ANTIBODIES TO SARS-COV-2

RELATED APPLICATIONS

This application claims priority under 35 U.S.C. §119(e) to U.S. Provisional Patent Application No. 63/231,848 filed August 11, 2021, which is incorporated herein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on , is named and is bytes in size.

BACKGROUND OF THE INVENTION

A virus is a submicroscopic infectious agent that replicates within a living host cell of another organism. When the host cell is infected by a virus, the virus causes the host cell to produce additional copies of the virus that may then infect other cells within the same organism or spread to other organisms.

When outside of a host a cell, a virus exists as an independent particle that may be referred to as a virion. Typically, a virion will include genetic material enclosed in a capsid consisting of protein and, in some cases, a lipid bilayer. The genetic material may be a molecule of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).

Various types of viruses infect all types of life forms. Viruses are responsible for causing many diseases within the human species, including the common cold, influenza, chickenpox, rabies, acquired immune deficiency syndrome (AIDS), and many others. As another example, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the 2019-20 coronavirus pandemic, has infected humans around the world, causing the coronavirus disease 2019 (CO VID- 19).

SARS-CoV-2 has four major structural proteins, specifically the spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. The N protein holds the RNA genome, while the other three structural proteins are components of the viral envelope. The S protein is responsible for allowing the virus to attach and fuse to the membrane of a host cell. It comprises an SI domain which mediates the attachment and an S2 domain which mediates the fusion of the viral cellular membrane with the host cell. The SI domain comprises the receptor binding domain (RBD), the binding site to the receptor angiotensin converting enzyme 2 (ACE2) on human host cells. Therefore, the RBD is a binding site of neutralizing antibodies which block the interaction between the virus and its host cells, thus conferring immunity. By contrast to SARS-CoV-1 and SARS- CoV-2, which are associated with a high mortality and severe illness, other coronaviruses exist which are associated with a mild and passing illness, such as coronaviruses 229E, NL63, OC43 and HKU 1. These coronaviruses are frequently associated with common cold, especially among children.

Once an organism is infected by a virus, it may release virion that can infect other organisms. For example, the organism may spread virion through coughing, sneezing, or even exhaling. Infected individuals may be asked or required to quarantine to prevent spreading of the virus to others. Unfortunately, quarantine is only effective in preventing the spread of virus by those individuals who have been identified as being infected.

In view of the current severe threat posed by the ongoing global SARS-CoV-2 pandemic, there is an urgent need in the art for improved, and in particular, more sensitive antibodies, that may be used in methods for diagnosing a SARS-CoV-2 infection, particularly for the early diagnosis of a SARS-CoV-2 infection, and for differentiation thereof from infections with other coronaviruses, and also for treating coronavirus infection. The current disclosure addresses this need.

SUMMARY OF THE INVENTION

The disclosure provides for new therapeutic and diagnostic antibodies to coronaviruses, and, in particular, to SARS-CoV-2 and its variants. Generally, the disclosure provides monoclonal antibodies or antigen-binding fragments that selectively bind to a protein of a coronavirus (e.g., SARS-CoV-2), such as the spike protein, nucleocapsid protein, envelope protein, and membrane protein.

In some embodiments, the disclosure provides for a monoclonal antibody that selectively binds to a nucleocapsid protein, an envelope protein, a membrane protein, or a spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) comprising or consisting of a heavy chain complementarity determining region 1 (CDR1) region, a heavy chain CDR2 region, and a heavy chain CDR3 region, wherein the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise or consist of amino acid sequences of: a) SEQ ID NOS: 1, 51, and 101, respectively; b) SEQ ID NOS: 3, 53, and 103, respectively; c) SEQ ID NOS: 5, 55, and 105, respectively; d) SEQ ID NOS: 7, 57, and 107, respectively; e) SEQ ID NOS: 9, 59, and 109, respectively; f) SEQ ID NOS: 11, 61, and 111, respectively; g) SEQ ID NOS: 13, 63, and 113, respectively; h) SEQ ID NOS: 15, 65, and 115, respectively; i)SEQ ID NOS: 17, 67, and 117, respectively; j) SEQ ID NOS: 19, 69, and 119, respectively; k) SEQ ID NOS: 20,

70, and 120, respectively; 1) SEQ ID NOS: 23, 73, and 123, respectively; m) SEQ ID NOS: 26, 76, and 126, respectively; n) SEQ ID NOS: 28, 78, and 128, respectively; o) SEQ ID NOS: 30, 80, and 130, respectively; p) SEQ ID NOS: 32, 82, and 132, respectively; q) SEQ ID NOS: 35, 85, and 135, respectively; r) SEQ ID NOS: 37, 87, and 137, respectively; s) SEQ ID NOS: 39, 89, and 139, respectively; t) SEQ ID NOS: 41, 91, and 141, respectively; u) SEQ ID NOS: 43, 93, and 143, respectively; v) SEQ ID NOS: 45, 95, and 145, respectively; w) SEQ ID NOS: 47, 97, and 147, respectively; or x) SEQ ID NOS: 49, 99, and 149, respectively; and the monoclonal antibody comprising a light chain CDR1 region, a light chain CDR2 region, and a light chain CDR3 region, wherein the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: aa) SEQ ID NOS: 2, 52, and 102, respectively; bb) SEQ ID NOS: 4, 54, and 104, respectively; cc) SEQ ID NOS: 6, 56, and 106, respectively; dd) SEQ ID NOS: 8, 58, and 108, respectively; ee) SEQ ID NOS: 10, 60, and 110, respectively; ff) SEQ ID NOS: 12, 62, and 112, respectively; gg) SEQ ID NOS: 14, 64, and 114, respectively; hh) SEQ ID NOS: 16, 66, and 116, respectively; ii) SEQ ID NOS: 18, 68, and 118, respectively; jj) SEQ ID NOS: 21, 71, and 121, respectively; kk) SEQ ID NOS: 22, 72, and 122, respectively; 11) SEQ ID NOS: 24, 74, and 124, respectively; mm) SEQ ID NOS: 25, 75, and 125, respectively; nn) SEQ ID NOS: 27, 77, and 127, respectively; oo) SEQ ID NOS: 29, 79, and 129, respectively; pp) SEQ ID NOS: 31, 81, and 131, respectively; qq) SEQ ID NOS: 33, 83, and 133, respectively; rr) SEQ ID NOS: 34, 84, and 134, respectively; ss) SEQ ID NOS: 36, 86, and 136, respectively; tt) SEQ ID NOS: 38, 88, and 138, respectively; uu) SEQ ID NOS: 40, 90, and 140, respectively; vv) SEQ ID NOS: 42, 92, and 142, respectively; ww) SEQ ID NOS: 44, 94, and 144, respectively; xx) SEQ ID NOS: 46, 96, and 146, respectively; yy) SEQ ID NOS: 48, 98, and 148, respectively; or zz) SEQ ID NOS: 50, 100, and 150, respectively.

In some embodiments, a monoclonal antibody may comprise or consist of a variable heavy chain region and a variable light chain region, wherein each of the variable heavy chain region and the variable light chain region comprises or consists of : a) SEQ ID NOS: 151 and 152, respectively; b) SEQ ID NOS: 153 and 154, respectively; c) SEQ ID NOS: 155 and 156, respectively; d) SEQ ID NOS: 157 and 158, respectively; e) SEQ ID NOS: 159 and 160, respectively; f) SEQ ID NOS: 161 and 162, respectively; g) SEQ ID NOS: 163 and 164, respectively; h) SEQ ID NOS: 165 and 166, respectively; i) SEQ ID NOS: 167 and 168, respectively; j) SEQ ID NOS: 169 and 171, respectively; k) SEQ ID NOS: 169 and 172, respectively; 1) SEQ ID NOS: 170 and 171, respectively; m) SEQ ID NOS: 170 and 172, respectively; n) SEQ ID NOS: 173 and 174, respectively; o) SEQ ID NOS: 176 and 177, respectively; p) SEQ ID NOS: 178 and 179, respectively; q) SEQ ID NOS: 180 and 181, respectively; r) SEQ ID NOS: 182 and 183, respectively; s) SEQ ID NOS: 182 and 184, respectively; t) SEQ ID NOS: 185 and 186, respectively; u) SEQ ID NOS: 187 and 188, respectively; v) SEQ ID NOS: 189 and 190, respectively; w) SEQ ID NOS: 191 and 192, respectively; x) SEQ ID NOS: 193 and 194, respectively; y) SEQ ID NOS: 195 and 196, respectively; z) SEQ ID NOS: 197 and 198, respectively; aa) SEQ ID NOS: 199 and 200, respectively.

In other embodiments, a monoclonal antibody may comprise or consist of a heavy chain and a light chain, wherein the heavy chain and the light chain each comprise or consist of an amino acid sequence: a) SEQ ID NOS: 201 and 202, respectively; b) SEQ ID NOS: 203 and 204, respectively; c) SEQ ID NOS: 205 and 206, respectively; d) SEQ ID NOS: 207 and 208, respectively; e) SEQ ID NOS: 209 and 210, respectively; f) SEQ ID NOS: 211 and 212, respectively; g) SEQ ID NOS: 213 and 214, respectively; h) SEQ ID NOS: 215 and 216, respectively; or i) SEQ ID NOS: 217 and 218, respectively.

The disclosure also provides for a polynucleotide encoding a variable heavy chain region and a variable light chain region, wherein the DNA sequence of the variable heavy chain region and a variable light chain region comprises or consists of : a) SEQ ID NO: 237 and SEQ ID NO: 239, respectively; b) SEQ ID NO: 237 and SEQ ID NO: 240, respectively; c) SEQ ID NO: 238 and SEQ ID NO: 239, respectively; d) SEQ ID NO: 238 and SEQ ID NO: 240, respectively; e) SEQ ID NO: 238 and SEQ ID NO: 240, respectively; f) SEQ ID NO: 241 and SEQ ID NO: 242, respectively; g) SEQ ID NO: 241 and SEQ ID NO: 243, respectively; h) SEQ ID NO: 244 and SEQ ID NO: 245, respectively; i) SEQ ID NO: 246 and SEQ ID NO: 247, respectively; j) SEQ ID NO: 248 and SEQ ID NO: 249, respectively; k) SEQ ID NO: 250 and SEQ ID NO: 251, respectively; 1) SEQ ID NO: 250 and SEQ ID NO: 252, respectively; m) SEQ ID NO: 253 and SEQ ID NO: 254, respectively; n) SEQ ID NO: 255 and SEQ ID NO: 256, respectively; o) SEQ ID NO: 257 and SEQ ID NO: 258, respectively; p) SEQ ID NO: 259 and SEQ ID NO: 260, respectively; q) SEQ ID NO: 261 and SEQ ID NO: 262, respectively; r) SEQ ID NO: 263 and SEQ ID NO: 264, respectively; s) SEQ ID NO: 265 and SEQ ID NO: 266, respectively; or t) SEQ ID NO: 267 and SEQ ID NO: 268, respectively.

In other embodiments, a polynucleotide encoding a heavy chain, wherein the heavy chain DNA sequence comprises or consists of any one of SEQ ID NOS: 219, 221, 223, 225, 227, 229, 231, 233, and 235; and/or a DNA sequence encoding a light chain, wherein the light chain DNA sequence comprises or consists of any one of SEQ ID NOS: 220, 22, 224, 226, 228, 230, 232, 234, and 236.

