WO2023240246A1

WO2023240246A1 - Computationally engineered monocolonal antibodies and antigen binding fragments specific for sars-cov-2 spike proteins and uses thereof

Info

Publication number: WO2023240246A1
Application number: PCT/US2023/068215
Authority: WO
Inventors: Zuben SAUNA; Nancy HERNANDEZ; Wojciech JANKOWSKI; Jeffrey Gray; Rahel FRICK; Simon KELOW; Roland Dunbrack
Original assignee: The United States Of America, As Represented By The Secretary, Department Of Health And Human Services; The Johns Hopkins University; Institute For Cancer Research D/B/A The Research Institute Of Fox Chase Cancer Center
Priority date: 2022-06-10
Filing date: 2023-06-09
Publication date: 2023-12-14

Abstract

This disclosure concerns antibodies that are computationally designed and engineered to specifically bind to the spike protein of SARS-CoV-2 strains and variants with high affinity. The disclosure also concerns uses of the antibodies for the detection, prophylaxis, and treatment of SARS-CoV-2 infection.

Description

COMPUTATIONALLY ENGINEERED MONOCOLONAL ANTIBODIES AND ANTIGEN BINDING FRAGMENTS SPECIFIC FOR SARS-COV-2 SPIKE PROTEINS AND USES THEREOF

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 63/351,312, filed June 10, 2022, which is incorporated by reference in its entirety.

FIELD

This disclosure relates to engineered antibodies (e.g., monoclonal antibodies or antigen binding fragments) that specifically bind the spike protein of SARS-CoV-2, and uses thereof.

ACKNOWLEDGMENT OF GOVERNMENT SUPPORT

This invention was made with government support under grant GM078221 awarded by the National Institutes of Health. The government has certain rights in the invention.

INCORPORATION OF SEQUENCE LISTING

The Sequence Listing is submitted as an XML file named “Sequence. xml”, created on June 8, 2023, 110,592 bytes, which is incorporated by reference herein.

BACKGROUND

The novel human infectious disease severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) has become a major threat to global public health. Following the original SARS-CoV-2 strain (WA-1), which initiated the pandemic in the United States and in the rest of the world, a series of new variants of concern (VOCs) have subsequently emerged as the result of viral evolution, including Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). Omicron contains an unprecedented number of mutations and is rapidly spreading worldwide, and new Omicron subvariants are emerging almost regularly.

As with all viral diseases, a vaccine represents the most effective public health measure against this pandemic. Current vaccines and therapies have been shown to be less effective against the new and often more transmissible VOCs. Furthermore, vaccines are not effective on all individuals, and “vaccine hesitancy” has resulted in a significant unvaccinated population. The development of new antibodies that may provide greater effectiveness against SARS-CoV-2 VOCs requires experimental evolution or identification of novel antibodies from people previously infected with the virus. This constraint slows the discovery of new vaccines, for example, that are effective against new and existing SARS-CoV-2 variants. Consequently, despite the availability of vaccines, the USA and other countries continue to suffer through waves of new cases of SARS-CoV-2. SUMMARY

Disclosed herein are antibodies (e.g., monoclonal antibodies or antigen binding fragments, such as human monoclonal antibodies or antigen binding fragments) engineered by a rational computational design method, which specifically bind the spike protein of SARS-CoV-2 with high affinity, for example, to neutralize a SARS-CoV-2 infection in a human subject. Such antibodies are useful, for example, for the detection, diagnosis, and treatment of SARS-CoV-2. The disclosed antibodies and functional fragments may also be useful as a prophylactic treatment, such as for those who are unable or unwilling to receive a SARS-CoV-2 vaccine, or do not elicit a sufficient immune response to such vaccines.

Accordingly, provided herein are monoclonal antibodies and antigen binding fragments that specifically bind a SARS-CoV-2 spike protein, for example, the spike protein of the wild-type strain SARS- CoV-2 (WA-1; referred to herein as WT SARS-CoV-2) and/or the spike protein of a variant of concern (VOC), such as Beta (B.1.351), Delta (B.1.617.2), or Omicron (B.1.1.529). In some aspects, a monoclonal antibody or antigen binding fragment disclosed herein specifically binds to a plurality of SARS-CoV-2 spike proteins; for example, a plurality of any of: the WT SARS-CoV-2 spike protein, the WT S6P SARS-CoV-2 spike protein, the Beta SARS-CoV-2 spike protein, the Beta S6P SARS-CoV-2 spike protein, the Delta SARS-CoV-2 spike protein, and the Omicron SARS-CoV-2 spike protein.

The monoclonal antibodies and antigen binding fragments disclosed herein include a light chain variable domain (VL) and a heavy chain variable domain (VH). In some examples, the VL and the HL include complementarity determining regions (CDRs) of the VL and/or VH identified in any of the computationally designed antibodies referred to herein as: 80R_5, 8OR_18, 80R_19, and 80R_23 (see, e.g., Table 1). In specific examples, the monoclonal antibody or antigen binding fragment disclosed herein include a VL that is at least 90% identical to any of 80R_5 VL (SEQ ID NO: 1), 80R_18 VL (SEQ ID NO: 9), 80R_19 VL (SEQ ID NO: 17), and 80R_23 VL (SEQ ID NO:25), and a VH that is at least 90% identical to any of 80R_5 VH (SEQ ID NO: 2), 80R_18 VH (SEQ ID NO: 10), 80R_19 VH (SEQ ID NO: 18), and 80R_23 VH (SEQ ID NO:26). Further provided are bispecific antibodies or multispecific antibodies that include at least one of the monoclonal antibodies or antigen binding fragments disclosed herein.

Further provided are nucleic acid molecules comprising a polynucleotide that encodes a computationally engineered monoclonal antibody or antigen binding fragment disclosed herein, or a VH and/or VL of a monoclonal antibody or antigen binding fragment disclosed herein. In some aspects, the polynucleotide is designed or optimized in silico, for example, the polynucleotide is codon-optimized for expression in a particular host (for example, a human cell). In various aspects, a nucleic acid molecule disclosed herein includes a promoter. In some examples, a polynucleotide disclosed herein is operably linked to a promoter; for example, a promoter that is capable of controlling expression of the polynucleotide in a host cell (e.g., a human cell). Also provided are vectors that include a nucleic acid molecule disclosed herein, and host cells that include such a vector.

Also provided are compositions including an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody), nucleic acid molecule, or vector disclosed herein; and a pharmaceutically acceptable carrier. In some examples, the composition is a pharmaceutical composition.

Methods for producing a monoclonal antibody or antigen binding fragment that specifically binds to one or more SARS-CoV-2 spike protein are further provided. In some aspects, the method includes expressing at least one polynucleotide encoding a disclosed monoclonal antibody or antigen binding fragment in a host cell; and purifying the monoclonal antibody or antigen binding fragment.

Further provided are methods for detecting the presence of a coronavirus in a biological sample from a subject. In some aspects, the method includes contacting the biological sample with an effective amount of an antibody disclosed herein (e.g., a monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody disclosed herein), under conditions sufficient to form an immune complex of the coronavirus and the antibody; and detecting the presence of the immune complex in the biological sample. The presence of the immune complex in the biological sample indicates the presence of the coronavirus in the sample.

Further provided are methods for inhibiting a coronavirus infection in a subject. In some aspects, the method includes administering an effective amount of a monoclonal antibody, antigen binding fragment, bispecific antibody, multispecific antibody, nucleic acid molecule, vector, or composition disclosed herein to the subject. In some aspects of the provided methods, the coronavirus is a WT SARS-CoV-2 or SARS- CoV-2 variant, (e.g., a VOC). In particular examples, the coronavirus is a WT SARS-CoV-2, a WT SARS- CoV-2 variant with a spike protein including S6P mutations, a Beta SARS-CoV-2, a Beta SARS-CoV-2 variant with a spike protein including S6P mutations, a Delta SARS-CoV-2, or an Omicron SARS-CoV-2 variant.

Further provided are methods for the detection, diagnosis, prevention, inhibition, and/or treatment of SARS-CoV-2 infection that utilize an antibody disclosed herein (e.g., a monoclonal antibody, antigen binding fragment, bispecific or multispecific antibody disclosed herein).

The foregoing and other aspects and features of the disclosure will become more apparent from the following detailed description, which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: A schematic of computational engineering of antibodies and antigen binding fragments that specifically bind SARS-CoV-2 spike proteins. The design process begins with (1) the structure of the 80R antibody single-chain Fv bound to the SARS-CoV-1 receptor binding domain (RBD) (PDB 2GHW). (2) The SARS-CoV-2 RBD (PDM 6M0J) is aligned with the SARS-CoV-1 RBD to produce a complex structure of 80R bound to SARS-CoV-2, and (3) the complex structure is energy minimized to create decoys. (4) The top scoring decoy is selected as an input file for RosettaAntibodyDesign (RAbD), and then (5) renumbered and (6) submitted to a RabD protocol, with various design settings. (7) The 30 top scoring designs were selected for SARS-CoV-2 spike protein binding analysis. FIG. 2: (Left) A model of 80R (a high-affinity, neutralizing recombinant human monoclonal antibody against SARS-CoV-1 that does not cross-react with or neutralize SARS-CoV-2) bound to the SARS-CoV-1 RBD with the extrapolated binding interface. (Right) Surface sequence alignments between SARS-CoV-1 spike protein RBD and the variant SARS-CoV-2 spike protein RBDs from SARS-CoV-2, Delta SARS-CoV-2, Beta S6P SARS-CoV-2, and Omicron SARS-CoV-2. The amino acid differences between SARS-CoV-1 spike protein RBD and the SARS-CoV-2 spike protein RBD are shown in dark gray. Mutations found in the variant SARS-CoV-2 spike protein RBDs are shown in black.

FIG. 3: Sequence logo for designs based on 80R as the template (SEQ ID NO: 100).

FIG. 4: Sequence alignment of VLs of 80R and the top 30 80R-based designs engineered by RabD. Conserved amino acid positions in 80R_5 (SEQ ID NO: 1), 80R_18 (SEQ ID NO: 9), 80R_19 (SEQ ID NO: 17), and 80R_23 (SEQ ID NO: 25) VLs with respect to 80R VL (SEQ ID NO: 45) are indicated with an asterisk. Amino acid differences found in particular designs, 80R_5, 8OR_1 , 80R_19, and 80R_23, are shown in white font on a black background. 80R_l through 80R_4 VLs are SEQ ID NOs: 46-49, respectively. 80R_6 through 80R_17 VLs are SEQ ID NOs: 50-61, respectively. 80R_20 through 80R_22 VLs are SEQ ID NOs: 62-64, respectively. 80R_24 through 8OR_3O VLs are SEQ ID NOs: 65-71, respectively.

FIG. 5: Sequence alignment of VHs of 80R and the top 30 80R -based designs engineered by RabD. Conserved amino acid positions in 80R_5 (SEQ ID NO: 2), 80R_18 (SEQ ID NO: 10), 80R_19 (SEQ ID NO: 18), and 80R_23 (SEQ ID NO: 26) VHs with respect to 80R VH (SEQ ID NO: 72) are indicated with an asterisk. Amino acid differences found in particular designs, 80R_5, 80R_18, 80R_19, and 80R_23, are shown in white font on a black backgound. 80R_l through 80R_4 VHs are SEQ ID NOs: 73-76, respectively. 80R_6 through 80R_17 VHs are SEQ ID NOs: 77-88, respectively. 80R_20 through 80R_22 VHs are SEQ ID NOs: 89-91, respectively. 80R_24 through 8OR_3O VHs are SEQ ID NOs: 92-98, respectively.

FIGs. 6A-6B: Binding curves to SARS-CoV-2 full length spike proteins for 80R (control) and representative 80R antibody designs. (FIG. 6A) Binding curves for 80R (80R_wild-type; negative control), 80R_5, 80R_6, 80R_7, 80R_8, 80R_10, 80R_18, 80R_19, and 80R_23 to WT SARS-CoV-2 full length spike protein. (FIG. 6B) Binding curves for 80R_5, 8OR_18, 80R_19, 80R_23, and 80R (80R_wild-type; negative control) to variant SARS-CoV-2 spike proteins; WT S6P SARS-CoV-2 (“Wuhan S6P”), Beta S6P SARS-CoV-2 (“South African S6P”), and Delta SARS-CoV-2.

FIGs. 7A-7C: Models of VL and VH of selected variant 80R designs bound to the WT SARS- CoV-2 spike protein RBD. (FIG. 7A) VL and VH of 80R_23 bound to WT SARS-CoV-2 spike protein RBD, showing the locations of LCDR1 (LI), LCDR2 (L2), LCDR3 (L3), HCDR1 (Hl), HCDR2 (H2), and HCDR3 (H3), as well as the DE loop framework regions (DE) for reference. (FIG. 7B) VL and VH of 80R_5 bound to WT SARS-CoV-2 spike protein RBD. Residues of the VL and VH CDRs that contact the binding interface of the spike protein are shown in light gray . (FIG. 7C) Amino acid sequences of 80R_5 VL (SEQ ID NO: 1) and HL (SEQ ID NO: 2), and 80R_23 VL (SEQ ID NO: 25) and HL (SEQ ID NO: 26), showing substitutions in the 80R_WT sequence (bold and larger font) and contact residues with SARS-CoV- 2 RED (underlined).

FIG. 8: Models of 80R_5 VL and VH bound to the Omicron SARS-CoV-2 spike protein RBD, the Delta SARS-CoV-2 spike protein RBD, and the Beta S6P SARS-CoV-2 spike protein RBD.

FIG. 9: Model showing mutations in the PDB 2GHW (top figure) containing antibody 80R (light gray) selected through RAbD that form favorable interactions with the SARS-CoV-2 spike protein (gray). Examples of mutations (black sticks) in both VH (left; light gray) and VL (right, light gray) of the 80R antibody, and a favorable electrostatic interaction between SARS-CoV-2 spike protein Q493 and VL T39 (bottom figure).

SEQUENCE LISTING

The amino acid sequences listed herein are shown using standard three letter code for amino acids, as defined in 37 C.F.R. § 1.822.

The amino acid sequences listed define molecules or parts thereof (e.g., proteins and polypeptides) comprising contiguous amino acids arranged in the manner described. The amino acid sequences listed also each define a genus of polynucleotides, each comprising a coding sequence having codons arranged in a manner such that they are expressible in a host cell (for example, a host cell comprised in an organism, or a cultured cell) to produce a protein or polypeptide comprising contiguous amino acids arranged in the manner described by the amino acid sequence. According to the redundancy of the genetic code, it is understood by those in the art that a coding sequence may at least be modified to substitute nucleotides therein without impacting the structure of the encoded polypeptide, often in the third (and sometimes second) position of a codon.

The Sequence Listing is submitted as an XML file in the form of the file named “Sequence.xml” (110,592 bytes), created on June 8, 2023, which is incorporated by reference herein. In the accompanying sequence listing:

SEQ ID NOs: 1 and 2 are the amino acid sequences of the 80R_5 VL and VH, respectively.

SEQ ID NOs: 3-8 are the amino acid sequences of the LCDR1, LCDR2, LCDR3, HCDR1, HCDR2, and HCDR3 of 80R_5 antibody.

SEQ ID NOs: 9 and 10 are the amino acid sequences of the 8OR_18 VL and VH, respectively.

SEQ ID NOs: 11-16 are the amino acid sequences of the LCDR1, LCDR2, LCDR3, HCDR1, HCDR2, and HCDR3 of 8OR_18 antibody.

SEQ ID NOs: 17 and 18 are the amino acid sequences of the 80R_19 VL and VH, respectively.

SEQ ID NOs: 19-24 are the amino acid sequences of the LCDR1, LCDR2, LCDR3, HCDR1, HCDR2, and HCDR3 of 80R_19 antibody.

SEQ ID NOs: 25 and 26 are the amino acid sequences of the 80R_23 VL and VH, respectively.

SEQ ID NOs: 27-32 are the amino acid sequences of the LCDR1, LCDR2, LCDR3, HCDR1, HCDR2, and HCDR3 of 80R_23 antibody. SEQ ID NOs: 33-38 are consensus amino acid sequences for the LCDR1, LCDR2, LCDR3,

HCDR1, HCDR2, and HCDR3 based on the 80R_5, 8OR_18, 80R_19, and 80R_23 antibodies.

SEQ ID NOs: 39-44 are consensus amino acid sequences for the LCDR1, LCDR2, LCDR3,

HCDR1, HCDR2, and HCDR3 based on the 80R_5 and 80R_23 antibodies.

SEQ ID NOs: 45-49 are the amino acid sequences of the 80R VL and 80R_l through 80R_4 VLs, respectively.

SEQ ID NOs: 50-61 are the amino acid sequences of the 80R_6 through 80R_17 VLs, respectively.

SEQ ID NOs: 62-64 are the amino acid sequences of the 80R_20 through 80R_22 VLs, respectively.

SEQ ID NOs: 65-71 are the amino acid sequences of the 80R_24 through 8OR_3O VLs, respectively.

SEQ ID NOs: 72-76 are the amino acid sequences of the 80R VH and 80R_l through 80R_4 VHs, respectively.

SEQ ID NOs: 77-88 are the amino acid sequences of the 80R_6 through 80R_17 VHs, respectively.

SEQ ID NOs: 89-91 are the amino acid sequences of the 80R_20 through 80R_22 VHs, respectively.

SEQ ID NOs: 92-98 are the amino acid sequences of the 80R_24 through 8OR_3O VHs, respectively.

SEQ ID NO: 99 is the amino acid sequence of the 80R H3 loop (HCDR3). ARDRSYYLDY

SEQ ID NO: 100 is the sequence logo of FIG. 3.

SEQ ID NO: 101 is the amino acid sequence of an 80R_5 scFv.

TTLTQSPATLSLSPGERATLSCKASEDIGTALAWYQQKPGQAPRPLIFDGAILAPGIPDRFSGSGSGT

DFTLTISRLEPEDFAVYYCHNVYSWPPTFGQGTKVEVKSEVQLVQSGGGVVQPGKSLRLSCKASGF AFSNYAMHWVRQAPGKGLEWVAVISYDGSYKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT AVYYCARDRSYYLDYWGQGTLVTVSS

SEQ ID NO: 102 is the amino acid sequence of an 80R_18 scFv.

