WO2022224203A1 - Antibodies that bind sars-cov-2 spike protein - Google Patents

Antibodies that bind sars-cov-2 spike protein Download PDF

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Publication number
WO2022224203A1
WO2022224203A1 PCT/IB2022/053756 IB2022053756W WO2022224203A1 WO 2022224203 A1 WO2022224203 A1 WO 2022224203A1 IB 2022053756 W IB2022053756 W IB 2022053756W WO 2022224203 A1 WO2022224203 A1 WO 2022224203A1
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seq
antibody
cov
coronavirus
sars
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Jamshid Tanha
Martin A. ROSSOTTI
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National Research Council of Canada
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National Research Council of Canada
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Priority to JP2023560880A priority Critical patent/JP2024515525A/en
Priority to EP22791236.7A priority patent/EP4326763A4/en
Priority to CA3216274A priority patent/CA3216274A1/en
Priority to US18/556,415 priority patent/US20240270826A1/en
Publication of WO2022224203A1 publication Critical patent/WO2022224203A1/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—RNA viruses
    • C07K16/102—Coronaviridae (F)
    • C07K16/104—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56983—Viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
    • A61K2039/541—Mucosal route
    • A61K2039/544—Mucosal route to the airways
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/22—Immunoglobulins specific features characterized by taxonomic origin from camelids, e.g. camel, llama or dromedary
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/64—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising a combination of variable region and constant region components
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/005—Assays involving biological materials from specific organisms or of a specific nature from viruses
    • G01N2333/08—RNA viruses
    • G01N2333/165—Coronaviridae, e.g. avian infectious bronchitis virus
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2469/00—Immunoassays for the detection of microorganisms
    • G01N2469/10—Detection of antigens from microorganism in sample from host
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • coronavirus spike polypeptide particularly the spike polypeptide of SARS-CoV-2 and variants thereof, and to the use of such antibodies for various applications including the detection of a coronavirus and/or treatment or prevention of a coronavirus infection.
  • Coronavirus is a single-stranded enveloped RNA virus belonging to the subfamily Coronavirinae in the order Nidovirales.
  • coronaviruses Based on genomic structure, coronaviruses have been classified into four genera; Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus; two of which (alphacoronaviruses and betacoronaviruses) infect mammals. Seven coronaviruses are known to cause human disease: HCoV 229E, HCov OC43, HCoVNL63, HCoVHKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2. Three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, cause serious illness in humans, whereas the remaining four human coronaviruses are associated with mild illness.
  • coronavirus spike protein which is a homotrimeric glycoprotein.
  • the spike polypeptide includes three segments, an ectodomain, a single-pass transmembrane anchor, and an intracellular tail.
  • the spike ectodomain is made up of a receptor-binding subunit (S1) and a membrane-fusion subunit (S2).
  • S1 includes two major domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), which is also known as the receptor binding domain (RBD).
  • S1 contains two subdomains (SD1 and S1-SD2) as described in Lan et al., 2020.
  • S1 binds to a host cell surface receptor and S2 fuses the host and viral membranes (Li, 2016).
  • the host cell surface receptor bound by both SARS-CoV and SARS-CoV- 2 is a zinc peptidase angiotensin-converting enzyme 2 (ACE2), whereas MERS-CoV recognizes a serine peptidase (DPP4) (Li, 2016; Zhou et al, 2020).
  • ACE2 zinc peptidase angiotensin-converting enzyme 2
  • DPP4 serine peptidase
  • the receptor binding domain (RBD) of SARS-CoV-2 has been characterized and the binding mode of the SARS-CoV-2 RBD to ACE2 has been found to be nearly identical to that observed for SARS-CoV (Lan et al., 2020).
  • RBD receptor binding domain
  • Antibodies that neutralize coronaviruses have significant potential as therapeutic agents. Further antibodies with high affinity for coronaviruses, such as SARS-CoV-2, may allow for detection, quantification, or capture of coronaviruses with high sensitivity and specificity.
  • an isolated or purified antibody that specifically recognizes at least one coronavirus spike polypeptide, wherein the antibody comprises an antigen binding portion of an antibody heavy chain, wherein the antigen binding portion comprises a first complementarity determining region (CDR1), a second complementarity determining region (CDR2), and a third complementarity determining region (CDR3), and wherein CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 1, SEQ ID NO:
  • the antibody is a neutralizing antibody and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100;
  • the antibody specifically binds the S1-NTD domain of the coronavirus spike polypeptide and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126; SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128; or SEQ ID NO: 38, SEQ ID NO: 83, and SEQ
  • the antibody specifically binds the S2 subunit of the coronavirus spike polypeptide and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 34, SEQ ID NO: 78, and SEQ ID NO: 124; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO:
  • the antibody specifically binds the S1-RBD domain of the coronavirus spike polypeptide and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 9,
  • the antibody is cross-reactive with the spike polypeptide of SARS- CoV-2 and SARS-CoV, and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 92; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO:
  • the antibody recognizes a linear epitope, and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 27, SEQ ID NO
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 183.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; or SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126 or SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128.
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 184.
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 158, SEQ ID NO: 157, SEQ ID NO: 172, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 159, or SEQ ID NO: 162, or an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 158, SEQ ID NO: 157, SEQ ID NO: 172, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 159, and/or SEQ ID NO: 162.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118.
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 185.
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 166, SEQ ID NO: 177, SEQ ID NO: 179, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 181, SEQ ID NO: 165, or SEQ ID NO: 178, or an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 166, SEQ ID NO: 177, SEQ ID NO: 179, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 180, SEQ ID
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; or SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127.
  • CDR1, CDR2, and CDR3, respectively comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; or SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125.
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 186.
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 171, SEQ ID NO: 173, SEQ ID NO: 149, SEQ ID NO: 155, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 154, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 156, SEQ ID NO: 174, SEQ ID NO: 137, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 141, SEQ ID NO: 146, SEQ ID NO: 150, or SEQ ID NO: 151, or an amino acid sequence having at least 75%, at least 80%, at least 85%, at
  • the antibody is a single domain antibody. In a further embodiment, the antibody is a V H H. [0040] In an embodiment the antibody is of camelid origin. [0041] In an embodiment, the antibody is in a multivalent display format. In a further embodiment, the antibody is linked to an Fc fragment. In a further embodiment, the Fc-linked antibody is in a bivalent display format. [0042] In an embodiment of the antibody, the at least one coronavirus spike polypeptide specifically binds an ACE2 receptor. [0043] In an embodiment of the antibody, the at least one coronavirus spike polypeptide comprises a SARS-CoV-2 spike polypeptide.
  • the at least one coronavirus spike polypeptide is comprised within a homotrimer.
  • an antibody cocktail composition comprising two or more of the antibodies as described herein.
  • the composition may comprise two, three, four, five, or more different antibodies as described herein.
  • the antibody cocktail composition may further comprise a pharmaceutically acceptable carrier and/or diluent.
  • Another embodiment is a nucleic acid molecule encoding an antibody as described herein.
  • a further embodiment is a vector comprising the nucleic acid molecule. In an embodiment of the vector, the nucleic acid molecule is operably linked to at least one promoter and/or regulatory element to enable expression in a host cell.
  • An additional embodiment is a host cell comprising the vector.
  • Another embodiment is a pharmaceutical composition comprising at least one antibody as defined herein and a pharmaceutically acceptable carrier and/or diluent. In an embodiment, the pharmaceutical composition is for delivery by inhalation or nebulization.
  • Another embodiment is a composition comprising at least one antibody as defined herein, linked to another molecule. In an embodiment, the other molecule is a label or polypeptide. In an embodiment, the other molecule is an ACE2 polypeptide or a fragment thereof.
  • Another embodiment is a composition or apparatus comprising at least one antibody as defined herein immobilized on a substrate.
  • a further embodiment is a method for capturing a coronavirus or a coronavirus spike polypeptide or fragment thereof from a sample, the method comprising exposing the sample to the composition or apparatus.
  • the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
  • the coronavirus is SARS-CoV-2 or SARS-CoV.
  • Another embodiment is use of an antibody as described herein to treat or detect a coronavirus infection.
  • the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
  • the coronavirus infection is caused by SARS-CoV-2 and/or SARS-CoV.
  • Another embodiment is use of an antibody or composition as described herein to detect, quantify and/or capture a coronavirus; or to detect, quantify and/or capture a coronavirus spike polypeptide or fragment thereof.
  • the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
  • the coronavirus is SARS-CoV-2 or SARS-CoV.
  • Another embodiment is a method for treating or preventing a coronavirus infection, the method comprising administering at least one antibody or composition as described herein to a subject in need thereof.
  • the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
  • the coronavirus infection is caused by SARS-CoV-2 and/or SARS-CoV.
  • the administration is by inhalation or nebulization.
  • Another embodiment is a method for detecting the presence of a coronavirus or a coronavirus spike polypeptide or fragment thereof in a sample, the method comprising exposing the sample to at least one antibody or composition as described herein and assaying for specific binding between the at least one antibody and the sample, wherein specific binding indicates a presence of the at least one coronavirus or coronavirus spike polypeptide or fragment thereof in the sample.
  • the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
  • coronavirus is SARS-CoV-2 or SARS-CoV
  • the coronavirus spike polypeptide or fragment thereof is a SARS-CoV-2 or SARS-CoV coronavirus spike polypeptide or fragment thereof.
  • Another embodiment is an antibody or composition as described herein for use to detect or treat a coronavirus infection.
  • the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
  • the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV.
  • Another embodiment is an antibody composition as described herein for use to detect, quantify and/or capture a coronavirus; or to detect, quantify and/or capture a coronavirus spike polypeptide or fragment thereof.
  • the coronavirus is a coronavirus that specifically binds an ACE2 receptor, or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
  • the coronavirus is SARS-CoV-2 or SARS-CoV or the coronavirus spike polypeptide or fragment thereof is a SARS- CoV-2 or SARS-CoV spike polypeptide or fragment thereof.
  • Another embodiment is use of an antibody as described herein in the manufacture of a medicament for prevention or treatment of a coronavirus infection.
  • the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
  • the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV.
  • the medicament is for delivery by inhalation or nebulization.
  • Figures 1A and 1B describe antigen validation by ELISA.
  • Fig.1A shows the results of an ELISA assessing the binding of microtiter-well-adsorbed (S, S1, S2, S1-RBD) and microtiter- well-captured (AviTag-S1, AviTag-S1-RBD) SARS-CoV-2 spike protein fragments to cognate ACE2 receptor (ACE2-hFc).
  • AviTag-S1 and AviTag-S1-RBD were captured on streptavidin- coated microtiter wells through their C-terminal biotins.
  • FIG. 1B shows the results of an ELISA confirming the binding of microtiter-well-adsorbed SARS-CoV-2 spike protein fragments S, S1, S2 and S1-RBD to a commercial rabbit anti-SARS-CoV-2 S polyclonal antibody (pAb).
  • Figures 2A and 2B show the results of llama serology.
  • Fig. 2A shows the results of an ELISA performed with pre-immune (day 0) and immune (day 21 and 28) sera, demonstrating that spike protein-immunized Maple Red and Eva Green llamas generated a strong immune response against target antigens S, S1, S2 and S1-RBD.
  • ELISA performed with day 0, 21 and 28 sera showed spike protein-immunized llamas did not react with non-target antigens (casein and dipeptidase 1 [DPEP1]), demonstrating specificity of the immune response.
  • Fig.2B shows flow cytometry surrogate neutralization assays performed with pre-immune (day 0) and immune (day 21 and 28) sera demonstrating that the Eva Green llama mounted a polyclonal immune response that was more potent in inhibiting the binding of SARS-CoV-2 S to ACE2 than Maple Red’s. Due to a lack of complete curves, inhibitory serum titers for Maple Red sera were estimated assuming similar upper plateaus as those for Eva Green sera.
  • Figure 3 provides a schematic representation of three different antibody formats: monomeric V H H, bivalent V H H-Fc and monovalent V H H-Fc.
  • Figures 4A and 4B show size-exclusion chromatogram (SEC) profiles of anti-SARS- CoV-2 spike protein V H Hs.
  • Fig.4A shows SEC profiles of Eva Green V H Hs.
  • Fig.4B shows SEC profiles of Maple Red V H Hs. V e , elution volume: mAU, milliabsorbance unit.
  • Figures 5A and 5B show data on the thermostability of anti-SARS-CoV-2 spike protein V H Hs.
  • Fig.5A provides representative examples showing the thermal unfolding of NRCoV2-1d, NRCoV2-02, NRCoV2-07 and NRCoV2-11, as determined using CD spectroscopy.
  • Fig. 5B provides a summary of V H H T m s. The dotted line across the graph in Fig.5B represents the median T m (70.4 ).
  • Figures 6A, 6B, 6C, 6D and 6E show SPR/ELISA binding affinity, specificity and cross- reactivity data for anti-SARS-CoV-2 V H Hs and V H H-Fcs. Figs.
  • FIGS. 6A and 6B show the results of ELISA assessing the cross-reactivity of anti-SARS-CoV-2 V H H-Fcs against to a collection of spike glycoproteins from various coronavirus genera and SARS-CoV-2 variants. Assays were performed at a fixed V H H-Fc concentration (13 nM). The V H H-72 (Wrapp et al., 2020) benchmark and human ACE-2 were included for comparison. The epitope bin numbers provided along the bottom of Fig. 6B correspond to the bins shown in Fig. 9G. Fig.
  • 6C shows representative SPR sensorgrams showing single-cycle kinetic analysis of NRCoV2-02, NRCoV2-07, NRCoV2-SR03 and NRCoV2-S2A4 VHH binding to SARS-CoV S and SARS-CoV-2 S, S1, S2 and S1-RBD.
  • Spike proteins were captured on CM5 sensorchip surfaces, followed by flowing V H Hs over the sensorchip surfaces at the concentration ranges shown in each panel.
  • “NRCoV2-02/NRCoV2- 07”, “SR03” and “S2A4” represent SPR binding profiles for V H Hs specific to SARS-CoV-2 S1- RBD, S1-NTD and S2, respectively.
  • NRCoV2-07 also represents binding profiles for V H Hs that cross-react with SARS-CoV.
  • Figs. 6D and 6E show the results of ELISA assessing the domain specificity of a set of anti-SARS-CoV-2 V H H-Fcs. Assays were performed against SARS-CoV-2 S, S1, S1-NTD and S1-RBD at a fixed concentration (13 nM) (Fig.6D) or varying concentrations (Fig. 6E) of V H H-Fcs. In the graphs shown in Fig. 6E, NRCoV2-02 is included as an internal control (dashed line).
  • Figures 7A and 7B show on-/off-rate maps summarizing V H H kinetic rate constants, k a s and k d s. Diagonal lines represent equilibrium dissociation constants, K D s. Maps were constructed using the V H H binding data against SARS-CoV-2 S (Fig.7A) and SARS-CoV S (Fig.7B). In Fig. 7A, V H Hs are clustered based on subunit/domain specificity determined in Example 5.
  • FIGS. 8A and 8B show the results of flow cytometry assessing the binding of V H H-Fcs to SARS-CoV-2 S-expressing CHO-S cells.
  • Fig. 8A shows representative examples.