In still other embodiments, a polynucleotide encodes a heavy chain and a light chain, wherein the DNA sequence of the heavy chain and the light chain comprise or consist of: a) SEQ ID NO: 219 and SEQ ID NO: 220, respectively; b) SEQ ID NO: 221 and SEQ ID NO: 222, respectively; c) SEQ ID NO: 223 and SEQ ID NO: 224, respectively; d) SEQ ID NO: 225 and SEQ ID NO: 226, respectively; e) SEQ ID NO: 227 and SEQ ID NO: 228, respectively; f) SEQ ID NO: 229 and SEQ ID NO: 230, respectively; g) SEQ ID NO: 231 and SEQ ID NO: 232, respectively; h) SEQ ID NO: 233 and SEQ ID NO: 234, respectively; or i) SEQ ID NO: 235 and SEQ ID NO: 236, respectively;

The present invention and its attributes and advantages will be further understood and appreciated with reference to the detailed description below of presently contemplated embodiments, taken in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the specification and are included to further demonstrate certain embodiments or various aspects of the invention. In some instances, embodiments of the invention can be best understood by referring to the accompanying drawings in combination with the detailed description presented herein. The description and accompanying drawings may highlight a certain specific example, or a certain aspect of the invention. However, one skilled in the art will understand that portions of the example or aspect may be used in combination with other examples or aspects of the invention.

FIG. 1. illustrates a list of amino acid and DNA sequences of certain embodiments of the disclosure; and

FIG. 2 illustrates amino acid and DNA sequences of certain embodiments of disclosure. DETAILED DESCRIPTION OF THE INVENTION

Definitions

The following definitions are included to provide a clear and consistent understanding of the specification and claims. As used herein, the recited terms have the following meanings. All other terms and phrases used in this specification have their ordinary meanings as one of skill in the art would understand. Such ordinary meanings may be obtained by reference to technical dictionaries, such as Hawley ’s Condensed Chemical Dictionary 14 ^th Edition, by R. J. Lewis, John Wiley & Sons, New York, N.Y., 2001 or Singleton, et al., Dictionary of Microbiology and Molecular Biology, 2d ed., John Wiley and Sons, New York (1994), and Hale & Markham, The Harper Collins Dictionary of Biology. Harper Perennial, N.Y. (1991).

References in the specification to "one embodiment", "an embodiment", etc., indicate that the embodiment described may include a particular aspect, feature, structure, moiety, or characteristic, but not every embodiment necessarily includes that aspect, feature, structure, moiety, or characteristic. Moreover, such phrases may, but do not necessarily, refer to the same embodiment referred to in other portions of the specification. Further, when a particular aspect, feature, structure, moiety, or characteristic is described in connection with an embodiment, it is within the knowledge of one skilled in the art to affect or connect such aspect, feature, structure, moiety, or characteristic with other embodiments, whether or not explicitly described.

The singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to "a compound" includes a plurality of such compounds, so that a compound X includes a plurality of compounds X. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for the use of exclusive terminology, such as "solely," "only," and the like, in connection with any element described herein, and/or the recitation of claim elements or use of "negative" limitations.

The term "and/or" means any one of the items, any combination of the items, or all of the items with which this term is associated. The phrases "one or more" and "at least one" are readily understood by one of skill in the art, particularly when read in context of its usage. For example, the phrase can mean one, two, three, four, five, six, ten, 100, or any upper limit approximately 10, 100, or 1000 times higher than a recited lower limit. For example, one or more substituents on a phenyl ring refers to one to five, or one to four, for example if the phenyl ring is di substituted. As will be understood by the skilled artisan, all numbers, including those expressing quantities of ingredients, properties such as molecular weight, reaction conditions, and so forth, are approximations and are understood as being optionally modified in all instances by the term "about." These values can vary depending upon the desired properties sought to be obtained by those skilled in the art utilizing the teachings of the descriptions herein. It is also understood that such values inherently contain variability necessarily resulting from the standard deviations found in their respective testing measurements. When values are expressed as approximations, by use of the antecedent "about," it will be understood that the particular value without the modifier "about" also forms a further aspect.

The term "about" can refer to a variation of ± 5%, ± 10%, ± 20%, or ± 25% of the value specified. For example, "about 50" percent can in some embodiments carry a variation from 45 to 55 percent, or as otherwise defined by a particular claim. For integer ranges, the term "about" can include one or two integers greater than and/or less than a recited integer at each end of the range. Unless indicated otherwise herein, the term "about" is intended to include values, e.g., weight percentages, proximate to the recited range that are equivalent in terms of the functionality of the individual ingredient, composition, or embodiment. The term about can also modify the endpoints of a recited range as discussed above in this paragraph.

As will be understood by one skilled in the art, for any and all purposes, particularly in terms of providing a written description, all ranges recited herein also encompass any and all possible sub-ranges and combinations of sub-ranges thereof, as well as the individual values making up the range, particularly integer values. It is therefore understood that each unit between two particular units are also disclosed. For example, if 10 to 15 is disclosed, then 11, 12, 13, and 14 are also disclosed, individually, and as part of a range. A recited range (e.g., weight percentages or carbon groups) includes each specific value, integer, decimal, or identity within the range. Any listed range can be easily recognized as sufficiently describing and enabling the same range being broken down into at least equal halves, thirds, quarters, fifths, or tenths. As a non-limiting example, each range discussed herein can be readily broken down into a lower third, middle third and upper third, etc. As will also be understood by one skilled in the art, all language such as "up to", "at least", "greater than", "less than", "more than", "or more", and the like, include the number recited and such terms refer to ranges that can be subsequently broken down into sub-ranges as discussed above. In the same manner, all ratios recited herein also include all sub-ratios falling within the broader ratio. Accordingly, specific values recited for radicals, substituents, and ranges, are for illustration only; they do not exclude other defined values or other values within defined ranges for radicals and substituents. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint.

One skilled in the art will also readily recognize that where members are grouped together in a common manner, such as in a Markush group, the invention encompasses not only the entire group listed as a whole, but each member of the group individually and all possible subgroups of the main group. Additionally, for all purposes, the invention encompasses not only the main group, but also the main group absent one or more of the group members. The invention therefore envisages the explicit exclusion of any one or more of members of a recited group. Accordingly, provisos may apply to any of the disclosed categories or embodiments whereby any one or more of the recited elements, species, or embodiments, may be excluded from such categories or embodiments, for example, for use in an explicit negative limitation.

The term "contacting" refers to the act of touching, making contact, or of bringing to immediate or close proximity, including at the cellular or molecular level, for example, to bring about a physiological reaction, a chemical reaction, or a physical change, e.g., in a solution, in a reaction mixture, in vitro, or in vivo.

The terms "treating", "treat" and "treatment" include (i) preventing a disease, pathologic or medical condition from occurring (e.g., prophylaxis); (ii) inhibiting the disease, pathologic or medical condition or arresting its development; (iii) relieving the disease, pathologic or medical condition; and/or (iv) diminishing symptoms associated with the disease, pathologic or medical condition. Thus, the terms "treat", "treatment", and "treating" can extend to prophylaxis and can include prevent, prevention, preventing, lowering, stopping or reversing the progression or severity of the condition or symptoms being treated. As such, the term "treatment" can include medical, therapeutic, and/or prophylactic administration, as appropriate.

The terms "inhibit", "inhibiting", and "inhibition" refer to the slowing, halting, or reversing the growth or progression of a disease, infection, condition, or group of cells. The inhibition can be greater than about 20%, 40%, 60%, 80%, 90%, 95%, or 99%, for example, compared to the growth or progression that occurs in the absence of the treatment or contacting.

The term "antibody" as used herein refers to a polypeptide (or set of polypeptides) of the immunoglobulin family that is capable of binding an antigen non- covalently, reversibly and specifically. For example, a naturally occurring "antibody" of the IgGtype is a tetramer comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. The heavy chain constant region is comprised of three domains, CHI, CH2 and CH3. Each light chain is comprised of a light chain variable region (abbreviated herein as VL) and a light chain constant region. The light chain constant region is comprised of one domain, CL. The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs arranged from amino-terminus to carboxy -terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen, which is sometimes referred to herein as the antigen binding domain. The constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system. The term "antibody" includes, but is not limited to, monoclonal antibodies, human antibodies, humanized antibodies, camelised antibodies, chimeric antibodies, bispecific or multispecific antibodies and anti -idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies described herein), single chain variable fragments, and single domain antibodies. The antibodies can be of any isotype/class (e.g., IgG, IgE, IgM, IgD, IgA and IgY) or subclass (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2). Both the light and heavy chains are divided into regions of structural and functional homology. The terms "constant" and "variable" are used functionally. In this regard, it will be appreciated that the variable domains of both the light (VL) and heavy (VH) chain portions determine antigen recognition and specificity. Conversely, the constant domains of the light chain (CL) and the heavy chain (CHI, CH2 or CH3) confer important biological properties such as secretion, transplacental mobility, Fc receptor binding, complement binding, and the like. By convention the numbering of the constant region domains increases as they become more distal from the antigen binding site or amino- terminus of the antibody. The N-terminus is a variable region and at the C-terminus is a constant region; the CH3 and CL domains actually comprise the carboxy-terminus of the heavy and light chain, respectively.

A “monoclonal antibody” refers to a homogeneous antibody population involved in the highly specific recognition and binding of a single antigenic determinant, or epitope. This is in contrast to polyclonal antibodies that typically include different antibodies directed against different antigenic determinants. The term “monoclonal antibody” encompasses both intact and full-length monoclonal antibodies as well as antibody fragments (such as Fab, Fab', F(ab')2, F _v ), single chain (scFv) mutants, fusion proteins comprising an antibody portion, and any other modified immunoglobulin molecule comprising an antigen recognition site. Furthermore, “monoclonal antibody” refers to such antibodies made in any number of manners including but not limited to by hybridoma, phage selection, recombinant expression, and transgenic animals.

As used herein, “humanized” antibodies refer to forms of non-human (e.g., murine) antibodies that are specific chimeric immunoglobulins, immunoglobulin chains, or fragments thereof that contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a complementarity determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat, or rabbit having the desired specificity, affinity, and biological activity. In some instances, Fv framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, the humanized antibody may comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences but are included to further refine and optimize antibody performance. In general, a humanized antibody comprises substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region or domain (Fc), typically that of a human immunoglobulin. Antibodies may have Fc regions modified as described in, for example, WO 99/58572. Other forms of humanized antibodies have one or more CDRs (one, two, three, four, five, or six) which are altered with respect to the original antibody, which are also termed one or more CDRs “derived from” one or more CDRs from the original antibody. (Jones et al., Nature 321 :522-525, 1986; Riechmann et al., Nature 332:323-327, 1988; Verhoeyen et al., Science 239: 1534-1536, 1988).

A “variable region” of an antibody refers to the variable region of the antibody light chain or the variable region of the antibody heavy chain, either alone or in combination. The variable regions of the heavy and light chain each consist of four framework regions (FR) connected by three complementarity determining regions (CDRs) also known as hypervariable regions. The CDRs in each chain are held together in close proximity by the FRs and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies. There are at least two techniques for determining CDRs: (1) an approach based on cross-species sequence variability (i.e., Kabat et al. Sequences of Proteins of Immunological Interest, 5th ed., 1991, National Institutes of Health, Bethesda Md.); and (2) an approach based on crystallographic studies of antigen-antibody complexes (Al-lazikani et al., J. Molec. Biol. 273:927-948, 1997). In addition, combinations of these two approaches are sometimes used in the art to determine CDRs.

The term “chimeric antibodies” refers to antibodies wherein the amino acid sequence of the immunoglobulin molecule is derived from two or more species. Typically, the variable region of both light and heavy chains corresponds to the variable region of antibodies derived from one species of mammals (e.g., mouse, rat, rabbit, etc.) with the desired specificity, affinity, and capability while the constant regions are homologous to the sequences in antibodies derived from another (usually human) to avoid or reduce the chance of eliciting an immune response in that species (e.g., human). In certain embodiments, chimeric antibody may include an antibody or antigen-binding fragment thereof comprising at least one human heavy and/or light chain polypeptide, such as, for example, an antibody comprising murine light chain and human heavy chain polypeptides.