TTLTQSPATLSLSPGERATLSCQASEDIGTNLAWYQQKPGQAPRPLIFDAAQLAPGIPDRFSGSGSGT

QFTLTISRLEPEDFAVYYCQQIYNWPPSFGQGTKVEVKSEVQLVQSGGGVVQPGKSLRLSCVASGF NFSEYAMHWVRQAPGKGLEWVAVISYDGSYKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT AVYYCARDNAYYLDYWGQGTLVTVSS

SEQ ID NO: 103 is the amino acid sequence of an 80R_19 scFv.

TTLTQSPATLSLSPGERATLSCHASEDIGTNLAWYQQKPGQAPRPLIFDAAQLAPGIPDRFSGSGSGT

DFTLTISRLEPEDFAVYYCMQIHNWPPSFGQGTKVEVKSEVQLVQSGGGVVQPGKSLRLSCVASGF DFKSYAMHWVRQAPGKGLEWVAVISYDGSYKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT AVYYCARDNAYYLDYWGQGTLVTVSS

SEQ ID NO: 104 is the amino acid sequence of an 80R_23 scFv.

TTLTQSPATLSLSPGERATLSCHASEDIGTNLAWYQQKPGQAPRPLIFDGAQLAPGIPDRFSGSGSGT

DFTLTISRLEPEDFAVYYCQQIYNWPPSFGQGTKVEVKSEVQLVQSGGGVVQPGKSLRLSCVASGF DFKSYAMHWVRQAPGKGLEWVAVISYDGSYKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT AVYYCARDNAYYLDYWGQGTLVTVSS DETAILED DESCRIPTION

I. Overview

There is a clear, unmet global need for the development of therapeutics to combat SARS-CoV-2 that can be generalizable to current SARS-CoV-2 variants, and may also be expected to be generalizable to future VOCs. Current monoclonal antibody therapies and vaccines have been shown to be less effective against SARS-CoV-2 variants than against WT SARS-CoV-2 (WA-1). Given the scope and severity of the SARS-CoV-2 pandemic, antibodies useful for diagnosing, preventing, and treating infections by multiple SARS-CoV-2 strains, and which may be rapidly deployed to combat SARS-CoV-2 variants that emerge in the future, are needed. The monoclonal antibodies and antigen binding fragments described herein are either generalizable or specific against a wide range of SARS-CoV-2 viruses (for example, WT SARS-CoV-2 S6P, Delta (B.1.617.2), Beta (B.1.351), Beta S6P, and Omicron (B.1.1.529)), with binding affinities in the nM range. The structural information contained within the genus of these monoclonal antibodies and antigen binding fragments constitutes a computational design platform based around binding requirements for SARS-CoV-2 RBD-antibody binding that requires no experimental evolution or in situ isolation to engineer antibodies that are effective against new and existing SARS-CoV-2 variants.

II. Abbreviations

ACE2 angiotensin converting enzyme 2

CDR complementarity determining region

CoV coronavirus

COVID-19 coronavirus disease 2019

FSC Fourier shell correlation

PDB Protein Data Bank

RAbD RosettaAntibodyDesign

RBD receptor binding domain

S spike protein

SARS severe acute respiratory syndrome

VH variable region of the heavy chain

VL variable region of the light chain

VOC variant of concern

III. Summary of Terms

Unless otherwise noted, technical terms are used according to conventional usage in the relevant field. Definitions of many common terms in molecular biology may be found in Krebs et al. (eds.), Lewin’s genes XII, published by Jones & Bartlett Learning, 2017. As used herein, the singular forms “a,” “an,” and “the,” refer to both the singular as well as plural, unless the context clearly indicates otherwise. For example, the term “an antigen” includes singular or plural antigens, and can be considered equivalent to the phrase “at least one antigen.” As used herein, the term “comprises” means “includes.” It is further understood that all values, such as molecular weight or molecular mass, are approximate and provided for descriptive purposes, unless otherwise indicated. Although many methods and materials similar or equivalent to those described herein can be used, particular suitable methods and materials are described herein. The materials, methods, and examples disclosed herein are illustrative only and non-limiting.

In case of conflict, the present specification, including the following definitions of terms, will control. To facilitate review of the various aspects, the following explanations of terms are provided:

About: Unless context indicated otherwise, “about” refers to plus or minus 5% of a reference value. For example, “about” 100 refers to 95 to 105.

Administration: The introduction of an agent, such as a disclosed antibody (e.g., a monoclonal antibody, antigen binding fragment, or multispecific antibody disclosed herein) or composition, into a subject by a chosen route. Administration can be local or systemic. For example, if the chosen route is intravascular, the agent (e.g., an antibody or composition disclosed herein) is administered by introducing the composition into a blood vessel of the subject. Exemplary routes of administration include, but are not limited to, oral, injection (e.g., subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), sublingual, rectal, transdermal (e.g., topical), intranasal, vaginal, and inhalation routes.

Amino Acid Substitution: The replacement of one amino acid in a polypeptide with a different amino acid.

Antibody: An immunoglobulin, or a derivative thereof (e.g., antigen binding fragment), that specifically binds and recognizes an analyte (antigen) such as a coronavirus spike protein, such as a spike protein from SARS-CoV-2. The unmodified term “antibody” is used herein in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, antigen binding fragments, bispecific antibodies, multispecific antibodies, and polyclonal antibodies, so long as they exhibit the desired antigen binding activity, such as binding affinity for a coronavirus spike protein (e.g., a spike protein from SARS-CoV-2).

Antigen binding fragments include those produced by the modification of whole antibodies, and those synthesized de novo using recombinant DNA methodologies (see, e.g., Kontermann and Diibel (Eds.), Antibody Engineering, Vols. 1-2, 2^nd ed., Springer- Verlag, 2010). Examples of antigen binding fragments include, but are not limited to:.

(1) Fab, a fragment that contains a monovalent antigen binding fragment, as can typically be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;

(2) Fab', a fragment as can be obtained by digestion whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain;

(3) (Fab')z, a dimer of two Fab' fragments held together by two disulfide bonds;

(4) Fv, a genetically engineered fragment containing the VH and VL expressed as two chains; (5) scFv, a genetically engineered fragment containing the VH and the VL in either possible intramolecular orientation (VH domain-linker-VL domain, or VL do main-linker- VH domain) linked by a suitable polypeptide linker (see, e.g., Ahmad et al., Clin. Dev. Immunol., 2012, doi: 10.1155/2012/980250; Marbry and Snavely, IDrugs, 13(8):543-549, 2010); and

(6) SCFV2 (also referred to as a “miniantibody”), a dimer of a scFv.

Antigen binding fragments also include Fab'-SH, diabodies, linear antibodies, and single-chain antibody molecules (e.g. scFv). Antibodies include genetically engineered forms, for example, chimeric antibodies (e.g., humanized antibodies) and heteroconjugate antibodies (e.g., bispecific antibodies).

An antibody may have one or more binding sites. If there is more than one binding site, the binding sites may be identical to one another or may be different. For instance, a naturally -occurring immunoglobulin has two identical binding sites, a single-chain antibody or Fab fragment has one binding site. A bispecific or bifunctional antibody is an engineered antibody that has two different binding sites (e.g., binds two epitopes of a coronavirus spike protein). A multispecific antibody is an engineered antibody that has a plurality of binding sites and binds two or more epitopes (e.g., two or more epitopes of a coronavirus spike protein).

Typically, a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. Each heavy and light chain contains a constant region (or constant domain) and a variable region (or variable domain). In combination, the heavy and the light chain variable regions specifically bind the antigen. Mammalian immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable domain genes. There are two types of light chain, lambda (X) and kappa (K), and there are five main heavy chain classes (or isotypes): IgM, IgD, IgG, IgA, and IgE.

References to “VH” or “VH” refer to the variable region of an antibody heavy chain, including that of an antigen binding fragment, such as, for example, Fv, scFv, dsFv, and Fab. References to “VL” or “VL” refer to the variable domain of an antibody light chain or antigen binding fragment.

The VH and VL contain a “framework” region interrupted by three hypervariable regions, also called “complementarity -determining regions” or “CDRs” (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, 5^th ed., NIH Publication No. 91-3242, Public Health Service, National Institutes of Health, U.S. Department of Health and Human Services, 1991). The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.

The CDRs are primarily responsible for binding to an epitope of an antigen. The amino acid sequence boundaries of a given CDR can be readily determined using any of a number of well-known schemes, including those described by Kabat et al. (Sequences of Proteins of Immunological Interest, 5^th ed., NIH Publication No. 91-3242, Public Health Service, National Institutes of Health, U.S. Department of Health and Human Services, 1991; “Kabat” numbering scheme), Al-Lazikani et al., (“Standard conformations for the canonical structures of immunoglobulins,” J. Mol. Bio., 273(4):927-948, 1997; “Chothia” numbering scheme), and Lefranc et al. (“IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains,” Dev. Comp. Immunol., K,i .55-1~l , 2003; “IMGT” numbering scheme). The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3 (from the N-terminus to C-terminus), and are also typically identified by the chain in which the particular CDR is located. Thus, a VH CDR3 is the CDR3 from the VH of the antibody (e.g., monoclonal antibody or antigen binding fragment) in which it is found, whereas a VL CDR1 is the CDR1 from the VL of the antibody (e.g., monoclonal antibody or antigen binding fragment) in which it is found. Light chain CDRs are sometimes referred to as LCDR1, LCDR2, and LCDR3. Heavy chain CDRs are sometimes referred to as HCDR1, HCDR2, and HCDR3.

Aspects herein include monoclonal antibodies and antigen binding fragments, where the term indicates high affinity binding (for example, binding with a KD less than about 10 nM) to SARS-CoV-2 spike proteins from more than one SARS-CoV-2 strain (e.g., spike proteins from WT SARS-CoV-2, Beta SARS-CoV-2, Delta SARS-CoV-2, Omicron SARS-CoV-2, and further variants of the foregoing comprising S6P mutations).

In some aspects, a disclosed antibody may comprise a constant domain that includes one or more modifications (such as the “LS” mutation) to increase half-life.

A “monoclonal antibody” is an antibody obtained from a population of substantially homogeneous antibodies, that is, the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, for example, containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. Thus, the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies disclosed herein may be made by a variety of techniques, including but not limited to the hybridoma method, recombinant DNA methods, phage-display methods, and methods utilizing transgenic animals containing all or part of the human immunoglobulin loci, such methods and other exemplary methods for making monoclonal antibodies being described herein. Monoclonal antibodies can have conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions (See, for example, Greenfield (Ed.), Antibodies: A Laboratory Manual, 2^nd ed. New York: Cold Spring Harbor Laboratory Press, 2014).

A “humanized” antibody (e.g., monoclonal antibody or antigen binding fragment) includes a human framework region and one or more CDRs from a computationally designed antibody; for example, 80R_5, 8OR_18, 80R_19, and 80R_23. The human antibody providing the framework is termed an “acceptor.” Human antibodies can be identified and isolated using technologies for creating antibodies based on sequences derived from the human genome, for example by phage display or using transgenic animals (see, e.g., Barbas et ah Phage display: A Laboratory Manuel. 1^st Ed. New York: Cold Spring Harbor Laboratory Press, 2004. Print.; Lonberg, Nat. Biotech., 23: 1117-1125, 2005; Lonenberg, Curr. Opin. Immunol., 20:450-459, 2008). In one aspect, all the CDRs of a humanized antibody are from 80R_5, 8OR_18, 80R_19, and/or 80R_23, and the acceptor is 80R. Constant regions need not be present, but if they are, they can be substantially identical to human immunoglobulin constant regions, such as at least about 85- 90%, such as about 95%, or more identical. Hence, all parts of a humanized antibody, except possibly the CDRs, are substantially identical to corresponding parts of natural human antibody sequences.

A “chimeric antibody” is an antibody which includes sequences derived from two different antibodies. In one aspect, a chimeric antibody includes (1) one or more CDRs taken from 80R_5 VL, 8OR_18 VL, 80R_19 VL, 80R_23 VL, 80R_5 VH, 80R_18 VH, 80R_19 VH, and/or 80R_23 VH, (see, e.g., Table 1) and (2) constant region amino acid sequences derived from, for example and without limitation, mice, hamsters, rabbits, and non-human primates. In some examples, a chimeric antibody includes CDRs from a computationally designed antibody, and framework regions from a mouse antibody.

Antibody that Neutralizes SARS-CoV-2: An antibody (e.g., a monoclonal antibody or antigen binding fragment) that specifically binds to a SARS-CoV-2 antigen (such as the spike protein) in such a way as to inhibit a biological function associated with SARS-CoV-2 that inhibits infection. The antibody (e.g., a monoclonal antibody or antigen binding fragment) can thereby neutralize the activity of SARS-CoV-2. Lor example, an antibody that neutralizes SARS-CoV-2 may interfere with the virus by binding it directly and limiting entry into cells. Alternately, an antibody (e.g., a monoclonal antibody or antigen binding fragment) may interfere with one or more post-attachment interactions of the virus with its receptor (ACE2), for example, by interfering with viral entry using the receptor. In some examples, a disclosed bispecific or multispecific antibody that is specific for the WT SARS-CoV-2 spike protein and the spike protein of one or more SARS-CoV-2 variants neutralizes and inhibits SARS-CoV-2 infection.

In some aspects, an antibody (e.g., a monoclonal antibody or antigen binding fragment) that specifically binds to SARS-CoV-2 and neutralizes SARS-CoV-2 inhibits infection of cells, for example, by at least 50% compared to a control.

A “broadly neutralizing” antibody (e.g., a monoclonal antibody or antigen binding fragment) binds to and inhibits the function of related antigens, such as antigens that share at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity. With regard to an antigen from a pathogen, such as a virus, the antibody can bind to and inhibit the function of an antigen from more than one class and/or subclass of the pathogen. Bor example, with regard to a SARS-CoV-2, the antibody (e.g., a monoclonal antibody or antigen binding fragment) can bind to and inhibit the function of an antigen thereof, such as the spike protein from WT SARS-CoV-2 and one or more SARS-CoV-2 variant.

Binding Affinity: Affinity of an antibody for an antigen. In one aspect, affinity is calculated by a modification of the Scatchard method described by Erankel et al., Mol. Immunol., 16:101-106, 1979. In another aspect, binding affinity is measured by an antigen/antibody dissociation rate. In another aspect, a high binding affinity is measured by a competition radioimmunoassay. In another aspect, binding affinity is measured by ELISA. In some aspects, binding affinity is measured using an optical biosensing technology, such as bio-layer interferometry (BLI). In other aspects, binding affinity is measured using surface plasmon resonance assays. In still other aspects, antibody affinity is measured by flow cytometry or by surface plasmon reference. An antibody that “specifically binds” an antigen (such as a coronavirus spike protein) is an antibody that binds the antigen with high affinity (for example, with a KD less than about 10 nM, less than about 5 nM, less than about 1 nM, less than about 0.5 nM, less than about 0.1 nM, less than about 0.05 nM, and less than about 0.01 nM), and does not significantly bind other unrelated antigens with high affinity.

Biological Sample: A sample obtained from a subject. Biological samples include all clinical samples useful for detection of disease or infection in subjects, including, but not limited to, sputum, saliva, mucus, nasal wash, peripheral blood, tissue, cells, urine, tissue biopsy (e.g., lung biopsy), fine needle aspirate, surgical specimen, feces, cerebral spinal fluid (CSF), bronchoalveolar lavage (BAL) fluid, nasopharyngeal samples, oropharyngeal samples, and autopsy material. Biopsied or surgically removed tissue samples can be unfixed, frozen, or fixed in formalin or paraffin. In a particular example, a biological sample is obtained from a subject having or suspected of having a SARS-CoV-2 infection.

Bispecific Antibody: A recombinant molecule composed of two different antigen binding domains that consequently binds to two different antigenic epitopes. Bispecific antibodies include chemically or genetically linked molecules of two antigen binding domains. The antigen binding domains can be linked using a linker. The antigen binding domains can be monoclonal antibodies, antigen binding fragments (e.g., Fab, scFv), or combinations thereof. A bispecific antibody can include one or more constant domains, but does not necessarily include a constant domain.

Conditions Sufficient to Form an Immune Complex: Conditions which allow an antibody (e.g., a monoclonal antibody or antigen binding fragment) to bind to its cognate epitope to a detectably greater degree than (for example, to the substantial exclusion of) binding to substantially all other epitopes. Conditions sufficient to form an immune complex are dependent upon the format of the binding reaction and typically are those utilized in immunoassay protocols or those conditions encountered in vivo. See, Greenfield (Ed.), Antibodies: A Laboratory Manual, 2^nd ed. New York: Cold Spring Harbor Laboratory Press, 2014, for a description of immunoassay formats and examples of conditions sufficient to form an immune complex. The conditions employed in the methods are “physiological conditions,” which references conditions (e.g., temperature, osmolarity, and pH) that are typical inside a living mammal or a mammalian cell. While it is recognized that some organs are subject to extreme conditions, the intra- organismal and intracellular environment normally lies around pH 7 (e.g., from pH 6.0 to pH 8.0, more typically pH 6.5 to 7.5), contains water as the predominant solvent, and exists at a temperature above 0 °C and below 50 °C. Osmolarity is within the range that is supportive of cell viability and proliferation.

The formation of an immune complex can be detected through any of a variety of conventional methods, for example, immunohistochemistry (IHC), immunoprecipitation (IP), flow cytometry, biolayer interferometry (BLI), immunofluorescence microscopy, ELISA, immunoblotting (for example, Western blot), magnetic resonance imaging (MRI), computed tomography (CT) scans, radiography, and affinity chromatography .

Conjugate: A complex of two molecules linked together, for example, by a covalent bond. In some aspects, a conjugate comprises an antibody linked to an effector molecule. For example, a conjugate in particular aspects is a complex of an antibody (e.g., a monoclonal antibody or antigen binding fragment) that binds with high-affinity to SARS-CoV-2 spike proteins, covalently linked to an effector molecule (e.g., a detectable label). The linkage can be by chemical or recombinant means. In one aspect, the linkage is chemical, wherein a reaction between the antibody moiety and the effector molecule has produced a covalent bond formed between the two molecules to form one molecule. A peptide linker (short peptide sequence) can optionally be included between the antibody and the effector molecule. Because conjugates can be prepared from two molecules with separate functionalities, for example, an antibody and an effector molecule, they are also sometimes referred to as “chimeric molecules.”

