism software. A full dose-response neutralization assay was not performed for antibody 54042-11 due to insufficient quantity at the time of experiment. The NT50 of the donor sample was comparable to previously reported data for other donors for SARS-CoV-2 antibody discovery efforts. Epitope mapping of antibodies by alanine scanning. Epitope mapping was performed essentially as described previously using a SARS-CoV-2 (strain Wuhan-Hu-1) spike protein RBD shotgun mutagenesis mutation library, made using an expression construct for full-length spike protein. 184 residues of the RBD (between spike residues 335 and 526) were mutated individually to alanine, and alanine residues to serine and clones arrayed in 384-well plates, one mutant per well. Antibody binding to each mutant clone was determined, in duplicate, by high-throughput flow cytometry. Each spike protein mutant was transfected into HEK- 293T cells and allowed to express for 22 hrs. Cells were fixed in 4% (v/v) paraformaldehyde (Electron Microscopy Sciences), and permeabilized with 0.1% (w/v) saponin (Sigma-Aldrich) in PBS plus calcium and magnesium (PBS++) before incubation with antibodies diluted in PBS++, 10% normal goat serum (Sigma), and 0.1% saponin. Antibody screening concentrations were determined using an independent immunofluorescence titration curve against cells expressing wild-type spike protein to ensure that signals were within the linear range of detection. Antibodies were detected using 3.75 μg/mL of AlexaFluor488-conjugated secondary antibody (Jackson ImmunoResearch Laboratories) in 10% normal goat serum with 0.1% saponin. Cells were washed three times with PBS++/0.1% saponin followed by two washes in PBS, and mean cellular fluorescence was detected using a high-throughput Intellicyte iQue flow cytometer (Sartorius). Antibody reactivity against each mutant spike protein clone was calculated relative to wild-type spike protein reactivity by subtracting the signal from mock- transfected controls and normalizing to the signal from wild-type S-transfected controls. Mutations within clones were identified as critical to antibody binding if they did not support reactivity of the test antibody, but supported reactivity of other SARS-CoV-2 antibodies. This counter-screen strategy facilitates the exclusion of spike mutants that are locally misfolded or have an expression defect. Plaque reduction neutralization test (PRNT) The virus neutralization with live authentic SARS-CoV-2 virus was performed in the BSL- 3 facility of the Galveston National Laboratory using Vero E6 cells (ATCC CRL-1586) following the standard procedure. Briefly, Vero E6 cells were cultured in 96-well plates (104 cells/well). Next day, 4-fold serial dilutions of antibodies were made using MEM-2% FBS, as to get an initial concentration of 100 µg/ml. Equal volume of diluted antibodies (60 µl) were mixed gently with authentic virus (60 µl containing 200 pfu) and incubated for 1 h at 37°C/5% CO2 atmosphere. The virus-serum mixture (100 µl) was added to cell monolayer in duplicates and incubated for 1 at h 37°C/5% CO2 atmosphere. Later, virus-serum mixture was discarded gently, and cell monolayer was overlaid with 0.6% methylcellulose and incubated for 2 days. The overlay was removed, and the plates were fixed in 4% paraformaldehyde twice following BSL-3 protocol. The plates were stained with 1% crystal violet and virus-induced plaques were counted. The percent neutralization and/or NT50 of antibody was calculated by dividing the plaques counted at each dilution with plaques of virus-only control. For antibodies, the inhibitory concentration at 50% (IC50) values were calculated in GraphPad Prism software by plotting the midway point between the upper and lower plateaus of the neutralization curve among dilutions. The Alpha variant virus incorporates the following substitutions: Del 69-70, 144 Del, E484K, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H. The Beta variant incorporates the following substitutions: 24 Del, 242-243 Del, D80A, D215G, K417N, E484K, N501Y, D614G, H665Y, T1027I. The Delta variant incorporates the following substitutions: T19R, G142D, Del 156-157, R158G, L452R, T478K, D614G, P681R, Del 689-691, D950N; the deletion at positions 689-691 has not been observed in nature, and was identified upon one passage of the virus. The Gamma variant incorporates the following substitutions: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I. BioLayer Interferometry (BLI) Purified 54042-4 IgG was immobilized to AHC sensortips (FortéBio) to a response level of approximately 1.4 nm in a buffer composed of 10 mM HEPES pH 7.5, 150 mM NaCl, 3 mM EDTA, 0.05% Tween 20 and 0.1% (w/v) BSA. Immobilized IgG was then dipped into wells containing four-fold dilutions of SARS-CoV-2 RBD-SD1 ranging in concentration from 100- 