The terms “epitope” or “antigenic determinant” are used interchangeably herein and refer to that portion of an antigen capable of being recognized and specifically bound by a particular antibody. When the antigen is a polypeptide, epitopes can be formed both from contiguous amino acids and noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained upon protein denaturing, whereas epitopes formed by tertiary folding are typically lost upon protein denaturing. An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation.

As used herein, “fused” means to couple directly or indirectly one molecule with another by whatever means, e.g., by covalent bonding, by non-covalent bonding, by ionic bonding, or by non-ionic bonding. Covalent bonding includes bonding by various linkers such as thioether linkers or thioester linkers. Direct fusion involves one molecule attached to the molecule of interest. Indirect fusion involves one molecule attached to another molecule which in turn is attached directly or indirectly to the molecule of interest.

As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprising amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein's or peptide's sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides, and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.

By the term “specifically binds,” as used herein, is meant a molecule, such as an antibody, which recognizes and binds to another molecule or feature, but does not substantially recognize or bind other molecules or features in a sample.

The term “binding affinity” generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, “binding affinity” refers to intrinsic binding affinity which reflects a 1 : 1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd) or the half-maximal effective concentration (ECso). Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present invention. Specific illustrative embodiments are described herein.

The term "sample" from a subject may be a sample of any bodily fluid or tissue of said subject that may comprise an antibody. Exemplary bodily fluids include for example blood, saliva, nasal mucus or lymph fluid. In some embodiments, the sample is a blood sample, preferably selected from the group comprising whole blood, serum, plasma, capillary blood, arterial blood, venous blood or any mixture thereof. The capillary blood is preferably in the form of a dried blot spot, which may be prepared by the patient, sent to the lab, followed by extraction of the blood. The person of ordinary skill is aware of various means and methods that may be applied to obtain a sample from a subject suitable for the purposes of the herein disclosed methods, products and uses and in the required quantities. In certain embodiments, the sample may be obtained from the subject by a physician, whereas in other cases, the sample may be obtained by the subject itself, for example, by using minimal invasive means, such as finger pricking to draw blood ("fingerstick blood"). In preferred embodiments, the sample is a saliva sample or nasal swab.

As used herein, “sequence identity” or “identity” in the context of two nucleic acid or polypeptide sequences makes reference to a specified percentage of residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window, as measured by sequence comparison algorithms or by visual inspection. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity.” Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).

As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.

The term “substantial identity” in the context of a peptide indicates that a peptide comprises a sequence with at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, or 94%, or even 95%, 96%, 97%, 98% or 99%, sequence identity to the reference sequence over a specified comparison window. In certain embodiments, optimal alignment is conducted using the homology alignment algorithm of Needleman and Wunsch (Needleman and Wunsch, JMB, 48, 443 (1970)). An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide. Thus, a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution. Thus, the invention also provides nucleic acid molecules and peptides that are substantially identical to the nucleic acid molecules and peptides presented herein.

For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

Nucleic acid sequences cited herein are written in a 5' to 3' direction unless indicated otherwise. The term "nucleic acid" refers to either DNA or RNA or a modified form thereof comprising the purine or pyrimidine bases present in DNA (adenine "A", cytosine "C", guanine "G", thymine "T") or in RNA (adenine "A", cytosine "C", guanine "G", uracil "U"). Interfering RNAs provided herein may comprise "T" bases, for example at 3' ends, even though "T" bases do not naturally occur in RNA. In some cases, these bases may appear as "dT" to differentiate deoxyribonucleotides present in a chain of ribonucleotides.

The term “polynucleotide” refers to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. Polynucleotides can have any three- dimensional structure and may perform any function, known or unknown. The following are nonlimiting examples of polynucleotides: a gene or gene fragment (for example, a probe, primer, or EST), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, RNAi, siRNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers. A polynucleotide can comprise, or alternatively consist essentially of, or yet further consist of modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after assembly of the polynucleotide. The sequence of nucleotides can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component. The term also refers to both double- and single-stranded molecules. Unless otherwise specified or required, any embodiment of this invention that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.

A polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for thymine when the polynucleotide is RNA. Thus, the term “polynucleotide sequence” is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching.

A polynucleotide of this invention can be delivered to a cell or tissue using a gene delivery vehicle. “Gene delivery,” “gene transfer,” “transducing,” and the like as used herein, are terms referring to the introduction of an exogenous polynucleotide (sometimes referred to as a “transgene”) into a host cell, irrespective of the method used for the introduction. Such methods include a variety of well-known techniques such as vector-mediated gene transfer (by, e.g., viral infection/transfection, or various other protein-based or lipid-based gene delivery complexes) as well as techniques facilitating the delivery of “naked” polynucleotides (such as electroporation, “gene gun” delivery and various other techniques used for the introduction of polynucleotides). The introduced polynucleotide may be stably or transiently maintained in the host cell. Stable maintenance typically requires that the introduced polynucleotide either contains an origin of replication compatible with the host cell or integrates into a replicon of the host cell such as an extrachromosomal replicon (e.g., a plasmid) or a nuclear or mitochondrial chromosome. A number of vectors are known to be capable of mediating transfer of genes to mammalian cells, as is known in the art and described herein.

A “viral vector” is defined as a recombinantly produced virus or viral particle that comprises, or alternatively consists essentially of, or yet further consists of a polynucleotide to be delivered into a host cell, either in vivo, ex vivo or in vitro. Examples of viral vectors include retroviral vectors, adenovirus vectors, adeno-associated virus vectors, alphavirus vectors and the like. Alphavirus vectors, such as Semliki Forest virus-based vectors and Sindbis virus-based vectors, have also been developed for use in gene therapy and immunotherapy. See, Schlesinger and Dubensky (1999) Curr. Opin. Biotechnol. 5:434-439 and Ying, et al. (1999) Nat. Med. 5(7):823-827. In aspects where gene transfer is mediated by a retroviral vector, a vector construct refers to the polynucleotide comprising, or alternatively consisting essentially of, or yet further consisting of the retroviral genome or part thereof, and a therapeutic gene.

As used herein, “retroviral mediated gene transfer” or “retroviral transduction” carries the same meaning and refers to the process by which a gene or nucleic acid sequences are stably transferred into the host cell by virtue of the virus entering the cell and integrating its genome into the host cell genome. The virus can enter the host cell via its normal mechanism of infection or be modified such that it binds to a different host cell surface receptor or ligand to enter the cell. As used herein, retroviral vector refers to a viral particle capable of introducing exogenous nucleic acid into a cell through a viral or viral-like entry mechanism.

Retroviruses carry their genetic information in the form of RNA; however, once the virus infects a cell, the RNA is reverse transcribed into the DNA form which integrates into the genomic DNA of the infected cell. The integrated DNA form is called a provirus.

In aspects where gene transfer is mediated by a DNA viral vector, such as an adenovirus (Ad) or adeno-associated virus (AAV), a vector construct refers to the polynucleotide comprising, or alternatively consisting essentially of, or yet further consisting of the viral genome or part thereof, and a transgene. Adenoviruses (Ads) are a relatively well characterized, homogenous group of viruses, including over 50 serotypes. See, e.g., International PCT Application No. WO 95/27071. Ads do not require integration into the host cell genome. Recombinant Ad derived vectors, particularly those that reduce the potential for recombination and generation of wild-type virus, have also been constructed. See, International PCT Application Nos. WO 95/00655 and WO 95/11984. Wild-type AAV has high infectivity and specificity integrating into the host cell's genome. See, Hermonat et al., (1984) Proc. Natl. Acad. Sci. USA 81 :6466-6470 and Lebkowski et al. (1988) Mol. Cell. Biol. 8:3988-3996.

Vectors that contain both a promoter and a cloning site into which a polynucleotide can be operatively linked are well known in the art. Such vectors are capable of transcribing RNA in vitro or in vivo and are commercially available from sources such as Stratagene (La Jolla, Calif.) and Promega Biotech (Madison, Wis.). In order to optimize expression and/or in vitro transcription, it may be necessary to remove, add or alter 5' and/or 3' untranslated portions of the clones to eliminate extra, potential inappropriate alternative translation initiation codons or other sequences that may interfere with or reduce expression, either at the level of transcription or translation. Alternatively, consensus ribosome binding sites can be inserted immediately 5' of the start codon to enhance expression.

A “plasmid” is an extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA. In many cases, it is circular and double-stranded. Plasmids provide a mechanism for horizontal gene transfer within a population of microbes and typically provide a selective advantage under a given environmental state. Plasmids may carry genes that provide resistance to naturally occurring antibiotics in a competitive environmental niche, or alternatively the proteins produced may act as toxins under similar circumstances.

“Plasmids” used in genetic engineering are called “plasmid vectors”. Many plasmids are commercially available for such uses. The gene to be replicated is inserted into copies of a plasmid containing genes that make cells resistant to particular antibiotics and a multiple cloning site (MCS, or polylinker), which is a short region containing several commonly used restriction sites allowing the easy insertion of DNA fragments at this location. Another major use of plasmids is to make large amounts of proteins. In this case, researchers grow bacteria containing a plasmid harboring the gene of interest. Just as the bacterium produces proteins to confer its antibiotic resistance, it can also be induced to produce large amounts of proteins from the inserted gene. This is a cheap and easy way of mass-producing a gene or the protein it then codes for.

Embodiments of the disclosure

The disclosure provides for antibodies and antigen-binding fragments that selectively bind to an antigenic protein of a coronavirus, and methods of use. Exemplary coronaviruses include severe acute respiratory syndrome associate coronavirus (SARS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or its variants (e.g., B. l.1.7, B.1.351, B.1.525, B.1.617, B.1.429, B.1.427, B.1.1.207, and P.l), or Middle East Respiratory Syndrome Coronavirus (MERS-CoV). In some embodiments, the disclosed antibodies or antigen-binding fragments may specifically bind to the nucleocapsid protein, the envelope protein, the membrane protein, or the spike protein of SARS-CoV-2, the amino acid sequences of which may be found, for example, at the UniProt database (www.uniprot.org), Sequence P0DTC9, P0DTC4, P0DTC5, and P0DTC2, respectively. In some embodiments, the antibodies or antigen-binding fragments specifically bind to the nucleocapsid protein of SARS-CoV-2. In preferred embodiments, the antibodies and antigen-binding fragments are monoclonal antibodies or antigen-binding fragments derived from monoclonal antibodies.

In some embodiments, an antibody of the disclosure comprises, consists essentially of, or consists of a variable heavy chain (VH ) region and a variable light (VL) chain region , the VH chain region comprising (a) a VH complementarity determining region 1 (CDR1) having an amino acid sequence of any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 23, 28, 30, 32, 35, 37, 39, 41, 43, 45, 47, and 49, (b) a VH CDR2 having an amino acid sequence of any one of SEQ ID NOS: 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 70, 73, 76, 78, 80, 82, 85, 87, 89, 91, 93, 95, 97, and 99, (c) a VH CDR3 having an amino acid sequence of any one of SEQ ID NOS: 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 120, 123, 126, 128, 130, 132, 135, 137, 139, 141, 143, 145, 147, and 149; and the VL chain comprises, consists essentially of, or consists of (d) a VL CDR1 having an amino acid sequence of any one of SEQ ID NOS: 2,4,6, 8, 10, 12, 14, 16, 21, 22, 24, 25, 27, 29, 31, 33, 34, 36, 38, 40, 42, 44, 46, 48, and 50, (e) a VL CDR2 having an amino acid sequence of any one of SEQ ID NOS: 52, 54, 56, 58, 60, 62, 64, 66, 68, 71, 72, 74, 75, 77, 79, 81, 83, 84, 86, 88, 90, 92, 94, 96, 98, and 100, and (f) a VL CDR3 having an amino acid sequence of any one of SEQ ID NOS: 102, 104, 106, 108, 110, 112, 114, 116, 118, 121, 122, 124, 125, 127, 129, 131, 133, 134, 136, 138, 140, 142, 144, 146, 148, and 150.