  • Fig. 8B summarizes affinity values, i.e., EC 50 s, determined from graphs in Fig.8A.
  • V H H-72 (Wrapp et al., 2020; open circle) is included for comparison. The line through the data points is the median.
  • Figures 9A, 9B, 9C, 9D, 9E, 9F, and 9G show epitope typing and binning data obtained by SDS-PAGE/WB, sandwich ELISA and SPR.
  • Fig.9A and 9B show the results of epitope typing of anti-SARS-CoV-2 V H Hs by SDS-PAGE/WB. Binding of biotinylated V H Hs or V H H-Fcs to denatured SARS-CoV-2 S was detected using streptavidin-peroxidase conjugate (Fig.9A) or anti- human Ig Fc antibody-peroxidase conjugate (Fig. 9B), respectively. Presence of binding signals indicates V H H recognizing a linear epitope.
  • FIG.9C shows representative sensorgrams showing SPR epitope binning on SARS-CoV-2 S-immobilized surfaces.
  • Figs. 9D and 9E show epitope binning of S1-RBD-specific V H Hs by competitive sandwich ELISA. ELISA binding results for pair-wise combinations of V H Hs against S1 are presented as a heat map.
  • Binding pairs giving binding signal were considered as recognizing non-overlapping epitopes hence belonging to different epitope bins or V H H clusters, while those giving no/week binding signals (colorless/pale shading) were considered to be recognizing overlapping epitopes belonging to the same epitope bins.
  • ACE2-Fc and V H H-72 V H H/V H H-Fc benchmark were also included in assays.
  • Fig.9F provides a schematic summary of the initial epitope binning results.
  • NRCoV2- 1c and NRCoV2-MRed02 were assigned to bin 1 since their CDRs were essentially the same as to those of NRCoV2-1a/1d and NRCoV2-MRed04, respectively, with experimentally defined bins.
  • Fig. 9G provides a schematic summary of binning results after further characterization. Unless specified otherwise, references to epitope bin numbers throughout the present disclosure refer to the bins identified in Fig.9F. The bin numbers provided in Fig.9E correspond to the bins shown in Fig.9G.
  • FIG 10 shows the results of ELISA assessing the ability of monomeric V H Hs in blocking (“neutralizing”) the binding of human ACE2 receptor (ACE2-Fc) to its SARS-CoV-2 S1-RBD ligand (i.e., S).
  • a 450 nm is a measure of blocking.
  • V H H-72 V H H (Wrapp et al., 2020) and monomeric ACE2-H 6 served as positive antibody controls, while toxin A-specific A20.1 V H H (Hussack et al., 2011) was a negative antibody control.
  • PBS represents assays in which VHH was substituted with PBS and, similar to the A20.1 control, provides a reference binding signal for lack of any blocking (“min inhibition”).
  • FIG. 11 shows sensorgrams showing the ability of monomeric V H Hs in blocking (“neutralizing”) the binding of ACE2 receptor to its ligand SARS-CoV-2 S.
  • a tandem SPR in two different orientation formats were performed where injection of V H H (orientation #1) or ACE2 (orientation #2) at 20 – 40 ⁇ K D concentration (V H H) or 1 ⁇ M (ACE2) over sensor chip- immobilized S was followed by injection of V H H + ACE2 mix at the same V H H and ACE2 concentrations.
  • Solid and dashed profiles represent binding results with the two orientation formats.
  • NRCoV2-02:ACE2 represents profiles for blocking (neutralizing) VHHs where the addition of the V H H or ACE2 results in no significant increase in binding over that achieved by the injection of the ACE2 or V H H over the antigen surface.
  • “NRCoV2-11:ACE2” represents profiles for non-blocking (non-neutralizing V H Hs where the addition of the V H H or ACE2 results in significant increase in binding over that achieved by the injection of the ACE2 or V H H over the antigen surface.
  • RUs, representing binding differences between the first and second injection were calculated from the sensorgrams and used to identify V H Hs that block (neutralize) the binding of ACE2 receptor to its ligand S1-RBD.
  • FIG. 12A and 12B show the results of flow cytometry assessing the ability of monomeric V H Hs in blocking (“neutralizing”) the binding of SARS-CoV-2 S to ACE2-expressing Vero E6 cells at 100 nM (Fig. 12A) or increasing (Fig. 12B) V H H concentrations.
  • Fig. 12B provides plots showing inhibition of SARS-CoV-2 S binding to Vero E6 cells as a function of V H H concentration.
  • the NRCoV2-1d, NRCoV2-02, NRCoV2-05, and NRCoV2-11 V H Hs are S1-RBD, SR13, S1-NTD-specific.
  • Monomeric ACE2 (ACE2-H 6 ) serves as positive “antibody” control and reference, and V H H-72 V H H (Wrapp et al., 2020) is included as benchmark.
  • A20.1 and PBS represent negative control assays in which V H Hs were replaced with C. difficile toxin A-specific A20.1 V H H (Hussack et al., 2011) and PBS, respectively.
  • Figures 13A and 13B show virus-neutralizing potential of V H H-Fcs in flow cytometry- based surrogate virus neutralization assays.
  • Fig.13A shows flow cytometry assessing the ability of bivalent VHH-Fcs in blocking (“neutralizing”) the binding of SARS-CoV-2 S to ACE2- expressing Vero E6 cells at 250 nM V H H-Fc concentrations.
  • Fig. 13B shows flow cytometry assessing the ability of bivalent V H H-Fcs in blocking (“neutralizing”) the binding of SARS-CoV- 2 S to ACE2-expressing Vero E6 cells at increasing V H H-Fc concentrations.
  • V H H-Fcs are S1-RBD- specific, while NRCoV2-SR01 and NRCoV2-SR13 V H H-Fcs are S1-NTD-specific.
  • V H H-72 V H H- Fc (Wrapp et al., 2020) is included as a benchmark.
  • A20.1” and “PBS” represent negative control assays in which V H Hs were replaced with C. difficile toxin A-specific A20.1 V H H (Hussack et al., 2011) and PBS, respectively.
  • Figures 14A and 14B show the results of a V H H-Fc in vitro live-virus micro- neutralization assay. Antibody concentrations that gave 100% neutralization, i.e., MN100s, were used to rank the neutralizing potency of V H H-Fcs. A lower MN 100 means a higher neutralization potency. V H H-72 (Wrapp et al., 2020) is included as benchmark.
  • Fig.14A provides a plot showing the MN 100 s of bivalent V H H-Fcs. The inset shows MN 100 s of monomeric NRCoV2-02 and V H H- 72 V H Hs.
  • Fig.14B provides a plot comparing the MN 100 s of bivalent V H H-Fcs to monovalent V H H-Fcs. Monovalent V H H-72-Fc did not show MN 100 at the highest concentration tested (350 nM). In monovalent V H H-Fc constructs, one heavy chain displays an S- specific V H H, while the other displays a C. difficile toxin A-specific, mock V H H (A26.8) (Hussack et al., 2011).
  • FIG. 15A shows inhibition capability of S1-RBD-specific V H H-Fcs at high (312.5 nM) and low (2.5 nM) V H H-Fc concentrations.
  • NRCoV2-08, NRCoV2-19 and NRCoV2-21 which showed no binding to spike protein-expressing CHO cells (CHO-S), do not neutralize either.
  • V H H-72 Wrapp et al., 2020
  • C. difficile toxin A-specific V H H A20.1 are included as benchmark and negative control, respectively.
  • Figs.15B-D provide representative examples showing inhibition capability of V H H-Fcs as a function of V H H- Fc concentration, for select S-RBD specific antibodies (Fig. 15B), S1-NTD-specific antibodies (Fig. 15C), and S2-specific antibodies (Fig. 15D).
  • Antibody concentrations that gave 50% neutralization, i.e., IC 50 s, were calculated from graphs and used to rank the neutralizing potency of VHH-Fcs.
  • Fig. 15E shows a summary of IC50 categorized based on subunit/domain specificity and epitope bin. A lower IC 50 means a higher neutralization potency.
  • V H H-72 is shown as open circle in bin 1.
  • FIG. 16A shows SEC profiles of pre- vs post-aerosolized V H Hs, for representative V H Hs.
  • NRCoV2-1d, NRCoV2-02 and NRCoV2-07 represent the vast majority of V H Hs which were resistant to aerosolization-induced aggregation, showing a homogenously monomeric peak.
  • the V H H-72 benchmark forms a significant amount of soluble aggregates following aerosolization.
  • NRCoV2-11 on the other hand represents the few V H Hs that formed visible, precipitating aggregates reflected in significant reduction of their monomeric peak areas (compare monomeric peak for pre- vs post-aeosolized NRCoV2-11). V e , elution volume.
  • Fig. 16B summarizes the % recovery of all V H Hs and
  • Fig. 16C summarizes the % recovery of a subset of V H Hs.
  • % recovery represents the proportion of a V H H that remained monomerically soluble following aerosolization.
  • the open circle in Fig.16B represents benchmark V H H-72. The line through the data points is the median.
  • FIG.16D shows the results of ELISA assessing the effect of aerosolization on the functionality of V H Hs by comparing the binding activity of pre- vs post- aerosolized V H Hs against SARS-CoV-2 S.
  • Essentially identical EC 50 s for pre- vs post-aerosolized V H Hs clearly indicate aerosolization had no effect on the functional activity of V H Hs.
  • Figure 17 provides the results of sandwich ELISA demonstrating the potential utility of V H Hs in detecting/capturing SARS-CoV-2, SARS-CoV and related viruses, as well as their spike proteins.
  • SARS-CoV-2 S, S1 and S1-RBD antigens were used as surrogates for viruses. Specific detection of S, S1 and S1-RBD was achieved using NRCoV2-02 V H H as the capture antibody and NRCoV2-1d, NRCoV2-02, NRCoV2-04, NRCoV2-07, or NRCoV2-11 V H H-Fcs as detecting antibodies. SC 50 is the concentration of antigen that gives 50% binding and were calculated from graphs. [0076] Figure 18 shows an alignment of amino acid sequences of S-specific V H H antibodies described herein. [0077] Figure 19 shows an alignment of amino acid sequences of S1-NTD-specific V H H antibodies described herein.
  • Figure 20 shows an alignment of amino acid sequences of S2-specific V H H antibodies described herein.
  • Figure 21 shows an alignment of amino acid sequences of S1-RBD-specific V H H antibodies described herein.
  • Figures 22A, 22B, 22C, and 22D show the results of efficacy tests of V H H-Fcs in hamsters challenged with SARS-CoV-2.
  • Fig.22A shows lung viral load in V H H-Fc-treated (V H H- 72 benchmark, 1d, 05, MRed05, SR01, S2A3, 1d/MRed05, 1d/SR01) and control groups treated with PBS or isotype A20.1 V H H-Fc at 5 dpi.
  • Fig.22B shows the percent body weight change for antibody-treated and control groups.
  • Fig. 22C shows the percent body weight change at 5 dpi.
  • treatment effects assessed by one-way ANOVA with Dunnett’s multiple comparison post hoc test, were significant (*p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001 or ****p ⁇ 0.0001).
  • Dunnett’s test was performed by comparing treatment groups against the isotype control. ns, not significant.
  • FIG 23 shows immunohistochemical demonstration of SARS-CoV-2 nucleocapsid (N) protein in the lungs of V H H-Fcs-treated animals.
  • Untreated (PBS) and A20.1 isotype-treated animals showed strong viral N protein immunoreactivity which was mainly found in large multifocal patches of consolidated areas.
  • Black arrow indicates the presence of viral N protein in bronchiolar epithelial cells.
  • Omission of anti-nucleocapsid antibody eliminated the staining (Negative). Shown also is the absence of staining in healthy animals (Na ⁇ ve).
  • a marked reduction in viral N protein staining was seen in all lung tissues examined from V H H-Fc-treated animals (middle and bottom panels).
  • FIG. 24 shows immunohistochemical detection of infiltrating macrophages in the lungs of V H H-Fc-treated animals. Untreated (PBS) and A20.1 isotype-treated animals showed an intense immune reaction to anti-Iba-1 antibody and an increased number of Iba-1-positive macrophagesin the consolidated areas.
  • FIG. 25 shows immunohistochemical detection of T lymphocytes in the lungs of V H H- Fc-treated animals. Untreated (PBS) and A20.1 isotype-treated animals showed an increased number of T lymphocytes in the pulmonary interstitium. A dramatic decrease in the number of T lymphocytes was seen in the lungs of V H H-Fc-treated animals. Representative images are shown from a single experiment.
  • Figure 26 shows immunohistochemical detection of apoptotic cells in the lungs of V H H- Fc-treated animals.
  • Untreated (PBS) and A20.1 isotype-treated animals showed an increase in the number of TUNEL-positive cells with classical features of apoptotic cells in the pulmonary interstitium.
  • a marked reduction in the TUNEL- positive cells was seen in the lungs of NRCoV2-05- and NRCoV2-MRed05-treated animals. Black arrows indicate occasional TUNEL-positive cells. Representative images are shown from a single experiment.
  • Figure 27 shows on-/off-rate maps summarizing V H H kinetic rate constants, kas and kds determined by SPR for the binding of V H Hs to SARS-CoV S.
  • Figures 28A and 28B show on-/off-rate maps summarizing V H H kinetic rate constants, kas and kds determined by SPR for the binding of V H Hs to SARS-CoV-2 Alpha S (Fig.28A) and SARS-CoV-2 Beta S (Fig.28B).
  • Figure 29 shows representative SPR sensorgrams showing single-cycle kinetics analysis of NRCoV2-02, NRCoV2-15 and NRCoV2-MRed05 binding to Wuhan, Alpha and Beta S (NRCoV2-02, NRCoV2-15) and RBD (NRCoV2-MRed05).
  • Figure 30 shows a summary of IC 50 s obtained by live virus neutralization assays (LVNAs) for V H H-Fcs against Wuhan, Alpha, and Beta SARS-CoV-2 variants.
  • the epitope bin numbers provided in Fig.30 correspond to the bins shown in Fig.9G.
  • Figures 31A, 31B, 31C, and 31D show results from live virus neutralization assays assessing the ability of SARS-CoV-2 V H H-Fcs in blocking the infection of ACE2-expressing Vero E6 cells by SARS-CoV-2 Alpha (Fig. 31A and Fig. 31C) and Beta (Fig. 31B and Fig. 31D) variants at fixed (Fig. 31A and Fig. 31B) or varying (Fig. 31C and Fig. 31D) V H H-Fc concentrations.
  • Inhibition assays shown in Fig.31A and Fig.31B were performed at 312, 12.5 or 0.5 nM V H H-Fc concentrations.
  • FIG. 31C and Fig. 31D are recorded in Table 19.
  • V H H-72 and C. difficile toxin A-specific V H H A20.1 are included as a benchmark and negative antibody control, respectively.
  • the epitope bin numbers provided in Figs. 31C and 31D correspond to the bins shown in Fig.9G.
  • Figure 32 shows in vivo stability and persistence of V H Hs. Stability and persistence were determined by monitoring the concentration of a representative VHH-Fc (NRCoV2-1d) in hamster blood at various days post-injection by ELISA. V H H-72 V H H-Fc was used as the benchmark.