Conservative Substitution/Variation: “Conservative” amino acid substitutions include those substitutions where an amino acid residue is substituted for another amino acid in the same class. A nonconservative amino acid substitution is one where the residues do not fall into the same class, for example, substitution of a basic amino acid for a neutral or non-polar amino acid. In most cases, a single amino acid is considered to be a member of more than one class. Classes of amino acids that may be defined for the purpose of performing a conservative substitution are known in the art. Conservative amino acid substitutions either do not substantially affect or decrease a function of a protein (such as the ability of an antibody variable domain to interact with a target antigen), or alter the function of a protein in a desired way (for example, to change the binding specificity of an antibody variable domain between viral variants). In introducing a conservative substitution for such an amino acid, structural information regarding the chemical environment of the amino acid in its polypeptide context when the polypeptide is in its desired conformation (for example, the environment of a CDR amino acid in an antigen binding fragment bound to the RBD of a SARS-CoV-2 spike protein) can be used to select among alternative substitute amino acid; for example, so as to avoid steric hinderance, or introduce or maintain favorable hydrophobic and/or electrostatic interactions.

The following seven example classes include amino acids that are considered conservative substitutions for one another:

1) Aliphatic amino acids: Gly, Ala, Pro, He, Leu, Vai, and Met;

2) Aromatic amino acids: His, Phe, Trp, and Tyr;

3) Hydrophobic amino acids: Ala, Vai, He, Leu, Met, Phe, Tyr, and Trp;

4) Polar amino acids: Ser, Thr, Asn, Gin, Cys, Gly, Pro, Arg, His, Lys, Asp, and Glu

5) Electrically neutral amino acids: Gly, Ser, Thr, Cys, Asn, Gin, and Tyr;

6) Non-polar amino acids: Ala, Vai, Leu, He, Phe, Trp, Pro, and Met;

The selection of a conservative substitution is often made to maximize the number of the foregoing classes to which the first and second amino acids both belong. Thus, if the first amino acid is Ser (a polar, non-aromatic, and electrically neutral amino acid), the second amino acid may be another polar amino acid (e.g., Thr, Asn, Gin, Cys, Gly, Pro, Arg, His, Lys, Asp, and Glu); another non-aromatic amino acid (e.g., Thr, Asn, Gin, Cys, Gly, Pro, Arg, His, Lys, Asp, Glu, Ala, He, Leu, Vai, and Met); or another electrically- neutral amino acid (e.g., Gly, Thr, Cys, Asn, Gin, and Tyr). However, it may be preferred that the second amino acid in this case be one of Thr, Asn, Gin, Cys, and Gly, because these amino acids share all the classifications according to polarity, non-aromaticity, and electrical neutrality. Additional criteria that may optionally be used to select a particular second amino acid to be used in a conservative substitution are known in the art. For example, when Thr, Asn, Gin, Cys, and Gly are available to be used in a conservative substitution for Ser, Cys may be eliminated from selection in order to avoid the formation of undesirable cross-linkages and/or disulfide bonds. Likewise, Gly may be eliminate from selection because it lacks an alkyl side chain. In this case, Thr may be selected, e.g., in order to retain the functionality of a side chain hydroxyl group.

Selecting an amino acid for a conservative substitution can be performed by myriad techniques available in the art; for example, scanning mutagenesis, experimental evolution, modeling, and inspection). In aspects disclosed herein, variable regions of the SARS-CoV-1 -specific antibody 80R, which does not specifically bind SARS-CoV-2 spike protein, is used as a template sequence for introduction of conservative substitutions that confer desired binding specificity towards SARS-CoV-2 spike proteins. The combination of detailed structural information regarding binding of 80R to SARS-CoV-1 and the results disclosed herein for different combinations of energy-minimized substituted 80R VL and VH designs allow the rational identification of functionally equivalent and desirably modified antibodies and antigen binding fragments derived from the specific examples herein.

In some aspects disclosed herein, an antibody (e.g., a monoclonal antibody or antigen binding fragment) against a SARS-CoV-2 epitope includes less than or equal to any of 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, and 1 substitutions compared to a reference antibody sequence, and retains specific binding activity for spike protein binding, and/or SARS-CoV-2 neutralization activity. In some examples, a monoclonal antibody or antigen binding fragment disclosed herein includes less than 20 conservative substitutions, such as less than 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 conservative substitutions. In particular examples, the foregoing substitutions are introduced in one or more variable region of the monoclonal antibody or antigen binding fragment disclosed herein, for example, in the CDRs of the variable region(s). The term conservative variation also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid. Accordingly, in particular aspects, individual substitutions, deletions, or additions that alter, add, or delete a single amino acid or a small percentage of amino acids (for example, less than 10%, less than 5%, and less than 1%) in an encoded sequence are conservative variations.

Contacting: Placement in direct physical association; including both in solid and liquid form, which can take place either in vivo or in vitro. Contacting includes contact between one molecule and another molecule, for example the amino acid on the surface of one polypeptide, such as an antigen, that contacts another polypeptide, such as an antibody. Contacting can also include contacting a cell for example by placing an antibody in direct physical association with a cell.

Control: A reference standard. A control can be a negative control, such as sample obtained from a healthy patient not infected with a coronavirus. A control can be a positive control, such as a tissue sample obtained from a patient diagnosed with a coronavirus infection. In some examples, the control is a historical control or standard reference value or range of values (such as a previously tested control sample, such as a group of patients with known prognosis or outcome, or group of samples that represent baseline or normal values).

A difference between a test sample and a control can be an increase or conversely a decrease. The difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference. In some examples, a difference is an increase or decrease, relative to a control, of at least about 5%, such as 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 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, or at least about 500%.

Coronavirus: A family of positive-sense, single-stranded RNA viruses that are known to cause severe respiratory illness. Viruses from the coronavirus family that are currently known to infect humans from the alphacoronavirus and betacoronavirus genera. Additionally, it is believed that the gammacoronavirus and deltacoronavirus genera may infect humans in the future.

Non-limiting examples of betacoronaviruses include SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV or SARS- CoV-1), human coronavirus HKU1 (HKUl-CoV), human coronavirus OC43 (OC43-CoV), murine hepatitis virus (MHV-CoV), bat SARS-like coronavirus WIV1 (WIVl-CoV), and human coronavirus HKU9 (HKU9- CoV). Non-limiting examples of alphacoronaviruses include human coronavirus 229E (229E-CoV), human coronavirus NL63 (NL63-CoV), porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV). A non-limiting example of a deltacoronaviruses is the swine delta coronavirus (SDCV).

The viral genome is capped, polyadenylated, and covered with nucleocapsid proteins. The coronavirus virion includes a viral envelope containing type I fusion glycoproteins referred to as the spike (S) protein. Most coronaviruses have a common genome organization with the replicase gene.

CO VID- 19: The disease caused by the coronavirus SARS-CoV-2.

Detectable Marker: A detectable molecule (also known as a label) that is conjugated directly or indirectly to a second molecule, such as an antibody (e.g., a monoclonal antibody or antigen binding fragment), to facilitate detection of the second molecule. For example, the detectable marker can be capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy, or diagnostic imaging techniques (for example, CT scans, MRIs, ultrasound, fiberoptic examination, and laparoscopic examination). Specific, non-limiting examples of detectable markers include fluorophores, chemiluminescent agents, enzymatic linkages, radioactive isotopes, and heavy metals or compounds (for example super paramagnetic iron oxide nanocrystals for detection by MRI). Methods for using detectable markers and guidance in the choice of detectable markers appropriate for various purposes are discussed for example in Green and Sambrook (Molecular Cloning: A Laboratory Manual, 4^th ed., New York: Cold Spring Harbor Laboratory Press, 2012) and Ausubel et al. (Eds.) (Current Protocols in Molecular Biology, New York: John Wiley and Sons, including supplements, 2017).

Detect or Detecting: To identify the existence, presence, or fact of something.

Dual Variable Domain (DVD) Immunoglobulin: A bispecific antibody that includes two heavy chain variable domains and two light chain variable domains. Unlike IgG, however, both heavy and light chains of a DVD-immunoglobulin molecule contain an additional variable domain (VD) connected via a linker sequence at the N-termini of the VH and VL of an existing monoclonal antibody (mAh). Thus, when the heavy and the light chains combine, the resulting DVD-immunoglobulin molecule contains four antigen recognition sites (see Jakob et al., Mabs 5: 358-363, 2013; see FIG. 1 of Jaakob et al. for schematic and space-filling diagrams). A DVD-Ig™ molecule functions to bind two different antigens on each DFab simultaneously.

Effective Amount: A quantity of a specific substance sufficient to achieve a desired effect in a subject to whom the substance is administered. For instance, this can be the amount necessary to inhibit a coronavirus infection, such as a SARS-CoV-2 infection, or to measurably alter outward symptoms of such an infection. In some examples, the desired effect is to detect, inhibit, reduce, or prevent SARS-CoV-2 infection. The SARS-CoV-2 infection does not need to be detected with perfect accuracy, or be completely inhibited, reduced, or prevented, for the method to be effective.

In some aspects, administration of an effective amount of a disclosed antibody (e.g., a monoclonal antibody or antigen binding fragment) that binds to a coronavirus spike protein reduces or inhibits a SARS- CoV-2 infection (for example, as measured by infection of cells, by number or percentage of subjects infected by the coronavirus, by an increase in the survival time of infected subjects, and/or by reduction in symptoms associated with the infection) by a desired amount, for example by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even about 100% (100% reduction or inhibition signifies elimination or prevention of detectable infection), as compared to a suitable control.

The effective amount of an antibody (e.g., monoclonal antibody or antigen binding fragment) that specifically binds the coronavirus spike protein that is administered to a subject to inhibit infection will vary depending upon a number of factors associated with that subject, for example the overall health and/or weight of the subject. An effective amount can be determined by varying the dosage and measuring the resulting response, such as, for example, a reduction in pathogen titer. Effective amounts also can be determined through various in vitro, in vivo, or in situ immunoassays.

An effective amount encompasses a fractional dose that contributes, in combination with any previous or subsequent administrations, to attaining an effective response. For example, an effective amount of an agent can be administered in a single dose, or in several doses, for example daily, during a course of treatment lasting several days or weeks. However, the effective amount can depend on the subject being treated, the severity and type of the condition being treated, and the manner of administration. A unit dosage form of the agent can be packaged in an amount, or in multiples of the effective amount, for example, in a vial (e.g., with a pierceable lid) or syringe having sterile components.

Effector Molecule: A molecule intended to have or produce a desired effect; for example, a desired effect on a cell to which the effector molecule is targeted, or a detectable marker. Effector molecules include, for example and without limitation, polypeptides and small molecules. Some effector molecules have or produce more than one desired effect.

Epitope: An antigenic determinant. These are particular chemical groups or peptides of a molecule that are antigenic, such that they elicit a specific immune response; for example, an epitope is the region of an antigen to which B and/or T cells respond. An antibody (e.g., a monoclonal antibody or antigen binding fragment) can bind to a particular antigenic epitope, such as an epitope on a coronavirus spike protein.

Expression: Transcription or translation of a nucleotide sequence. For example, a coding polynucleotide (such as a gene) can be expressed when it is transcribed into RNA or an RNA fragment, which in some examples is processed to become mRNA. An mRNA molecule “expressed” when its coding polyribonucleotide is translated into a polypeptide, such as a protein or a protein fragment. Tn a particular example, a heterologous gene is expressed when it is transcribed into an RNA. In another example, a heterologous gene is expressed when its RNA is translated into an amino acid sequence. Regulation of expression can include controls on transcription, translation, RNA transport and/or processing, degradation of intermediary molecules (e.g., mRNA), or through activation, inactivation, compartmentalization, or degradation of specific polypeptides after they are produced.

Expression Control Sequence: A nucleotide sequence that regulates the expression of a coding polynucleotide to which it is operatively linked. An expression control sequence is operatively linked to a polynucleotide when the expression control sequence initiates and/or regulates the transcription or, in some examples, translation of the polynucleotide to produce a polypeptide encoded thereby. Thus, expression control sequences can include appropriate promoters, enhancers, transcriptional terminators, a start codon (ATG) in front of a protein-encoding gene, splice signals for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The term “control sequence” includes components whose presence can influence expression, and additional components whose presence may be advantageous in specific applications; for example, leader sequences and fusion partner sequences. Some aspects of the disclosure utilize a promoter as an expression control sequence, wherein the promoter is operable (i.e., it functions to regulate expression) in a host cell, including a nucleic acid molecule comprising the promoter and an operably linked coding polynucleotide, or into which such a nucleic acid molecule is to be introduced.

Expression Vector: A vector comprising expression control sequences operatively linked to a polynucleotide to be expressed. An expression vector comprises sufficient cis- acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Non-limiting examples of expression vectors include cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the polynucleotide to be expressed.

A polynucleotide can be inserted into an expression vector that contains a promoter sequence that facilitates the efficient transcription of the inserted polynucleotide in a host cell. The expression vector typically contains an origin of replication, a promoter, as well as specific elements that allow phenotypic selection of the transformed cells.

Fc Region: The constant region of an antibody, excluding the first heavy chain constant domain. “Fc region” generally refers to the last two heavy chain constant domains of IgA, IgD, and IgG, and the last three heavy chain constant domains of IgE and IgM. An Fc region may also include part or all of the flexible hinge N-terminal to these domains. For IgA and IgM, an Fc region may or may not include the tailpiece, and may or may not be bound by the J chain. For IgG, the Fc region is typically understood to include immunoglobulin domains Cy2 and Cy3 and optionally the lower part of the hinge between Cyl and Cy2. Although the boundaries of the Fc region may vary, the human IgG heavy chain Fc region is usually defined to include residues following C226 or P230 to the Fc carboxyl-terminus, wherein the numbering is according to Kabat. For IgA, the Fc region includes immunoglobulin domains Ca2 and Ca3 and optionally the lower part of the hinge between Cal and Ca2.

Fusion Protein: A protein comprising at least a portion of two different (heterologous) proteins.

Heterologous: The term “heterologous,” as applied to polynucleotides and polypeptides herein, means of different origin. As used herein, a heterologous polypeptide or nucleic acid molecule is not naturally occurring. For example, if a host cell is transformed with a polynucleotide that does not occur in the untransformed host cell in nature, then that polynucleotide is heterologous to the host cell. Furthermore, different elements (e.g., promoters, enhancers, coding polynucleotides, and terminators) of a transforming nucleic acid may be heterologous to one another and/or to the transformed host. The term heterologous may also be applied to a polynucleotide that is identical in sequence to a polynucleotide already present in a host cell, but which is linked to different additional control sequences and/or is present at a different copy number, etc. In one specific, non-limiting example, a heterologous nucleic acid molecule encoding a protein, such as an scFv, is expressed in a cell, such as a mammalian cell. Methods for introducing a heterologous nucleic acid molecule in a cell or organism are well known in the art, for example transformation with a nucleic acid, including electroporation, lipofection, particle gun acceleration, and homologous recombination.

Host Cell: Cells in which a vector can be propagated, and its DNA expressed. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the subject host cell. It is understood that all progeny need not be identical to the parental cell, since mutations can occur during replication. However, such progeny are included when the term “host cell” is used. IgA: A polypeptide belonging to the class of antibodies that are substantially encoded by a recognized immunoglobulin alpha gene. In humans, this class or isotype comprises IgAi and IgAz. IgA antibodies can exist as monomers, polymers (referred to as plgA) of predominantly dimeric form, and secretory IgA. Tire constant chain of wild-type IgA contains an 18-amino-acid extension at its C-terminus called the tail piece (tp). Polymeric IgA is secreted by plasma cells with a 15-kDa peptide called the J chain linking two monomers of IgA through the conserved cysteine residue in the tail piece.

IgG: A polypeptide belonging to the class or isotype of antibodies that are substantially encoded by a recognized immunoglobulin gamma gene. In humans, this class comprises IgGi, IgG2, IgG?, and IgG4.

Immune Complex: A complex that is formed when an antibody (e.g., a monoclonal antibody or antigen binding fragment (e.g., a scFv)) binds a soluble antigen (for example, a virus spike protein RBD). The formation of an immune complex can be detected through conventional methods, for instance immunohistochemistry, immunoprecipitation, flow cytometry, biolayer interferometry, immunofluorescence microscopy, ELISA, immunoblotting (for example, Western blot), magnetic resonance imaging, CT scans, radiography, and affinity chromatography.

Inhibiting or Treating a Disease: Inhibiting the full development of a disease or condition, for example, in a subject who is at risk for a disease such as a SARS-CoV-2 infection. “Treatment” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease, or pathological condition after it has begun to develop. The term “ameliorating,” with reference to a disease or pathological condition, refers to any observable beneficial effect of the treatment. Inhibiting a disease can include preventing or reducing the risk of the disease, such as preventing or reducing the risk of viral infection. The beneficial effect can be evidenced, for example, by a delayed onset of clinical symptoms of the disease in a susceptible subject, a reduction in severity of some or all clinical symptoms of the disease, a slower progression of the disease, a reduction in the viral load, an improvement in the overall health or well-being of the subject, or by other parameters that are specific to the particular disease. A “prophylactic” treatment is a treatment administered to a subject who does not exhibit signs of a disease or exhibits only early signs for the purpose of decreasing the risk of developing pathology.

The term “reduces” is a relative term, such that an agent reduces a disease or condition if the disease or condition is quantitatively diminished following administration of the agent, or if it is diminished following administration of the agent, as compared to a reference agent. Similarly, the term “prevents” does not necessarily mean that an agent completely eliminates the disease or condition, so long as at least one characteristic of the disease or condition is eliminated. Thus, a composition that reduces or prevents an infection, can, but does not necessarily completely, eliminate such an infection, so long as the infection is measurably diminished, for example, by at least about 50%, such as by at least about 70%, or about 80%, or even by about 90% of the infection in the absence of the agent, or in comparison to a reference agent.

Isolated: A biological component (such as for example, polynucleotides, polypeptides, and protein complexes; for example, antibodies) that has been substantially separated, produced apart from, or purified away from other biological components in the cell of the organism in which the component naturally occurs (i.e., other chromosomal and extra-chromosomal DNA and RNA, and proteins), while effecting a chemical or functional change in the component (e.g., a polynucleotide may be isolated from a chromosome by breaking chemical bonds connecting the polynucleotide to the remaining DNA in the chromosome). Thus, isolated polynucleotides, polypeptides, peptides, and proteins include those purified by standard purification methods. The term also embraces polynucleotides, polypeptides, peptides, and proteins prepared by recombinant expression in a host cell, as well as those chemically synthesized. An isolated polynucleotide, polypeptide, peptide, or protein (for example, an antibody (e.g., a monoclonal antibody or antigen binding fragment) can be at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% pure.