In some embodiments, the antibodies include a VH chain region further comprises a variable region sequence, the variable region sequence having an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or identical to any one of SEQ ID NOS: 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 170, 173, 176, 178, 180, 182, 185, 187, 189, 191, 193, 195, 197, and 199. In some embodiments, the VH chain variable region has an amino acid sequence of any one of SEQ ID NOS: 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 170, 173, 176, 178, 180, 182, 185, 187, 189, 191, 193, 195, 197, and 199.

In some embodiments, the antibodies include a VL chain further comprising a variable region sequence, the variable region sequence having an amino acid sequence at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or identical to any one of SEQ ID NOS: 152, 154, 156, 158, 160, 162, 164, 166, 168, 171, 172, 174, 175, 177, 179, 181, 183, 184, 186, 188, 190, 192, 194, 196, 198, and 200. In some embodiments, the variable region sequence has an amino acid sequence of any one of SEQ ID NOS: 152, 154, 156, 158, 160, 162, 164, 166, 168, 171, 172, 174, 175, 177, 179, 181, 183, 184, 186, 188, 190, 192, 194, 196, 198, and 200.

In some embodiments, the disclosure provides for a monoclonal antibody that selectively binds to a nucleocapsid protein, an envelope protein, a membrane protein, or a spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) comprising a heavy chain complementarity determining region 1 (CDR1) region, a heavy chain CDR2 region, and a heavy chain CDR3 region, wherein the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: a) SEQ ID NOS: 1, 51, and 101, respectively; b) SEQ ID NOS: 3, 53, and 103, respectively; c) SEQ ID NOS: 5, 55, and 105, respectively; d) SEQ ID NOS: 7, 57, and 107, respectively; e) SEQ ID NOS: 9, 59, and 109, respectively; f) SEQ ID NOS: 11, 61, and 111, respectively; g) SEQ ID NOS: 13, 63, and 113, respectively; h) SEQ ID NOS: 15, 65, and 115, respectively; i)SEQ ID NOS: 17, 67, and 117, respectively; j) SEQ ID NOS: 19, 69, and 119, respectively; k) SEQ ID NOS: 20, 70, and 120, respectively; 1)SEQ ID NOS: 23, 73, and 123, respectively; m) SEQ ID NOS: 26, 76, and 126, respectively; n) SEQ ID NOS: 28, 78, and 128, respectively; o) SEQ ID NOS: 30, 80, and 130, respectively; p) SEQ ID NOS: 32, 82, and 132, respectively; q) SEQ ID NOS: 35, 85, and 135, respectively; r) SEQ ID NOS: 37, 87, and 137, respectively; s) SEQ ID NOS: 39, 89, and 139, respectively; t)SEQ ID NOS: 41, 91, and 141, respectively; u) SEQ ID NOS: 43, 93, and 143, respectively; v) SEQ ID NOS: 45, 95, and 145, respectively; w) SEQ ID NOS: 47, 97, and 147, respectively; or x) SEQ ID NOS: 49, 99, and 149, respectively; and the monoclonal antibody comprising a light chain CDR1 region, a light chain CDR2 region, and a light chain CDR3 region, wherein the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: aa) SEQ ID NOS: 2, 52, and 102, respectively; bb) SEQ ID NOS: 4, 54, and 104, respectively; cc) SEQ ID NOS: 6, 56, and 106, respectively; dd) SEQ ID NOS: 8, 58, and 108, respectively; ee) SEQ ID NOS: 10, 60, and 110, respectively; ff) SEQ ID NOS: 12, 62, and 112, respectively; gg) SEQ ID NOS: 14, 64, and 114, respectively; hh) SEQ ID NOS: 16, 66, and 116, respectively; ii) SEQ ID NOS: 18, 68, and 118, respectively; jj) SEQ ID NOS: 21, 71, and 121, respectively; kk) SEQ ID NOS: 22, 72, and 122, respectively; 11) SEQ ID NOS: 24, 74, and 124, respectively; mm) SEQ ID NOS: 25, 75, and 125, respectively; nn) SEQ ID NOS: 27, 77, and 127, respectively; oo) SEQ ID NOS: 29, 79, and 129, respectively; pp) SEQ ID NOS: 31, 81, and 131, respectively; qq) SEQ ID NOS: 33, 83, and 133, respectively; rr) SEQ ID NOS: 34, 84, and 134, respectively; ss) SEQ ID NOS: 36, 86, and 136, respectively; tt) SEQ ID NOS: 38, 88, and 138, respectively; uu) SEQ ID NOS: 40, 90, and 140, respectively; vv) SEQ ID NOS: 42, 92, and 142, respectively; ww) SEQ ID NOS: 44, 94, and 144, respectively; xx) SEQ ID NOS: 46, 96, and 146, respectively; yy) SEQ ID NOS: 48, 98, and 148, respectively; or zz) SEQ ID NOS: 50, 100, and 150, respectively.

In some embodiments, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: a) SEQ ID NOS: 1, 51, and 101, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 151; b) SEQ ID NOS: 3, 53, and 103, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 153; c) SEQ ID NOS: 5, 55, and 105, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 155; d) SEQ ID NOS: 7, 57, and 107, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 157; e) SEQ ID NOS: 9, 59, and 109, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 159; f) SEQ ID NOS: 11, 61, and 111, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 161; g) SEQ ID NOS: 13, 63, and 113, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 163; h) SEQ ID NOS: 15, 65, and 115, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 165; i) SEQ ID NOS: 17, 67, and 117, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 167; j) SEQ ID NOS: 19, 69, and 119, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 169; k) SEQ ID NOS: 20, 70, and 120, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 170; 1) SEQ ID NOS: 23, 73, and 123, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 173; m) SEQ ID NOS: 26, 76, and 126, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 176; n) SEQ ID NOS: 28, 78, and 128, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 178; o) SEQ ID NOS: 30, 80, and 130, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 180; p) SEQ ID NOS: 32, 82, and 132, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 182; q) SEQ ID NOS: 35, 85, and 135, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 185; r) SEQ ID NOS: 37, 87, and 137, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 187; s) SEQ ID NOS: 39, 89, and 139, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 189; t) SEQ ID NOS: 41, 91, and 141, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 191; u) SEQ ID NOS: 43, 93, and 143, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 193; v) SEQ ID NOS: 45, 95, and 145, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 195; w) SEQ ID NOS: 47, 97, and 147, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 197; or x) SEQ ID NOS: 49, 99, and 149, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 199.

In some embodiments, the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: a) SEQ ID NOS: 2, 52, and 102, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 152; b) SEQ ID NOS: 4, 54, and 104, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 154; c) SEQ ID NOS: 6, 56, and 106, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 156; d) SEQ ID NOS: 8, 58, and 108, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 158; e) SEQ ID NOS: 10, 60, and 110, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 160; f) SEQ ID NOS: 12, 62, and 112, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 162; g) SEQ ID NOS: 14, 64, and 114, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 164; h) SEQ ID NOS: 16, 66, and 116, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 166; i) SEQ ID NOS: 18, 68, and 118, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 168; jj) SEQ ID NOS: 21, 71, and 121, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 171; kk) SEQ ID NOS: 22, 72, and 122, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 172; 11) SEQ ID NOS: 24, 74, and 124, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 174; mm) SEQ ID NOS: 25, 75, and 125, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 175; nn) SEQ ID NOS: 27, 77, and 127, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 177; oo) SEQ ID NOS: 29, 79, and 129, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 179; pp) SEQ ID NOS: 31, 81, and 131, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 181; qq) SEQ ID NOS: 33, 83, and 133, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 183; rr) SEQ ID NOS: 34, 84, and 134, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 184; ss) SEQ ID NOS: 36, 86, and 136, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 186; tt) SEQ ID NOS: 38, 88, and 138, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 188; uu) SEQ ID NOS: 40, 90, and 140, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 190; vv) SEQ ID NOS: 42, 92, and 142, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 192; ww) SEQ ID NOS: 44, 94, and 144, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 194; xx) SEQ ID NOS: 46, 96, and 146, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 196; yy) SEQ ID NOS: 48, 98, and 148, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 198; or zz) SEQ ID NOS: 50, 100, and 150, respectively, and further comprising a variable region sequence having an amino acid sequence at least 95% identical to SEQ ID NO: 200.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 1, 51, and 101, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 2, 52, and 102, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 3, 53, and 103, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 4, 54, and 104, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 5, 55, and 105, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 6, 56, and 106, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 7, 57, and 107, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 8, 58, and 108, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 9, 59, and 109, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 10, 60, and 110, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 11, 61, and 111, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 12, 62, and 112, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 13, 63, and 113, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 14, 64, and 114, respectively. In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 15, 65, and 115, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 16, 66, and 116, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 17, 67, and 117, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 18, 68, and 118, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 19, 69, and 119, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 21, 71, and 121, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 19, 69, and 119, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 22, 72, and 122, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 20, 70, and 120, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 21, 71, and 121, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 20, 70, and 120, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 22, 72, and 122, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 23, 73, and 123, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 24, 74, and 124, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 23, 73, and 123, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 25, 75, and 125, respectively. In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 26, 76, and 126, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 27, 77, and 127, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 28, 78, and 128, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 29, 79, and 129, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 30, 80, and 130, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 31, 81, and 131, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 32, 82, and 132, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 33, 83, and 133, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 32, 82, and 132, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 34, 84, and 134, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 35, 85, and 135, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 36, 86, and 136, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of SEQ ID NOS: 37, 87, and 137, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 38, 88, and 138, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 39, 89, and 139, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 40, 90, and 140, respectively. In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 41, 91, and 141, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 42, 92, and 142, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 43, 93, and 143, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 44, 94, and 144, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 45, 95, and 145, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 46, 96, and 146, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 47, 97, and 147, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 48, 98, and 148, respectively.

In one embodiment, the heavy chain CDR1 region, the heavy chain CDR2 region, and the heavy chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 49, 99, and 149, respectively; and the light chain CDR1 region, the light chain CDR2 region, and the light chain CDR3 region comprise amino acid sequences of: SEQ ID NOS: 50, 100, and 150, respectively.

In other embodiments, a monoclonal antibody may comprise a variable heavy chain region and a variable light chain region, wherein each of the variable heavy chain region and the variable light chain region comprises: a) SEQ ID NOS: 151 and 152, respectively; b) SEQ ID NOS: 153 and 154, respectively; c) SEQ ID NOS: 155 and 156, respectively; d) SEQ ID NOS: 157 and 158, respectively; e) SEQ ID NOS: 159 and 160, respectively; f) SEQ ID NOS: 161 and 162, respectively; g) SEQ ID NOS: 163 and 164, respectively; h) SEQ ID NOS: 165 and 166, respectively; i) SEQ ID NOS: 167 and 168, respectively; j) SEQ ID NOS: 169 and 171, respectively; k) SEQ ID NOS: 169 and 172, respectively; 1) SEQ ID NOS: 170 and 171, respectively; m) SEQ ID NOS: 170 and 172, respectively; n) SEQ ID NOS: 173 and 174, respectively; o) SEQ ID NOS: 176 and 177, respectively; p) SEQ ID NOS: 178 and 179, respectively; q) SEQ ID NOS: 180 and 181, respectively; r) SEQ ID NOS: 182 and 183, respectively; s) SEQ ID NOS: 182 and 184, respectively; t) SEQ ID NOS: 185 and 186, respectively; u) SEQ ID NOS: 187 and 188, respectively; v) SEQ ID NOS: 189 and 190, respectively; w) SEQ ID NOS: 191 and 192, respectively; x) SEQ ID NOS: 193 and 194, respectively; y) SEQ ID NOS: 195 and 196, respectively; z) SEQ ID NOS: 197 and 198, respectively; aa) SEQ ID NOS: 199 and 200, respectively.