  • DETAILED DESCRIPTION [0091] The following is a detailed description provided to aid those skilled in the art in practicing the present disclosure.
  • coronavirus spike polypeptide or “coronavirus spike protein” (S) is the major coronavirus surface protein, and is a glycosylated homotrimer that binds to a host cell receptor and mediates coronavirus entry into a host cell.
  • the coronavirus may be SARS-CoV-2, SARS-CoV, or another coronavirus.
  • SARS-CoV-2 may be used herein to refer to any strain or variant of the SARS-CoV-2 virus.
  • SARS-CoV may be used to refer to any strain or variant of the SARS-CoV virus.
  • a SARS-CoV-2 variant is a strain of SARS-CoV-2 that comprises one or more mutations relative to the Wuhan strain of SARS-CoV-2.
  • a variant may be, but need not be, a variant that has been designated as a variant of concern or a variant of interest by the World Health Organization.
  • the term “polypeptide” refers to a molecule comprising two or more amino acid residues linked by peptide bonds.
  • a polypeptide may have primary, secondary, and/or tertiary structure.
  • a “protein” comprises at least one polypeptide and may have primary, secondary, tertiary, and/or quaternary structure.
  • polypeptide and “protein” are often used interchangeably, and a polypeptide may be comprised by a protein.
  • a protein may be a homo- or hetero-multimer that comprises two or more polypeptides, or a protein may comprise a single polypeptide.
  • a polypeptide or protein may include one or more post- translational modifications, such as, but not limited to, glycosylation, phosphorylation, lipidation, S-nitrosylation, N-acetylation, or methylation.
  • fragment in the context of a polypeptide, refers to a portion of a polypeptide comprising a series of consecutive amino acid residues from a parent polypeptide.
  • fragment refers to an amino acid sequence of at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive amino acid residues from a parent polypeptide.
  • a fragment may comprise an epitope or binding domain from a parent polypeptide.
  • a fragment may be a biologically active fragment that retains one or more functional characteristics of a parent polypeptide.
  • antibody refers to an antigen binding protein comprising at least a heavy chain variable region (V H ) that binds a target epitope.
  • the term antibody includes monoclonal antibodies comprising immunoglobulin heavy and light chain molecules, single heavy chain variable domain antibodies, and variants and derivatives thereof, including chimeric variants of monoclonal and single heavy chain variable domain antibodies.
  • the antibody may be a naturally-occurring antibody, it may be obtained by manipulation of a naturally-occurring antibody, or it may be produced using recombinant methods.
  • an antibody may include, but is not limited to a Fv, single-chain Fv (scFv; a molecule consisting of VL and VH connected with a peptide linker), Fab, F(ab')2, single domain antibody (sdAb; an antibody composed of a single V L or V H ), or a multivalent presentation of any of these.
  • Antibodies such as those just described may require linker sequences, disulfide bonds, or other types of covalent bond to link different portions of the antibody.
  • the antibody may be a single domain antibody derived from a naturally- occurring source.
  • Heavy chain antibodies of camelid origin Hamers-Casterman et al, 1993
  • V H H sdAbs have also been observed in shark and are termed VNAR (Nuttall et al, 2003).
  • single domain antibody includes single domain antibodies directly isolated from V H , V H H, V L , or VNAR reservoir of any origin through phage display or other technologies, single domain antibodies derived from the aforementioned single domain antibodies, recombinantly produced single domain antibodies, as well as single domain antibodies generated through further modification of such single domain antibodies by humanization, affinity maturation, stabilization, solubilization, camelization, or other methods of antibody engineering.
  • Single domain antibodies possess desirable properties for antibody molecules, such as high thermostability, high detergent resistance, relatively high resistance to proteases (Dumoulin et al, 2002) and high production yield (Arbabi-Ghahroudi et al, 1997). They can also be engineered to have very high affinity by isolation from an immune library (Li et al, 2009) or by in vitro affinity maturation (Davies & Riechmann, 1996).
  • a person of skill in the art would be well-acquainted with the structure of a single-domain antibody.
  • a single domain antibody comprises a single immunoglobulin domain that retains the immunoglobulin fold; most notably, only three CDR/hypervariable loops form the antigen-binding site. However, and as would be understood by one of skill in the art, not all CDRs may be required for binding the antigen.
  • one, two, or three of the CDRs may contribute to binding and recognition of the antigen by a single domain antibody.
  • the CDRs of the single domain antibody or variable domain are referred to herein as CDR1, CDR2, and CDR3, and numbered as defined by Lefranc et al., 2003.
  • the amino acid sequence and structure of a heavy chain variable domain can be considered—without however being limited thereto—to be comprised of four framework regions or ‘FR’, which are referred to in the art and herein as ‘Framework region 1’ or ‘FR1’; as ‘Framework region 2’ or ‘FR2’; as ‘Framework region 3’ or ‘FR3’; and as ‘Framework region 4’ or ‘FR4’, respectively; which framework regions are interrupted by three complementarity determining regions or ‘CDR s’, which are referred to in the art as ‘Complementarity Determining Region 1’ or ‘CDR1’; as ‘Complementarity Determining Region 2’ or ‘CDR2’; and as ‘Complementarity Determining Region 3’ or ‘CDR3’, respectively.
  • FR framework regions or ‘FR’, which are referred to in the art and herein as ‘Framework region 1’ or ‘FR1’; as ‘Framework region 2’ or ‘FR2’
  • binding refers to the process of a non-covalent interaction between molecules. Preferably, said binding is specific.
  • the terms ‘specific’ or ‘specificity’ or grammatical variations thereof refer to the number of different types of antigens or their epitopes to which a particular antibody such as a V H H can bind.
  • the specificity of an antibody also referred to as “specific binding”, can be determined based on affinity.
  • a specific antibody preferably has a binding affinity (Kd) for its epitope of less than 10 7 M, preferably less than 10 8 M.
  • affinity refers to the strength of a binding reaction between a binding domain of an antibody and an epitope. It is the sum of the attractive and repulsive forces operating between the binding domain and the epitope.
  • affinity refers to the equilibrium dissociation constant, Kd.
  • epitope refers to a part of an antigen that is recognized by an antibody.
  • epitope includes linear epitopes and conformational epitopes.
  • a linear epitope is an epitope that is recognized by an antibody based on its primary structure, and a stretch of contiguous amino acids is sufficient for binding.
  • a conformational epitope is based on 3-D surface features and shape and/or tertiary structure of the antigen.
  • neutralizing antibody refers to an antibody that, when bound to an epitope, interferes with at least one of the steps leading to the release of a virus genome, such as a coronavirus genome, into a host cell.
  • subject refers to an animal that is susceptible to infection by a coronavirus.
  • the subject may be an animal that is susceptible to infection by a coronavirus that binds an ACE2 receptor, such as SARS-CoV-2 or SARS-CoV.
  • the subject may be a human or non-human animal.
  • the subject is a human or non-human mammal.
  • the ACE2 receptor may be a human ACE2 receptor or an animal ACE2 receptor.
  • administration routes include, but are not limited to, parenteral (intravenous, intramuscular, and subcutaneous), oral, nasal, ocular, transmucosal (buccal, vaginal, and rectal), transdermal, and pulmonary administration.
  • strong interaction and strong binding refer to the presence of salt bridges and cation-pi interactions between amino acid residues, as is known to the skilled person.
  • weak interaction and weak binding refer to the presence of hydrogen bonds and non-bonded/hydrophobic interactions, as is known to the skilled person.
  • purified refers to a molecule, e.g. a polypeptide or protein that has been identified and substantially separated and/or recovered from the components of its natural environment.
  • isolated antibody refers to an antibody that is substantially freed from other antibody molecules having different antigenic specificities. Further, a purified or isolated antibody may be substantially free of one or more other cellular and/or chemical substances. Absolute purity is not required for a molecule to be considered purified or isolated.
  • pharmaceutically acceptable means generally regarded as safe when administered to humans.
  • the term “pharmaceutically acceptable” is approved by a federal or state government regulatory agency for use in animals, more preferably in humans.
  • carrier means a diluent, adjuvant, excipient, or vehicle with which a compound is formulated and/or administered.
  • Such pharmaceutical carriers can be water and sterile liquids, such as petroleum, animal, vegetable or synthetically derived oils such as peanut oil, soybean oil, mineral oil, sesame oil. Water or saline solutions and aqueous dextrose and glycerol solutions are preferably used as carriers for injectable solutions. Suitable pharmaceutical carriers are, for example, described in “Remington (23 rd edition), The Science and Practice of Pharmacy”.
  • linker refers to a chemical group or molecule that can be used to join one molecule to another.
  • An antibody may be linked to another molecule by a linker or an antibody may be directly linked (aka joined, fused, or bonded) to another molecule, without the use of a linker.
  • Suitable linkers are known in the art and may be selected based on the chemical nature of the molecules being joined. Examples of linkers include peptide linkers and chemical cross-linkers. Peptide linkers may comprise a single amino acid residue or a plurality of amino acid residues.
  • label refers to a molecule or compound that can be used to label a molecule, such as an antibody, to allow detection of the molecule. Suitable labels will be known to one skilled in the art and include, but are not limited to, radioisotopes; enzymes, such as horse radish peroxidase (HRP) or calf intestinal alkaline phosphate (AP); fluorophores; antigen binding fragments from cleaved antibodies (Fabs); and colloidal gold.
  • HRP horse radish peroxidase
  • AP calf intestinal alkaline phosphate
  • fluorophores antigen binding fragments from cleaved antibodies (Fabs)
  • colloidal gold colloidal gold.
  • nucleic acid molecule refers to any nucleic acid-containing molecule including, but not limited to, DNA, RNA, and DNA/RNA hybrids, in any form and/or conformation.
  • the term encompasses nucleic acids that include any of the known base analogs of DNA and RNA. For example, single-stranded, double-stranded, nuclear, extranuclear, extracellular, and isolated nucleic acids are all contemplated.
  • vector refers to a synthetic nucleotide sequence used for manipulation of genetic material, including but not limited to cloning, subcloning, sequencing, or introduction of exogenous genetic material into cells, tissues or organisms. It is understood by one skilled in the art that vectors may contain synthetic DNA sequences, naturally occurring DNA sequences, or both. Examples of commonly used vectors include plasmids, viral vectors, cosmids, and artificial chromosomes.
  • the term “regulatory sequence” includes promoters, enhancers and other expression control elements, such as polyadenylation sequences, matrix attachment sites, insulator regions for expression of multiple genes on a single construct, ribosome entry/attachment sites, introns that are able to enhance expression, and silencers. Promoters may be cell-specific or tissue- specific to facilitate expression in a desired target.
  • promoters include promoters, enhancers and other expression control elements, such as polyadenylation sequences, matrix attachment sites, insulator regions for expression of multiple genes on a single construct, ribosome entry/attachment sites, introns that are able to enhance expression, and silencers. Promoters may be cell-specific or tissue- specific to facilitate expression in a desired target.
  • the term “operably linked” is used herein to mean that the two sequences are associated in a manner that allows the regulatory sequence to affect expression of the other nucleotide sequence.
  • the term “host cell” refers to a cell into which a nucleic acid molecule or vector may be introduced, for example to allow for replication of the nucleic acid molecule or vector by the host cell and/or to allow for expression of the nucleic acid molecule, or of a nucleic acid molecule comprised by the vector, by the host cell to produce a product of interest, such as an RNA or protein.
  • the nucleic acid molecule may encode an antibody as described herein, and introduction of the nucleic acid molecule into the host cell may allow the antibody to be expressed by the host cell.
  • a host cell may be any suitable cell, such as a bacterial cell or eukaryotic cell.
  • host cells include E. coli, yeast, and mammalian cells, such as, but not limited to, Chinese hamster ovary (CHO) cells, mouse myeloma cells, and human embryonic kidney (HEK) cells.
  • CHO Chinese hamster ovary
  • HEK human embryonic kidney
  • invention refers to the prophylactic administration of a therapeutic molecule or composition to a subject to prevent the occurrence of, or to reduce the severity of, an illness or disease in the subject.
  • sample refers to a sample in which a coronavirus presence is suspected or expected.
  • the sample may be a biological sample from a subject, such as, but not limited to, blood or a fraction thereof, saliva, cellular material, urine, or feces; a sample from a bioreactor; or an environmental sample.
  • sequence identity refers to the percentage of sequence identity between two amino acid sequences or two nucleic acid sequences. To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g. gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the determination of percent identity between two sequences can also be accomplished using a mathematical algorithm.
  • One non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, modified as in Karlin and Altschul, 1993. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990.
  • BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g.
  • Gapped BLAST can be utilized as described in Altschul et al., 1997.
  • PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules.
  • XBLAST and NBLAST can be used (see, e.g. the NCBI website).
  • Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
  • ALIGN program version 2.0
  • a PAM120 weight residue table When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.
  • the percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
  • the phrase "at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements.
  • This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase "at least one" refers, whether related or unrelated to those elements specifically identified.
  • Description [00127] The present disclosure relates to SARS-CoV-2 spike protein-specific antibodies and uses thereof. Provided are isolated or purified antibodies comprising complementarity determining region (CDR) 1, CDR2, and CDR3 sequences as outlined in Table 6.
  • the antibodies described herein recognize a variety of spike protein epitopes in different subunit and domains of the coronavirus spike protein, specifically S2, the N-terminal domain of S1 (S1-NTD), and the receptor binding domain of S1 (S1-RBD). Within these subunits/domains, antibodies described herein recognize several different epitopes. Because of this epitopic diversity, antibodies described herein may be used in combination, for example for combination therapy, or as bi- specific or multi-specific antibodies.
  • An antibody as described herein comprises an antigen binding portion of an antibody heavy chain, wherein the antigen binding portion comprises a first complementarity determining region (CDR1), a second complementarity determining region (CDR2), and a third complementarity determining region (CDR3), and wherein CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7,
  • the antibody comprises the amino acid sequence set forth in SEQ ID NO: 183, 184, 185, or 186.
  • an antibody as described herein comprises the amino acid sequence set forth in SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO:
  • the antibody comprises an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO:
  • nucleic acid molecule encoding an antibody as described herein.
  • a further embodiment is a vector comprising the nucleic acid molecule.
  • the nucleic acid molecule may be operably linked to at least one promoter and/or regulatory element to enable expression in a host cell.
  • a further embodiment is a host cell comprising the nucleic acid or vector.
  • An antibody as described herein may be comprised within a composition.
  • the antibody may be comprised within a pharmaceutical composition that comprises a pharmaceutically acceptable carrier and/or diluent, the antibody may be linked to another molecule, or the antibody may be immobilized on a substrate.
  • the pharmaceutical composition may be for delivery by inhalation or nebulization.
  • Antibodies and compositions as described herein may be used, or for use, to treat or prevent a coronavirus infection, including an infection caused by at least one coronavirus that specifically binds an ACE2 receptor. Antibodies as described herein may also be used in the manufacture of a medicament for prevention or treatment of a coronavirus infection.
  • the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV.
  • a method for prevention or treatment of a coronavirus infection comprising administering an antibody or composition as described herein to a subject in need thereof. In an embodiment, the administration is by inhalation or nebulization.