1.5625 nM, to measure association. Dissociation was measured by dipping sensortips into wells containing only running buffer. Data were reference subtracted and kinetics were calculated in Octet Data Analysis software v10.0 using a 1:1 binding model. ACE2 Binding Inhibition Assay 96-well plates were coated with 2 μg/mL purified recombinant SARS-CoV-2 at 4°C overnight. The next day, plates were washed three times with PBS supplemented with 0.05% Tween-20 (PBS-T) and coated with 5% milk powder in PBS-T. Plates were incubated for one hour at room temperature and then washed three times with PBS-T. Purified antibodies were diluted in blocking buffer at 10 μg/mL in triplicate, added to the wells, and incubated at room temperature. Without washing, recombinant human ACE2 protein with a mouse Fc tag was added to wells for a final 0.4 μg/mL concentration of ACE2 and incubated for 40 minutes at room temperature. Plates were washed three times with PBS-T, and bound ACE2 was detected using HRP-conjugated anti- mouse Fc antibody and TMB substrate. The plates were incubated at room temperature for ten minutes, and then 1N sulfuric acid was added to stop the reaction. Plates were read at 450 nm. ACE2 binding without antibody served as a control. Experiment was done in biological replicate and technical triplicates. RTCA Neutralization Assay with Known Antibody Escape Mutants A real-time cell analysis assay (RTCA) and xCELLigence RTCA MP Analyzer (ACEA Biosciences Inc.) were used with modification of previously described assays (Gilchuk et al., 2020a; Weisblum et al., 2020, Suryadevara et al.,2021). Fifty (50) μL of cell culture medium (DMEM supplemented with 2% FBS) was added to each well of a 96-well E-plate to obtain a background reading. Eighteen thousand (18,000) Vero E6 cells in 50 μL of cell culture medium were seeded per each well, and plates were placed on the analyzer. Measurements were taken automatically every 15 min and the sensograms were visualized using RTCA software version 2.1.0 (ACEA Biosciences Inc). wtEscape mutant VSV-SARS-CoV-2 or wild-type VSV-SARS- CoV-2 virus (5e3 plaque forming units [PFU] per well, ∼0.3 MOI) was mixed with a saturating neutralizing concentration of individual antibody (5 μg/mL) in a total volume of 100 μL and incubated for 1 h at 37°C. At 16-20 h after seeding the cells, the virus-antibody mixtures were added into 8 to 96 replicate wells of 96-well E-plates with cell monolayers. Wells containing only virus in the absence of antibody and wells containing only Vero E6 cells in medium were included on each plate as controls. Plates were measured continuously (every 15 min) for 72 h. The lack of neutralization for the individual escape mutant viruses from 54042-4 was confirmed by delayed CPE in wells containing antibody while COV2-2381 was used as positive control. EM sample prep and data collection To form the spike-Fab complex, a final concentration of 0.5 mg/mL spike protein and 5X molar excess of Fab were combined in buffer containing 2mM Tris-Cl pH 8.0, 200 mM NaCl, and 0.02% NaN3. The complex was incubated on ice for 30 min before 3 µL of the sample was deposited on Au-3001.2/1.3 grids (UltrAuFoil) that had been plasma cleaned in a Solarus 950 plasma cleaner (Gatan) for 4 minutes using a 4:1 ratio of O2:H2. A force of -4 was used to blot excess liquid for 3 s using a Vitrobot Mark IV (Thermo Fisher) followed by plunge-freezing with liquid ethane. 3,762 micrographs were collected from a single grid using a Titan Krios (Thermo Fisher) equipped with a K3 detector (Gatan) with the stage set at a 30° tilt. SerialEM was used to collect movies at 29,000X nominal magnification with a calibrated pixel size of 0.81 Å/pixel. Additional details about data collection parameters can be found in Table 4. Cryogenic electron microscopy (Cryo-EM) Motion correction, CTF estimation, particle picking, and preliminary 2D classification were performed using cryoSPARC v3.2.0 live processing. The final iteration of 2D class averaging distributed 374,669 particles into 60 classes using an uncertainty factor of 2. From that, 241,732 particles were used to perform an ab inito reconstruction with four classes followed by heterogeneous refinement of those four classes. Particles from the two highest quality classes were used for homogenous refinement of the best volume with applied C3 symmetry. Non-uniform refinement was performed on the resulting volume using per-particle defocus and per-group CTF optimizations applied. To improve the 54042-4 Fab-RBD density, C3 symmetry expansion was performed followed by local refinement using a mask created in ChimeraX that encompassed the entire 54042-4 Fab and RBD. Local refinement was performed using a pose/shift gaussian prior during alignment, 3° standard deviation of prior over rotation and 1 Å standard deviation