In other embodiments, a monoclonal antibody may comprise a heavy chain and a light chain, wherein the heavy chain and the light chain each comprise an amino acid sequence comprising: a) SEQ ID NOS: 201 and 202, respectively; b) SEQ ID NOS: 203 and 204, respectively; c) SEQ ID NOS: 205 and 206, respectively; d) SEQ ID NOS: 207 and 208, respectively; e) SEQ ID NOS: 209 and 210, respectively; f) SEQ ID NOS: 211 and 212, respectively; g) SEQ ID NOS: 213 and 214, respectively; h) SEQ ID NOS: 215 and 216, respectively; or i) SEQ ID NOS: 217 and 218, respectively.

In some embodiments, the antibodies or antigen-binding fragments comprise or consist of one or more of the amino acid sequences listed in Example 1, or two or more of the amino acid sequences listed in Example 1, or three or more of the amino acid sequences listed in Example 1.

In some embodiments, the antibodies have a binding affinity for a target protein of less than 200 nanomolar (nM), less than 150 nM, less than 100 nM, less than 75 nM, less than 50 nM, less than 25 nM, less than 10 nM, less than 5 nM, or less than 1 nM. In some embodiments, the binding affinity of the antibody or antigen-binding fragment is less than 0.9 nM, less than 0.8 nM, less than 0.7 nM, less than 0.6 nM, less than 0.5 nM, less than 0.4 nM, less than 0.3 nM, less than 0.2 nM, less than 0.1 nM, less than 0.05 nM, less than .025 nM, or less than .001 nM. In some embodiments, the binding affinity is determined by surface plasmon resonance at 25 °C in PBS buffer at pH 7. Table 1 discloses some specificity and binding data of selected antibodies or antigen-binding fragments. In some embodiments, the monoclonal antibody comprises a binding affinity of less than 100 nanomolar for the nucleocapsid protein, the envelope protein, the membrane protein, or the spike protein. In other embodiments, certain antibodies have a binding affinity according to Table 1 below.

Table 1. Antigen specificity and binding data of certain antibodies or antigen-binding fragments.

In some embodiments, the antibodies or antigen-binding fragments comprise or consist of one or more of the amino acids and/or DNA sequences listed in Example 1, Figure 1, or Figure 2.

Antibodies and antigen-binding fragments used in the embodiments disclosed herein may be obtained by conventional antibody development techniques. See, e.g., Harlow and Lane, eds., ANTIBODIES; A LABORATORY MANUAL, Coldspring Harbor Laboratory, Coldspring, N.Y. Suitable inoculant for preparing the antibodies includes but not limited to the whole virus obtained from a clinical sample from an infected individual or a recombinant virus or virus protein. Suitable antibodies should be immunoreactive under aqueous and ionic and non-ionic detergent buffer conditions.

Polyclonal antibodies may be prepared, e.g., as described in Harboe and Ingild, Scand. J. Immun. 2 (Suppl. 1), p. 161-164, (1973). More specifically, polyclonal antibodies can be obtained by inoculating any of various host animals, including but not limited to rabbits, mice, rats, sheep, goats and the like, with the above-described inoculant in a suitable adjuvant, such as Freund’s incomplete or complete adjuvant. The inoculation may be followed by one or more booster injections at suitable intervals (e.g., one or two weeks to a month). The animals are bled regularly, for instance at weekly intervals, and the antibody is isolated from the serum.

Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein (1975) Nature 256:495 and U.S. Pat. No. 4,707,442. Using the hybridoma method, a mouse, hamster, or other appropriate host animal, is immunized to elicit the production by lymphocytes of antibodies that will specifically bind to an immunizing antigen. Lymphocytes can also be immunized in vitro. Following immunization, the lymphocytes are isolated and fused with a suitable myeloma cell line using, for example, polyethylene glycol, to form hybridoma cells that can then be selected away from unfused lymphocytes and myeloma cells. Hybridomas that produce monoclonal antibodies directed specifically against a chosen antigen as determined by immunoprecipitation, immunoblotting, or by an in vitro binding assay (e.g., radioimmunoassay (RIA); enzyme-linked immunosorbent assay (ELISA)) can then be propagated either in vitro culture using standard methods (Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, 1986) or in vivo as ascites tumors in an animal. The monoclonal antibodies can then be purified from the culture medium or ascites fluid as described for polyclonal antibodies.

Alternatively monoclonal antibodies can also be made using recombinant DNA methods as described in U.S. Pat. No. 4,816,567. The polynucleotides encoding a monoclonal antibody are isolated from mature B-cells or hybridoma cells, such as by RT-PCR using oligonucleotide primers that specifically amplify the genes encoding the heavy and light chains of the antibody, and their sequence is determined using conventional procedures. The isolated polynucleotides encoding the heavy and light chains are then cloned into suitable expression vectors, which when transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, monoclonal antibodies are generated by the host cells. Also, recombinant monoclonal antibodies or fragments thereof of the desired species can be isolated from phage display libraries expressing CDRs of the desired species as described U.S. Pat. No. 11,021,531; McCafferty et al., Nature 348:552-554, 1990; Clackson et al., Nature, 352:624-628, 1991; and Marks et al., J. Mol. Biol. 222:581-597, 1991).

Antigen-binding fragments of the disclosure refers to a portion of an intact antibody and refers to the antigenic determining variable regions of an intact antibody. Examples of antibody fragments include, but are not limited to, Fab, Fab', F(ab')2, and F _v fragments, linear antibodies, single chain antibodies, and multispecific antibodies formed from antibody fragments. The term “antigen-binding fragment” of an antibody includes one or more fragments of an antibody that retain the ability to specifically bind to an antigen. It has been shown that the antigenbinding function of an antibody can be performed by certain fragments of a full-length antibody. Examples of binding fragments encompassed within the term “antigen-binding fragment” of an antibody include (without limitation): (i) an Fab fragment, a monovalent fragment consisting of the VL, VH, CL, and CHI domains (e.g., an antibody digested by papain yields three fragments: two antigen-binding Fab fragments, and one Fc fragment that does not bind antigen); (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region (e.g., an antibody digested by pepsin yields two fragments: a bivalent antigenbinding F(ab')2 fragment, and a pFc' fragment that does not bind antigen) and its related F(ab') monovalent unit; (iii) a Fa fragment consisting of the Vu and CHI domains (i.e., that portion of the heavy chain which is included in the Fab); (iv) a F _v fragment consisting of the VL and VH domains of a single arm of an antibody, and the related disulfide linked F _v ; (v) a dAb (domain antibody) or sdAb (single domain antibody) fragment (Ward et al., Nature 341 :544-546, 1989), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). is an Fab, Fab', F(ab')2, Fa, single chain Fv or scFv, disulfide linked F _v , V-NAR domain, IgNar, intrabody, IgGACFh, minibody, F(ab')3, tetrabody, triabody, diabody, single-domain antibody, DVD-Ig, Fcab, mAb2, (scFv)2, or scFv-Fc.

Various techniques for the production of antibody fragments are known in the art. Traditionally, these fragments are derived via proteolytic digestion of intact antibodies (for example Morimoto et al., Journal of Biochemical and Biophysical Methods 24: 107-117, 1993; Brennan et al., Science 229:81, 1985). In certain embodiments, antibody fragments are produced recombinantly. Fab, Fv, and scFv antibody fragments can all be expressed in and secreted from E. coli or other host cells, thus allowing the production of large amounts of these fragments. Such antibody fragments can also be isolated from antibody phage libraries. The antibody fragment can also be linear antibodies as described in U.S. Pat. No. 5,641,870, for example, and can be monospecific or bispecific. Other techniques for the production of antibody fragments will be apparent to a person of ordinary skill in the art.

In some embodiments, an antibody or fragment thereof may be modified to include other amino acid sequence variants of the modified antibody which can be prepared by introducing appropriate nucleotide changes into the modified antibody DNA, or by synthesis of the desired modified antibody polypeptide. Such variants include, for example, deletions from, or insertions or substitutions of, residues within the amino acid sequences of the first and second polypeptides forming the modified antibody. Any combination of deletion, insertion, and substitution is made to arrive at the final construct, provided that the final construct possesses the desired antigenbinding characteristics. The amino acid changes also may alter post-translational processes of the modified antibody, such as changing the number or position of glycosylation sites. “Alanine scanning mutagenesis” can be a useful method for identification of certain residues or regions of the modified antibody polypeptides that might be preferred locations for mutagenesis. Here, a residue or group of target residues are identified (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively charged amino acid (for example, alanine or polyalanine) to affect the interaction of the amino acids with the surrounding aqueous environment in or outside the cell. Those domains demonstrating functional sensitivity to the substitutions then are refined by introducing further or other variants at or for the sites of substitution. Thus, while the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined. Normally the mutations can involve conservative amino acid replacements in nonfunctional regions of the modified antibody. Exemplary mutations are shown below.

Original Preferred

Residue Exemplary Substitutions Substitutions

Ala (A) Vai; Leu; He Vai

Arg (R) Lys; Gin; Asn Lys

Asn (N) Gin; His; Lys; Arg Gin

Asp (D) Glu Glu

Cys (C) Ser Ser

Gin (Q) Asn Asn

Glu (E) Asp Asp

Gly (G) Pro; Ala Ala

His (H) Asn; Gin; Lys; Arg Arg

He (I) Leu; Vai; Met; Ala; Phe; Norleucine Leu

Leu (L) Norleucine; He; Vai; Met; Ala; Phe He

Lys (K) Arg; Gin; Asn Arg

Met (M) Leu; Phe; He Leu

Phe (F) Leu; Vai; He; Ala; Tyr Leu

Pro (P) Ala Ala

Ser (S) Thr Thr Original Preferred

Residue Exemplary Substitutions Substitutions

Thr (T) Ser Ser

Trp (W) Tyr; Phe Tyr

Tyr (Y) Trp; Phe; Thr; Ser Phe

Vai (V) He; Leu; Met; Phe; Ala; Norleucine Leu

Covalent modifications of antibody, antigen-binding fragment, or modified antibody polypeptides are included within the scope of this disclosure. Covalent modifications of the modified antibody can be introduced into the molecule by reacting targeted amino acid residues of the modified antibody or fragments thereof with an organic derivatizing agent that can be capable of reacting with selected side chains or the N- or C-terminal residues. Another type of covalent modification of the modified antibody polypeptide can comprise altering the native glycosylation pattern of the polypeptide. Herein, “altering” can mean deleting one or more carbohydrate moieties found in the original modified antibody, and/or adding one or more glycosylation sites that are not present in the original modified antibody. Addition of glycosylation sites to the modified antibody polypeptide can be accomplished by altering the amino acid sequence such that it contains one or more N-linked glycosylation sites. The alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the original modified antibody sequence (for O-linked glycosylation sites). For ease, the modified antibody amino acid sequence can be altered through changes at the DNA level, particularly by mutating the DNA encoding the modified antibody polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids. Another means of increasing the number of carbohydrate moieties on the modified antibody polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Removal of carbohydrate moieties present on the modified antibody can be accomplished chemically or enzymatically.

Another type of covalent modification of modified antibody comprises linking the modified antibody polypeptide to one of a variety of non-proteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes. Methods for complexing binding agents or the antibody or antigen-binding fragments herein with another agent are known in the art. Such methods may utilize one of several available heterobifunctional reagents used for coupling or linking molecules.

In one instance, Fc portions of antibodies can be modified to increase half-life of the molecule in the circulation in blood when administered to a subject.