  • Antibodies and compositions as described herein may also be used, or for use, to detect, quantify, and/or capture a coronavirus, a coronavirus spike polypeptide or a coronavirus spike polypeptide fragment. Further provided are methods for detecting, quantifying, and/or capturing a coronavirus, a coronavirus spike polypeptide or a coronavirus spike polypeptide fragment using an antibody or composition as described herein.
  • the coronavirus or spike polypeptide is a coronavirus or spike polypeptide that specifically binds an ACE2 receptor.
  • the ACE2 receptor may be a human ACE2 receptor or an animal ACE2 receptor.
  • the coronavirus is SARS-CoV-2 or SARS-CoV
  • the spike polypeptide or fragment thereof is from SARS-CoV-2 or SARS-CoV
  • the antibodies described herein have the characteristics of neutralizing antibodies, and some have been demonstrated to be cross-reactive with the spike protein of other coronaviruses, such as SARS-CoV and related coronaviruses that infect bats, pangolin, and civet, suggesting that antibodies described herein may be useful for binding the spike protein of more than one coronavirus; including coronaviruses that bind an ACE2 receptor, such as SARS-CoV-2 and SARS-CoV.
  • Antibodies described herein have also been demonstrated to bind various SARS- CoV-2 spike protein variants, such as the Wuhan-Hu-1 variant that was first identified in China; the B.1.1.7 variant that was first identified in the United Kingdom (also referred to herein as the UK variant, or the Alpha variant); the B.1.352 variant that was first identified in South Africa (also referred to herein as the South Africa variant, or the Beta variant), the B.1.617.1 variant that was first detected in India (also referred to herein as Kappa); the B.1.617.2 variant that was first detected in India (also referred to herein as Delta); and the B.1.1.529 variant that was first detected in South Africa (also referred to herein as Omicron).
  • SARS- CoV-2 spike protein variants such as the Wuhan-Hu-1 variant that was first identified in China; the B.1.1.7 variant that was first identified in the United Kingdom (also referred to herein as the UK variant, or the Alpha variant); the B.1.352 variant that was first identified in South Africa (also referred
  • Antibodies described herein may be linked to another molecule or substrate.
  • they may be linked to a detectable label to allow detection, quantification, and/or visualization; they may be linked to a molecule that extends antibody half-life, such as polyethylene glycol (PEG), Ig Fc, serum albumin, serum-albumin-specific antibody, serum- albumin-specific peptide, or Fc-specific peptides, proteins or antibodies; they may be linked to a therapeutic molecule; they may be immobilized onto a substrate, such as a plastic surface, a magnetic bead or a protein sheet or bead; and/or they may be linked to a polypeptide.
  • PEG polyethylene glycol
  • Ig Fc Ig Fc
  • serum albumin serum-albumin-specific antibody
  • serum- albumin-specific peptide serum- albumin-specific peptide
  • Fc-specific peptides proteins or antibodies
  • antibodies described herein may be linked to an ACE2 polypeptide or a fragment thereof.
  • Antibodies described herein may also be employed in various formats and combinations.
  • antibodies described herein may be monoparatropic or multiparatropic (including biparatropic), or monospecific or multispecific (including bispecific).
  • Antibodies described herein may be in a monovalent format or in a multivalent format (including a bivalent format).
  • Antibodies described herein that are specific for the same or different epitopes, or for the same or different spike protein subunit or domains may be linked, for example to produce antibodies with different affinities and/or specificities.
  • antibodies described herein may be linked to one or more other antibodies or antibody fragments.
  • antibodies described herein may be used individually or in combination.
  • a combination may comprise any two or more antibodies described herein, or it may comprise at least one antibody described herein and another antibody.
  • the antibodies are V H H antibodies or V H H-Fc antibodies.
  • Antibodies described herein may be useful for a variety of applications.
  • they may be useful for detecting the presence of a coronavirus or a coronavirus spike polypeptide or fragment thereof; for capturing a coronavirus or a coronavirus spike polypeptide or fragment thereof; for quantifying the amount of a coronavirus or a coronavirus spike polypeptide or fragment thereof in a sample; for treatment or prevention of a coronavirus infection; for diagnosing a coronavirus infection; for monitoring the production of a coronavirus spike protein or fragment thereof; for purification of a coronavirus spike protein or fragment thereof; for detecting the level of expression of a coronavirus spike protein or fragment thereof, and/or for quantifying the amount of a coronavirus.
  • cross-reactive antibodies described herein have been shown to be stable against aerosolization, indicating that they may be suitable for delivery to the lungs by inhalation or nebulization.
  • cross-reactive antibodies may have general applicability for the treatment, prevention, detection, quantification or capture of coronaviruses, in addition to SARS-CoV-2, or coronavirus spike polypeptides or fragments thereof from coronaviruses in addition to SARS-CoV-2.
  • cross-reactive antibodies may be used to bind coronaviruses or coronavirus spike polypeptides that bind an ACE2 receptor, including fragments of such coronavirus spike polypeptides.
  • Antibodies described herein may be classified based on the spike protein subunit or domain to which they bind. Nine antibodies were generated that bind to the S1-NTD domain, 24 antibodies were generated that bind to the S1-RBD domain, and 14 antibodies were generated that bind to the S2 subunit (see Tables 5 and 6). Neutralization assays, as described in the Examples, identified antibodies with neutralizing properties within each of these three groups. To the inventors’ knowledge, this is the first known observation of single domain antibodies neutralizing the SARS-CoV-2 virus by targeting a non-S1-RBD region of S, i.e., S1-NTD or S2.
  • Antibodies described herein may also be classified based on their pattern of cross- reactivity with different coronavirus spike proteins and/or spike protein variants, as shown in Figures 6A and 6B. Antibodies that recognize the same set of spike proteins and/or spike protein variants may be viewed as a single group.
  • V H H spike protein antibody V H H-72 (Wrapp et al., 2020). Further, many of the antibodies described herein are demonstrated to outperform V H H-72 in neutralization assays, and some are demonstrated to be more broadly neutralizing than V H H-72. Additionally, some antibodies described herein are demonstrated to be more broadly cross-reactive than V H H-72. [00142]
  • the antibodies described in the following examples may be modified, while still retaining antigen specificity. For example, changes may be introduced into the amino acid sequence of the framework regions, or the antibodies may be humanized. The antibodies may also be linked to other molecule(s).
  • Coronavirus spike protein fragments used for library selection, binding and epitope study experiments Reference Accession describing RBD/SD1 (aa319-591) b Wrapp et al., (Wuhan) QHD43416.1 NRC 6xHis 2020 t SARS-CoV S AAU04646.1 NRC F Galipeau et al., Cive 1 a b LAG-Dual Strep-6xHis 2021 na, not applicable
  • spike protein fragments used in the following Examples were produced as described in Stuible et al., 2021.
  • Materials and Methods Binding to cognate human angiotensin converting enzyme (ACE2) receptor
  • ELISA was performed to determine if spike proteins were able to bind to human ACE2 when passively adsorbed (S, S1, S1-RBD and S2) or captured (S1, S1-RBD) on microtiter wells.
  • Table 2 Binding affinity (EC 50 ) of passively absorbed spike fragments and streptavidin- captured spike fragments to ACE2 Antigen S S1 S2 S1-RBD AviTag-S1-RBD AviTag-S1 “nb”
  • Table 3 Binding affinity (EC 50 ) of passively absorbed spike fragments to a polyclonal antibody known to be specific for SARS-CoV-2 spike protein Antigen S S1 S2 S1-RBD
  • Example 2 Llama Immunization and Serum Analyses Introduction
  • two llamas were immunized with SARS-CoV-2 S or S/S1-RBD to trigger the generation of a diverse pool of antibodies targeting manifold sites over the surface of S, and targeting the S1-RBD sub-domain of S which is used by the virus to start the process of host cell infection through interaction with the ACE2 receptor.
  • Llama sera were assessed by ELISAs for generation of immune responses against SARS-CoV-2 spike proteins, and by flow cytometry surrogate neutralization assays for generation of neutralizing antibodies.
  • Materials and Methods [00155] Llama immunization [00156] Immunizations were performed at Cedarlane Laboratories (Burlington, ON, Canada) and essentially as described (Hussack et al., 2011).
  • a second llama (Maple Red) was immunized with 100 g of S in 500 ⁇ L PBS combined with 500 ⁇ L of Freund’s complete adjuvant on day 0, followed by immunization with 100 g of S mixed with Freund’s incomplete adjuvant on day 7, and immunization with 50 g of S mixed with Freund’s incomplete adjuvant on each of days 14 and 21.
  • Serum ELISA [00158] Llama sera were tested for antigen-specific immune response by ELISA essentially as described (Hussack et al., 2011; Henry et al., 2016). Briefly, dilutions of sera in PBST were added to wells pre-coated with S, S1, S2 or S1-RBD.
  • Negative antigen control wells were pre-coated with casein (100 ⁇ L of 1% v/w) or recombinant human dipeptidase 1 ectodomain, DPEP1 (50 ng/well; Sino Biological, Cat#13543-H08H). Following 1 h incubation at room temperature, wells were washed 10 times with PBST and incubated with HRP-conjugated polyclonal goat anti-llama IgG heavy and light chain antibody (Bethyl, Cat#A160-100P) for 1 h at room temperature. After 10 washes, the peroxidase activity was determined as described above.
  • Trimeric SARS-CoV-2 S was chemically biotinylated using EZ-LinkTM NHS-LC-LC- Biotin following manufacturer’s instructions (Thermo Fisher, Cat#21343). Vero E6 cells (ATCC, Cat#CRL-1586) were maintained according to ATCC protocols.
  • DMEM medium Thermo Fisher, Cat#11965084
  • FBS Thermo Fisher, Cat#10438034
  • 2 mM Glutamax TM Thermofisher, Cat#35050061
  • Percent inhibition 100 x [1 - (F n - F min ) / (F max - F min )], where, F n is the measured fluorescence at any given competitor serum dilution, F min is the baseline fluorescence measured in the presence of cells and SAPE only, and F max is the maximum fluorescence, measured in the absence of competitor serum.
  • Phage display library construction [00166] On day 28, 100 mL of blood from each of the two llamas was drawn and peripheral blood mononuclear cells (PBMCs) were purified by Ficoll® gradient at Cedarlane Laboratories (Burlington, ON, Canada). Two independent phage-displayed V H /V H H libraries were constructed from 5 ⁇ 10 7 PBMCs as described previously (Henry et al., 2016; Rossotti et al., 2015; Henry et al., 2015).
  • PBMCs peripheral blood mononuclear cells
  • V H /V H H genes were amplified using semi-nested PCR and cloned into the phagemid vector pMED1, followed by transformation of E. coli TG1 to construct two libraries with sizes of 1 ⁇ 10 7 and 2 ⁇ 10 7 independent transformants for Eva Green and Maple Red, respectively.
  • library phages were diluted at 1 x 10 11 colony-forming units (cfu)/mL in PBSBT [PBS supplemented with 1% [w/v] BSA and 0.05% Tween® 20] and incubated in antigen-coated microtiter wells for 2 h at 4°C.
  • phages were added to wells with passively-adsorbed S (10 pg/well; PI), passively-adsorbed S2 (10 pg/well; P2), streptavidin-captured biotinylated SI (0.5 pg/well; P3) and streptavidin-captured biotinylated Sl-RBD (0.5 pg/well; P4).
  • phages were pre-absorbed on passively-adsorbed Sl-RBD wells (10 pg/well) for 1 h at 4°C and then the unbound phage in the solution was transferred to wells with streptavidin-captured biotinylated SI (0.5 pg/well) in the presence of non-biotinylated Sl-RBD competitor in solution (10 pg/well).
  • wells were washed 10 times with PBST and bound phages were eluted by treatment with 100 mM glycine pH 2.2 for 10 min at room temperature, followed by immediate neutralization of phages with 2 M Tris.
  • phages were bound on streptavidin-captured biotinylated Sl-RBD but elution of bound phages were carried out competitively with 50 nM ACE2-Fc following the washing step.
  • a small aliquot of eluted phage was used to determine their titer on LB-agar/ampicillin plates and the remaining were used for their subsequent amplification in E.coli TGI strain (Hussack et al., 2011).
  • the amplified phages were used as input for the next round of selection as described above.
  • Example 4 V H H Cloning/Expression in E. coli, Stability/Affinity Validation and Cross- Reactivity Studies Introduction [00171] Hits identified by monoclonal phage ELISA and DNA sequencing were cloned into the expression vector pMRo.BAP.H 6 (Rossotti et al., 2019), produced as His 6 -tagged V H Hs in the periplasmic space of E. coli BL21(DE3) and purified by immobilized metal-ion affinity chromatography (IMAC). V H Hs were subsequently validated for binding and further explored for cross-reactivity soluble ELISA against SARS-CoV-2, SARS-CoV and MERS-CoV spike proteins.
  • IMAC immobilized metal-ion affinity chromatography
  • V H Hs were validated for aggregation resistance by size exclusion chromatography (SEC) and thermostability by circular dichroism T m measurement assays.
  • Lead V H Hs were produced in mammalian cells in fusion with human IgG1 Fc and were subsequently tested in a comprehensive cross-reactivity ELISA against a collection of various coronavirus spike proteins (S).
  • SEC size exclusion chromatography
  • S coronavirus spike proteins
  • V H Hs were subsequently cloned into pET expression vector (Novagen, Madison, WI) for their production in BL21(DE3) E.coli as monomeric soluble protein (Rosotti et al., 2019). Briefly, individual colonies were cultured overnight in 10 mL of LB supplemented with 50 ⁇ g/mL of kanamycin (LB/Kan) at 37°C and 250 rpm. After 16 h, cultures were added to 250 mL LB/Kan and grown to an OD 600 of 0.6. Expression of V H Hs was induced with 10 ⁇ M of IPTG (isopropyl -D-1-thiogalactopyranoside) overnight at 28°C and 250 rpm.
  • IPTG isopropyl -D-1-thiogalactopyranoside
  • V H /V H Hs were extracted by sonication and purified by IMAC as described previously (Rosotti et al., 2019).
  • ELISA see below
  • a small fraction was biotinylated by incubating 1 mg of purified V H Hs with 10 ⁇ M of ATP (Alfa Aesar, Cat#CAAAJ61125-09), 100 ⁇ M of D-(+)-biotin (VWR, Cat#97061-446) and a bacterial cell extract overexpressing E.coli BirA as described previously (Rossotti et al., 2015b).
  • V H H binding validation and preliminary cross-reactivity studies by ELISA Binding validation studies were performed with S1-RBD-specific clones. Briefly, microtiter well plates were coated with 50 ng/well SARS-CoV-2 S1-RBD in 100 ⁇ L PBS overnight at 4 .
  • V H H T m s were measured by circular dichroism as previously described (Henry et al., 2017). Ellipticity of V H Hs were determined at 200 ⁇ g/mL V H H concentrations and 205 nm wavelength in 100 mM sodium phosphate buffer, pH 7.4.
  • V H Hs Production of V H Hs in mammalian cells in fusion with human IgG1 Fc
  • Codon-optimized genes for bivalent V H H-Fcs were synthesized (GenScript).