Kabat Position: A position of a residue in an amino acid sequence that follows the numbering convention delineated by Kabat et al. (Sequences of Proteins of Immunological Interest, 5^lh Edition, Department of Health and Human Services, Public Health Service, National Institutes of Health, Bethesda, NIH Publication No. 91-3242, 1991).

Linker: A bi-functional molecule that can be used to link two molecules into one contiguous molecule, for example, linking a detectable marker to an antibody. Non-limiting examples of peptide linkers include glycine- serine linkers.

The terms “conjugating,” “joining,” “bonding,” and “linking” can refer to making two molecules into one contiguous molecule; for example, linking two polypeptides into one contiguous polypeptide, or covalently attaching an effector molecule or detectable marker radionuclide or other molecule to a polypeptide, such as an scFv. The linkage can be either by chemical or recombinant means. “Chemical means” refers to a reaction between the antibody moiety and the effector molecule, such that there is a covalent bond formed between the two molecules to form one molecule.

Nucleic Acid Molecule: A polymeric form of nucleotides, which may include both sense and antisense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above, being defined by the nucleotide sequence thereof. A nucleotide may refer to a ribonucleotide, deoxyribonucleotide, or a modified form of either type of nucleotide. A “nucleic acid molecule” as used herein is synonymous with “nucleic acid” and “polynucleotide.” A nucleic acid molecule is usually at least 10 bases in length, unless otherwise specified. The term includes single- and double-stranded forms of DNA. A nucleic acid molecule can include either or both naturally occurring and modified nucleotides linked together by naturally occurring and/or non-naturally occurring nucleotide linkages.

“cDNA” refers to a DNA that is complementary to an mRNA, in either single stranded or double stranded form.

“Encoding” refers to the inherent property of specific nucleotide sequences 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 produced by that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and non-coding strand, used as the template for transcription, of a gene or cDNA can be referred to as encoding the protein or other product of that gene or cDNA. Unless otherwise specified, a “coding polynucleotide” or “polynucleotide encoding a polypeptide” includes polynucleotides comprising any of the nucleotide sequences that are degenerate versions of each other and encode a polypeptide comprising the same amino acid sequence. Polynucleotides that encode proteins and RNA may include introns.

Operably Linked: A first polynucleotide is operably linked with a second polynucleotide when the first polynucleotide is placed in a functional relationship with the second polynucleotide. For example, a promoter (e.g., the CMV promoter) is operably linked to a coding polynucleotide if the promoter affects the transcription or expression of the coding polynucleotide. Generally, though not necessarily, operably linked polynucleotides are contiguous in a nucleic acid molecule, and, where necessary to join two protein-coding regions, in the same reading frame.

Pharmaceutically Acceptable Carriers: The pharmaceutically acceptable carriers of use in the present disclosure are conventional. Remington: The Science and Practice of Pharmacy, 22^nd ed., London, UK: Pharmaceutical Press, 2013, describes compositions and formulations suitable for pharmaceutical delivery of the disclosed agents.

In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually include injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol, or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers include, for example, pharmaceutical grades of mannitol, lactose, starch, and magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances (for example, wetting or emulsifying agents, added natural or non-natural preservatives, and pH buffering agents (e.g., sodium acetate and sorbitan monolauratc). In particular examples, the pharmaceutically acceptable carrier is sterile and suitable for parenteral administration to a subject; for example, by injection. In some examples, the active agent and pharmaceutically acceptable carrier are provided in a unit dosage form, such as a pill or in a selected quantity in a vial. Unit dosage forms can include one dosage or multiple dosages (for example, in a vial from which metered dosages of the agents can selectively be dispensed).

Polypeptide: A polymer in which the monomers are amino acid residues that are joined together through amide bonds. When the amino acids are alpha-amino acids, either the L-optical isomer or the D- optical isomer can be used, the L-isomers being preferred. The terms “polypeptide” and “protein” as used herein are intended to encompass any amino acid polymer, and include modified sequences; for example, glycoproteins. “Polypeptides” include naturally occurring proteins and fragments thereof, as well as those that are recombinantly or synthetically produced. A polypeptide has an amino terminal (N-terminal) end and a carboxy-terminal (C-terminal) end. In some implementations, a polypeptide is a disclosed antibody (e.g., a monoclonal antibody or antigen binding fragment) disclosed herein.

Purified: The term purified does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified peptide or polypeptide preparation is one in which the peptide or polypeptide (such as a monoclonal antibody or antigen binding fragment) is more enriched than the peptide or polypeptide is in its natural environment, such as within a cell. In one example, a preparation is purified such that a peptide or polypeptide represents at least 50% of the total peptide or polypeptide content of the preparation, for example, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or at least 99% of the total peptide or polypeptide content of the preparation.

Recombinant: A recombinant nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished by chemical synthesis, or, more commonly, by the artificial manipulation of isolated polynucleotide segments of the nucleic acid, for example, by genetic engineering techniques. A recombinant protein is one that has an amino acid sequence that is not naturally occurring or is made by an artificial combination of two otherwise separated polypeptides. In an example, a recombinant protein is encoded by a heterologous polynucleotide that has been introduced into a host cell, such as a bacterial or eukaryotic cell. A polynucleotide can be introduced, for example, on an expression vector having expression control sequences capable of expressing the protein encoded by the introduced polynucleotide, or the polynucleotide can be integrated into the host cell chromosome.

SARS-CoV-2: A coronavirus of the genus betacoronavirus that first emerged in humans in 2019. This virus is also known as Wuhan coronavirus, 2019-nCoV, or 2019 novel coronavirus, and is referred to herein as “wild-type SARS-CoV-2” or “WT SARS-CoV-2.” The term “SARS-CoV-2” includes both the original WA-1 strain of SARS-CoV-2, and variants thereof, such as WT S6P SARS-CoV-2, and VOCs (e.g., B.1.1.7, Alpha; B.1.351, Beta; P.l, Gamma; B.l.617.2, Delta; and B.l.1.529, Omicron). SARS-CoV-2 is a positive-sense, single stranded RNA virus that has emerged as a highly fatal cause of severe acute respiratory infection. The viral genome is capped, poly adenylated, and covered with nucleocapsid proteins. The SARS-CoV-2 virion includes a viral envelope with large spike glycoproteins. The SARS-CoV-2 genome, like most coronaviruses, has a common genome organization, with the replicase gene included in the 5'-two thirds of the genome, and structural genes included in the 3'-third of the genome. The SARS- CoV-2 genome encodes the canonical set of structural protein genes in the order 5' - spike (S) - envelope (E) - membrane (M) and nucleocapsid (N) - 3'. Symptoms of SARS-CoV-2 infection include, but are not limited to, fever, respiratory illness (e.g., dry cough or shortness of breath), myalgia, fatigue, loss of taste, loss of smell, and gastrointestinal upset. Cases of severe infection can progress to severe pneumonia, multiorgan failure, and death. The time from exposure to onset of symptoms is approximately 2 to 14 days.

Standard methods for detecting viral infection may be used to detect SARS-CoV-2 infection, including but not limited to, assessment of patient symptoms and background (e.g., known exposure to SARS-CoV-2), and genetic tests such as reverse transcription-polymerase chain reaction (rRT-PCR). The test can be done on patient samples such as respiratory or blood samples.

SARS Spike (S) Protein: A class I fusion glycoprotein initially synthesized as a precursor protein of approximately 1256 amino acids in size for SARS-CoV-1, and 1273 for SARS-CoV-2. Individual precursor S polypeptides form a homotrimer and undergo glycosylation within the Golgi apparatus, as well as processing to remove the signal peptide, and cleavage by a cellular protease between approximately position 679/680 for SARS-CoV-1, and 685/686 for SARS-CoV-2, to generate separate SI and S2 polypeptide chains, which remain associated as S1/S2 protomers within the homotrimer and is therefore a trimer of heterodimers. The SI subunit is distal to the virus membrane and contains the N-terminal domain (NTD) and the receptor-binding domain (RBD) that mediates virus attachment to its host receptor. The S2 subunit contains fusion protein machinery, such as the fusion peptide, two heptad-repeat sequences (HR1 and HR2) and a central helix typical of fusion glycoproteins, a transmembrane domain, and the cytosolic tail domain.

Specific SARS-CoV-2 variants herein include a “S6P” spike protein, which refers to a SARS-CoV-2 spike protein with the “6P” or “Hexapro” mutations - F817P, A892P, A899P, A942P, K986P, and V987P. The 6P mutations stabilize the spike ectodomain in the prefusion conformation.

Sequence Identity: A measure of similarity between a query sequence and a reference sequence. Sequence identity can be applied to nucleic acid sequences or amino acid sequences. Suitable methods of determining sequence identity are known and have been described. Non-limiting examples of programs and alignment algorithms are described in: Smith and Waterman, Adv. Appl. Math. 2(4):482-489, 1981; Needleman and Wunsch, J. Mol. Biol. 48(3):443-453, 1970; Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85(8):2444-2448, 1988; Higgins and Sharp, Gene, 73(l):237-244, 1988; Higgins and Sharp, Bioinformatics, 5(2): 151-3, 1989; Corpet, Nucleic Acids Res. 16(22): 10881-10890, 1988; Huang et al. Bioinformatics, 8(2): 155- 165, 1992; and Pearson, Methods Mol. Biol. 24:307-331, 1994., Altschul et al., J. Mol. Biol. 215(3):403-410, 1990, presents a detailed consideration of sequence alignment methods and homology calculations. The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol. 215(3):403-410, 1990) is available from several sources, including the National Center for Biological Information and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn, and tblastx. Blastn is used to compare nucleic acid sequences, while blastp is used to compare amino acid sequences. Additional information can be found at the NCBI website. In some examples, sequence identity is determined using a BLAST tool under default parameters.

Sequence identity can be expressed in terms of percentage identity (or percent identity); the higher the percentage, the more identical the sequences. “Substantially identical” antibodies (e.g., monoclonal antibodies or antigen binding fragments) comprise polypeptides (e.g., VHs and VLs) having amino acid sequences that are more than 85% identical. For example, a substantially identical amino acid sequence is at least 85.5%; at least 86%; at least 87%; at least 88%; at least 89%; at least 90%; at least 91%; at least 92%; at least 93%; at least 94%; at least 95%; at least 96%; at least 97%; at least 98%; at least 99%; or at least 99.5% identical to the reference sequence.

Specifically Bind: When referring to an antibody (e.g., monoclonal antibody or antigen binding fragment), “specifically bind” or “specific binding” refers to a binding reaction that determines the presence of a target protein in the presence of a heterogeneous population of proteins and other biologies. Thus, under designated conditions, an antibody (e.g., monoclonal antibody or antigen binding fragment) binds preferentially to a particular target protein, peptide, or polysaccharide (for example, an antigen present on the surface of a pathogen, such as a coronavirus spike protein), and does not bind in a significant amount to other proteins, peptides, or polysaccharides present in the sample or subject. With regard to the binding of an antibody to a coronavirus spike protein, the antibody may bind a particular SARS-CoV-2 spike protein (e.g., the spike protein of a SARS-CoV-2 variant), such that the antibody binds to particular SARS-CoV-2 spike protein, but does not significantly bind to other proteins, including spike proteins from other SARS- CoV viruses. In some aspects herein, an antibody (e.g., monoclonal antibody or antigen binding fragment) is an antibody that binds to a plurality of different SARS-CoV-2 spike proteins (for example, from different SARS-CoV-2 strains or variants), and does not bind in a significant amount to other SARS-CoV spike proteins present in the sample or subject. Specific binding can be determined by standard methods. See Harlow & Lane, Antibodies, A Laboratory Manual, 2^nd ed., Cold Spring Harbor Publications, New York (2013), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity.

With reference to an antibody-antigen complex, specific binding indicates a KD of less than about 10 nM; for example, less than about 5 nM, less than about 1 nM, less than about 0.5 nM, less than about 0.1 nM, less than about 0.05 nM, less than about 0.01 nM, or even lower. KD refers to the dissociation constant for a given interaction, such as a polypeptide-ligand interaction. For example, for the bimolecular interaction of an antibody and an antigen it is the concentration of the individual components of the bimolecular interaction divided by the concentration of the complex.

An antibody that specifically binds to an epitope on a coronavirus spike protein is an antibody that binds substantially to the coronavirus spike protein, such as the NTD or RBD of a spike protein from SARS- CoV-2, including viruses, substrate to which the spike protein is attached, or the protein in a biological specimen. It is, of course, recognized that a certain degree of non-specific interaction may occur between an antibody and a non-target. Typically, specific binding results in a much stronger association between the antibody and a spike protein than between the antibody and other different coronavirus proteins (such as MERS), or from non-coronavirus proteins. Specific binding typically results in greater than 2-fold, such as greater than 5 -fold, greater than 10-fold, or greater than 100-fold increase in amount of bound antibody (per unit time) to a protein including the epitope or cell or tissue expressing the target epitope as compared to a protein or cell or tissue lacking this epitope. Specific binding to a protein under such conditions requires an antibody that is selected for its specificity for a particular protein. A variety of immunoassay formats are appropriate for selecting antibodies or other ligands specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with a protein.

Subject: Living multi-cellular vertebrate organisms, a category that includes human and nonhuman mammals, such as non-human primates, pigs, camels, bats, sheep, cows, dogs, cats, rodents, and the like. In a particular example, the subject is a human. In an additional example, a subject is selected that is in need of inhibiting a SARS-CoV-2 infection. For example, the subject is either uninfected and at risk of the SARS-CoV-2 infection or is infected and in need of treatment.

Synthetic: Produced by artificial means in a laboratory, for example a synthetic nucleic acid molecule or protein (for example, an antibody) can be chemically synthesized in a laboratory.

Transformed: A transformed cell is a cell into which a nucleic acid molecule has been introduced by molecular biology techniques. As used herein, the term transformed and the like (e.g., transformation, transfection, transduction, etc.) encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transduction with viral vectors, transformation with plasmid vectors, and introduction of DNA by electroporation, lipofection, and particle gun acceleration.

Vector: An entity containing a nucleic acid molecule (such as a DNA or RNA molecule) bearing a promoter(s) that is operationally linked to the coding sequence of a protein of interest and can express the coding sequence. Non-limiting examples include a naked or packaged (lipid and/or protein) DNA, a naked or packaged RNA, a subcomponent of a virus or bacterium or other microorganism that may be replicationincompetent, or a virus or bacterium or other microorganism that may be replication-competent. A vector is sometimes referred to as a construct. Recombinant DNA vectors are vectors having recombinant DNA. A vector can include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication. A vector can also include one or more selectable marker genes and other genetic elements. Viral vectors are recombinant nucleic acid vectors having at least some nucleic acid sequences derived from one or more viruses. In some aspects, a viral vector comprises a nucleic acid molecule encoding a disclosed antibody (e.g., a monoclonal antibody or antigen binding fragment) that specifically binds to a coronavirus spike protein and neutralizes the coronavirus. In some aspects, the viral vector can be an adeno-associated virus (AAV) vector.

Under Conditions Sufficient for: A phrase used to describe any environment that permits a desired activity.

IV. Antibodies

Monoclonal antibodies (mAbs) represent one of the most effective therapeutic options for treatment of a SARS-CoV-2 infection, as they provide immediate protection in the absence of significant side effects. They may be especially helpful in unvaccinated individuals and in those who respond poorly to vaccination or have a waning immunity, as well as against emergent antigenically distinct variants or strains of SARS- CoV-2. A primary target of neutralizing antibodies is the receptor binding domain (RBD) within the SARS- CoV-2 spike (S) protein, which interacts with the host angiotensin-converting enzyme 2 (ACE2) viral receptor on the surface of susceptible cells. Efforts to identify SARS-CoV-2 neutralizing antibodies are slowed by the need to isolate antibodies from convalescent COVID-19 patients, or subject known antibodies to experimental evolutionary selection.

Described herein are the results of a rational, computational design platform based on energy - minimization of complex structures of SARS-CoV-2 RBD and the 80R antibody, which is a high-affinity, neutralizing recombinant human monoclonal antibody against SARS-CoV-1 that does not cross-react with or neutralize SARS-CoV-2. This design platform is made possible by the facts that: (1) the spike protein RBDs of SARS-CoV-2 and SARS-CoV-1 are similar in sequence and structure with minimal amino acid differences (Yuan, M. et al. A highly conserved cryptic epitope in the receptor-binding domains of SARS- CoV-2 and SARS-CoV. Science (80-). 7269, eabb7269 (2020); Tai, W., He, L., Zhang, X., Pu, J. & Voronin, D. Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine. Cell. Mol. Immunol. (2020). doi:10.1038/s41423-020-0400-4); and (2) that the antigen-bound 80R structure is well-characterized. By utilizing the foregoing platform, many novel 80R-derived antibodies were identified that specifically bind the SARS-CoV-2 spike protein with high affinity. Of these, 4 were found to bind multiple SARS-CoV-2 spike proteins, including those of VOCs, with high affinity.

The SARS-CoV-2-binding specificity of the monoclonal antibodies and antigen binding fragments herein are determined by the LCDR and HCDR sequences of VL and VH from exemplary 80R-derived antigen binding fragments referred to herein as 80R_5, 80R_18, 80R_19, and 80R_23. In some aspects, a monoclonal antibody or antigen binding fragment that binds a plurality of SARS-CoV-2 spike protein variants with high affinity comprises LCDR and HCDR sequences of VL and VH polypeptides from 80R_5, 8OR_18, 80R_19, and/or 80R_23. In particular aspects, the monoclonal antibody or antigen binding fragment comprises LCDR and HCDR sequences of VL and VH polypeptides from 80R_5 or 80R_23.

The amino acid sequences of the four spike protein-specific monoclonal antibodies are provided below in Table 1. CDR sequences determined using the method of IMGT are indicated by bold underline. Table 1 also lists the VH domain and VL domain CDR sequences of each antibody using IMGT. However, one of skill in the art could readily determine the CDR boundaries using an alternative numbering scheme, such as the Kabat or Chothia numbering scheme.

Table 1. VL, VH, and CDR sequences of 80R_5, 8OR_18, 80R_19, and 80R_23 antibodies.