Additionally, antibodies may be produced or expressed so that they do not contain fucose on their complex N-glycoside-linked sugar chains to increase effector functions. Similarly, antibodies can be attached at their C-terminal end to all or part of an immunoglobulin heavy chain derived from any antibody isotype, e.g., IgG, IgA, IgE, IgD, and IgM and any of the isotype subclasses, e.g., IgGl, IgG2b, IgG2a, IgG3, and IgG4.

Accordingly, in some embodiments, the antibody or the antigen-binding fragment is an IgG, an IgM, an IgE, an IgA, an IgD, or is derived therefrom. In other embodiments, the antibody is an IgG selected from the group consisting of an IgGl, an IgG2a, an IgG2b, an IgG3, and an IgG4.

Glycosylation of immunoglobulins has been shown to have significant effects on their effector functions, structural stability, and rate of secretion from antibody-producing cells. Antibodies and antigen-binding fragments herein may be glycosylated. Glycosylation at a variable domain framework residue can alter the binding interaction of the antibody with antigen. The present disclosure includes criteria by which a limited number of amino acids in the framework or CDRs of an immunoglobulin chain can be chosen to be mutated (e.g., by substitution, deletion, and/or addition of residues) in order to increase the affinity of an antibody.

Linkers for conjugating antibodies to other moieties are within the scope of the present disclosure. Associations (binding) between antibodies and labels include, but are not limited to, covalent and non-covalent interactions, chemical conjugation, as well as recombinant techniques.

Antibodies, or antigen-binding fragments thereof, can be modified for various purposes such as, for example, by addition of polyethylene glycol (PEG). PEG modification (PEGylation) can lead to one or more of improved circulation time, improved solubility, improved resistance to proteolysis, reduced antigenicity and immunogenicity, improved bioavailability, reduced toxicity, improved stability, and easier formulation.

The polynucleotide(s) encoding, for example, a monoclonal antibody or antigen-binding fragment can further be modified in a number of different manners using recombinant DNA technology to generate alternative antibodies. In some embodiments, the constant domains of the light and heavy chains of, for example, a mouse monoclonal antibody can be substituted 1) for those regions of, for example, a human antibody to generate a chimeric antibody, or, 2) for a nonimmunoglobulin polypeptide to generate a fusion antibody. In some embodiments, the constant regions are truncated or removed to generate the desired antibody fragment of a monoclonal antibody. Site-directed or high-density mutagenesis of the variable region can be used to optimize specificity, affinity, etc. of a monoclonal antibody.

In certain embodiments, polynucleotide sequences encoding a particular antibody or antigen-binding fragment of interest can be inserted into an expression vector and operatively linked to an expression control sequence appropriate for expression of the protein in a desired host. Proper assembly can be confirmed by nucleotide sequencing, restriction mapping, and expression of a biologically active polypeptide in a suitable host. As is well known in the art, in order to obtain high expression levels of a transfected gene in a host, the gene must be operatively linked to transcriptional and translational expression control sequences that are functional in the chosen expression host.

In certain embodiments, recombinant expression vectors are used to amplify and express DNA encoding antibodies, or fragments thereof, against the SARS-Cov-2 N-protein. Recombinant expression vectors are replicable DNA constructs which have synthetic or cDNA-derived DNA fragments encoding a polypeptide chain of an anti-N-protein antibody or antigen-binding fragment, operatively linked to suitable transcriptional or translational regulatory elements derived from mammalian, microbial, viral or insect genes. A transcriptional unit generally comprises an assembly of (1) a genetic element or elements having a regulatory role in gene expression, for example, transcriptional promoters or enhancers, (2) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (3) appropriate transcription and translation initiation and termination sequences. Such regulatory elements can include an operator sequence to control transcription. The ability to replicate in a host, usually conferred by an origin of replication, and a selection gene to facilitate recognition of transformants can additionally be incorporated. DNA regions are operatively linked when they are functionally related to each other. For example, DNA for a signal peptide (secretory leader) is operatively linked to DNA for a polypeptide if it is expressed as a precursor which participates in the secretion of the polypeptide; a promoter is operatively linked to a coding sequence if it controls the transcription of the sequence; or a ribosome binding site is operatively linked to a coding sequence if it is positioned so as to permit translation. Structural elements intended for use in yeast expression systems include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it can include an N-terminal methionine residue. This residue can optionally be subsequently cleaved from the expressed recombinant protein to provide a final product.

The choice of expression control sequence and expression vector will depend upon the choice of host. A wide variety of expression host/vector combinations can be employed. Useful expression vectors for eukaryotic hosts, include, for example, vectors comprising expression control sequences from SV40, bovine papilloma virus, adenovirus, and cytomegalovirus. Useful expression vectors for bacterial hosts include known bacterial plasmids, such as plasmids from Escherichia coH, including pCR 1, pBR322, pMB9 and their derivatives, wider host range plasmids, such as M13 and filamentous single-stranded DNA phages.

Suitable host cells for expression of an antibody or antigen-binding fragment include prokaryotes, yeast, insect, or higher eukaryotic cells under the control of appropriate promoters. Prokaryotes include gram-negative or gram-positive organisms, for example E. coli or bacilli. Higher eukaryotic cells include established cell lines of mammalian origin, such as CHO cells. Cell-free translation systems could also be employed. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts are described by Pouwels et al. (Cloning Vectors: A Laboratory Manual, Elsevier, N.Y., 1985), the relevant disclosure of which is hereby incorporated by reference. Additional information regarding methods of protein production, including antibody production, can be found, e.g., in U.S. Patent Pub. No. 2008/0187954, U.S. Pat. Nos. 6,413,746 and 6,660,501, and PCT Patent Publication No. W004009823.

Various mammalian or insect cell culture systems are advantageously employed to express a recombinant antibody or antigen-binding fragment. Expression of such recombinant proteins in mammalian cells can be performed because the proteins are generally correctly folded, appropriately modified and completely functional. Examples of suitable mammalian host cell lines include HEK-293 and HEK-293T, the COS-7 lines of monkey kidney cells, described by Gluzman et al., Cell 23: 175, 1981, and other cell lines including, for example, L cells, CI 27, 3T3, Chinese hamster ovary (CHO), HeLa and BHK cell lines. Mammalian expression vectors can comprise non-transcribed elements such as an origin of replication, a suitable promoter and enhancer linked to the gene to be expressed, and other 5' or 3' flanking non-transcribed sequences, and 5' or 3' nontranslated sequences, such as necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, and transcriptional termination sequences. Baculovirus systems for production of heterologous proteins in insect cells are reviewed by Luckow and Summers, Bio/Technology 6:47 (1988). Other methods of producing recombinant antibodies are disclosed in, for example, in U.S. Pat. No. 4,816,567.

For high level production, a widely used mammalian expression system is one which utilizes Lonza's GS Gene Expression System™. This system uses a viral promoter and selection via glutamine metabolism to provide development of high-yielding and stable mammalian cell lines.

For alternative high-level production, a widely used mammalian expression system is one which utilizes gene amplification by dihydrofolate reductase deficient (“dhfir”) Chinese hamster ovary cells. The system is based upon the dihydrofolate reductase “dhfir” gene, which encodes the DHFR enzyme, which catalyzes conversion of dihydrofolate to tetrahydrofolate. In order to achieve high production, dhfr-CHO cells are transfected with an expression vector containing a functional DHFR gene, together with a gene that encodes a desired protein. For example, the desired protein is recombinant antibody heavy chain and/or light chain.

By increasing the amount of the competitive DHFR inhibitor methotrexate (MTX), the recombinant cells develop resistance by amplifying the dhfr gene. In standard cases, the amplification unit employed is much larger than the size of the dhfr gene, and as a result the antibody heavy /light chain is co-amplified.

Accordingly, in some embodiments, a polynucleotide encodes a variable heavy region and a variable light region, wherein the variable heavy chain region comprises the DNA sequence of any one of SEQ ID NOS: 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 238, 241, 244, 246, 248, 250, 253, 255, 257, 259, 261, 263, 265, and 267; and the variable light chain region comprises the DNA sequence of any one of SEQ ID NOS: 220, 22, 224, 226, 228, 230, 232, 234, 236, 239, 240, 242, 243, 245, 247, 249, 251, 252, 254, 256, 258, 260, 262, 264, 266, and 268.

In other embodiments, a polynucleotide encodes a variable heavy region and a variable light region comprising: a) SEQ ID NO: 237 and SEQ ID NO: 239, respectively; b) SEQ ID NO: 237 and SEQ ID NO: 240, respectively; c) SEQ ID NO: 238 and SEQ ID NO: 239, respectively; d) SEQ ID NO: 238 and SEQ ID NO: 240, respectively; e) SEQ ID NO: 238 and SEQ ID NO: 240, respectively; f) SEQ ID NO: 241 and SEQ ID NO: 242, respectively; g) SEQ ID NO: 241 and SEQ ID NO: 243, respectively; h) SEQ ID NO: 244 and SEQ ID NO: 245, respectively; i) SEQ ID NO: 246 and SEQ ID NO: 247, respectively; j) SEQ ID NO: 248 and SEQ ID NO: 249, respectively; k) SEQ ID NO: 250 and SEQ ID NO: 251, respectively; 1) SEQ ID NO: 250 and SEQ ID NO: 252, respectively; m) SEQ ID NO: 253 and SEQ ID NO: 254, respectively; n) SEQ ID NO: 255 and SEQ ID NO: 256, respectively; o) SEQ ID NO: 257 and SEQ ID NO: 258, respectively; p) SEQ ID NO: 259 and SEQ ID NO: 260, respectively; q) SEQ ID NO: 261 and SEQ ID NO: 262, respectively; r) SEQ ID NO: 263 and SEQ ID NO: 264, respectively; s) SEQ ID NO: 265 and SEQ ID NO: 266, respectively; or t) SEQ ID NO: 267 and SEQ ID NO: 268, respectively.

In other embodiments, a polynucleotide encoding a heavy chain comprises the DNA sequence of any one of SEQ ID NOS: 219, 221, 223, 225, 227, 229, 231, 233, and 235; and/or a light chain comprising a DNA sequence of any one of SEQ ID NOS: 220, 222, 224, 226, 228, 230, 232, 234, and 236.

In still other embodiments, a polynucleotide encodes a heavy chain and a light chain comprising: a) SEQ ID NO: 219 and SEQ ID NO: 220, respectively; b) SEQ ID NO: 221 and SEQ ID NO: 222, respectively; c) SEQ ID NO: 223 and SEQ ID NO: 224, respectively; d) SEQ ID NO: 225 and SEQ ID NO:226, respectively; e) SEQ ID NO: 227 and SEQ ID NO: 228, respectively; f) SEQ ID NO: 229 and SEQ ID NO: 230, respectively; g) SEQ ID NO: 231 and SEQ ID NO: 232, respectively; h) SEQ ID NO: 233 and SEQ ID NO: 234, respectively; or i) SEQ ID NO: 235 and SEQ ID NO: 236, respectively.

Some embodiments of the disclosure include a recombinant cell comprising a polynucleotide comprising one or more of the preceding DNA sequences. Various eukaryotic and prokaryotic host cells, including mammalian cells, may be used as hosts for expression of an anti- CoV-S antigen-binding protein. Such host cells are well known in the art and many are available from the American Type Culture Collection (ATCC). These host cells include, inter alia, Chinese hamster ovary (CHO) cells, NS0, SP2 cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (e.g., Hep G2), A549 cells, 3T3 cells, HEK-293 cells and a number of other cell lines. Mammalian host cells include human, mouse, rat, dog, monkey, pig, goat, bovine, horse and hamster cells. Other cell lines that may be used are insect cell lines (e.g., Spodoptera frugiperda or Trichoplusia ni), amphibian cells, bacterial cells, plant cells and fungal cells. Fungal cells include yeast and filamentous fungus cells including, for example, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia koclamae, Pichia membranaefaciens, Pichia minuta (Ogataea minuta, Pichia lindneri), Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia guercuum, Pichia pijperi, Pichia stiptis, Pichia methanolica, Pichia sp., Saccharomyces cerevisiae, Saccharomyces sp., Hansenula polymorpha, Kluyveromyces sp., Kluyveromyces lactis, Candida albicans, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Chrysosporium lucknowense, Fusarium sp., Fusarium gramineum, Fusarium venenatum, Physcomitrella patens and Neurospora crassa. The present invention includes an isolated host cell (e.g., a CHO cell) comprising an antibody or antibi fragment, such as those of Example 1, Figure 1, or Figure 2; or a polynucleotide encoding such a polypeptide thereof.