of prior over shifts. Additionally, maximum alignment resolution was limited to 2.8 Å resolution to avoid over-refining. To improve map quality, the focused refinement volumes were processed using the DeepEMhancer tool via COSMIC science gateway, which included the use of a refinement mask to help define noise while sharpening. An initial model was generated by docking PDBID: 6XKL and a Fab model based on the 54042-4 sequence built using SAbPred ABodyBuilder into map density via ChimeraX. The model was iteratively refined and completed using a combination of Phenix, Coot, and ISOLDE. Details on structure validation and the full cryo-EM processing workflow can be found in Figures 10 and 11. GISAID Mutation Frequency Calculation To evaluate the conservation of 54042-4 epitope residues, the GISAID database was utilized, comprising sequences from 1229459 SARS-CoV-2 variants (as of May 6th, 2021). The spike glycoprotein sequences were extracted and translated, and pairwise sequence alignment with the reference sequence hCoV-19/Wuhan/WIV04/2019 was then performed. After removing incomplete sequences and sequences with alignment errors, the pairwise alignments for the remaining 1,148,887 spike protein sequences were combined to compute the conservation of each residue position using in-house perl scripts. RMSD Calculation Differences in Angle of Antigen Approach for Different Antibodies The SARS-CoV-2 spike receptor binding domain coordinates present in each antibody- antigen complex were aligned in PyMOL (The PyMOL Molecular Graphics System, Version 2.3.5, Schrödinger, LLC.) using an all-atom alignment with 5 cycles of outlier rejection of atom pairs having an RMSD greater than 2. The alignment was performed for RBD residues 329-529 in antibody 54042-4 (PDB ID: TBD chain A), 329-529 in antibody 2-7 (PDB ID: 7LSS chain B), 333-526 in antibody REGN10987 (PDB ID: 6XDG chain A), and 334-527 in antibody LY- COV1404 (PDB ID: 7MMO chain C). This resulted in RMSD values of 0.751 Å between 54042- 4 and REGN10987’s RBDs, 1.044 Å between 54042-4 and antibody 2-7’s RBDs, 0.632 Å between 54042-4 and LY-COV1404’s RBDs, 1.067 Å between REGN10987 and antibody 2-7’s RBDs, and 0.751 Å between LY-COV1404 and antibody 2-7’s RBDs with well-aligned epitope residues. Next the residues comprising the N-termini through the end of framework region 3 were determined for the heavy and light chains of all three antibodies using IMGT Domain Gap Align. Each pair of antibodies was aligned using a pairwise sequence alignment of this region in PyMOL. Finally, the alpha carbon root mean square deviation between antibodies was calculated over this region in the heavy and light chains using residue pairs from the sequence alignment. RMSD values were calculated from 183, 183, and 180 alpha carbon pairs for the 54042-4 vs REGN1087, REGN1087 vs 2-7, and 54042-4 vs 2-7 comparisons respectively. In the examples above, large numbers of antibody sequences were determined (see sequences provided below). The following paired heavy chain and light chain sequences are used herein for methods of treating, preventing, or detecting coronavirus infections. Table 1. Paired heavy and light chains and the CDRs thereof
Figure imgf000059_0001
Table 2. Additional paired heavy and light chains and the CDRs thereof
Figure imgf000060_0001
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Figure imgf000064_0001
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
Figure imgf000076_0001
Figure imgf000077_0001
Figure imgf000078_0001
Figure imgf000079_0001
Figure imgf000080_0001
Figure imgf000081_0001
Figure imgf000082_0001
Figure imgf000083_0001
Figure imgf000084_0001
Figure imgf000085_0001
Figure imgf000086_0001
Table 3. PDB files Used for Epitope Comparisons
Figure imgf000086_0002
Figure imgf000087_0001
Table 4. PDB validation report EM data collection
Figure imgf000087_0002
Figure imgf000088_0001
Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of skill in the art to which the disclosed invention belongs. Publications cited herein and the materials for which they are cited are specifically incorporated by reference. Those skilled in the art will appreciate that numerous changes and modifications can be made to the preferred embodiments of the invention and that such changes and modifications can be made without departing from the spirit of the invention. It is, therefore, intended that the appended claims cover all such equivalent variations as fall within the true spirit and scope of the invention.

Claims

WHAT IS CLAIMED IS: 1. A recombinant antibody, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and/or a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH3 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11188-11196; and CDRL3 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11224-11232.