The HCDRs of the 80R_5, 80R_18, 80R_19, and 80R_23 antibodies, and the LCDRs of the 80R_5, 8OR_18, 80R_19, and 80R_23 antibodies share significant sequence homology. Further, structural studies presented in the examples show CDR residues important for antigen binding. Based on this information, consensus CDR sequences based on the CDRs of the 80R_5, 8OR_18, 80R_19, and 80R_23 antibodies, or just the 80R_5 and 80R_23 antibodies were generated that confer binding to SARS-CoV-2 spike RBD from multiple strains of SARS-CoV-2. These consensus CDRs are listed in Tables 2 and 3. Table 2. Consensus CDR sequences based on the 80R_5, 8OR_18, 80R_19, and 80R_23 antibodies.

Table 3. Consensus CDR sequences based on the 80R_5 and 80R_23 antibodies.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2. In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 39, 40, and 41, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 42, 43, and 44, respectively, and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2. In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 45, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 45, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 72, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 72, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 1, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 1, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 2, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 2, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and/or a Vn comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 9, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 9, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 10, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 10, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 17, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 17, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 18, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 18, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2. In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 25, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 25, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 26, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 26, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 39, 40, and 41, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 42, 43, and 44, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 45, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 45, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 72, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 72, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 39, 40, and 41, respectively, and/or a Vn comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 42, 43, and 44, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 1, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 1, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 2, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 2, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 39, 40, and 41, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 with consensus amino acid sequences set forth as SEQ ID NOs: 42, 43, and 44, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 25, such as 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 25, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 26, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 26, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2. Antibodies Based on 80R_5

In some implementations, the monoclonal antibody or antigen binding fragment is based on, or derived from, the 80R_5 antibody disclosed herein, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, the monoclonal antibody or antigen binding fragment based on, or derived from, the 80R_5 antibody disclosed herein neutralizes SARS-CoV-2. In some examples, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising the LCDR1, the LCDR2, and the LCDR3, and the HCDR1, the HCDR2, and the HCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 80R_5 antibody (see e.g., Table 1), and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 1, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 2, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a V and a VH independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 1 and 2, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising or consisting of an amino acid sequence set forth as SEQ ID NO: 1, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising or consisting of the amino acid sequence set forth as SEQ ID NO: 2, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising or consisting of amino acid sequences set forth as SEQ ID Nos: 1 and 2, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID Nos: 3, 4, and 5, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID Nos: 6, 7, and 8, respectively, and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 having amino acid sequences set forth as SEQ ID Nos: 3, 4, and 5, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 having amino acid sequences set forth as SEQ ID Nos: 6, 7, and 8, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 1, such as at least 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 1, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 2, such as at least 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 2, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the antigen binding fragment is a scFv. A non-limiting example of an amino acid sequence for a scFv comprising a VL and VH based on those of the 80R_5 antibody is provided as SEQ ID NO: 101.

In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed herein inhibit viral entry and/or replication of SARS-CoV-2.

Antibodies Based on 80R_18

In some implementations, the monoclonal antibody or antigen binding fragment is based on, or derived from, the 80R_18 antibody disclosed herein, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, the monoclonal antibody or antigen binding fragment based on, or derived from, the 80R_l 8 antibody disclosed herein neutralizes SARS-CoV-2. In some examples, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising the LCDR1, the LCDR2, and the LCDR3, and the HCDR1, the HCDR2, and the HCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 8OR_18 antibody (see e.g.. Table 1), and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 9, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 10, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a VL and a VH independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID Nos: 9 and 10, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising or consisting of an amino acid sequence set forth as SEQ ID NO: 9, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising or consisting of the amino acid sequence set forth as SEQ ID NO: 10, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising or consisting of amino acid sequences set forth as SEQ ID Nos: 9 and 10, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 11, 12, and 13, respectively, and/or a V_H comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 14, 15, and 16, respectively, and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 having amino acid sequences set forth as SEQ ID NOs: 11, 12, and 13, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 having amino acid sequences set forth as SEQ ID NOs: 14, 15, and 16, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 9, such as at least 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 9, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 10, such as at least 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 10, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the antigen binding fragment is a scFv. A non-limiting example of an amino acid sequence for a scFv comprising a VL and VH based on those of the 80R_18 antibody is provided as SEQ ID NO: 102.

Antibodies Based on 80R_19

In some implementations, the monoclonal antibody or antigen binding fragment is based on or derived from the 80R_19 antibody disclosed herein, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, the monoclonal antibody or antigen binding fragment based on, or derived from, the 80R_19 antibody disclosed herein neutralizes SARS-CoV-2. In some examples, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising the LCDR1, the LCDR2, and the LCDR3, and the HCDR1, the HCDR2, and the HCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 80R_19 antibody see e.g., Table 1), and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 17, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 18, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a VL and a VH independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 17 and 18, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising or consisting of an amino acid sequence set forth as SEQ ID NO: 17, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising or consisting of the amino acid sequence set forth as SEQ ID NO: 18, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising or consisting of amino acid sequences set forth as SEQ ID NOs: 17 and 18, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 19, 20, and 21, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 22, 23, and 24, respectively, and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 having amino acid sequences set forth as SEQ ID NOs: 19, 20, and 21, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 having amino acid sequences set forth as SEQ ID NOs: 22, 23, and 24, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 17, such as at least 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 17, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 18, such as at least 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 18, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the antigen binding fragment is a scFv. A non-limiting example of an amino acid sequence for a scFv comprising a VL and VH based on those of the 80R_19 antibody is provided as SEQ ID NO: 103.

In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed herein inhibit viral entry and/or replication of SARS-CoV-2. Antibodies Based on 80R_23

In some implementations, the monoclonal antibody or antigen binding fragment is based on or derived from the 80R_23 antibody disclosed herein, and specifically binds to SARS-CoV-2 spike RBD.In some implementations, the monoclonal antibody or antigen binding fragment based on, or derived from, the 80R_23 antibody disclosed herein neutralizes SARS-CoV-2. In some examples, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising the LCDR1, the LCDR2, and the LCDR3, and the HCDR1, the HCDR2, and the HCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 80R_23 antibody (see e.g., Table 1), and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 25, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 26, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a V and a VH independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 25 and 26, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising or consisting of an amino acid sequence set forth as SEQ ID NO: 25, and specifically binds to SARS-CoV-2 spike RBD. In more implementations, the monoclonal antibody or antigen binding fragment comprises a VH comprising or consisting of the amino acid sequence set forth as SEQ ID NO: 26, and specifically binds to SARS-CoV-2 spike RBD. In additional implementations, the monoclonal antibody or antigen binding fragment comprises a VL and a VH comprising or consisting of amino acid sequences set forth as SEQ ID NOs: 25 and 26, respectively, and specifically binds to SARS-CoV-2 spike RBD. In some implementations, any of the monoclonal antibodies or antigen binding fragments disclosed above neutralize SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 27, 28, and 29, respectively, and/or a V_H comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 30, 31, and 32, respectively, and specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS-CoV-2.

In some implementations, the monoclonal antibody or antigen binding fragment comprises a VL comprising a LCDR1, a LCDR2, and a LCDR3 having amino acid sequences set forth as SEQ ID NOs: 27, 28, and 29, respectively, and/or a VH comprising a HCDR1, a HCDR2, and a HCDR3 having amino acid sequences set forth as SEQ ID NOs: 30, 31, and 32, respectively, wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 25, such as at least 95%, 96%, 97%, 98% to 99% identical to SEQ ID NO: 25, and wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 26, such as at least 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 26, and the monoclonal antibody or antigen binding fragment specifically binds to SARS-CoV-2 spike RBD, and neutralizes SARS- CoV-2.

In some implementations, the antigen binding fragment is a scFv. A non-limiting example of an amino acid sequence for a scFv comprising a VL and VH based on those of the 80R_23 antibody is provided as SEQ ID NO: 104.

Additional Description of the Disclosed Antibodies

In some aspects, the monoclonal antibody or antigen binding fragment specifically binds the spike proteins of a plurality of SARS-CoV-2 variants; for example, the spike protein of wild-type SARS-CoV-2 (WA-1), and further the spike protein of at least one SARS-CoV-2 VOC (for example and without limitation, Beta, Delta, and Omicron) or engineered forms of these spike proteins, including the S6P mutations (F817P, A892P, A899P, A942P, K986P and V987P).

Antibody fragments as disclosed herein are “antigen binding” fragments due to their retention of the ability to selectively bind to least one coronavirus spike protein (for example, at least one of WT S ARS- CoV-2, SARS-CoV-2 VOCs (e.g., Alpha, Beta, Gamma, Delta, and Omicron SARS-CoV-2 variants), and variants of any of the foregoing comprising the S6P mutations) with high affinity. Such antigen binding fragments include, for example and without limitation:

(4) Fv, a genetically engineered fragment containing the VH and VL expressed as two chains;

(5) scFv, a genetically engineered fragment containing the VH and the VL in either possible intramolecular orientation (VH domain-linker-VL domain, or VL do main-linker- VH domain) linked by a suitable polypeptide linker (see, e.g., Ahmad et al., Clin. Dev. Immunol., 2012, doi: 10.1155/2012/980250; Marbry and Snavely, IDrugs, 13(8):543-549, 2010); and

(6) SCFV2 (also referred to as a “miniantibody”), a dimer of a scFv.

Any suitable method of producing the foregoing antigen binding fragments may be used. Nonlimiting examples are provided in Harlow and Lane, Antibodies: A Laboratory Manual, 2^nd, Cold Spring Harbor Laboratory, New York, 2013. For example, antigen binding fragments can be prepared by expression in a host cell (such as an E. coli cell or human cell) of a polynucleotide encoding the fragment. Other methods for producing antigen binding fragments include, for example, separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, and other enzymatic, chemical, and genetic techniques.

In some aspects, the monoclonal antibody or antigen binding fragment includes a recombinant constant domain that includes a modification that increases the half-life of the monoclonal antibody. In some examples, the modification increases binding to the neonatal Fc receptor. Several such substitutions are known to the person of ordinary skill in the art, such as substitutions at IgG constant regions T250Q and M428L (see, e.g., Hinton et al., J Immunol., 176:346-356, 2006); M428L and N434S (the “LS” mutation, see, e.g., Zalevsky, etal., Nature Biotechnology, 28:157-159, 2010); N434A (see, e.g., Petkova et al., Int. Immunol., 18:1759-1769, 2006); T307A, E38OA, and N434A (see, e.g., Petkova et a/., Int. Immunol., 18:1759-1769, 2006); and M252Y, S254T, and T256E (see, e.g., Dall’Acqua et al., J. Biol. Chem., 281:23514-23524, 2006). The disclosed monoclonal antibodies and antigen binding fragments can be linked to a Fc polypeptide including any of the substitutions listed above, for example, an Fc polypeptide comprising the M428L and N434S substitutions.

Also provided herein are bispecific antibodies that include any of the monoclonal antibodies or antigen binding fragments disclosed herein. In some aspects, the bispecific antibody is a dual variable domain immunoglobulin. In some implementations, the bispecific antibody includes an antigen binding fragment selected from SEQ ID NOs: 94-97 and a second antigen binding fragment or antibody. In some implementations, the bispecific antibody includes two antigen binding fragments selected from SEQ ID Nos: 94-97. Also disclosed are multispecific antibodies that include any of the monoclonal antibodies or antigen binding fragments disclosed herein. A multispecific antibody includes a plurality of binding sites, and binds two or more epitopes (e.g., two or more epitopes of a coronavirus spike protein). In a non-limiting example, a multispecific antibody includes an antigen binding fragment selected from SEQ ID NOs: 94-97. In some implementations, a multispecific antibody includes three or more antigen binding fragments selected from SEQ ID NOs: 94-97.

An antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific, or multispecific antibody)disclosed herein can be a humanized antibody. Chimeric antibodies are also provided. The antibody can include any suitable framework region in the heavy or light chain of the antibody; for example and without limitation, human framework regions, optimized framework regions, and heterologous framework regions (e.g., a mouse or monkey framework region). In particular aspects, a monoclonal antibody herein includes a human constant domain. A monoclonal antibody herein can be of any isotype. The antibody can be, for example, an IgA, IgM or an IgG antibody, such as IgG i . IgGi, IgG s, or IgG ,. In some examples, the disclosed antibodies are oligomers of antibodies, such as dimers, trimers, tetramers, pentamers, hexamers, septamers, octomers, and so on. An antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific, or multispecific antibody) disclosed herein can be derivatized or linked to another molecule (such as another peptide or protein). In general, the antibody is derivatized, such that the binding to the spike protein is not affected adversely by the derivatization or labeling. For example, a monoclonal antibody or antigen binding fragment disclosed herein can be functionally linked (by chemical coupling, genetic fusion, noncovalent association, or otherwise) to one or more other molecular entities; for example and without limitation, to another antibody (for example, a bispecific antibody, multispecific antibody, or a diabody), a detectable marker, an effector molecule, or a protein or peptide that can mediate association of the monoclonal antibody or fragment with another molecule (such as a streptavidin core region or a poly histidine tag).

In some aspects, the antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific, or multispecific antibody) is conjugated to a detectable marker, for example, a detectable marker capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy, or diagnostic imaging techniques. Specific, non-limiting examples of detectable markers include fluorophores, chemiluminescent agents, enzymatic linkages, radioactive isotopes and heavy metals or compounds (for example super paramagnetic iron oxide nanocrystals for detection by MRI). For example, useful detectable markers include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-l- napthalenesulfonyl chloride, phycoerythrin, lanthanide phosphors and the like. Bioluminescent markers are also of use, such as luciferase, green fluorescent protein (GFP), and yellow fluorescent protein (YFP). An antibody can also be conjugated with enzymes that are useful for detection, such as horseradish peroxidase, P- galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like. When an antibody is conjugated with a detectable enzyme, it can be detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present, the addition of hydrogen peroxide and diaminobenzidine leads to a colored reaction product, which is visually detectable. An antibody may also be conjugated with biotin and detected through indirect measurement of avidin or streptavidin binding.

In some aspects, an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific, or multispecific antibody) is altered to increase or decrease the extent to which the antibody is glycosylated. Addition or deletion of glycosylation sites may be conveniently accomplished by altering the amino acid sequence such that one or more glycosylation sites is created or removed.

Where an antigen binding fragment is an Fc fragment, or where an antibody comprises an Fc region, the carbohydrate attached thereto may be altered. Native antibodies produced by mammalian cells typically comprise a branched, biantennary oligosaccharide that is generally attached by an N-linkage to Asn297 of the CH2 domain of the Fc region. See, e.g., Wright etal. Trends Biotechnol. 15(l):26-32, 1997. The oligosaccharide may include various carbohydrates, e.g., mannose, N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as a fucose attached to a GlcNAc in the “stem” of the biantennary oligosaccharide structure. In some aspects, modifications of the oligosaccharide may be made in order to create variants with certain improved properties. Further provided are antibodies having a carbohydrate structure that lacks fucose attached (directly or indirectly) to an Fc region. For example, the amount of fucose attached to the Fc may be from 1% to 80%, from 1% to 65%, from 5% to 65% or from 20% to 40%. The amount of fucose is determined by calculating the average amount of fucose within the sugar chain at Asn297, relative to the sum of all glycostructures attached to Asn 297 (e.g. complex, hybrid and high mannose structures) as measured by MALDI-TOF mass spectrometry, as described in WO 2008/077546, for example. Asn297 refers to the asparagine residue located at about position 297 in the Fc region; however, Asn297 may also be located about ±3 amino acids upstream or downstream of position 297, i.e., between positions 294 and 300, due to minor sequence variations in antibodies. Such fucosylation variants may have improved ADCC function. See, e.g., US Patent Publication Nos. US 2003/0157108 (Presta, L.); US 2004/0093621 (Kyowa Hakko Kogyo Co., Ltd). Examples of publications related to “defucosylated” or “fucose-deficient” antibody variants include: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US 2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO 2005/035586; WO 2005/035778; W02005/053742; WO 2002/031140; Okazaki et al., J. Mol. Biol., 336(5): 1239-1249, 2004; Yamane-Ohnuki et al., Bioteclmol. Bioeng. 87(5):614-622, 2004. Examples of cell lines capable of producing defucosylated antibodies include Lee 13 CHO cells deficient in protein fucosylation (Ripka et al., Arch. Biochem. Biophys. 249(2):533-545, 1986; US Pat. Appl. No. US 2003/0157108 and WO 2004/056312, especially at Example 11), and knockout cell lines, such as alpha- 1,6-fucosyltransferase gene, FUT8, knockout CHO cells (see, e.g., Yamane-Ohnuki et al., Bioteclmol. Bioeng., 87(5): 614-622, 2004; Kanda et a/., Biotechnol. Bioeng., 94(4):680-688, 2006; and W02003/085107).

Further provided are antibodies, including antigen binding fragments, with bisected oligosaccharides, e.g., in which a biantennary oligosaccharide attached to the Fc region is bisected by GlcNAc. Such antibodies may have reduced fucosylation and/or improved ADCC function. Examples are described, e.g., in WO 2003/011878 (Jean-Mairet et al.)', U.S. Pat. No. 6,602,684 (Umana et al.),' and US 2005/0123546 (Umana et al.). Antibodies with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such antibodies may have improved CDC function. Examples are described, e.g., in WO 1997/30087; WO 1998/58964; and WO 1999/22764.

In some aspects, an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific, or multispecific antibody) provided herein may be further modified to contain additional nonproteinaceous moieties. The moieties suitable for derivatization of the antibody include, for example and without limitation, water soluble polymers. Non-limiting examples of water soluble polymers include, for example; polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1, 3-dioxolane, poly-l,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), dextran or poly(n- vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody may vary, and if more than one polymer are attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization are determined based on considerations including, for example, the particular properties or functions of the antibody to be improved, and whether the antibody derivative will be used in an application under defined conditions.