The disclosure also provides for methods of treating a SARS-CoV-2 viral infection or COVID-19 disease in a subject in need thereof, comprising administering to the subject an effective amount of an antibody or the antigen-binding fragment listed in Example 1, Figure 1, or Figure 2, or a composition thereof. Optionally, the method may include also administering one or more additional anti-viral agents or other agents to the subject either simultaneously with or sequentially with the disclosed antibodies or antigen-binding fragments.

Exemplary antivirals or other agents include: one or more blood thinners or anticoagulants; statins; hydroxy chloroquine; intubation; one or more antibiotics (e.g., doxycycline, Azithromycin, etc.); one or more decongestants (e.g., Mucinex, Sudafed, etc.); one or more antihistamines and/or glucocorticoids (e.g., Zyrtec, Claritin, Allegra, fluticasone luroate, etc.); one or more pain relievers (e.g., acetominophen); one or more zinc-containing medications (e.g., Zycam, etc.); Azithromycin, hydroquinolone, or a combination thereof; one or more integrase inhibitors (e.g., Bictegravir, dolutegravir (Tivicay), elvitegravir, raltegravir, or a combination thereof); one or more nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs; e.g., abacavir (Ziagen), emtricitabine (Emtriva), lamivudine (Epivir), tenofovir alafenamide fumarate (Vemlidy), tenofovir disoproxil fumarate (Viread), zidovudine (Retrovir), didanosine (Videx, Videx EC), stavudine (Zerit), or a combination thereof); a combination of NRTIs (e.g., (i) abacavir, lamivudine, and zidovudine (Trizivir), (ii) abacavir and lamivudine (Epzicom), (iii) emtricitabine and tenofovir alafenamide fumarate (Descovy), (iv) emtricitabine and tenofovir disoproxil fumarate (Truvada), (v) lamivudine and tenofovir disoproxil fumarate (Cimduo, Temixys), (vi) lamivudine and zidovudine (Combivir), etc.); a combination of Descovy and Truvada; one or more non-nucleoside reverse transcriptase inhibitors (NNRTIs; e.g., doravirine (Pifeltro), efavirenz (Sustiva), etravirine (Intelence), nevirapine (Viramune, Viramune XR), rilpivirine (Edurant), delavirdine (Rescriptor), or a combination thereof); one or more Cytochrome P4503A (CYP3A) inhibitors (e.g., cobicistat (Tybost), ritonavir (Norvir), etc.); one or more protease inhibitors (Pls; e.g., atazanavir (Reyataz), darunavir (Prezista), fosamprenavir (Lexiva), lopinavir, ritonavir (Norvir), tipranavir (Aptivus), etc.); one or Pls in combination with cobicistat, ritonavir, Lopinavir, Tipranavir, Atazanavir, fosamprenavir, indinavir (Crixivan), nelfinavir (Viracept), saquinavir (Invirase), or a combination thereof; Atazanavir; fosamprenavir; a combination of Atazanavir, darunavir and cobicistat; one or more fusion inhibitors (e.g., enfuvirtide (Fuzeon); one or more post-attachment inhibitors (e.g., ibalizumab-uiyk (Trogarzo)); one or more Chemokine coreceptor antagonists (CCR5 antagonists; e.g., maraviroc (Selzentry)); and one or more viral entry inhibitors (e.g., enfuvirtide (Fuzeon), ibalizumab-uiyk (Trogarzo), maraviroc (Selzentry), etc.); or a combination thereof.

An effective or therapeutically effective dose of an antibody or antigen-binding fragment (e.g., of Example 1, Figure 1, or Figure 2), for treating or preventing a viral infection refers to the amount of the antibody or fragment sufficient to alleviate one or more signs and/or symptoms of the infection in the treated subject, whether by inducing the regression or elimination of such signs and/or symptoms or by inhibiting the progression of such signs and/or symptoms. The dose amount may vary depending upon the age and the size of a subject to be administered, target disease, conditions, route of administration, and the like. In an embodiment of the invention, an effective or therapeutically effective dose of antibody or antigen-binding fragment thereof of the present invention, for treating or preventing viral infection, e.g., in an adult human subject, is about 0.01 to about 200 mg/kg, e.g., up to about 150 mg/kg. In an embodiment of the invention, the dosage is up to about 10.8 or 11 grams (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 grams). Depending on the severity of the infection, the frequency and the duration of the treatment can be adjusted. In certain embodiments, the antigen-binding protein of the present invention can be administered at an initial dose, followed by one or more secondary doses. In certain embodiments, the initial dose may be followed by administration of a second or a plurality of subsequent doses of antibody or antigen-binding fragment thereof in an amount that can be approximately the same or less than that of the initial dose, wherein the subsequent doses are separated by at least 1 day to 3 days; at least one week, at least 2 weeks; at least 3 weeks; at least 4 weeks; at least 5 weeks; at least 6 weeks; at least 7 weeks; at least 8 weeks; at least 9 weeks; at least 10 weeks; at least 12 weeks; or at least 14 weeks.

Embodiments of the disclosure also provide a composition comprising one or more of the monoclonal antibodies as described herein, and pharmaceutically acceptable carrier. In another embodiment, the disclosure provides a method of detecting SARS-CoV-2 virus comprising contacting a sample obtained from a subject suspected of having the SARS-CoV-2 virus with an antibody or the antigen-binding fragment listed in Example 1, Figure 1, or Figure 2, and detecting the presence or absence of an antibody/SARS-CoV-2 virus complex or an antigenbinding fragment/SARS-CoV-2 virus complex, wherein the detection of the antibody/SARS-CoV- 2 virus complex or the antigen-binding fragment/SARS-CoV-2 virus complex indicates an active infection.

In some embodiments, an antibody or antigen-binding fragment as described herein can neutralize the activity of SARS-Cov-2. Neutralization ability of the disclosed antibody or antigenbinding fragment can be assessed using any suitable means including, but not limited to, an in vitro pseudovirus assay. For example, nucleocapsid encoding genes from a SARS-Cov-2 virus are codon-optimized for human cells and cloned into eukaryotic expression plasmids to generate envelope recombinant plasmids; mammalian cells are then transfected with the plasmids. The transfected mammalian cells are contacted with an antibody or antigen-binding fragment as described herein and trypsinization is determined as a measure of neutralization. In some instances, an antibody or antigen-binding fragment neutralize SARS-Cov-2 by at least 5%, 10%, 15%, 20%, 25%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or more compared to a non-specific antibody, or compared to an antibody that selectively binds to SARS-Cov-1 or MERS. The neutralization ability antibody or antigen-binding fragment can also be assessed using, for example, an in vivo hamster animal model. For example, hamsters can be injected with either saline or a disclosed antibody or antigen-binding fragment. Body weight and viable signs (e.g., ruffled hair and movement) are recorded. Viral titers are assessed in homogenates of lung tissues and/or by immunohistochemistry of lung tissue. An antibody or antigen-binding fragment herein reduces viral titers compared to controls. Other methods of testing various antibody characteristics are known in the art and discloses, for example, in U.S. Pat. No. 10,954,289.

In some embodiments, the SARS-CoV-2/antibody complexes may be detected using a secondary antibody. As used herein, the term "secondary antibody" in its broadest sense is to be understood to refer to any kind of "binding moiety", preferably binding protein, capable of specific binding to an IgA, IgG and/or IgM class antibody or a fragment thereof such as a constant domain of a particular Ig class of a selected species, preferably human species. Non-limiting examples of binding moieties include antibodies, for example antibodies immunologically or genetically derived from any species, for example human, chicken, camel, llama, lamprey, shark, goat, rodent, cow, dog, rabbit, etc., antibody fragments, domains or parts thereof, for example Fab, Fab', F(ab')2, scFab, Fv, scFv, VH, VHH, VL, VLRs, and the like, diabodies, monoclonal antibodies (mAbs), polyclonal antibodies (pAbs), mAbdAbs, phage display-derived binders, affibodies, heteroconjugate antibodies, bispecific antibodies, evibodies, lipocalins, anticalins, affibodies, avimers, maxibodies, heat shock proteins such as GroEL and GroES, trans-bodies, DARPins, aptamers, C-type lectin domains such as tetranectins; human y-crystallin and human ubiquitinderived binders such as affilins, PDZ domain-derived binders; scorpion toxin and/or Kunitz-type domain binders, fibronectin-derived binders such as adnectins, receptors, ligands, lectins, streptavidin, biotin, including derivatives and/or combinations thereof such as bi-/multi-specific formats formed from two or more of these binding molecules. Various antibody-derived and alternative (i.e. non-antibody) binding protein scaffolds including methods of generation thereof are known in the art (e.g. reviewed in Chiu ML et al., Antibodies (Basel), (2019); 8(4) : 55 ; Simeon R. & Chen Z., Protein Cell. (2018);9(1):3-14; and Chapter 7 - Non-Antibody Scaffolds from Handbook of Therapeutic Antibodies (2007) edited by Stefan Dubel.

In some embodiments, the secondary antibody is an immunoglobulin (Ig), preferably IgG raised in a non-human species, wherein said secondary antibody specifically binds immunoglobulins of one or more specific Ig classes or fragments thereof (e.g. a constant domain of a particular Ig class) of another selected species, preferably human species. An example is a polyclonal antibody raised in goat that specifically recognizes human IgA (i.e., a polyclonal goat anti-human IgA antibody). In another preferred embodiment, the secondary antibody is a monoclonal antibody that specifically binds immunoglobulins of one or more specific Ig classes or fragments thereof (e.g. a constant domain of a particular Ig class) of another selected species, preferably human species. Means and methods for producing (mono- or polyclonal) antibodies capable of specific binding of one or more selected target antigens are well known in the art.

In certain embodiments, the secondary antibody may be chosen to specifically bind to only one, only two, or all three classes of Ig antibodies, i.e. IgA, IgG and/or IgM. In certain embodiments, instead of using only one single kind of secondary antibody, a mixture of several different secondary antibodies may be used, wherein the different secondary antibodies either bind to the same one or different Ig classes (e.g., a mixture of different antibodies (e.g., polyclonal antibodies) all binding to IgA), or to, e.g. IgA and IgG or IgM or wherein the different secondary antibodies bind to different individual target structures (e.g. one kind of secondary antibody specifically binding to IgA, and another specifically binding to IgG). In some embodiments, the antibodies and/or antigen-binding fragments may be conjugated to one or more detectable agents that may be a diagnostic agent useful for diagnosis. Examples of detectable agents include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, green fluorescence protein (GFP), a variant of GFP, a resonance energy transfer (RET) donor molecule, a RET acceptor molecule, radioactive nuclides, positron emitting metals (for use in positron emission tomography), and nonradioactive paramagnetic metal ions. See generally U.S. Pat. No. 4,741,900 for metal ions which can be conjugated to antibodies for use as diagnostics. Suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; suitable prosthetic groups include streptavidin, avidin and biotin; suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride and phycoerythrin; suitable luminescent materials include luminol; suitable bioluminescent materials include luciferase, luciferin, and aequorin; and suitable radioactive nuclides include ¹²⁵ I, ^{13 X} I, ^U1 ln and "Tc.