  • VHH genes were PCR amplified as described previously and cloned into pTT5-hIgG1Fc between the genes for human V H leader sequence and the human IgG1 hinge/Fc sequences, using NarI/HindIII restriction sites.
  • Bivalent V H H-Fcs were produced by transient transfection of HEK293-6E cells followed by protein A affinity chromatography as previously described (Rosotti et al., 2019).
  • Heterodimeric monovalent V H H-Fcs were produced by co-transfection of HEK293-6E cells with two pTT5 vectors, one encoding for a 6xHis-tagged heavy chain (V H H1-hinge-C H 2-C H 3-His 6 ), the other for a non-tagged heavy chain of a different V H H (V H H2-hinge-C H 2-C H 3).
  • the heterodimeric antibodies were purified by sequential protein A affinity chromatography and IMAC.
  • V H H The sequence of the V H H was ordered as GeneBlock (IDT DNA) flanked by SfiI sites for cloning into pMRo.BAP.H6, and NarI/HindIII for cloning into pTT5-hIgG1Fc. Protein purity was evaluated by SDS-PAGE using 4–20% Mini-PROTEAN® TGX Stain-FreeTM Gels (Bio-Rad, Cat#17000435).
  • V H H-Fcs were washed five times with PBSTC and binding of V H H-Fcs was detected using 1 ⁇ g/mL HRP-conjugated goat anti-human IgG. Finally plates were washed five times and peroxidase (HRP) activity was measured as described above.
  • HRP-conjugated goat anti-human IgG HRP-conjugated goat anti-human IgG.
  • HRP-conjugated goat anti-human IgG HRP-conjugated goat anti-human IgG.
  • HRP-conjugated goat anti-human IgG HRP-conjugated goat anti-human IgG
  • V H H hits were cloned in E. coli, confirmed by DNA sequencing, and expressed and purified by IMAC. Following expression of V H Hs, the binding of a sample set of V H Hs was validated by ELISA. Affinities, expressed as EC 50 s, were high, ranging from 0.4 to 7.2 nM (data not shown). V H Hs were also tested for aggregation resistance and stability, and cross-reactivity.
  • Aggregation resistance and stability are desirable attributes of biotherapeutics, as they affect both efficacy and manufacturability.
  • V H Hs tested were found to be aggregation resistant (Figs.4A and 4B), except for NRCoV2-08, which showed some degree of aggregation
  • the V H Hs were also tested for thermal stability and found to be highly thermostable. With the exception of NRCoV2-11, which had a relatively lower T m of 60.4°C, the remaining 25 V H Hs tested had T m s higher than 65°C, with a T m range and median of 65.5 – 79.8°C and 70.4°C, respectively (Figs.5A and 5B).
  • V H Hs had T m s that were higher than that of the V H H-72 benchmark (73.0°C).
  • V H Hs with antigen binding activity were produced as monomeric and dimeric V H H-Fcs for subsequent binding and neutralization assays.
  • the schematic formats of these fusion molecules are depicted in Fig.3.
  • Fig.6A and 6B The results of cross-reactivity studies using SARS-CoV-2 variants and various coronaviruses are shown in Fig.6A and 6B. Initial experiments showed that for the UK (Alpha) and South Africa (Beta) variants of SARS-CoV-2, eight out of nine S1-NTD-specific V H Hs tested were cross-reactive to both variants (Fig.6A).
  • S1-RBD-specific V H Hs 15/20 cross- reacted to both variants and an additional four cross-reacted with the UK variant. Only one (NRCoV2-08) V H H was not cross-reactive at all. Additionally, one S1-NTD-specific V H H, six S1- RBD-specfic and eight S2-specific V H Hs cross-reacted with SARS-CoV. Many antibodies also cross-reacted with pangolin CoV, with fewer, but still significant, numbers cross-reacting to SARS-like CoV W1V1, bat SARS-like CoV and civet SARS-CoV with similar cross-reactivity patterns.
  • V H H-Fcs cross-reacted with the S protein from variants Alpha, Beta, Gamma, Delta and Kappa (B.1.617.1; Variant Being Monitored [VBM]).
  • VBM Variant Being Monitored
  • the exceptions were: 1) RBD-specific V H Hs NRCoV2-02/ NRCoV2-05 did not cross-react with Beta and Gamma and NRCoV2-04/ NRCoV2-14/ NRCoV2-15, did not cross- react with Kappa and 2) S2-specific V H Hs NRCoV2-MRed18 and NRCoV2-MRed19 did not cross-react with Kappa. All nine NTD-specific V H Hs cross-reacted with all variants tested.
  • VHHs cross-reacted with pangolin CoV with fewer cross-reacting to SARS- CoV, SARS-like CoV WIV1, bat SARS-like CoV and civet SARS CoV.
  • These viruses, including variants, are all of the Betacoronavirus Sarbecovirus subgenus. None of the antibodies tested cross- reacted with the remaining 11 non-Sarbecovirus Betacoronavirus, or with Alphacoronavirus, Deltacoronavirus or Gammacoronavirus. 29 V H Hs cross-reacted with the Omicron variant (Fig. 6B).
  • V H Hs recognizing 10 – 12 viruses, including SARS-CoV-2 variants, were two NTD binders (NRCoV2-SR01, NRCoV2-SR02), six RBD binders (NRCoV2-1d, NRCoV2-07, NRCoV2-11, NRCoV2-12, NRCoV2-20, NRCoV2- MRed04) and six S2 binders (NRCoV2-S2F3, NRCoV2-S2G3, NRCoV2-S2G4, NRCoV2- MRed18, NRCoV2-MRed19, NRCoV2-MRed20).
  • the VHH-72 benchmark was also broadly cross-reactive.
  • V H Hs had similar cross-reactivity profiles to human ACE2, except that ACE2 did not bind civet SARS-CoV S and, unsurprisingly, bound HCoV-NL63 S.
  • ACE2 did not bind civet SARS-CoV S and, unsurprisingly, bound HCoV-NL63 S.
  • 12 out of 14 ELISA-positive V H Hs cross- reacted with SARS-CoV S, most with comparably high affinities (Table 11. Seven of these V H Hs were S2-specific, four were RBD-specific and one was NTD-specific.
  • the SPR cross-reactivity data performed with 37 V H Hs, were consistent with ELISA, except for NRCoV2-04 and NRCoV2-14, which were negative or very weak for binding to the Beta variant by SPR (Tables 11 and 12). All 37 V H Hs tested bound the Alpha variant S protein, and 34 were also cross-reactive to the Beta variant S protein (Figs.28A (Alpha) and 28B (Beta); Fig.29; Table 11; Table 12).
  • VHHs bound all three variants with similar affinities, except for V H Hs NRCoV2-10, NRCoV2-15 and NRCoV2-17 which bound to the Beta variant with 40 – 50-fold weaker affinity; the remaining four that did not bind the Beta variant showed cross-reactivity with the Alpha variant with similar (NRCoV2-04, NRCoV2-14) or reduced ( ⁇ 5-fold [NRCoV2-05] and ⁇ 20-fold [NRCoV2-02]) affinity relative to the Wuhan variant. All NTD-specific and S2-specific V H Hs cross-reacted with the three variants with essentially the same or similar affinities.
  • V H Hs and V H H-Fcs The cross-reactivity of the V H Hs and V H H-Fcs is significant, as it is believed that the progenitor of SARS-CoV was generated by recombination among bat SARS-like coronaviruses that spread to humans via civet cat as an intermediate host (Zheng et al, 2020). Further, most new emerging viruses are derived from strains circulating in zoonotic reservoirs. Antibodies that can cross-react against a variety of animal and human coronaviruses have potential to be used for detection and/or treatment of emerging coronavirus outbreaks.
  • V H Hs and V H H-Fcs Surface Plasmon Resonance (SPR) and ELISA Binding Studies Introduction
  • SPR Surface Plasmon Resonance
  • ELISA ELISA Binding Studies Introduction
  • Binding of anti-SARS-CoV-2 V H Hs against various SARS-CoV-2 spike protein fragments (Wuhan) was assayed using SPR and ELISA to determine their affinity and domain/sub- domain specificity.
  • Binding of V H Hs against SARS-CoV, SARS-CoV-2 UK (Alpha) variant and SARS-CoV-2 South African (Beta) variant spike protein S was also carried out to determine their virus cross-reactivity patterns.
  • V H Hs, ACE2 receptor Prior to SPR analyses all analytes in flow (V H Hs, ACE2 receptor) were SEC-purified on a Superdex TM 75 Increase 10/300 GL column (Cytiva) in HBS-EP buffer at a flow rate of 0.8 mL/min to obtain monomeric proteins.
  • SARS-CoV spike (S), SARS-CoV-2 spike trimer (S) and various SARS-CoV-2 spike fragments were immobilized on CM5 sensor chips through standard amine coupling (10 mM acetate buffer, pH 4.0; Cytiva).
  • V H Hs at various concentration ranges were flowed over all surfaces at a flow rate of 40 ⁇ L/min with 180 s of contact time and 600 s of dissociation time.
  • Surfaces were regenerated with a 12 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 100 ⁇ L/min.
  • V H H EK2 Injection of EGFR-specific V H H EK2 served as a negative control for the SARS-CoV and SARS-CoV-2 surfaces and as a positive control for the EGFR surface.
  • the ACE2 affinity was determined using similar conditions by flowing a range of monomeric ACE2 concentrations (31.53 – 500 nM). All affinities were calculated by fitting reference flow cell-subtracted data to a 1:1 interaction model using BIAevaluation Software v3.0 (Cytiva). [00193] For V H H 12 and MRed05, V H H-Fc formats were used in SPR experiments.
  • V H H-Fcs Approximately 200 RUs of V H H-Fcs (2 ⁇ g/mL) were captured on goat anti-human IgG surfaces (4000 RUs, Jackson ImmunoResearch, Cat#109-005-098) at a flow rate of 10 ⁇ L/min for 30 s.
  • a range of SEC-purified RBD fragments (Table 1; SARS-CoV, Wuhan, Alpha and Beta) at 0.62 – 10 nM were flowed over the captured V H H-Fc at a flow rate of 40 ⁇ L/min with 180 s of contact time and 300 s of dissociation. Surfaces were regenerated with a 120 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 50 ⁇ L/min.
  • V H Hs that bound to the S1 subunit but not its S1-RBD domain in SPR assays, were further examined by ELISA to determine if they were binding to the S1-NTD domain of S1. Briefly, S, S1, S1-NTD and S1-RBD were coated onto NUNC® MaxiSorpTM 4BX plates (Thermo Fisher) at 100 ng/well in 100 ⁇ L PBS, pH 7.4.
  • V H Hs were tested by SPR against SARS-CoV-2 S, S1, S1-RBD and S2 to determine their affinity and domain/sub-domain specificity. Binding data are presented in Fig. 6C, Figs. 7A-B, Table 8 and Table 9.
  • SPR binding assays NRCoV2-SR01, NRCoV2-SR02, NRCoV2-SR03, NRCoV2-SR04, NRCoV2-SR13, NRCoV2-SR16, NRCoV2-MRed03, NRCoV2-MRed06 and NRCoV2-MRed07 bound to the S1 subunit but not to its S1-RBD domain.
  • V H Hs were S1-NTD-specific (Figs. 6D and 6E and Table 10).
  • V H Hs displayed high affinity towards their target (i.e., S) with the vast majority having K D s in the range of single-digit-nM to pM.
  • Three clusters of V H Hs based on domain/subdomain specificity were identified: (i) S1-RBD-specific V H Hs; (ii) S1-NTD- spepcfic V H Hs; and (iii) S2-specific V H Hs (Fig.7A).
  • V H Hs As for the S1-RBD-specific V H Hs, with the exception of NRCoV2-06, which had an affinity of 223 nM (Table 11), the remaining 16 cluster members displayed high affinities ranging from 0.02 - 10 nM, all vastly outperforming the benchmark V H H-72 V H H, which had a K D of 86.2 nM.
  • V H Hs were S1-NTD-specific and, similar to S1-RBD-specific V H Hs, displayed high affinities (K D s) in the range of 0.1 – 5.2 nM.
  • 11 V H Hs were S2 subunit-specific, with similarly high affinities (K D s) ranging from 0.09 – 12.8 nM.
  • V H Hs were tested against SARS-CoV (S) in SPR assays for quantitative determination of cross-reactivity.
  • V H Hs were first screened for cross-reactivity at fixed concentrations. Twelve out of 37 V H Hs screened showed cross-reactivity to SARS-CoV S. These 12 V H Hs were subsequently subjected to comprehensive binding analysis against both SARS-CoV S and SARS- CoV-2 S at multiple V H H concentrations.
  • the SPR cross-reactivity results which agreed with those from ELISAs, are presented in Fig.27 and Table 11. Seven out of the 12 VHHs tested were S2-specific, four were S1-RBD-specific and one was S1-NTD-specific.
  • NRCoV2-MRed04 showed weak binding to SARS-CoV S compared to SARS-CoV-2 S (300 nM for SARS-CoV S vs 1 nM for SARS-CoV-2 S), but the remaining V H Hs cross-reacted with high/comparable affinities to both SARS-CoV-2 S and SARS-CoV S.
  • NRCoV2-07, NRCoV2-12, NRCoV2-MRed18, NRCoV2-MRed19 and NRCoV2-MRed20 cross-reacted with SARS-CoV S with relatively lower affinities in comparison to SARS-CoV-2 S, but nonetheless with high absolute affinities in the low nanomolar KD range.
  • V H Hs bound all three variants with similar affinities, except for V H Hs NRCoV2-10, NRCoV2-15 and NRCoV2-17 which bound to the Beta variant with 40 – 50-fold weaker affinity; the remaining four that did not bind the Beta variant showed cross- reactivity with the Alpha variant with similar (NRCoV2-04, NRCoV2-14) or reduced ( ⁇ 5-fold [NRCoV2-05] and ⁇ 20-fold [NRCoV2-02]) affinity relative to the Wuhan variant. All NTD- specific and S2-specific V H Hs cross-reacted with the three variants with essentially the same or similar affinities.
  • Example 6 Cell Binding Assays by Flow Cytometry Introduction
  • a stable Chinese hamster ovary (CHO) cell line CHO BRI TM /55E1 (Stuible et al., 2021) overexpressing SARS-CoV-2 S (CHO-S) was grown in BalanCDTM CHO Growth A medium (Irvine Scientific) supplemented with 50 ⁇ M of methionine sulfoximine (MSX) at 120 rpm and 37°C in a humidified 5% CO 2 atmosphere. When the cell count reached 2 x 10 6 /mL, the expression of the membrane anchored SARS-CoV-2 trimeric spike protein (SmT1, described in Stuible et al, 2021) was induced by adding cumate at 2 ⁇ g/mL.
  • SmT1 membrane anchored SARS-CoV-2 trimeric spike protein
  • V H H-Fcs V-Bottom 96-well microtest plates (Globe Scientific, Cat# 120130) and mixed with 50 ⁇ L of CHO-S cells.
  • VHH-Fcs (NRCoV2-08, NRCoV2-19, NRCoV2-21, NRCoV2-S202) which bound to SARS-CoV-2 S in purified form did not bind to SARS-CoV-2 S-displaying target cells.