In some aspects, an antibody, including a monoclonal antibody or antigen binding fragment disclosed herein, specifically binds at least one (for example, at least two, three, or four) SARS-CoV-2 spike protein with an affinity (e.g., measured by KD of no more than about lOnM, no more than about 5 nM, no more than about 1 nM, no more than about 0.5 nM, no more than about 0.1 nM, no more than about 0.5 nM, no more than about 0.1 nM, no more than about 0.05 nM, or no more than about 0.01 nM. KD can be measured, for example, by a radiolabeled antigen-binding assay (RIA) performed with a Fab and its antigen. In one assay, solution binding affinity of Fabs for an antigen is measured by equilibrating Fab with a minimal concentration of (¹²⁵I)-labeled antigen in the presence of a titration series of unlabeled antigen, then capturing bound antigen with an anti-Fab antibody-coated plate (see, e.g., Chen et al., J. Mol. Biol. 293(4):865-881, 1999). To establish conditions for the assay, MICROTITER® multi-well plates (Thermo Scientific) are coated overnight with 5 |ig/mL of a capturing anti-Fab antibody (Cappel Labs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked with 2% (w/v) bovine serum albumin in PBS for two to five hours at room temperature (approximately 23 °C). In a non-adsorbent plate (NUNC™ Catalog #269620), 100 pM or 26 pM [¹²⁵I]-antigen are mixed with serial dilutions of a Fab of interest (e.g., consistent with assessment of the anti-VEGF antibody, Fab-12, in Presta et al., Cancer Res. 57(20):4593- 4599, 1997). The Fab of interest is then incubated overnight; however, the incubation may continue for a longer period (e.g., about 65 hours) to ensure that equilibrium is reached. Thereafter, the mixtures are transferred to the capture plate for incubation at room temperature (e.g., for one hour). The solution is then removed and the plate washed eight times with 0.1% polysorbate 20 (TWEEN-20®) in PBS. When the plates have dried, 150 pL/well of scintillant (MICROSCINT™-20; PerkinElmer) is added, and the plates are counted on a TOPCOUNT™ gamma counter (PerkinElmer) for ten minutes. Concentrations of each Fab that give less than or equal to 20% of maximal binding are chosen for use in competitive binding assays.

In particular aspects, KD is measured using surface plasmon resonance assays using biolayer interferometry (BLI). In other aspects, KD can be measured using a BIACORE®-2000 or a BIACORE®- 3000 (BIAcore, Inc., Piscataway, N.J.) at 25 °C with immobilized antigen CM5 chips at -10 response units (RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIACORE®, Inc.) are activated with N- ethyl-N'-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to the supplier's instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8, to 5 pg/mL (-0.2 pM) before injection at a flow rate of 5 L/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1 M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05% polysorbate 20 (TWEEN-20™) surfactant (PBST) at 25 °C at a flow rate of approximately 25 L/min. Association rates (k_on) and dissociation rates (kott) are calculated using a simple one-to-one Langmuir binding model (BIACORE® Evaluation Software version 3.2) by simultaneously fitting the association and dissociation sensorgrams. The equilibrium dissociation constant (KD) is calculated as the ratio k_of_t/k_on. See, e.g., Chen et al., J. Mol. Biol. 293:865-881 (1999). If the on-rate exceeds 10⁶ M^-1 s^-1 by the surface plasmon resonance assay above, then the on-rate can be determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity (excitation = 295 nm; emission = 340 nm, 16 nm band-pass) at 25 °C of a 20 nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophotometer (Aviv Instruments) or a 8000-series SLM-AMINCO™ spectrophotometer (ThermoSpectronic) with a stirred cuvette. Affinity can also be measured by high throughput SPR using the Carterra LSA.

In some aspects, a monoclonal antibody or antigen binding fragment disclosed herein can neutralize at least one coronavirus, such as WT SARS-CoV-2 or a SARS-CoV-2 VOC. In particular examples, the monoclonal antibody or antigen binding fragment can neutralize multiple SARS-CoV-2 variants, including, for example, a SARS-CoV-2 VOC against which available antibodies are ineffective. In some aspects, the monoclonal antibody or antigen binding fragment neutralizes more than one strain of SARS-CoV-2; for example, WT SARS-CoV-2, SARS-CoV-2 VOCs (e.g., Alpha, Beta, Gamma, Delta, and Omicron SARS- CoV-2 variants), and variants of any of the foregoing comprising the S6P mutations. Specific monoclonal antibodies and antigen binding fragments herein may inhibit a SARS-CoV-2 infection in vivo, and can be administered prior to, or after, an infection with SARS-CoV-2.

V. Nucleic Acids

Nucleic acid molecules (e.g., DNA molecules and RNA molecules (for example, mRNAs)) comprising a polynucleotide that encodes an antibody disclosed herein (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody or multispecific antibody disclosed herein), or a VH and/or VL domain thereof, are further provided. In some aspects, the nucleic acid molecule comprises a promoter operably linked to the polynucleotide encoding the antibody. The antibodies (e.g., monoclonal antibodies, antigen binding fragments), and variable domains herein were computationally designed, and so are not encoded by any naturally-occurring nucleotide sequence. A polynucleotide sequence encoding a monoclonal antibody, antigen binding fragment, VH domain, VL domain, or bispecific antibody disclosed herein can determined using the standard genetic code. In some examples, the nucleotide sequence of the polynucleotide is engineered, for example, codon-optimized for expression in a host cell. In some examples, the host cell is a human cell, such as a cultured human cell or a cell comprised in a human subject.

Nucleic acid molecules comprising a polynucleotide encoding a monoclonal antibody or antigen binding fragment disclosed herein can be prepared by any suitable method including, for example, by direct chemical synthesis by standard methods. Chemical synthesis produces a single -stranded oligonucleotide. This can be converted into double-stranded DNA by hybridization with a complementary sequence, or by polymerization with a DNA polymerase using the single strand as a template.

Nucleic acid molecules can also be prepared using molecular biology techniques, such as cloning and sub-cloning techniques, or amplification methods. Examples of suitable cloning and amplification techniques can be found, for example, in Green and Sambrook (Molecular Cloning: A Laboratory Manual, 4^th ed., New York: Cold Spring Harbor Laboratory Press, 2012) and Ausubel et al. (Eds.) (Current Protocols in Molecular Biology, New York: John Wiley and Sons, including supplements). Exemplary amplification methods include polymerase chain reaction (PCR), ligase chain reaction (LCR), transcription-based amplification system (TAS), and self-sustained sequence replication system (3SR).

The antibodies (e.g., monoclonal antibodies and antigen binding fragments) disclosed herein can be expressed as individual proteins including the VH and/or VL (linked to an effector molecule or detectable marker as needed), or can be expressed as a fusion protein. Any suitable method of expressing and purifying antibodies and antigen binding fragments may be used; non-limiting examples are provided in Al- Rubeai (Ed.), Antibody Expression and Production, Dordrecht; New York: Springer, 2011). An immunoadhesin can also be expressed. Thus, in some examples, polynucleotides encoding a Vu and Vj„ and immunoadhesin are provided. The polynucleotides may optionally encode a leader sequence.

To create a scFv, the VH- and Vr-encoding polynucleotides can be operatively linked to another polynucleotide encoding a flexible linker, e.g., encoding the amino acid sequence (Gly i-Ser)a, such that the VH and VL sequences are expressed as a contiguous single-chain protein, with the VL and VH domains joined by the flexible linker (see, e.g., Bird et al., Science, 242(4877):423-426, 1988; Huston et al., Proc. Natl. Acad. Sci. U.S.A., 85(16):5879-5883, 1988; McCafferty et al., Nature, 348:552-554, 1990; Kontermann and Diibel (Eds.), Antibody Engineering, Vols. 1-2, 2^nd ed., Springer- Verlag, 2010; Greenfield (Ed.), Antibodies: A Laboratory Manual, 2^nd ed. New York: Cold Spring Harbor Laboratory Press, 2014). The scFv may be monovalent, if only a single VH and VL are used, bivalent, if two VH and VL are used, or polyvalent, if more than two VH and VL are used. Polyvalent (e.g., multispecific) antibodies may be generated that bind specifically to a coronavirus spike protein and another antigen (for example, a different coronavirus spike protein). Optionally, a cleavage site can be included in a linker, such as a furin cleavage site.

Nucleic acid molecules comprising a polynucleotide encoding an antibody disclosed herein (e.g., a monoclonal antibody or antigen binding fragment disclosed herein) can be expressed in a recombinantly engineered cell; for example, by DNA transfer into the host cell. The cell may be prokaryotic or eukaryotic; for example, bacteria, plant, yeast, insect, and mammalian (e.g., human) cells. Numerous expression systems available for expression of proteins including E. coli, other bacterial hosts, yeast, and various higher eukaryotic cells (e.g., COS, CHO, HeLa, and myeloma cell lines) can be used to express the antibodies disclosed herein. Methods of stable transfer (meaning that the foreign DNA is continuously maintained in the host) may be used. Hybridomas expressing the antibodies are also encompassed by this disclosure.

The expression of polynucleotides encoding the antibodies (e.g., monoclonal antibodies and antigen binding fragments) disclosed herein can be achieved by operably linking the polynucleotide to a promoter (which may be either constitutive or inducible) that is operable in a host cell of interest, followed by incorporation into an expression cassette. The promoter can be any promoter of interest, including a cytomegalovirus promoter. Optionally, an enhancer, such as a cytomegalovirus enhancer, is included in the construct. The cassettes can be suitable for replication and integration in either prokaryotes or eukaryotes. Typical expression cassettes contain specific sequences useful for regulation of the expression of the polynucleotide encoding the protein. For example, the expression cassettes can include appropriate promoters, enhancers, transcription and translation terminators, a ribosome binding site for translational initiation (e.g., internal ribosomal binding sequences), initiation sequences, a start codon (i.e., ATG) in front of a protein-encoding gene, splicing signals for introns, sequences for the maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons. The vector can encode a selectable marker, such as a marker encoding drug resistance (for example, ampicillin or tetracycline resistance).

For expression of a polynucleotide in E. coli, an expression cassette may include a prokaryotic promoter, such as the T7, trp, lac, and lambda promoters, a ribosome binding site, and a transcription termination signal. For eukaryotic cells, the expression cassette can include a promoter, and, for example, an enhancer (e.g., an enhancer derived from an immunoglobulin gene, HTLV, SV40, or cytomegalovirus), and a polyadenylation sequence, and can further include splice donor and/or acceptor sequences (for example, CMV and/or HTLV splice acceptor and donor sequences).

Modifications can be made to a polynucleotide encoding an antibody (e.g., a monoclonal antibody or antigen binding fragment) disclosed herein without diminishing its biological activity. Some modifications can be made to facilitate the cloning, expression, or incorporation of the antibody into a fusion protein. Such modifications include, for example, termination codons, sequences to create conveniently located restriction sites, sequences to add a methionine at the amino terminus to provide an initiation site, and additional amino acids (such as poly His) to aid in purification steps.

Once expressed, the antibodies (e.g., a monoclonal antibodies or antigen binding fragments) can be purified according to standard procedures in the art, including ammonium sulfate precipitation, affinity columns, column chromatography, and the like (see, generally, Simpson et al. (Eds.), Basic methods in Protein Purification and Analysis: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press, 2009). The antibodies need not be 100% pure. Once purified, partially or to homogeneity as desired, if to be used prophylactically, the antibodies should be substantially free of endotoxin. Methods for expression of antibodies (e.g., monoclonal antibodies, antigen-binding fragments, bispecific antibodies, and multispecific antibodies) and conjugates, and/or refolding to an appropriate active form, from mammalian cells and bacteria such as E. coli, have been described and are applicable to the antibodies disclosed herein. See, e.g., Greenfield (Ed.), Antibodies: A Laboratory Manual, 2^nd ed. New York: Cold Spring Harbor Laboratory Press, 2014, Simpson et al. (Eds.), Basic methods in Protein Purification and Analysis: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press, 2009, and Ward et al., Nature 341(6242):544-546, 1989. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 1, 9, 17, or 25, and includes SEQ ID Nos: 32, 34, and 35. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 2, 10, 18, or 26, and includes SEQ ID Nos: 36, 37, and 38. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 1, 9, 17, or 25, and includes SEQ ID Nos: 32, 34, and 35; and encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 2, 10, 18, or 26, and includes SEQ ID Nos: 36, 37, and 38. Thus, in these examples, sequence variation lies outside of the CDRs.

In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 1 or 25, and includes SEQ ID Nos: 39, 40, and 41 . In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 2 or 26, and includes SEQ ID Nos: 42, 43, and 44. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 1 or 25, and includes SEQ ID Nos: 39, 40, and 41; and encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to any one of SEQ ID NOs: 2 or 26, and includes SEQ ID Nos: 42, 43, and 44. Thus, in these examples, sequence variation lies outside of the CDRs.

In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 1, and includes SEQ ID Nos: 3, 4, and 5. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 2, and includes SEQ ID Nos: 6, 7, and 8. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 1, and includes SEQ ID Nos: 3, 4, and 5; and encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 2, and includes SEQ ID Nos: 6, 7, and 8. Thus, in these examples, sequence variation lies outside of the CDRs. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 9, and includes SEQ ID Nos: 11, 12, and 13. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 10, and includes SEQ ID Nos: 14, 15, and 16. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 9, and includes SEQ ID Nos: 11, 12, and 13; and encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 10, and includes SEQ ID Nos: 14, 15, and 16. Thus, in these examples, sequence variation lies outside of the CDRs.

In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 17, and includes SEQ ID Nos: 19, 20, and 21. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 18, and includes SEQ ID Nos: 22, 23, and 24. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 17, and includes SEQ ID Nos: 19, 20, and 21; and encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 18, and includes SEQ ID Nos: 22, 23, and 24. Thus, in these examples, sequence variation lies outside of the CDRs.

In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 25, and includes SEQ ID Nos: 27, 28, and 29. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 26, and includes SEQ ID Nos: 30, 31, and 32. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 25, and includes SEQ ID Nos: 27, 28, and 29; and encodes an amino acid sequence having at least 90% sequence identity (for example, at least 93%, at least 95%, at least 98%, or at least 99% sequence identity) to SEQ ID NO: 26, and includes SEQ ID Nos: 30, 31, and 32. Thus, in these examples, sequence variation lies outside of the CDRs. In some implementations, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence comprising or consisting of the VL and/or VH of the 80R_5, 8OR_18, 80R_19, or 80R_23, as disclosed herein (see, e.g., Table 1). In some examples, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence comprising or consisting of the VL and/or VH of 80R_5 (see, e.g., Table 1, SEQ ID Nos: 1 and 2). In some examples, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence comprising or consisting of the VL and/or VH of 8OR_18 (see, e.g., Table 1, SEQ ID Nos: 9 and 10). In some examples, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence that comprises or consists of the VL and/or VH of 80R_19 (see, e.g., Table 1, SEQ ID Nos: 17 and 18). In some examples, the nucleic acid molecule comprises a polynucleotide that encodes an amino acid sequence comprising or consisting of the VL and/or VH of 80R_5 23 (see, e.g., Table 1, SEQ ID Nos: 25 and 26). Also provided are vectors comprising a nucleic acid molecule disclosed herein. In some aspects, the vector is an expression vector. In other aspects, the vector is a viral vector. Host cells (e.g., a human cell) that include a disclosed nucleic acid molecule or vector are also provided.

VI. Compositions

In addition, provided herein are compositions comprising one or more of the antibodies (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies), conjugates, nucleic acid molecules, and/or vectors disclosed herein. For example, compositions according to particular aspects may include at least one, at least two, at least three, at least four, or at least five different antibodies, conjugates, nucleic acid molecules, and vectors, disclosed herein. In compositions comprising at least two different antibodies (e.g., monoclonal antibodies and/or antigen binding fragments), each antibody can specifically bind the same SARS-CoV-2 spike protein, or each can specifically bind a different SARS- CoV-2 spike protein; for example, spike proteins from different SARS-CoV-2 strains, so as to detect the presence or absence of multiple SARS-CoV-2 strains in a sample, or treat and/or prevent multiple SARS- CoV-2 strains in a subject.

Compositions herein can be prepared in unit dosage forms, such as in a kit, for administration to a subject. The amount and timing of administration are at the discretion of the administering physician to achieve the desired purposes. The antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody), conjugate, nucleic acid molecule, or vector can be formulated for systemic or local administration. In one example, the composition is formulated for parenteral administration, such as intravenous administration. In other examples, the composition is formulated for administration by inhalation. In another example, the composition is formulated for intranasal administration.

In some aspects, an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody), antigen binding fragment, conjugate, nucleic acid or vector in the composition is at least 70% (for example, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%) pure. In some aspects, the composition contains less than 10% (for example, less than 5%, less than 4%, less than 3%, less than 2%, less than 1%, less than 0.5%, or even less) of macromolecular contaminants, such as other mammalian (e.g., human) proteins.

In some aspects, the composition further includes a pharmaceutically acceptable carrier. Compositions for administration can include a solution of the antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody), conjugate, nucleic acid molecule or vector dissolved in a pharmaceutically acceptable carrier. In some examples, the pharmaceutically acceptable carrier is an aqueous carrier. A variety of aqueous carriers can be used, for example, buffered saline and the like. These solutions are sterile and generally free of undesirable matter. These compositions may be sterilized by any suitable technique. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, toxicity adjusting agents, and the like; for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, and sodium lactate. The concentration of antibody, antigen binding fragment, conjugate, or nucleic acid molecule in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight, and the like in accordance with the particular agent and mode of administration selected and the subject’s needs.

A typical composition for intravenous administration comprises about 0.01 to about 30 mg/kg of an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody disclosed herein) per subject per day (or the corresponding dose of a conjugate including the antibody). Any suitable method may be used for preparing administrable compositions; non-limiting examples are provided in such publications as Remington: The Science and Practice of Pharmacy, 22^nd ed., London, UK: Pharmaceutical Press, 2013. In some aspects, the composition is a liquid formulation including one or more antibodies (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) in a concentration range from about 0.1 mg/mL to about 20 mg/mL, from about 0.5 mg/mL to about 20 mg/mL, from about 1 mg/mL to about 20 mg/mL, from about 0.1 mg/mL to about 10 mg/mL, from about 0.5 mg/mL to about 10 mg/mL, or from about 1 mg/mL to about 10 mg/mL.

Antibodies (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), conjugates, nucleic acid molecules or vectors disclosed herein, can be provided in lyophilized form and rehydrated with sterile water before use or administration, although they can also be provided in sterile solutions of known concentration. In one example a concentrated solution including at least one of the disclosed monoclonal antibodies, antigen binding fragments, conjugates, and nucleic acid molecules is added to an infusion bag containing, for example, 0.9% sodium chloride, USP, for administration to a subject. For infusion administration, a typical dose ranges from 0.5 to 15 mg/kg of body weight. Considerable experience is available in the art in the administration of antibodybased compositions, which have been marketed in the U.S. since the approval of Rituximab in 1997. Antibodies (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), conjugates, nucleic acid molecules and/or vectors disclosed herein can be administered by slow infusion or in an intravenous push or bolus. In one example, a higher loading dose is administered, with subsequent, maintenance doses being administered at a lower level. For example, an initial loading dose of 4 mg/kg may be infused over a period of some 90 minutes, followed by weekly maintenance doses for 4-8 weeks of 2 mg/kg infused over a 30-niinute period if the previous dose was well tolerated.