In some embodiments, a biological sample from a subject used to detect the presence or absence of SARS-CoV-2 is comprises a nasal swab, a tissue sample, a saliva sample, or a blood sample.

Pharmaceutical Formulations

The compounds described herein can be used to prepare therapeutic pharmaceutical compositions, for example, by combining the compounds with a pharmaceutically acceptable diluent, excipient, or carrier. The compounds may be added to a carrier in the form of a salt or solvate. For example, in cases where compounds are sufficiently basic or acidic to form stable nontoxic acid or base salts, administration of the compounds as salts may be appropriate. Examples of pharmaceutically acceptable salts are organic acid addition salts formed with acids that form a physiologically acceptable anion, for example, tosylate, methanesulfonate, acetate, citrate, malonate, tartrate, succinate, benzoate, ascorbate, a-ketoglutarate, and P-glycerophosphate. Suitable inorganic salts may also be formed, including hydrochloride, halide, sulfate, nitrate, bicarbonate, and carbonate salts.

Pharmaceutically acceptable salts may be obtained using standard procedures well known in the art, for example by reacting a sufficiently basic compound such as an amine with a suitable acid to provide a physiologically acceptable ionic compound. Alkali metal (for example, sodium, potassium or lithium) or alkaline earth metal (for example, calcium) salts of carboxylic acids can also be prepared by analogous methods.

The compounds of the formulas described herein can be formulated as pharmaceutical compositions and administered to a mammalian host, such as a human patient, in a variety of forms. The forms can be specifically adapted to a chosen route of administration, e.g., oral or parenteral administration, by intravenous, intramuscular, topical or subcutaneous routes.

The compounds described herein may be systemically administered in combination with a pharmaceutically acceptable vehicle, such as an inert diluent or an assimilable edible carrier. For oral administration, compounds can be enclosed in hard- or soft-shell gelatin capsules, compressed into tablets, or incorporated directly into the food of a patient's diet. Compounds may also be combined with one or more excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. Such compositions and preparations typically contain at least 0.1% of active compound. The percentage of the compositions and preparations can vary and may conveniently be from about 0.5% to about 60%, about 1% to about 25%, or about 2% to about 10%, of the weight of a given unit dosage form. The amount of active compound in such therapeutically useful compositions can be such that an effective dosage level can be obtained.

The tablets, troches, pills, capsules, and the like may also contain one or more of the following: binders such as gum tragacanth, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as com starch, potato starch, alginic acid and the like; and a lubricant such as magnesium stearate. A sweetening agent such as sucrose, fructose, lactose or aspartame; or a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring, may be added. When the unit dosage form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier, such as a vegetable oil or a polyethylene glycol. Various other materials may be present as coatings or to otherwise modify the physical form of the solid unit dosage form. For instance, tablets, pills, or capsules may be coated with gelatin, wax, shellac or sugar and the like. A syrup or elixir may contain the active compound, sucrose or fructose as a sweetening agent, methyl and propyl parabens as preservatives, a dye and flavoring such as cherry or orange flavor. Any material used in preparing any unit dosage form should be pharmaceutically acceptable and substantially non-toxic in the amounts employed. In addition, the active compound may be incorporated into sustained-release preparations and devices. The active compound may be administered intravenously or intraperitoneally by infusion or injection. Solutions of the active compound or its salts can be prepared in water, optionally mixed with a nontoxic surfactant. Dispersions can be prepared in glycerol, liquid polyethylene glycols, triacetin, or mixtures thereof, or in a pharmaceutically acceptable oil. Under ordinary conditions of storage and use, preparations may contain a preservative to prevent the growth of microorganisms.

Pharmaceutical dosage forms suitable for injection or infusion can include sterile aqueous solutions, dispersions, or sterile powders comprising the active ingredient adapted for the extemporaneous preparation of sterile injectable or infusible solutions or dispersions, optionally encapsulated in liposomes. The ultimate dosage form should be sterile, fluid and stable under the conditions of manufacture and storage. The liquid carrier or vehicle can be a solvent or liquid dispersion medium comprising, for example, water, ethanol, a polyol (for example, glycerol, propylene glycol, liquid polyethylene glycols, and the like), vegetable oils, nontoxic glyceryl esters, and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the formation of liposomes, by the maintenance of the required particle size in the case of dispersions, or by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and/or antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, buffers, or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by agents delaying absorption, for example, aluminum monostearate and/or gelatin.

Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in the appropriate solvent with various other ingredients enumerated above, as required, optionally followed by filter sterilization. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation can include vacuum drying and freeze-drying techniques, which yield a powder of the active ingredient plus any additional desired ingredient present in the solution.

Useful solid carriers include finely divided solids such as talc, clay, microcrystalline cellulose, silica, alumina, and the like. Useful liquid carriers include water, dimethyl sulfoxide (DMSO), alcohols, glycols, or water-alcohol/glycol blends, in which a compound can be dissolved or dispersed at effective levels, optionally with the aid of non-toxic surfactants. Adjuvants such as fragrances and additional antimicrobial agents can be added to optimize the properties for a given use. The resultant liquid compositions can be applied from absorbent pads, used to impregnate bandages and other dressings, or sprayed onto the affected area using a pump-type or aerosol sprayer.

Thickeners such as synthetic polymers, fatty acids, fatty acid salts and esters, fatty alcohols, modified celluloses, or modified mineral materials can also be employed with liquid carriers to form spreadable pastes, gels, ointments, soaps, and the like, for application directly to the skin of the user.

Useful dosages of the compositions described herein can be determined by comparing their in vitro activity, and in vivo activity in animal models. Methods for the extrapolation of effective dosages in mice, and other animals, to humans are known to the art; for example, see U.S. Patent No. 4,938,949. The amount of a compound, or an active salt or derivative thereof, required for use in treatment will vary not only with the particular compound or salt selected but also with the route of administration, the nature of the condition being treated, and the age and condition of the patient, and will be ultimately at the discretion of an attendant physician or clinician.

In general, however, a suitable dose will be in the range of from about 0.5 to about 100 mg/kg, e.g., from about 10 to about 75 mg/kg of body weight per day, such as 3 to about 50 mg per kilogram body weight of the recipient per day, preferably in the range of 6 to 90 mg/kg/day, most preferably in the range of 15 to 60 mg/kg/day.

The compound is conveniently formulated in unit dosage form; for example, containing 5 to 1000 mg, conveniently 10 to 750 mg, most conveniently, 50 to 500 mg of active ingredient per unit dosage form. In one embodiment, the invention provides a composition comprising a compound of the invention formulated in such a unit dosage form.

The compound can be conveniently administered in a unit dosage form, for example, containing 5 to 1000 mg/m ² , conveniently 10 to 750 mg/m ² , most conveniently, 50 to 500 mg/m ² of active ingredient per unit dosage form. The desired dose may conveniently be presented in a single dose or as divided doses administered at appropriate intervals, for example, as two, three, four or more sub-doses per day. The sub-dose itself may be further divided, e.g., into a number of discrete loosely spaced administrations.

The desired dose may conveniently be presented in a single dose or as divided doses administered at appropriate intervals, for example, as two, three, four or more sub-doses per day. The sub-dose itself may be further divided, e.g., into a number of discrete loosely spaced administrations; such as multiple inhalations from an insufflator or by application of a plurality of drops into the eye.

The following Examples are intended to illustrate the above invention and should not be construed as to narrow its scope. One skilled in the art will readily recognize that the Examples suggest many other ways in which the invention could be practiced. It should be understood that numerous variations and modifications may be made while remaining within the scope of the invention. EXAMPLES

Example 1. Embodiments of Certain Complementary Determinate Regions

Example 2. SARS-Cov-2 target Proteins

Nucleocapsid protein (Gene N) - Uniprot # P0DTC9

MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALT Q HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTG

PEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYA EG

SRGGSQ AS SRS S SRSRNS SRNSTPGS SRGTSP ARMAGNGGD AAL ALLLLDRLNQLESKM SGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQEL IRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQV ILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQ SMSSADSTQA (SEQ ID NO: 269)

2. Envelope Small Membrane Protein (Gene E) - Uniprot # P0DTC4

MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFY VYSR VKNLNSSRVPDLLV (SEQ ID NO: 270)

3. Membrane Protein (Gene M) - Uniprot # P0DTC5

MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLL WPV TLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYK LG ASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQ (SEQ ID NO: 271)

4. Spike Protein (Gene S) - Uniprot # P0DTC2

MF VFLVLLPL VS SQCVNLTTRTQLPP AYTNSFTRGVYYPDKVFRS SVLHSTQDLFLPFF S NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMD LEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGF S ALEPL VDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSET KCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRIS N CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIA DYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGST PCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKN KCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVS VITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEH VNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIP T NFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDK NTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQ Y GDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIP FAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQN AQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRA A EIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKN FTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVN NTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLN ESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCC KFDEDDSEPVLKGVKLHYT (SEQ ID NO: 272)

Example 3. Pharmaceutical Dosage Forms

The following formulations illustrate representative pharmaceutical dosage forms that may be used for the therapeutic or prophylactic administration of a compound or composition generically or specifically described herein (hereinafter referred to as 'Composition X'): (i) Tablet 1 mg/tablet

'Composition X' 100.0 Lactose 77.5

Povidone 15.0

Croscarmellose sodium 12.0 Microcrystalline cellulose 92.5 Magnesium stearate 3,0

300.0

(ii) Tablet 2 mg/tablet

'Composition X' 20.0 Microcrystalline cellulose 410.0 Starch 50.0

Sodium starch glycolate 15.0 Magnesium stearate 5,0

500.0

(iii) Capsule mg/capsule

'Composition X' 10.0 Colloidal silicon dioxide 1.5 Lactose 465.5

Pregelatinized starch 120.0 Magnesium stearate 3,0

600.0

(iv) Injection 1 (1 mg/mL) mg/mL

'Composition X' (free acid form) 1.0 Dibasic sodium phosphate 12.0 Monobasic sodium phosphate 0.7 Sodium chloride 4.5

1.0 N Sodium hydroxide solution q.s. (pH adjustment to 7.0-7.5) Water for injection q.s. ad 1 mL

(v) Injection 2 (10 mg/mL) mg/mL

'Composition X' (free acid form) 10.0 Monobasic sodium phosphate 0.3 Dibasic sodium phosphate 1.1 Polyethylene glycol 400 200.0

0.1 N Sodium hydroxide solution q.s. (pH adjustment to 7.0-7.5) Water for injection q.s. ad 1 mL

(vi) Aerosol mg/can 'Composition X' 20

Oleic acid 10

Trichloromonofluoromethane 5,000

Dichlorodifluoromethane 10,000

Di chlorotetrafluoroethane 5,000

These formulations may be prepared by conventional procedures well known in the pharmaceutical art. It will be appreciated that the above pharmaceutical compositions may be varied according to well-known pharmaceutical techniques to accommodate differing amounts and types of active ingredient 'Composition X'. Aerosol formulation (vi) may be used in conjunction with a standard, metered dose aerosol dispenser. Additionally, the specific ingredients and proportions are for illustrative purposes. Ingredients may be exchanged for suitable equivalents and proportions may be varied, according to the desired properties of the dosage form of interest.

While specific embodiments have been described above with reference to the disclosed embodiments and examples, such embodiments are only illustrative and do not limit the scope of the invention. Changes and modifications can be made in accordance with ordinary skill in the art without departing from the invention in its broader aspects as defined in the following claims.

All publications, patents, and patent documents are incorporated by reference herein, as though individually incorporated by reference. No limitations inconsistent with this disclosure are to be understood therefrom. The invention has been described with reference to various specific and preferred embodiments and techniques. However, it should be understood that many variations and modifications may be made while remaining within the spirit and scope of the invention.