  • the remaining 41 V H H-Fcs bound to cells in a dose dependent manner (Fig.8A- B; Table 13).
  • affinities for S2-specific V H H-Fcs were also high (EC 50 range: 0.1 – 6.5; EC 50 median: 1 nM).
  • Table 13 Summary of V H H-Fc bindings to SARS-CoV-2 S expressing CHO-S cells S1-RBD-specific S1-NTD-specific S2-specific x NRCoV2- 1.3 280 NRCoV2- 10 44 MRed18 0.9 10205
  • Example 7 Epitope Studies Introduction [00211] Western blotting experiments were performed to determine if V H Hs bind to conformational or linear epitopes.
  • V H H epitope binning was performed by SPR dual injection experiments on the SARS-CoV-2 S at a flow rate of 40 ⁇ L/min in HBS-EP buffer. Dual injections consisted of injection of V H H1 (at 50 – 100 ⁇ K D concentration) for 150 s, followed by immediate injection of a mixture of V H H1 + V H H2 (both at 50 – 100 ⁇ K D concentration) for 150 s. The opposite orientation was also performed (VHH2 followed by VHH2 + VHH1) (Fig.9C). Surfaces were regenerated using a 12 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 100 ⁇ L/min.
  • V H Hs All pairwise combinations of V H Hs were analyzed and distinct or overlapping epitope bins determined.
  • Epitope binning by ELISA [00217] The pairwise ability of V H Hs to bind to their antigen in a sandwich ELISA format was evaluated as described previously (Rosotti et al., 2015a; Delfin-Riela et al., 2020), (Fig. 9D).
  • a matrix of 14 wells (row) 23 wells (column) was generated using six NUNC® MaxiSorp TM 4BX plates (Thermo Fisher) and coated overnight at 4°C with 4 ⁇ g/mL streptavidin (Jackson ImmunoResearch, Cat#016-000-113) in 100 ⁇ L PBS, pH 7.4.
  • Wells were blocked with 200 ⁇ L PBSC for 1 h at room temperature and then biotinylated V H Hs (10 ⁇ g/mL in 100 ⁇ L PBSCT) were captured in each row (same V H H in each row; 14 rows for a total of 14 V H Hs) for 1 h at room temperature.
  • V H H-Fcs/ACE2-Fc at 1 ⁇ g/mL used as detector antibodies (same V H H-Fc in each column; 23 column for a total of 22 V H H-Fcs and ACE2-Fc).
  • the binding of V H H-Fcs/ACE2-Fc to S1 was detected using 100 ⁇ L 1 ⁇ g/mL HRP-conjugated goat anti-human IgG (SIGMA, Cat#A0170).
  • VHHs monomeric VHHs as probe
  • three out of 26 VHHs tested bound to denatured S indicating they were recognizing linear epitopes, while the remaining V H Hs appeared to be conformational epitope-specific based on their lack of significant binding to denatures S.
  • V H H-Fc was used instead of V H H
  • V H Hs linear epitope-specific V H Hs give the option of virus detection against denatured S by robust diagnostic techniques such as SDS-PAGE/Western blot, where the additional molecular weight information provided by the SDS-PAGE would serve as a second, confirmatory piece of information to eliminate/reduce false positives obtained by binding data alone.
  • V H Hs were subjected to epitope binning experiments by SPR and sandwich ELISA.
  • V H H1 V H H1
  • V H H2 V H H2 + VHH2
  • Fig.9C (left panel) exemplifies a V H H pair (NRCoV2-02/NRCoV2-05) binding to an overlapping epitope, hence belonging to the same epitope bin, as the addition of the second V H H does not result in any increased binding (i.e., increase in RU) over that obtained for the addition of the first V H H.
  • Fig. 9C (right panel), on the other hand, exemplifies a V H H pair (NRCoV2-02/NRCoV2-07) binding to non-overlapping epitopes, hence belonging to different epitope bins, as the addition of the second V H H results in significant increase in binding over that already achieved by the addition of the first V H H.
  • the ELISA experiments confirmed the results of epitope binning by SPR, expanded the number of binders within each epitope bin, and identified new epitope bins.
  • the epitope binning results obtained by SPR and ELISA are summarized in Figs. 9F (initial results), 9G (further results) and Table 14.
  • Initial binning results identified 14 non-overlapping/partially overlapping bins: six for S1-RBD-specific V H Hs, three for S1-NTD-specific V H Hs and five for S2-specific V H Hs.
  • Example 8 Surrogate Virus Neutralization Assays Introduction
  • Surrogate neutralization assays were performed to identify potential neutralizing V H Hs/V H H-Fcs, i.e., V H Hs/V H H-Fcs inhibiting SARS-CoV-2 viruses from entering host cells.
  • Three different surrogate assays were performed: ELISA, SPR and flow cytometry.
  • ELISA and SPR ACE2 and SARS-CoV-2 S acted as surrogates for an ACE2-containing host cell and an S- containing invading virus, respectively.
  • flow cytometry assays which were performed directly against the host cell (Vero E6), S1-RBD or S served as surrogate virus.
  • Antibodies that interfered with the binding of spike fragment proteins to ACE2 in the surrogate assays were considered to be neutralizing antibodies.
  • Materials and Methods [00222] ACE2 competition assay by ELISA [00223] Wells of NUNC® MaxiSorp TM microtiter plates (Thermo Fisher) were coated overnight at 4°C with 50 ng/well of S in 100 ⁇ L PBS, pH 7.4. Next day, plates were blocked with 250 ⁇ L PBSC for 1 h at room temperature.
  • ACE2-Fc (ACROBiosystems, Cat#AC2-H5257) at 400 ng/mL was mixed with 50 ⁇ L of V H H at 1 ⁇ M, and then transferred to SARS-CoV-2 S coated microtiter plate wells. After 1 h incubation at room temperature, plates were washed 10 times with PBST and the ACE2-Fc binding was detected using 1 ⁇ g/mL goat anti-human IgG (Fc specific) peroxidase antibody (SIGMA, Cat# A0170) in 100 ⁇ L PBSCT. After 10 washes with PBST, the peroxidase activity was determined as described above.
  • ACE2 competition assay by SPR [00225] Standard SPR techniques were used for binding studies. All SPR assays were performed on a Biacore TM T200 instrument (Cytiva) at 25°C with HBS-EP running buffer (10 mM HEPES, 150 mM NaCl, 3 mM EDTA, 0.005 % [v/v] Tween® 20, pH 7.4) and CM5 sensor chips (Cytiva).
  • V H Hs Prior to SPR analyses, all analytes in flow (V H Hs, ACE2 receptor) were SEC-purified on a Superdex TM 75 Increase 10/300 GL column (Cytiva) in HBS-EP buffer at a flow rate of 0.8 mL/min to obtain monomeric proteins.
  • V H Hs were analyzed for their ability to block the SARS- CoV-2 spike trimer (S) interaction with ACE2 using SPR dual injection experiments.
  • S SARS- CoV-2 spike trimer
  • V H Hs and ACE2 were flowed over the SARS-CoV-2 S surface at 40 ⁇ L/min in HBS-EP buffer.
  • Dual injections consisted of injection of ACE2 (1 ⁇ M) for 150 s, followed by immediate injection of a mixture of ACE2 (1 ⁇ M) + V H H (at 20 – 40 ⁇ K D concentration) for 150 s. The opposite orientation was also performed (V H H followed by V H H + ACE2). Surfaces were regenerated using a 12 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 100 ⁇ L/min. All pairwise combinations of VHHs and ACE2 were analyzed. V H Hs that competed with ACE2 for SARS-CoV-2 spike trimer binding showed no increase in binding response during the second injection. Conversely, a binding response was seen during the second injection for V H Hs that did not compete with ACE2.
  • ACE2 competition assay by flow cytometry [00226] Experiments were performed essentially as described in Example 2. Briefly, 400 ng of chemically biotinylated trimeric SARS-CoV-2 S was mixed with 5 10 4 Vero E6 cells in the presence of decreasing concentrations of V H Hs or V H H-Fcs in a final volume of 150 ⁇ L.
  • a competition assay with recombinant human ACE2-His 6 in lieu of V H H was also included.
  • A20.1 a C. difficile toxin A-specific V H H (Hussack et al., 2011) was used as negative control VHH.
  • V H Hs 14 S1-RBD-specific, 6 S1-NTD-specific and 6 S2-specific
  • a total of 26 V H Hs 14 S1-RBD-specific, 6 S1-NTD-specific and 6 S2-specific
  • a total of 26 V H Hs 14 S1-RBD-specific, 6 S1-NTD-specific and 6 S2-specific
  • a total of 26 V H Hs 14 S1-RBD-specific, 6 S1-NTD-specific and 6 S2-specific
  • Fig.10 the majority of S1-RBD binders were significantly neutralizing, with NRCoV2-1d, NRCoV2-02, NRCoV2-05 and NRCoV2-07 displaying essentially 100% inhibition and outperforming the V H H-72 benchmark.
  • NRCoV2-SR01 Two of the S1-NTD- specific V H Hs (NRCoV2-SR01, NRCoV2-SR02) showed significant neutralization, with NRCoV2-SR02 essentially neutralizing at 100%. None of the S2 binders showed significant neutralizing activity.
  • a conceptually similar assay to ELISA was performed by a competitive SPR. The results are shown in Fig. 11 and Table 16. The four lead neutralizers identified by ELISA, i.e., NRCoV2-01d, NRCoV2-02, NRCoV2-05 and NRCoV2-07, were confirmed by SPR to be complete neutralizers (‘blockers”).
  • NRCoV2-14, NRCoV2-15, NRCoV2-18 and NRCoV2-20 showed partial neutralization (“+/-“; Table 16). The remaining V H Hs tested were judged to be non-neutralizing. Although the ELISA and SPR results agreed in the case of the majority of V H Hs, there was some disagreement. For example, while NRCoV2-SR02, NRCoV2-06, NRCoV2-10, and NRCoV2-11 were neutralizing by ELISA, they were not found to be neutralizing by SPR. Conversely, NRCoV2-20 was judged to be somewhat neutralizing by SPR, but non-neutralizing by ELISA.
  • NRCoV2-1d, NRCoV2-02, NRCoV2-05 and NRCoV2-07 led others with IC 50 / I max % values of 8.6 nM/72%, 5.1 nM/100%, 9.5 nM/97%, and 7.5 nM/86%, respectively.
  • a second group of V H Hs, including NRCoV2-10, NRCoV2-14, NRCoV2-15, NRCoV2-18, NRCoV2-20 and NRCoV2-MRed04 were also potent/efficacious neutralizers (Table 17). All of these antibodies outperformed the benchmark V H H-72, which had a far higher IC 50 (59 nM).
  • NRCoV2-11 and NRCoV2-17 although showing high potencies (IC 50 s of 16.8 nM and 9.4 nM, respectively), had weak efficacies (I max % values of 20% and 18%, respectively). None of the S1-NTD or S2 binders was neutralizing. The results obtained by flow cytometry correlated well with those obtained by ELISA and SPR. [00230] To increase the neutralization potency and efficacy of the V H Hs, they were reformatted as bivalent V H H-Fcs.
  • V H H-Fcs were generated and tested in flow cytometry surrogate neutralization assays as described above.
  • the majority of V H H-Fcs demonstrated high potencies and efficacies (Figs.13A- B; Table 17). Reformatting had a significant effect on the neutralization potencies/efficacies of V H Hs.
  • NRCoV2-11 (anti- RBD) and SR01 (anti-NTD) were also efficient, achieving neutralization as potent as was observed against Wuhan spike protein. From the list of antibodies tested NRCoV2-12, -20, -11 and -SR01 are the leads, showing efficient pan-neutralization against the SARS-CoV-2 variants generated so far, and outperforming the benchmark VHH-72.
  • Table 15 Flow cytometry SVNAs against SARS-CoV-2 variants and SARS-CoV SVNA IC 50 (nM) SARS-CoV-2 S V H H-Fc SARS-CoV S VHH-72 5.6 10.6 5.1 3.3 10.5 8.5 - 7.8 3,4 17 8.6 10.6 26.4 214 - - 3.4 - 10 8.8 11.3 10.8 21.8 - - 4.3 - 7,9,10 SR13 7.7 22.4 - 16.5 - 12.2 - 15
  • Table 17 Neutralization capabilities of SARS-CoV-2-specific V H Hs/V H H-Fcs obtained by surrogate virus neutralization flow cytometry assays against SARS-CoV-2 S (Wuhan) V H H/ACE2-H 6 2 V H-Fc/ACE2-Fc 2 Domain/ H V H H/ACE2 bd i 3 3 3 3 3 3 NRCoV2-S2A4 S2 - - - - - - - NRCoV2-S2F3 S2 - - - - - app eric ACE2.
  • IC 50 concentration of V H H/V H H/Fc giving 50% neutralization
  • IC 99 concentration of V H H/V H H/Fc giving 99% neutralization
  • I max % maximal inhibitory effect
  • IC 50 , IC 99 and I max % values were extracted from graphs exemplified in Figs. 12B and Figs. 13B. Dash indicate V H H/V H H-Fc does not neutralize the interaction between Vero E6 cell-displayed ACE2 and soluble S. 4 ICs cannot be determined with certainty due to low I max % values. nd, not determined, due to lack of sufficient quantities and/or neutralization as V H H-Fc.
  • Example 9 Live-Virus Neutralization Assays Introduction [00235] V H H-Fcs were subjected to authentic-virus neutralizations assays, i.e., micro- neutralization assays, to identify those that neutralized infection of host cells by the invading SARS-CoV-2 virus. Materials and Methods Authentic-virus neutralizations assays [00236] Neutralization activity of antibodies to SARS-CoV-2 was determined with the microneutralization assay.
  • V H H-Fc and V H H were prepared at 1 mg/mL in PBS and sterilized by passing through 0.22 ⁇ M filters.1:5 serial dilutions of 50 ⁇ g/mL of each antibody was carried out in DMEM, high glucose media supplemented with 1 mM sodium pyruvate, 1mM non-essential amino acids, 100 U/ml penicillin-streptomycin, and 1% heat- inactivated fetal bovine serum.
  • SARS-CoV-2 strain SARS-CoV-2/Canada/VIDO-01/2020 was incubated at 250 pfu with antibody dilution in 1:1 ratio at 37 o C for 1 h.
  • Vero E6 cells seeded in 96-well plates were infected with virus/antibody mix and incubated at 37 o C in humidified/5% CO 2 incubator for 72 hours post-infection (hpi). Cells were then fixed in 10% formaldehyde overnight and virus infection was detected with mouse anti-SARS-CoV-2 nucleocapsid antibody (R&D Systems, clone #1035111) and counterstained with rabbit anti-mouse IgG-HRP (Rockland Inc.). Colorimetric development was obtained with o-phenylenediamine dihydrochloride peroxidate substrate (Sigma-Aldrich) and detected on Biotek Synergy H1 plate reader at 490 nm.