Controlled-release parenteral formulations can be made as implants, oily injections, or as particulate systems. For a broad overview of protein delivery systems see, Banga, Therapeutic Peptides and Proteins: Formulation, Processing, and Delivery Systems, Lancaster, PA: Technomic Publishing Company, Inc., 1995. Particulate systems include microspheres, microparticles, microcapsules, nanocapsules, nanospheres, and nanoparticles. Microcapsules contain the active protein agent, such as a cytotoxin or a drug, as a central core. In microspheres, the active protein agent is dispersed throughout the particle. Particles, microspheres, and microcapsules smaller than about 1 |im are generally referred to as nanoparticles, nanospheres, and nanocapsules, respectively. Capillaries have a diameter of approximately 5 |im, so that only nanoparticles are administered intravenously. Microparticles are typically around 100 |tm in diameter and are administered subcutaneously or intramuscularly. See, for example, Kreuter, Colloidal Drug Delivery Systems, J. Kreuter (Ed.), New York, NY: Marcel Dekker, Inc., pp. 219-342, 1994; and Tice and Tabibi, Treatise on Controlled Drug Delivery: Fundamentals, Optimization, Applications, A. Kydonieus (Ed.), New York, NY: Marcel Dekker, Inc., pp. 315-339, 1992.

Polymers can be used for ion-controlled release of the compositions disclosed herein. Any suitable polymer may be used, such as a degradable or nondegradable polymeric matrix designed for use in controlled drug delivery. Alternatively, hydroxyapatite has been used as a microcarrier for controlled release of proteins. In yet another aspect, liposomes are used for controlled release as well as drug targeting of the lipid-capsulated drug.

VII. Methods

The antibodies

monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), conjugates, nucleic acid molecules, vectors, host cells, and compositions herein can be used in myriad applications, including for research, diagnostic, treatment, and/or prophylactic purposes. For example, specific monoclonal antibodies and antigen binding fragments herein can be used to diagnose a subject with a SARS-CoV-2 infection, or can be administered to inhibit a SARS- CoV-2 infection in a subject. In some examples, the disclosed monoclonal antibodies and antigen binding fragments are useful for research, diagnosis, treatment, and/or prophylaxis of a SARS-CoV-2 VOC.

Methods of Detection and Diagnosis

Methods are provided for the detection of the presence of a coronavirus spike protein in vitro or in vivo. In one example, a sample obtained from a subject (e.g., a human subject) is contacted with an antibody disclosed herein (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), and specific binding of the antibody to its target (coronavirus spike protein) is detected, thereby detecting the presence of a coronavirus spike protein in the sample. In some implementations, the sample is contacted with the antibody under conditions sufficient to form an immune complex. In some examples, detecting specific binding of the antibody to a coronavirus spike protein includes detecting the formation of an immune complex, which includes the antibody and the coronavirus spike protein.

In some examples, the presence of a coronavirus spike protein in a biological sample from a subject, is used to identify a subject with an infection. The sample can be any sample, including, but not limited to, tissue from biopsies, autopsies, and pathology specimens. Biological samples also include sections of tissues, for example, frozen sections taken for histological purposes. Biological samples further include body fluids, such as sputum, saliva, mucus, nasal wash, nasopharyngeal samples, oropharyngeal samples, peripheral blood, tissue, cells, urine, tissue biopsy, fine needle aspirate, surgical specimen, feces, cerebral spinal fluid (CSF), and bronchoalveolar lavage (BAL) fluid. The method of detection can include contacting a cell or sample, with a monoclonal antibody or antigen binding fragment herein or conjugate thereof e.g., a conjugate including a detectable marker) that specifically binds to a coronavirus spike protein, under conditions sufficient to form an immune complex, and detecting the immune complex (e.g., by detecting a detectable marker conjugated to the monoclonal antibody or antigen binding fragment).

In one aspect, the antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) is directly labeled with a detectable marker to facilitate detection. In another aspect, the antibody that binds the coronavirus spike protein is unlabeled, and a secondary antibody or other molecule that specifically bind the antibody is utilized for detection. For example, if the antibody is a human IgG antibody, then the secondary antibody may be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.

Suitable labels for the antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, betagalactosidase, or acetylcholinesterase. Non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin. Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin. A non-limiting exemplary luminescent material is luminol; a non-limiting exemplary a magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include ¹²⁵I, ¹³¹I, ³⁵S or ³H. hi an alternative aspect, spike protein can be assayed in a biological sample by a competition immunoassay utilizing spike protein standards labeled with a detectable substance and an unlabeled antibody (e.g., monoclonal antibody or antigen binding fragment) that specifically binds spike protein. In this assay, the biological sample, the labeled spike protein standards, and the antibody that specifically binds the spike protein are combined, and the amount of labeled spike protein standard bound to the unlabeled antibody is determined. The amount of spike protein in the biological sample is inversely proportional to the amount of labeled spike protein standard bound to the antibody that specifically binds the spike protein.

The immunoassays and methods disclosed herein can be used for a number of purposes. In one aspect, the antibody disclosed herein (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) specifically binds coronavirus spike protein and is used to detect the production of spike protein in cells in cell culture. In another aspect, the antibody disclosed herein (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) is used to detect the amount of spike protein in a biological sample, such as a sample obtained from a subject having or suspected or having a coronavirus infection.

In one aspect, a kit is provided for detecting coronavirus spike protein in a biological sample, such as a nasopharyngeal, oropharyngeal, sputum, saliva, or blood sample. Kits for detecting a coronavirus infection will typically comprise an antibody that specifically binds coronavirus spike protein, such as any of the antibodies disclosed herein (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein). In a further aspect, the antibody is labeled (for example, with a fluorescent, radioactive, or an enzymatic label).

In one aspect, a kit includes instructional materials that disclose means of use of the antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) that binds coronavirus spike protein. The instructional materials may be written, in an electronic form (such as on a website, downloadable form from a cloud or website, or on a drive) or may be visual (such as video files). The kits may also include additional components to facilitate the particular application for which the kit is designed. Thus, for example, the kit may additionally contain means of detecting a label (for example, enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a secondary antibody, and the like). The kits may additionally include buffers and other reagents routinely used for the practice of a particular method. In specific examples, the kit includes a monoclonal antibody or antigen binding fragment disclosed herein, and one or more detection reagents, buffers, and solid supports.

In one aspect, the diagnostic kit comprises an immunoassay. Although the details of the immunoassays may vary with the particular format employed, the method of detecting spike protein in a biological sample generally includes the steps of contacting the biological sample with at least one antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) which specifically reacts, under immunologically reactive conditions, to coronavirus spike protein. The antibody specifically binds under immunologically reactive conditions to form an immune complex, and the presence of the immune complex (bound antibody) is detected directly or indirectly. The disclosed antibodies and antigen binding fragments can also be used in nanotechnology methods, such as microfluidic immunoassays, which can be used to capture coronavirus (e.g., WT SARS-CoV-2, and SARS- CoV-2 variants), or exosomes containing coronavirus. Suitable samples for use with a microfluidic immunoassay or other nanotechnology method, include but are not limited to, saliva, blood, and fecal samples. Microfluidic immunoassays are described in U.S. Patent Application No. 2017/0370921, 2018/0036727, 2018/0149647, 2018/0031549, 2015/0158026 and 2015/0198593; and in Lin et al., JALA June 2010, pages 254-274; Lin et al., Anal Chem 92: 9454-9458, 2020; and Herr et al., Proc Natl Acad Sci USA 104(13): 5268-5273, 2007).

In some aspects, a disclosed antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) is used to test vaccines. For example, to test if a vaccine composition including a coronavirus spike protein, or a fragment thereof, assumes a conformation including the epitope of the disclosed antibody. Thus, provided herein is a method for testing a vaccine, wherein the method includes contacting a sample containing the vaccine, such as a coronavirus spike protein immunogen, with at least one disclosed antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), under conditions sufficient for formation of an immune complex, and detecting the immune complex, to detect the vaccine including the epitope of interest in the sample. The detection of the immune complex in the sample indicates that vaccine component assumes a conformation capable of binding the antibody.

Methods of Treating or Inhibiting a Coronavirus Infection

Methods are disclosed herein for treating or inhibiting a coronavirus infection in a subject, such as a SARS-CoV-2 infection. Such methods include administering an effective amount of a disclosed antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), nucleic acid, vector, or composition to the subject. In some examples, the infecting SARS-CoV-2 is WT SARS-CoV-2, Alpha SARS-CoV-2, Beta SARS-CoV-2, Gamma SARS-CoV-2, Delta SARS-CoV-2, Omicron SARS-CoV-2, or any of the foregoing strains comprising the S6P mutations. In some implementations the method treats or inhibits infection by more than one SARS-CoV-2 strain or variant, for example, a plurality of SARS-CoV-2 strains or variants (e.g., WT SARS-CoV-2, Alpha SARS- CoV-2, Beta SARS-CoV-2, Gamma SARS-CoV-2, Delta SARS-CoV-2, Omicron SARS-CoV-2, or any of the foregoing strains comprising the S6P mutations). A single clinical tool that treats or inhibits a plurality of SARS-CoV-2 strains or variants is useful, for example, when the SARS-CoV-2 strain infecting a subject has not been identified.

In some implementations, the disclosed methods include administering to the subject an effective amount (such as an amount effective to inhibit the infection in the subject) of a disclosed antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), nucleic acid, vector, or composition to a subject at risk of a coronavirus infection or having a coronavirus infection. Particular methods can be carried out pre-exposure or post-exposure. In some examples, the monoclonal antibody or antigen binding fragment is included in a bispecific antibody, such as a DVD-Immunoglobulin. In some examples, the antigen binding fragment is an scFv.

The infection does not need to be completely eliminated or inhibited for the method to be effective. For example, the method can decrease the infection by a desired amount, for example by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable coronavirus infection), as compared to a suitable control (e.g., a measurement of coronavirus infection (e.g., viral titers or a disease symptom) in the absence of treatment, or a measurement prior to initiation of treatment). In some aspects, the subject can also be treated with an effective amount of an additional agent, such as an anti-viral agent.

In some aspects, administration of an effective amount of a disclosed antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein) nucleic acid, vector, or composition inhibits the establishment of an infection and/or subsequent disease progression in a subject, which can encompass any statistically significant reduction in activity (for example, virus replication) or symptom of the coronavirus infection in the subject (such as fever or cough).

Methods are also provided herein for the inhibition of coronavirus replication in a subject. Such methods include administering to the subject an effective amount (e.g., an amount effective to inhibit coronavirus replication in the subject) of a disclosed antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies disclosed herein), nucleic acid molecule, vector, or composition to a subject at risk of a coronavirus infection or having a coronavirus infection. Such methods can be used pre-exposure or post-exposure.

Further provided are methods for treating a coronavirus infection in a subject, and methods for preventing a coronavirus infection in a subject. These methods include administering to the subject one or more of the antibodies (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies) nucleic acid molecules, vectors, and compositions disclosed herein.

Antibodies (including antigen binding fragments) can be administered, for example, by intravenous infusion. Doses of the antibody (including antigen binding fragments) according to specific methods herein vary, but generally range between about 0.5 mg/kg to about 50 mg/kg; for example, about 1 mg/kg, about 5 mg/kg, about 10 mg/kg, about 20 mg/kg, about 30 mg/kg, about 40 mg/kg, or about 50 mg/kg. In some aspects, the dose of the antibody may be from about 0.5 mg/kg to about 5 mg/kg; for example, about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg or about 5 mg/kg. The antibody is administered according to a dosing schedule determined by a medical practitioner. In some examples, the antibody is administered weekly, every two weeks, every three weeks, or every four weeks.

In some examples, any of the methods disclosed herein further comprise administering one or more additional agents to the subject. Exemplary additional agents include, without limitation, anti-viral agents such as hydroxychloroquine, arbidol, remdesivir, favipiravir, baricitinib, lopinavir/ritonavir, Zinc ions, interferon beta-1 b, a second antibody, and their combinations. In some aspects, the methods include administering a first antibody (e.g., monoclonal antibodies, antigen binding fragments, bispecific antibodies, or multispecific antibodies) that specifically binds to a coronavirus spike protein as disclosed herein, and a second antibody that also specifically binds to a coronavirus protein, such as on a different epitope of the coronavirus protein.

In some aspects, a subject is administered DNA or RNA encoding a disclosed antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody) to provide in vivo antibody production, for example, using the cellular machinery of the subject. Any suitable method of nucleic acid administration may be used; non-limiting examples are provided in U.S. Patent No. 5,643,578, U.S. Patent No. 5,593,972, and U.S. Patent No. 5,817,637. U.S. Patent No. 5,880,103 describes several methods of delivery of nucleic acids encoding proteins to an organism. One approach for administering nucleic acids to a subject is direct administration of plasmid DNA, such as a mammalian expression plasmid encoding an antibody disclosed herein. The polynucleotide encoding the disclosed antibody can be placed under the control of a promoter to increase expression. The methods also include liposomal delivery of nucleic acids. In some implementations, a disclosed antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody) is expressed in a subject using the pVRC8400 vector (described in Barouch et al., J. Virol., 79(14), 8828-8834, 2005).

In several aspects, a subject (such as a human subject at risk of a coronavirus infection or having a coronavirus infection) is administered an effective amount of a viral vector comprising at least one polynucleotide encoding a disclosed antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody disclosed herein). The viral vector is designed for expression of the polynucleotide(s) encoding a disclosed antibody in a host cell (e.g., a cell of the subject). Administration of an effective amount of the viral vector to the subject results in expression of an effective amount of the antibody in the subject. Non-limiting examples of viral vectors that can be used to express a disclosed antibody in a subject include those provided in Johnson et al., Nat. Med., 15(8):901-906, 2009 and Gardner et al., Nature, 519(7541):87-91 , 2015.

In one aspect, a nucleic acid encoding an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody) disclosed herein is introduced directly into tissue or cells. For example, the nucleic acid can be loaded onto gold microspheres by standard methods, and introduced into the skin by a device such as Bio-Rad’s HELIOS™ Gene Gun. The nucleic acids can be “naked,” consisting of plasmids under the control of a strong promoter. Typically, the DNA is injected into muscle, although it can also be injected directly into other sites. Dosages for injection are usually from about 0.5 Jlg/kg to about 50 mg/kg, and more typically are from about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Patent No. 5,589,466).

Compositions including a disclosed antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody disclosed herein), nucleic acid or vector encoding such molecules can be singly or multiply administered depending on the dosage and frequency as required and tolerated by the patient. The dosage can be administered once, but may be applied periodically until either a desired result is achieved or until side effects warrant discontinuation of therapy. Generally, the dose is sufficient to inhibit a coronavirus infection without producing unacceptable toxicity to the patient.

Data obtained from cell culture assays and animal studies can support a range of dosage for use in humans. The dosage normally lies within a range of circulating concentrations that include the ED50, with little or minimal toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized.

Kits are also provided for treating or preventing a coronavirus infection, such as SARS-CoV-2 infection. Kits for treating or preventing a coronavirus infection include an antibody (e.g., monoclonal antibody, antigen binding fragment, bispecific antibody, or multispecific antibody disclosed herein), nucleic acid, vector, or composition disclosed herein. In some examples, the kit includes a means for administering the antibody, nucleic acid, vector, or composition to a subject. Such means include, for example and without limitation, syringes, needles, and/or nebulizers. In some examples, the kit includes additional therapeutic agents, for example and without limitation, one or more additional anti-viral agents, such as remdesivir, galidesivir, favipiravir, baricitinib, lopinavir/ritonavir, hydroxychloroquine, dexamethasone, molnupiravir (Merck), arbidol, zinc ions, and/or interferon beta-lb.

The following examples are provided to illustrate particular features of certain aspects of the disclosure, but the scope of the claims should not be construed as limited to those features exemplified.

EXAMPLES

EXAMPLE 1

Computational rational design of antibodies and antigen binding fragments capable of binding with high affinity to SARS-CoV-2

A novel workflow that uses the RosettaAntibodyDesign (RAbD) computational method was used to rationally design antibodies and antibody fragments capable of binding with high affinity to SARS-CoV-2. This approach allows for identification and evaluation of novel anti-viral antibodies on a time scale that is appropriate for public health emergencies.

The initial step of SARS-CoV-2 infection involves the engagement of the spike protein of the virus with the human ACE2 receptor located most abundantly in the lungs. The spike protein is a trimeric glycoprotein containing 3 receptor-binding domains (RBDs) that bind with high affinity to the ACE2 receptor. The antibody 80R was re-designed to bind the SARS-CoV-2 spike protein with high affinity. 80R was selected as the initial template because a crystal structure is available for the SARS-CoV-1 antigen-80R antibody complex, and 80Rhas been shown to bind and neutralize the highly -related virus, SARS-CoV-1 (but not SARS-CoV-2). A panel of antibody variants designed using RAbD were experimentally validated. Particular designs are able to bind to the spike proteins of multiple current clinically important variants, such as Omicron, Delta, WA-1, and Beta. The receptor-binding domains of the spike proteins of the virus surface glycoprotein for SARS- CoV-2 and SARS-CoV-1 are highly similar in sequence and structures, with minimal amino acid differences. As shown in FIG. 1, a co-crystal structure of the 80R single-chain Fv bound to the SARS-CoV- 1 RED (PDB 2GHW) was used as a starting point for design. Tire AHo-renumbered (PMID: 25392411) antibody Fv region and the SARS-CoV-2 RED (PDB 6M0J) were separately minimized into the Rosetta energy function using CDRDihedralConstraints (PMID: 29702641) for the CDR regions and dihedral and coordinate constraints for the framework. They were then brought into contact by aligning to the PDB 2GHW co-crystal structure.

A total of 30 designs were generated based on antibody 80R using different RAbD design approaches. Briefly, design runs allowing sequence design for the light chain CDR loops and the light chain DE loop, as well as heavy chain CDR loops 1 and 2, were set up. A designated CDR H3 design run was also set up, allowing sequence design for the H3 loop. Mutations were sampled from a manually curated set of CDR loops with the same canonical conformation that was identified for antibody 80R. CDR H3 mutations that were predicted to be beneficial with a regular design run were manually combined in designs 80R_18 through 8OR_3O.