2. The recombinant antibody of claim 1, wherein CDRH3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11188-11196.
3. The recombinant antibody of claim 1 or claim 2, wherein CDRL3 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11224-11232.
4. The recombinant antibody of any one of claims 1 to 3, wherein: CDRH1 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11170-11178; and/or CDRL1 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11206-11214.
5. The recombinant antibody of any one of claims 1 to 4, wherein CDRH1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11170-11178.
6. The recombinant antibody of any one of claims 1 to 5, wherein CDRL1 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11206-11214.
7. The recombinant antibody of any one of claims 1 to 6, wherein: CDRH2 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11179-11187; and/or CDRL2 comprises an amino acid sequence at least 60% identical to SEQ ID NOs: 11215-11223.
8. The recombinant antibody of any one of claims 1 to 7, wherein CDRH2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11179-11187.
9. The recombinant antibody of any one of claims 1 to 8, wherein CDRL2 comprises at least one amino acid substitution when compared to SEQ ID NOs: 11215-11223.
10. The recombinant antibody of any one of claims 1 to 9, wherein VH comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11161-11169.
11. The recombinant antibody of any one of claims 1 to 10, wherein VL comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 11197-11205.
12. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11170, CDRH2 is SEQ ID NO:11179, CDRH3 is SEQ ID NO:11188, CDRL1 is SEQ ID NO:11206, CDRL2 is SEQ ID NO:11215, and CDRL3 is SEQ ID NO:11224.
13. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11171, CDRH2 is SEQ ID NO:11180, CDRH3 is SEQ ID NO:11189, CDRL1 is SEQ ID NO:11207, CDRL2 is SEQ ID NO:11216, and CDRL3 is SEQ ID NO:11225.
14. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11172, CDRH2 is SEQ ID NO:11181, CDRH3 is SEQ ID NO:11190, CDRL1 is SEQ ID NO:11208, CDRL2 is SEQ ID NO:11217, and CDRL3 is SEQ ID NO:11226.
15. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11173, CDRH2 is SEQ ID NO:11182, CDRH3 is SEQ ID NO:11191, CDRL1 is SEQ ID NO:11209, CDRL2 is SEQ ID NO:11218, and CDRL3 is SEQ ID NO:11227.
16. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11174, CDRH2 is SEQ ID NO:11183, CDRH3 is SEQ ID NO:11192, CDRL1 is SEQ ID NO:11210, CDRL2 is SEQ ID NO:11219, and CDRL3 is SEQ ID NO:11228.
17. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11175, CDRH2 is SEQ ID NO:11184, CDRH3 is SEQ ID NO:11193, CDRL1 is SEQ ID NO:11211, CDRL2 is SEQ ID NO:11220, and CDRL3 is SEQ ID NO:11229.
18. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11176, CDRH2 is SEQ ID NO:11185, CDRH3 is SEQ ID NO:11194, CDRL1 is SEQ ID NO:11212, CDRL2 is SEQ ID NO:11221, and CDRL3 is SEQ ID NO:11230.
19. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11177, CDRH2 is SEQ ID NO:11186, CDRH3 is SEQ ID NO:11195, CDRL1 is SEQ ID NO:11213, CDRL2 is SEQ ID NO:11222, and CDRL3 is SEQ ID NO:11231.
20. The recombinant antibody of any one of claims 1 to 11, wherein the antibody comprises a light chain variable region (VL) that comprises a light chain complementarity determining region (CDRL)1, CDRL2, and CDRL3 and a heavy chain variable region (VH) that comprises a heavy chain complementarity determining region (CDRH)1, CDRH2, and CDRH3, wherein: CDRH1 is SEQ ID NO:11178, CDRH2 is SEQ ID NO:11187, CDRH3 is SEQ ID NO:11196, CDRL1 is SEQ ID NO:11214, CDRL2 is SEQ ID NO:11223, and CDRL3 is SEQ ID NO:11232.
21. A nucleic acid encoding the recombinant antibody of any one of claims 1-20.
22. A recombinant expression cassette or plasmid comprising a sequence to express a recombinant antibody of any one of claims 1-21.
23. A host cell comprising the expression cassette or the plasmid of claim 22.
24. A method of producing an antibody, comprising cultivating or maintaining the host cell of claim 23 under conditions to produce the antibody.
25. A method of treating a coronavirus infection in a subject, comprising administering to the subject a therapeutically effective amount of the recombinant antibody of any one of claims 1-20.
26. The method of claim 25, where the coronavirus is SARS-CoV-2.
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