  • IC 50 was determined from non-linear regression on GraphPad Prism 9. For determining neutralization potencies by measuring cytopathic effect (CPE), infected Vero E6 cells were incubated at 37 for 96 h until the virus-only control wells had nearly 100% CPE (cell-only controls were also included). Neutralization was scored by MN 100 , lowest antibody concentration that gave no CPE, i.e., 100% neutralization. Assays were performed in technical duplicates. [00237] Results and Discussion [00238] A select set of lead V H H-Fcs were subjected to preliminary authentic-virus micro- neutralization assays to assess their SARS-CoV-2 virus-neutralizing activity.
  • CPE cytopathic effect
  • S1-RBD binders The most potent neutralizers were amongst the S1-RBD binders: NRCoV2-02 (MN 100 0.01 nM); NRCoV2-1d (MN 100 0.25 nM); NRCoV2-04 and NRCoV2-07 (MN 100 1.25 nM); NRCoV2-03 (MN 100 6.25 nM). NRCoV2-02 and NRCoV2-1d were far more potent neutralizers than the benchmark (V H H-72), by five- and 125-fold, respectively.
  • S1-NTD binders had MN 100 s of 6.25 nM (NRCoV2-SR01, NRCoV2-SR02).
  • NRCoV2-02 also outperformed the benchmark in V H H format by 125-fold (Fig.14A inset).
  • monovalent V H H-Fc versions of select V H H-Fcs were generated. Based on MN 100 values, neutralization potencies were decreased by five-fold for NRCoV2-SR01, 25-fold for NRCoV2-1d and NRCoV2- 07 and more than 125-fold for NRCoV2-02, with their conversion from bivalent to monovalent V H H-Fcs, demonstrating the sizable contribution of bivalency to their neutralization potency.
  • V H H-Fcs recognized epitopes 2/3/4 and had IC 50 s of 0.0008- 3.1 nM (Fig.15E and Fig.30; Table 19).
  • the leads were NRCoV-05 (IC 50 0.0008 nM) followed closely by NRCoV-02 (IC 50 0.12 nM) and NRCoV2-MRed 05 (IC 50 0.17 nM).
  • V H H-Fcs recognizing epitope 1 showed intermediate potencies with IC 50 s of 1.94 – 9.6 nM, with V H H-72 (belonging to the same bin 1) having similar IC 50 (8.46 nM).
  • V H H- Fcs recognizing epitope 5 and 6 showed IC 50 s of 9.96 – 76 nM.
  • S1-NTD-specific V H H six out of nine V H H-Fcs tested were neutralizing, with the lead V H H-Fcs having IC 50 s of 9.42, 14.31 and 54.2 nM. The remaining two had IC 50 s in the high nM - micromolar range.
  • V H H-Fcs were neutralizing with IC 50 s from 12.2 nM for S2A3 to high nM - micromolar range for S2G3 and S2G4. These belonged to three different epitope bins.
  • V H H-Fcs outperformed the V H H-72 benchmark by 2.5 – 10,000-fold.
  • the NRCoV2-05, NRCoV2-02 and NRCoV2- MRed05 leads showed 10,000-fold, 70-fold and 50-fold higher potency than V H H-72, respectively.
  • Beta mutations in the RBD were completely abrogated presumably by the Beta mutations in the RBD (K417N, E484K, N501Y), several others including NRCoV2-MRed05, NRCoV2-10 and NRCov2-15 did retain their high neutralizing potencies against both Alpha and Beta variants.
  • MN 100 Neutralization capabilities (MN 100 ) of SARS-CoV-2-specific V H H-Fcs obtained by authentic-virus (aka live virus) neutralization assays
  • MN 100 H H (nM) NRCoV2-07 x S1-RBD x null 31.25 A26.8 1 V H H-72 ben SARS-CoV-2 S (Wrapp et al. tive control V H H (Hussack et al., 2011).
  • 2 MN 100 is the lowest antibody concentration that gave no cytopathic effect (100% neutralization). Dash indicate V H H-Fc does not neutralize SARS-CoV-2 virus at the highest V H H-Fc concentration used.
  • MN 100 values were used to construct Fig.14A-B graphs. 3
  • the MN 100 of monovalent V H H-72 and NRCoV2-02 V H Hs were 156.25 and 1.25 nM, respectively.
  • Table 19 Neutralization capabilities (IC 50 ) of SARS-CoV-2-specific V H H-Fcs obtained by authentic-virus (aka live virus) neutralization assays
  • IC 50 Neutralization capabilities
  • nM NTD specific V H 1 V H H-72 benchmark is a SARS-CoV S-specific V H H that cross-reacts with SARS-CoV-2 S (Wrapp et al., 2020);
  • A20.1 is C.
  • V H H H Hussack et al., 2011. Epitope bin numbers correspond to the bins shown in Fig.9G.
  • Example 10 Stability of V H Hs against Aerosolization Introduction
  • One effective therapeutic approach against COVID-19 might be the direct delivery of aerosolized antibodies to the nasal and lung epithelia by inhalation.
  • V H Hs in particular are advantageously fit for such administration approach due to their high stability and robustness. Since aerosolization could compromise the structural integrity and function of antibodies that lack sufficient stability, such as mAbs (Detalle et al., 2016; Respaud et al., 2015), the effect of aerosolization on the stability of V H Hs was tested.
  • Aerosolized V H Hs were collected into 15 mL Round-Bottom Polypropylene test tubes (Falcon, Cat#C352059) for 5 min to allow condensation and were subsequently quantified and kept at 4 C until use. Then 200 ⁇ L aliquots of pre- and post- aerosolized V H Hs were subjected to SEC to obtain chromatogram profiles. Additionally, condensed V H Hs were closely monitored for the formation of any visible aggregates, and in cases where aggregate formation was observed, aggregates were removed by centrifugation prior to concentration determination, SEC analysis and ELISA. % soluble aggregate was determined as the proportion of a V H H that gave elution volumes (V e s) smaller than that of the monomeric V H H fraction.
  • % recovery was determined as the proportion of a V H H that remained monomerically soluble following aerosolization.
  • V H Hs including the benchmark V H H-72 were examined for their aggregation resistance/stability against aerosolization.
  • V H Hs For a few V H Hs, e.g., NRCoV2-MRed20, NRCoV2- S2A4, as well as the V H H-72 benchmark, aerosolization induced some soluble aggregation formation as determined by SEC (Fig. 16A; Table 20).
  • V H Hs e.g., NRCoV2-11, NRCoV2-SR03
  • Fig. 16A-C the majority of VHHs (20 out of 30 VHHs tested) were highly stable against aerosolization, that is, they did not form any soluble or visible aggregates and demonstrated high % recovery upon aerosolization treatment.
  • V H Hs examples include NRCoV2-1c/1d, NRCoV2-02, NRCoV2-07, NRCoV2-17, NRCoV2-18 and NRCoV2-20.
  • High % recovery indicates these V H Hs advantageously lack non-specific binding to nebulizer surfaces. For therapeutic V H Hs, this is expected to translate to a more effective drug delivery to the site of viral infection.
  • V H Hs i.e., NRCoV2-04, NRCoV2-14, NRCoV2-15, NRCoV2-SR04 and NRCoV2-MRed04, while forming some visible aggregates, still showed a good % recovery upon aerosolization (52 – 69 %).
  • V H Hs the activities (EC 50 s) of post- aerosolized V H Hs were determined by ELISA and compared to those for pre-aerosolized V H Hs. ELISAs were performed on a sample of four V H Hs: NRCoV2-1d, NRCoV2-02, NRCoV2-07 and NRCoV2-11 (Fig. 16D). Comparison of EC 50 s for post-aerosolized V H Hs vs pre-aerosolized V H Hs demonstrated that aerosolization did not compromise the functionality of V H Hs (Fig.16D; Table 21).
  • V H Hs for Diagnosis and Capture of SARS-CoV-2 Introduction
  • Pre pre-aerosolized
  • Post post-aerosolized
  • V H Hs EC (nM) V H 50 H t
  • Example 11 V H Hs for Diagnosis and Capture of SARS-CoV-2 Introduction
  • V H Hs described herein are promising diagnostic/capture agents against SARS-CoV-2, SARS-CoV and related viruses as well as their spike proteins.
  • four of the V H Hs were tested in sandwich ELISA for their diagnostic/capturing capability against SARS-CoV-2.
  • V H H-Fc that binds to a non- overlapping epitope in relation to NRCoV2-02 was added as the detecting antibody followed by the addition of a HRP-conjugated probing antibody binding to the detecting antibody.
  • the different V H H-Fcs tested as detecting antibodies were: NRCoV2-1d, NRCoV2-04, NRCoV2-07, and NRCoV2-11. Very low SC 50 values were obtained in ELISA assays (Fig. 17, Table 22).
  • V H H-Fc was chosen as a representative V H H and VHH-72 V H H-Fc, whose modified/enhanced version is currently in a phase 1 clinical trial, was included as a reference.
  • Hamsters were injected intraperitoneally (IP) with 1 mg of each antibody and serum antibody concentration was monitored for up to four days by ELISA.
  • Significant and comparable VHH-Fc concentrations were present in the hamster sera for both 1d and VHH-72 V H H-Fcs on days 1 and 4 post injection (Fig. 32), indicating that V H H-Fcs would have the required serum stability and persistence in vivo for the duration of the animal studies.
  • V H H-Fcs which were neutralizing by live virus neutralization assay was then assessed in a hamster model of SARS-CoV-2 infection.
  • Five V H H- Fcs were selected to cover a wide range of important attributes including in vitro neutralization potencies and breadth, epitope bin, subunit/domain specificity and cross-reactivity pattern. These included three RBD-specific (1d, 05, MRed05), one NTD-specific (SR01) and one S2-specific (S2A3) V H H-Fcs.
  • V H H-Fcs Cocktails of two V H H-Fcs were also included to explore synergy between the antibody pairs recognizing distinct epitopes within the RBD (1d/MRed05) or RBD and NTD (1d/SR01).
  • Hamsters were administered IP with 1 mg of V H H-Fcs 24 h prior to intranasal challenge with SARS-CoV-2 Wuhan isolate. Daily weight change and clinical symptoms were monitored. At 5 dpi, lungs were collected to determine viral titers. Viral titer decrease and reversal of weight loss in antibody treated versus control animals were taken as measures of antibody efficacy.
  • Animals treated with RBD binders 1d, 05, and MRed05 showed reduced lung viral burden by three, five and six orders of magnitude, respectively, relative to PBS or VHH-Fc isotype controls, with 05 and MRed05 reducing viral burden to below detectable levels (Fig. 22A).
  • the RBD-specific VHH-72 benchmark caused a mean viral decrease of four orders of magnitude.
  • the NTD binder SR01, and interestingly, the S2 binder S2A3, were also effective neutralizers, decreasing mean viral titers by four and three orders of magnitude, respectively.
  • Both 1d/SR01 and 1d/MRed05 cocktails decreased viral titers by 6 orders of magnitude to undetectable levels of virus infection.
  • SARS-CoV-2 infection is characterized by an overt inflammatory response in the respiratory tract accompanied by an increased infiltration of inflammatory immune cells, e.g., macrophages and T lymphocytes, in the lung parenchyma 70. As expected, this was the case for the non-treated PBS and isotype control groups.
  • a neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science 369, 650-655. Colwill K, et al.

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Abstract

Described herein are antibodies that specifically recognize the SARS-CoV-2 spike (S) polypeptide,compositions comprising said antibodies, uses thereof, and methods employing said antibodies. Eachantibody specifically recognizes the S1-RBD domain, S1-NTD domain, or S2 subunit of the SARS-CoV-2 spike polypeptide. Some antibodies are cross-reactive with variants of SARS-CoV-2 and othercoronavirus spike polypeptides, such as SARS-CoV S, pangolin CoV S, bat SARS-like CoV S, andcivet SARS-CoV S.