Models of aligned binding interface for the 8OR-SARS-C0V-I RBD, and surface alignments of the interfaces of WT SARS-CoV-2 S6P RBD, Delta variant B.l .617.2, Beta variant B.l .351 (S6P), and Omicron variant B.l.1.529 are shown in FIG. 2. Energy minimization of the binding interface provided the most accurate representation of whether mutations are beneficial vis-a-vis binding affinity. The interface score thus provided the best computational parameter for monitoring an enhancement in antibody-antigen binding. Using interface energy score as the initial screen, the total energy score for the best-scoring interface score models was considered.

Following interface score-sorting, the mutations introduced in our RAbD-based designs were manually inspected to determine if any favorable interactions were introduced at the antibody- antigen interface. In the manual evaluation of the antibody variants, consideration was given to factors such as additional hydrogen bonds, filling hydrophobic pockets and increased contact between the two proteins.

EXAMPLE 2

Materials and Methods

Antibody production and purification

Full length IgG antibodies were codon-optimized, ordered, expressed, and purified by Genscript™. Designed heavy chain (HC/VH) and light chain (LC/BL) was used with Genscript’ s default CH/CL (human IgGl and human Ig kappa). The recombinant plasmids (pcDNA3.4 as the expression vector) encoding 30 designs based on the antibody 80R as a template, and the wild-type 80R antibody, were transiently cotransfected into suspension mammalian HD 293F cells. All proteins were expressed, purified by affinity purification column, and buffer exchanged into PBS buffer pH 7.2. The purified protein was analyzed by SDS-PAGE analysis to determine the molecular weight and purity (>95% purity). Biolayer interferometry

Recombinant SARS-CoV-2 RBD-His Tag protein (Genscript Cat. No. Z03483) was loaded onto Anti-Penta-HIS (HIS IK) biosensors at 20 nM concentrations, designed antibodies were added at various concentrations (20 nM and 10 nM) for real time association and dissociation analysis, and data analysis. Octet was used for data processing. Recombinant wild-type SARS-CoV-2 full length spike trimer protein, WT SARS-CoV-2 S6P full length trimer spike variant, Beta SARS-CoV-2 S6P full length trimer spike variant, Delta SARS-CoV-2 full length trimer spike variant, and Omicron SARS-CoV-2 full length trimer spike variant were loaded onto Anti-Human IgG-Fc Capture (AHC) biosensors and real time association and dissociation experiments were conducted. All Octet experiments used 96-well, black, flat bottom, polypropylene microplates.

EXAMPLE 3

Binding of computationally designed antibodies to SARS-CoV-2 wild- type spike and variants

The light and heavy chain variable regions from 80R and the 30 80R antibody designs contained a relatively small number of common mutations in the CDRs. See, FIG. 4 (VLs) and FIG. 5 (VHs). AH designs based on the 80R antibody showed no binding to the wild-type RBD, but 10 designs exhibited binding to the wild-type full-length trimeric spike protein with KD values ranging from 0.4 nM to 1 14 nM (Table 4). In addition, the 80R_5, 80R_18, 80R_19, and 80R_23 designs bound the wild-type full-length trimeric spike protein (FIG. 6A), and at least one other spike protein variant (FIG. 6B) with KD values ranging from <0.001 nM to 7.99 nM (Table 4). The 80R_5 and 80R_23 designs were able to bind the full- length spike proteins from WT SARS-CoV-2, and from Delta, Beta (S6P), and Omicron variants. (Table 4). Models of the 80R_23 (FIG. 7A) and 80R_5 (FIG. 7B) light and heavy chain variable regions bound to the WT SARS-CoV-2 spike protein RBD show the interfaces of the antibody-antigen complexes, and allow identification of the contact residues in the variable regions (FIG. 7C).

Table 4. Biolayer interferometry binding affinities for 80R designs to WT SARS-CoV-2 full length trimer spike protein, WT S6P SARS-CoV-2 spike protein, Delta spike variant, Beta S6P spike variant, and

Omicron spike variant.

*N: no binding

*ND: not determined

80R_5 was able to bind to all the full-length spike proteins tested including WT SARS-CoV-2, WT SARS-CoV-2 (S6P), Delta, Beta (S6P), and Omicron spike variants (Table 3; FIG. 6A-B; FIG. 8), making this antibody a potential generalizable antibody that could bind to any SARS-CoV-2 spike variant that emerges. This is a significant result considering the 80R wild-type antibody did not show any binding to either the RBD or the full-length wild-type trimer spike protein, indicating that the mutations sufficiently altered the protein-protein interface to permit high affinity binding to the target of interest. To further understand the binding results, models were generated (using RosettaFastRelax with constraints and no constraints) of the 80R_5 antibody design to the full Omicron spike. Focus was placed on the Omicron variant since, as of the end of December 2021, it was a fast-spreading variant that became the dominant strain of Covid-19 in the US according to the CDC, accounting for 73.2 percent of all new cases. It was observed in the models that, compared to wild-type RBD protein, the Omicron N440K breaks a bidente hydrogen bond to the Y67 on the H chain of the antibody. Mutation G446S also creates a spatial clash. In addition, Q493R exchanges a side chain hydrogen bond with T39 of the L chain for a bidente backbone hydrogen bond with D58, while also forming an intra-chain backbone bond with F490. Lastly, G496S and N501Y form an intra-chain sidechain hydrogen bond, replacing the backbone bond that was previously there before in the wild-type RBD. FIG. 9 illustrates mutations in both the heavy chain and light chain of the 80R antibody (green) with hydrophobic residues shown (purple), and a favorable electrostatic interaction between Q493 and T39.

EXAMPLE 4

Neutralization of SARS-CoV-2 variants.

80_R antibody designs are evaluated using recombinant antibodies (individually and as a cocktail) in vitro, and in vivo in an animal model, for their capacity to neutralize the WT SARS-CoV-2 virus and variants of concern (VOC).

8OR_18 is found to be potent in neutralizing WT SARS-CoV-2 and/or Omicron SARS-CoV-2, with IC50 values the nanomolar range. 80R_19 is found to be potent in neutralizing WT SARS-CoV-2 and/or Beta SARS-CoV-2, with IC50 values the nanomolar range. 80R_23 is found to be potent in neutralizing WT SARS-CoV-2, Delta SARS-CoV-2, Beta SARS-CoV-2, and/or Omicron SARS-CoV-2, with 1C50 values the nanomolar range. 80R_5 is found to be potent in neutralizing WT SARS-CoV-2, Delta SARS- CoV-2, Beta SARS-CoV-2, Omicron SARS-CoV-2, and/or SARS-CoV-2 (S6P) with IC50 values the nanomolar range.

EXAMPLE 5

Protection from SARS-CoV-2 infection

Broadly neutralizing 80_R antibody designs, 80R_5, 8OR_18, 80R_19, and/or 80R_23 are evaluated for in vivo prophylactic efficacy, including reduced incidence of COVID infection, and/or reduced incidence of severe disease (e.g., reduced incidence or severity of pneumonia caused by SARS-CoV-2 infection). The antibodies are tested in an animal model that supports efficient viral replication and mimics the severity of COVID- 19 in humans.

The animals are inoculated with mAbs or scFvs and control. Based on the in vitro neutralization results, 80R_5, 80R_18, 80R_19, and/or 80R_23 are tested against the WT SARS-CoV-2 WA-1 strain, 80R_5 and/or 80R_23 are tested against the Delta SARS-CoV-2 variant, 80R_5, 80R_19, and/or 80R_23 are tested against the Beta SARS-CoV-2 variant, and 80R_5, 80R_18, and/or 80R_23 are tested against the Omicron SARS-CoV-2 variant.

Treatment of animals with 80R_5, 80R_18, 80R_19, and/or 80R_23 significantly protects the animals from the WT SARS-CoV-2 WA-1 strain, with a significant number of animals showing reduced incidence of infection and/or reduced incidence of severe disease following infection. Treatment of animals with 80R_5 and/or 80R_23 significantly protects the animals from the Delta SARS-CoV-2 variant, with a significant number of animals showing reduced incidence of infection and/or reduced incidence of severe disease following infection. Treatment of animals with 80R_5, 80R_19, and/or 80R_23 significantly protects the animals from the Beta SARS-CoV-2 variant, with a significant number of animals showing reduced incidence of infection and/or reduced incidence of severe disease following infection. Treatment of animals with 80R_5, 8OR_18, and/or 80R_23 significantly protects the animals from the Omicron SARS- CoV-2 variant, with a significant number of animals showing reduced incidence of infection and/or reduced incidence of severe disease following infection.

In animals treated with 80R_5, 8OR_18, 80R_19, or 80R_23, post-infection titers of their target SARS-CoV-2 strains are significantly reduced in examined tissues compared to controls.

EXAMPLE 6

Therapeutic activity against SARS-CoV-2 strains

Antibody designs 80R_5, 80R_18, 80R_19, and/or 80R_23 are evaluated for in vivo therapeutic efficacy. The antibodies are tested in an animal model that supports efficient viral replication and mimics the severity of COVID-19 in humans.

The therapeutic efficacy is evaluated by administering the antibodies to the animals after challenge with WT SARS-CoV-2 (WA-1), Delta SARS-CoV-2, Beta SARS-CoV-2, Omicron SARS-CoV-2, or control. Post-challenge viral load is measured in animal tissue. Analysis of viral load in the tissue shows a significant reduction in viral titers as compared to control in animals infected with WA-1 that are treated with 80R_5, 8OR_18, 80R_19, or 80R_23. Analysis of viral load shows a significant reduction in viral titers as compared to control in animals infected with Delta SARS-CoV-2 that are treated with 80R_5 or 80R_23. Analysis of viral load shows a significant reduction in viral titers as compared to control in animals infected with Beta SARS-CoV-2 that are treated with 80R_5, 80R_19, or 80R_23. Analysis of viral load shows a significant reduction in viral titers as compared to control in animals infected with Omicron SARS-CoV-2 that are treated with 80R_5, 80R_18, or 80R_23.

It will be apparent that the precise details of the methods or compositions described may be varied or modified without departing from the spirit of the described aspects of the disclosure. We claim all such modifications and variations that fall within the scope and spirit of the claims below.

Claims

CLAIMS We claim:

1. A monoclonal antibody or antigen binding fragment, comprising: a light chain variable domain (VL) comprising a light chain complementarity determining region (LCDR)l, a LCDR2, and a LCDR3 comprising amino acid sequences set forth as SEQ ID NOs: 33, 34, and 35, respectively, and a heavy chain variable domain (VH) comprising a heavy chain complementarity determining region (HCDR)1, a HCDR2, and a HCDR3 comprising amino acid sequences set forth as SEQ ID NOs: 36, 37, and 38, respectively, wherein the monoclonal antibody or antigen binding fragment specifically binds to a receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein from multiple strains of SARS-CoV-2.

2. The monoclonal antibody or antigen binding fragment of claim 1, wherein the LCDR1, the LCDR2, and the LCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 39, 40, and 41, respectively, and the HCDR1, the HCDR2, and the HCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 42, 43, and 44, respectively.

3. The monoclonal antibody or antigen binding fragment of claim 1 or claim 2, wherein:

(A) the LCDR1, the LCDR2, and the LCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 3, 4, and 5, respectively, and the HCDR1, the HCDR2, and the HCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 6, 7, and 8, respectively;

(B) the LCDR1, the LCDR2, and the LCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 11, 12, and 13, respectively, and the HCDR1, the HCDR2, and the HCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 14, 15, and 16, respectively;

(C) the LCDR1, the LCDR2, and the LCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 19, 20, and 21, respectively, and the HCDR1, the HCDR2, and the HCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 22, 23, and 24, respectively; or

(D) the LCDR1, the LCDR2, and the LCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 27, 28, and 29, respectively, and the HCDR1, the HCDR2, and the HCDR3 comprise amino acid sequences set forth as SEQ ID NOs: 30, 31, and 32, respectively.

4. The monoclonal antibody or antigen binding fragment of any one of claims 1-3, wherein the VL and the VH comprise amino acid sequences at least at least 90% identical to SEQ ID NOs: 45 and 72, respectively.

5. The monoclonal antibody or antigen binding fragment of any one of claims 1-4, wherein the VL and the VH comprise amino acid sequences at least at least 90% identical to:

(A) SEQ ID NOs: 1 and 2, respectively;

(B) SEQ ID NOs: 9 and 10, respectively;

(C) SEQ ID NOs: 17 and 18, respectively; or

(D) SEQ ID NOs: 25 and 26, respectively.

6. The monoclonal antibody or antigen binding fragment of claim 5, wherein the VL and the VH comprise the amino acid sequences of:

(A) SEQ ID NOs: 1 and 2, respectively;

(B) SEQ ID NOs: 9 and 10, respectively;

(C) SEQ ID NOs: 17 and 18, respectively; or

(D) SEQ ID NOs: 25 and 26, respectively.

7. The monoclonal antibody or antigen binding fragment of any one of claims 1-6, wherein the monoclonal antibody or antigen binding fragment specifically binds to at least two of: wild-type, wild-type S6P, Beta, Beta S6P, and Omicron SARS-CoV-2 spike proteins.

8. The monoclonal antibody or antigen binding fragment of any one of claims 5-7, wherein the monoclonal antibody or antigen binding fragment comprises:

(A) a VL domain at least 90% identical to SEQ ID NO: 1, and a VH domain at least 90% identical to SEQ ID NO: 2, wherein the monoclonal antibody or antigen binding fragment specifically binds to the receptor binding domains (RBDs) of the wild-type, wild-type S6P, Beta S6P, Delta, and Omicron SARS-CoV-2 spike proteins with a KD less than 10 nM;

(B) a VL domain at least 90% identical to SEQ ID NO:9, and a VH domain at least 90% identical to SEQ ID NO: 10, wherein the monoclonal antibody or antigen binding fragment specifically binds to the RBDs of the wild-type and Omicron SARS-CoV-2 spike proteins with a KD less than 10 nM;

(C) a VL domain at least 90% identical to SEQ ID NO: 17, and a VH domain at least 90% identical to SEQ ID NO: 18, wherein the monoclonal antibody or antigen binding fragment specifically binds to the RBDs of the wild-type and Beta S6P SARS-CoV-2 spike proteins with a KD less than 10 nM; or

(D) a VL domain at least 90% identical to SEQ ID NO:25, and a VH domain at least 90% identical to SEQ ID NO: 26, wherein the monoclonal antibody or antigen binding fragment specifically binds to the RBDs of the wild-type, Beta S6P, Delta, and Omicron SARS-CoV-2 spike proteins with a KD less than 10 nM.

9. The monoclonal antibody or antigen binding fragment of any one of claims 1-8, wherein the monoclonal antibody or antigen binding fragment is a human monoclonal antibody or antigen binding fragment.

10. The monoclonal antibody or antigen binding fragment of any one of claims 1-9, comprising the monoclonal antibody.

11. The monoclonal antibody of claim 10, comprising a human constant domain.

12. The monoclonal antibody of claim 10 or claim 11, comprising a recombinant constant domain comprising a modification that increases the half-life of the monoclonal antibody.

13. The monoclonal antibody of claim 12, wherein the modification increases binding to the neonatal Fc receptor.

14. The monoclonal antibody or antigen binding fragment of any one of claims 1-9, wherein the antigen binding fragment is selected from a group consisting of Fv, Fab, F(ab’)2, scFv, and scFv2.

15. The antigen binding fragment of claim 14, wherein the antigen binding fragment is the scFv.

16. The monoclonal antibody or antigen binding fragment of any one of claims 1-15, wherein the monoclonal antibody or antigen binding fragment neutralizes at least one of: wild-type S6P, Beta S6P, Delta, and Omicron SARS-CoV-2.

17. The monoclonal antibody or antigen binding fragment of any one of claims 1-16, conjugated to a detectable marker.

18. A bispecific antibody comprising the monoclonal antibody or antigen binding fragment of any one of claims 1-17.

19. An isolated nucleic acid molecule comprising a polynucleotide encoding the monoclonal antibody or antigen binding fragment of any one of claims 1-17, a VH and/or VL of the monoclonal antibody or antigen binding fragment of any one of claims 1-17, or the bispecific antibody of claim 18.

20. The nucleic acid molecule of claim 19, wherein the polynucleotide is operably linked to a promoter.

21. A vector comprising the nucleic acid molecule of claim 19 or claim 20.

22. A host cell comprising the nucleic acid molecule or vector of any one of claims 19-21.

23. A composition comprising: the monoclonal antibody or antigen binding fragment of any one of claims 1-17, the bispecific antibody of claim 18, the nucleic acid molecule of claim 19 or claim 20, or the vector of claim 21; and a pharmaceutically acceptable carrier.

24. A method for producing a monoclonal antibody or antigen binding fragment that specifically binds to a SARS-CoV-2 spike protein, comprising: expressing one or more polynucleotides encoding the monoclonal antibody or antigen binding fragment of any one of claims 1-17 in a host cell; and purifying the monoclonal antibody or antigen binding fragment.

25. A method for detecting the presence of SARS-CoV-2 in a biological sample from a subject, comprising: contacting the biological sample with an effective amount of the monoclonal antibody or antigen binding fragment of any one of claims 1-17 under conditions sufficient to form an immune complex; and detecting the presence of the immune complex in the biological sample.

26. The method according to claim 25, wherein detecting the presence of the immune complex in the biological sample indicates that the subject has a SARS-CoV-2 infection.

27. A method for inhibiting a SARS-CoV-2 infection in a subject, comprising administering to the subject an effective amount of the monoclonal antibody or antigen binding fragment of any one of claims 1-17, the bispecific antibody of claim 18, the nucleic acid molecule of claim 19 or claim 20, or the vector of claim 21, wherein the subject has or is at risk of contracting a SARS-CoV-2 infection.

28. The method according to claim 27, wherein the SARS-CoV-2 is a SARS-CoV-2 variant selected from a group consisting of: Delta SARS-CoV-2, Beta SARS-CoV-2, and Omicron SARS-CoV-2.

29. A kit, comprising: the monoclonal antibody or antigen binding fragment of any one of claims 1-17; and one or more of: instructional materials, detection reagents, and buffers.

30. Use of the monoclonal antibody or antigen binding fragment of any one of claims 1-17, the bispecific antibody of claim 18, the nucleic acid molecule of claim 19 or claim 20, or the vector of claim 21, for inhibiting a SARS-CoV-2 infection in a subject or to detect the presence of SARS-CoV-2 in a biological sample.