Description

ANTIBODIES THAT BIND SARS-COV-2 SPIKE PROTEIN FIELD [0001] The present disclosure relates to antibodies that specifically bind a coronavirus spike polypeptide, particularly the spike polypeptide of SARS-CoV-2 and variants thereof, and to the use of such antibodies for various applications including the detection of a coronavirus and/or treatment or prevention of a coronavirus infection. BACKGROUND [0002] Coronavirus is a single-stranded enveloped RNA virus belonging to the subfamily Coronavirinae in the order Nidovirales. Based on genomic structure, coronaviruses have been classified into four genera; Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus; two of which (alphacoronaviruses and betacoronaviruses) infect mammals. Seven coronaviruses are known to cause human disease: HCoV 229E, HCov OC43, HCoVNL63, HCoVHKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2. Three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, cause serious illness in humans, whereas the remaining four human coronaviruses are associated with mild illness. [0003] Since 2002, there have been three coronavirus outbreaks causing serious human illness. The first outbreak, caused by SARS-CoV, originated in China with the first case reported in November 2002. By July 2003, there were 8098 cases and 774 deaths in 29 countries (Arora et al., 2020). The second outbreak, caused by MERS-CoV, originated in Saudi Arabia, with the first case reported in June 2012. The disease was ultimately identified in 26 countries, with 1621 confirmed cases and 584 deaths (Arora et al., 2020). The third outbreak, caused by SARS-CoV- 2, originated in China with the first case reported in December 2019. On March 11, 2020, the World Health Organization (WHO) declared the outbreak a pandemic. According to information provided by the Johns Hopkins Coronavirus Resource Center, as of April 22, 2021, the global case count was 144 million and there had been 3.06 million deaths worldwide. [0004] Coronavirus entry into host cells is mediated by the coronavirus spike protein (S), which is a homotrimeric glycoprotein. The spike polypeptide includes three segments, an ectodomain, a single-pass transmembrane anchor, and an intracellular tail. The spike ectodomain is made up of a receptor-binding subunit (S1) and a membrane-fusion subunit (S2). S1 includes two major domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), which is also known as the receptor binding domain (RBD). Following the RBD, S1 contains two subdomains (SD1 and S1-SD2) as described in Lan et al., 2020. [0005] During virus entry, S1 binds to a host cell surface receptor and S2 fuses the host and viral membranes (Li, 2016). The host cell surface receptor bound by both SARS-CoV and SARS-CoV- 2 is a zinc peptidase angiotensin-converting enzyme 2 (ACE2), whereas MERS-CoV recognizes a serine peptidase (DPP4) (Li, 2016; Zhou et al, 2020). The receptor binding domain (RBD) of SARS-CoV-2 has been characterized and the binding mode of the SARS-CoV-2 RBD to ACE2 has been found to be nearly identical to that observed for SARS-CoV (Lan et al., 2020). [0006] There are currently few treatments available for SARS-CoV-2 infection or other coronavirus infections and, while vaccines for SARS-CoV-2 are now coming onto the market, vaccine distribution is far from complete. Additionally, the duration and breadth of protection offered by SARS-CoV-2 vaccines is not yet known, meaning that vaccinated individuals may become increasingly susceptible to subsequent infection with time. Further, vaccination may be ineffective for immunocompromised individuals, leaving them susceptible to life-threatening coronavirus infections. Antibodies that neutralize coronaviruses, such as SARS-CoV-2, have significant potential as therapeutic agents. Further antibodies with high affinity for coronaviruses, such as SARS-CoV-2, may allow for detection, quantification, or capture of coronaviruses with high sensitivity and specificity. SUMMARY [0007] Provided is an isolated or purified antibody that specifically recognizes at least one coronavirus spike polypeptide, wherein the antibody comprises an antigen binding portion of an antibody heavy chain, wherein the antigen binding portion comprises a first complementarity determining region (CDR1), a second complementarity determining region (CDR2), and a third complementarity determining region (CDR3), and wherein CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 20, SEQ ID NO: 64, and SEQ ID NO: 110; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 34, SEQ ID NO: 78, and SEQ ID NO: 124; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127; SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128; SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135. [0008] In an embodiment, the antibody is a neutralizing antibody and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; or SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125. [0009] In an embodiment, the antibody specifically binds the S1-NTD domain of the coronavirus spike polypeptide and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126; SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128; or SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129. [0010] In an embodiment, the antibody specifically binds the S2 subunit of the coronavirus spike polypeptide and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 34, SEQ ID NO: 78, and SEQ ID NO: 124; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135. [0011] In an embodiment, the antibody specifically binds the S1-RBD domain of the coronavirus spike polypeptide and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 20, SEQ ID NO: 64, and SEQ ID NO: 110; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0012] In an embodiment, the antibody is cross-reactive with the spike polypeptide of SARS- CoV-2 and SARS-CoV, and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 92; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; or SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133. [0013] In an embodiment, the antibody recognizes a linear epitope, and CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; or SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132. [0014] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 183. [0015] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; or SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114. [0016] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129. [0017] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126 or SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128. [0018] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 184. [0019] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 158, SEQ ID NO: 157, SEQ ID NO: 172, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 159, or SEQ ID NO: 162, or an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 158, SEQ ID NO: 157, SEQ ID NO: 172, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 159, and/or SEQ ID NO: 162. [0020] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135. [0021] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123. [0022] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122. [0023] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117. [0024] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118. [0025] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 185. [0026] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 166, SEQ ID NO: 177, SEQ ID NO: 179, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 181, SEQ ID NO: 165, or SEQ ID NO: 178, or an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 166, SEQ ID NO: 177, SEQ ID NO: 179, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 170, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 181, SEQ ID NO: 165, and/or SEQ ID NO: 178. [0027] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0028] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0029] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0030] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97. [0031] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; or SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102. [0032] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0033] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0034] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0035] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; or SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127. [0036] In an embodiment of the antibody, CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; or SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125. [0037] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 186. [0038] In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 171, SEQ ID NO: 173, SEQ ID NO: 149, SEQ ID NO: 155, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 154, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 156, SEQ ID NO: 174, SEQ ID NO: 137, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 141, SEQ ID NO: 146, SEQ ID NO: 150, or SEQ ID NO: 151, or an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 171, SEQ ID NO: 173, SEQ ID NO: 149, SEQ ID NO: 155, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 139, SEQ ID NO: 142, SEQ ID NO: 154, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 156, SEQ ID NO: 174, SEQ ID NO: 137, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 140, SEQ ID NO: 143, SEQ ID NO: 141, SEQ ID NO: 146, SEQ ID NO: 150, and/or SEQ ID NO: 151. [0039] In an embodiment, the antibody is a single domain antibody. In a further embodiment, the antibody is a VHH. [0040] In an embodiment the antibody is of camelid origin. [0041] In an embodiment, the antibody is in a multivalent display format. In a further embodiment, the antibody is linked to an Fc fragment. In a further embodiment, the Fc-linked antibody is in a bivalent display format. [0042] In an embodiment of the antibody, the at least one coronavirus spike polypeptide specifically binds an ACE2 receptor. [0043] In an embodiment of the antibody, the at least one coronavirus spike polypeptide comprises a SARS-CoV-2 spike polypeptide. [0044] In an embodiment of the antibody, the at least one coronavirus spike polypeptide is comprised within a homotrimer. [0045] Another embodiment is an antibody cocktail composition comprising two or more of the antibodies as described herein. The composition may comprise two, three, four, five, or more different antibodies as described herein. The antibody cocktail composition may further comprise a pharmaceutically acceptable carrier and/or diluent. [0046] Another embodiment is a nucleic acid molecule encoding an antibody as described herein. A further embodiment is a vector comprising the nucleic acid molecule. In an embodiment of the vector, the nucleic acid molecule is operably linked to at least one promoter and/or regulatory element to enable expression in a host cell. An additional embodiment is a host cell comprising the vector. [0047] Another embodiment is a pharmaceutical composition comprising at least one antibody as defined herein and a pharmaceutically acceptable carrier and/or diluent. In an embodiment, the pharmaceutical composition is for delivery by inhalation or nebulization. [0048] Another embodiment is a composition comprising at least one antibody as defined herein, linked to another molecule. In an embodiment, the other molecule is a label or polypeptide. In an embodiment, the other molecule is an ACE2 polypeptide or a fragment thereof. [0049] Another embodiment is a composition or apparatus comprising at least one antibody as defined herein immobilized on a substrate. A further embodiment is a method for capturing a coronavirus or a coronavirus spike polypeptide or fragment thereof from a sample, the method comprising exposing the sample to the composition or apparatus. In an embodiment, the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor. In an embodiment, the coronavirus is SARS-CoV-2 or SARS-CoV. [0050] Another embodiment is use of an antibody as described herein to treat or detect a coronavirus infection. In an embodiment, the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor. In an embodiment, the coronavirus infection is caused by SARS-CoV-2 and/or SARS-CoV. [0051] Another embodiment is use of an antibody or composition as described herein to detect, quantify and/or capture a coronavirus; or to detect, quantify and/or capture a coronavirus spike polypeptide or fragment thereof. In an embodiment, the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor. In an embodiment, the coronavirus is SARS-CoV-2 or SARS-CoV. [0052] Another embodiment is a method for treating or preventing a coronavirus infection, the method comprising administering at least one antibody or composition as described herein to a subject in need thereof. In an embodiment, the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor. In an embodiment, the coronavirus infection is caused by SARS-CoV-2 and/or SARS-CoV. In an embodiment, the administration is by inhalation or nebulization. [0053] Another embodiment is a method for detecting the presence of a coronavirus or a coronavirus spike polypeptide or fragment thereof in a sample, the method comprising exposing the sample to at least one antibody or composition as described herein and assaying for specific binding between the at least one antibody and the sample, wherein specific binding indicates a presence of the at least one coronavirus or coronavirus spike polypeptide or fragment thereof in the sample. [0054] In an embodiment of the methods described in the preceding paragraphs, the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor. In an embodiment, coronavirus is SARS-CoV-2 or SARS-CoV, or the coronavirus spike polypeptide or fragment thereof is a SARS-CoV-2 or SARS-CoV coronavirus spike polypeptide or fragment thereof. [0055] Another embodiment is an antibody or composition as described herein for use to detect or treat a coronavirus infection. In an embodiment, the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor. In an embodiment, the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV. [0056] Another embodiment is an antibody composition as described herein for use to detect, quantify and/or capture a coronavirus; or to detect, quantify and/or capture a coronavirus spike polypeptide or fragment thereof. In an embodiment, the coronavirus is a coronavirus that specifically binds an ACE2 receptor, or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor. In an embodiment, the coronavirus is SARS-CoV-2 or SARS-CoV or the coronavirus spike polypeptide or fragment thereof is a SARS- CoV-2 or SARS-CoV spike polypeptide or fragment thereof. [0057] Another embodiment is use of an antibody as described herein in the manufacture of a medicament for prevention or treatment of a coronavirus infection. In an embodiment, the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor. In an embodiment, the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV. In an embodiment, the medicament is for delivery by inhalation or nebulization. BRIEF DESCRIPTION OF THE DRAWINGS [0058] Throughout the present disclosure, including in the drawings, antibodies may be referred to by their full name, e.g. NRCoV2-1d, NRCoV2-02, NRCoV2-SR03, or NRCoV2-MRed02, or by an abbreviation in which the “NRCoV2-” portion of the antibody name is omitted, e.g.1d, 02, SR03, or MRed02. Further, “RBD” and “S1-RBD” are used interchangeably, as are “NTD” and “S1-NTD”. [0059] Figures 1A and 1B describe antigen validation by ELISA. Fig.1A shows the results of an ELISA assessing the binding of microtiter-well-adsorbed (S, S1, S2, S1-RBD) and microtiter- well-captured (AviTag-S1, AviTag-S1-RBD) SARS-CoV-2 spike protein fragments to cognate ACE2 receptor (ACE2-hFc). AviTag-S1 and AviTag-S1-RBD were captured on streptavidin- coated microtiter wells through their C-terminal biotins. Fig. 1B shows the results of an ELISA confirming the binding of microtiter-well-adsorbed SARS-CoV-2 spike protein fragments S, S1, S2 and S1-RBD to a commercial rabbit anti-SARS-CoV-2 S polyclonal antibody (pAb). [0060] Figures 2A and 2B show the results of llama serology. Fig. 2A shows the results of an ELISA performed with pre-immune (day 0) and immune (day 21 and 28) sera, demonstrating that spike protein-immunized Maple Red and Eva Green llamas generated a strong immune response against target antigens S, S1, S2 and S1-RBD. ELISA performed with day 0, 21 and 28 sera showed spike protein-immunized llamas did not react with non-target antigens (casein and dipeptidase 1 [DPEP1]), demonstrating specificity of the immune response. Fig.2B shows flow cytometry surrogate neutralization assays performed with pre-immune (day 0) and immune (day 21 and 28) sera demonstrating that the Eva Green llama mounted a polyclonal immune response that was more potent in inhibiting the binding of SARS-CoV-2 S to ACE2 than Maple Red’s. Due to a lack of complete curves, inhibitory serum titers for Maple Red sera were estimated assuming similar upper plateaus as those for Eva Green sera. [0061] Figure 3 provides a schematic representation of three different antibody formats: monomeric VHH, bivalent VHH-Fc and monovalent VHH-Fc. [0062] Figures 4A and 4B show size-exclusion chromatogram (SEC) profiles of anti-SARS- CoV-2 spike protein VHHs. Fig.4A shows SEC profiles of Eva Green VHHs. Fig.4B shows SEC profiles of Maple Red VHHs. Ve, elution volume: mAU, milliabsorbance unit. [0063] Figures 5A and 5B show data on the thermostability of anti-SARS-CoV-2 spike protein VHHs. Fig.5A provides representative examples showing the thermal unfolding of NRCoV2-1d, NRCoV2-02, NRCoV2-07 and NRCoV2-11, as determined using CD spectroscopy. Fig. 5B provides a summary of VHH Tms. The dotted line across the graph in Fig.5B represents the median Tm (70.4 ). [0064] Figures 6A, 6B, 6C, 6D and 6E show SPR/ELISA binding affinity, specificity and cross- reactivity data for anti-SARS-CoV-2 VHHs and VHH-Fcs. Figs. 6A and 6B show the results of ELISA assessing the cross-reactivity of anti-SARS-CoV-2 VHH-Fcs against to a collection of spike glycoproteins from various coronavirus genera and SARS-CoV-2 variants. Assays were performed at a fixed VHH-Fc concentration (13 nM). The VHH-72 (Wrapp et al., 2020) benchmark and human ACE-2 were included for comparison. The epitope bin numbers provided along the bottom of Fig. 6B correspond to the bins shown in Fig. 9G. Fig. 6C shows representative SPR sensorgrams showing single-cycle kinetic analysis of NRCoV2-02, NRCoV2-07, NRCoV2-SR03 and NRCoV2-S2A4 VHH binding to SARS-CoV S and SARS-CoV-2 S, S1, S2 and S1-RBD. Spike proteins were captured on CM5 sensorchip surfaces, followed by flowing VHHs over the sensorchip surfaces at the concentration ranges shown in each panel. “NRCoV2-02/NRCoV2- 07”, “SR03” and “S2A4” represent SPR binding profiles for VHHs specific to SARS-CoV-2 S1- RBD, S1-NTD and S2, respectively. “NRCoV2-07” also represents binding profiles for VHHs that cross-react with SARS-CoV. Figs. 6D and 6E show the results of ELISA assessing the domain specificity of a set of anti-SARS-CoV-2 VHH-Fcs. Assays were performed against SARS-CoV-2 S, S1, S1-NTD and S1-RBD at a fixed concentration (13 nM) (Fig.6D) or varying concentrations (Fig. 6E) of VHH-Fcs. In the graphs shown in Fig. 6E, NRCoV2-02 is included as an internal control (dashed line). [0065] Figures 7A and 7B show on-/off-rate maps summarizing VHH kinetic rate constants, kas and kds. Diagonal lines represent equilibrium dissociation constants, KDs. Maps were constructed using the VHH binding data against SARS-CoV-2 S (Fig.7A) and SARS-CoV S (Fig.7B). In Fig. 7A, VHHs are clustered based on subunit/domain specificity determined in Example 5. Anti- SARS-CoV VHH-72, which cross-reacts with SARS-CoV-2 S1-RBD (Wrapp et al., 2020), and the monomeric ACE2 (ACE2-H6) are included as benchmark/reference binders. [0066] Figures 8A and 8B show the results of flow cytometry assessing the binding of VHH-Fcs to SARS-CoV-2 S-expressing CHO-S cells. Fig. 8A shows representative examples. Fig. 8B summarizes affinity values, i.e., EC50s, determined from graphs in Fig.8A. VHH-72 (Wrapp et al., 2020; open circle) is included for comparison. The line through the data points is the median. [0067] Figures 9A, 9B, 9C, 9D, 9E, 9F, and 9G show epitope typing and binning data obtained by SDS-PAGE/WB, sandwich ELISA and SPR. Fig.9A and 9B show the results of epitope typing of anti-SARS-CoV-2 VHHs by SDS-PAGE/WB. Binding of biotinylated VHHs or VHH-Fcs to denatured SARS-CoV-2 S was detected using streptavidin-peroxidase conjugate (Fig.9A) or anti- human Ig Fc antibody-peroxidase conjugate (Fig. 9B), respectively. Presence of binding signals indicates VHH recognizing a linear epitope. The absence of binding signals is an indirect indication of VHHs recognizing conformational epitopes. Toxin A-specific A20.1 VHH (Hussack et al., 2011) was used as a negative antibody control. “PBS” and “A20.1” represent experiments where VHH test articles were replaced with PBS and C. difficile toxin A-specific VHH A20.1. Fig.9C shows representative sensorgrams showing SPR epitope binning on SARS-CoV-2 S-immobilized surfaces. Figs. 9D and 9E show epitope binning of S1-RBD-specific VHHs by competitive sandwich ELISA. ELISA binding results for pair-wise combinations of VHHs against S1 are presented as a heat map. Binding pairs giving binding signal (shaded) were considered as recognizing non-overlapping epitopes hence belonging to different epitope bins or VHH clusters, while those giving no/week binding signals (colorless/pale shading) were considered to be recognizing overlapping epitopes belonging to the same epitope bins. ACE2-Fc and VHH-72 VHH/VHH-Fc benchmark (Wrapp et al., 2020) were also included in assays. Wells captured with C. difficile toxin A-specific VHH negative control, A20.1 (Hussack et al., 2011), did not give any binding. Fig.9F provides a schematic summary of the initial epitope binning results. NRCoV2- 1c and NRCoV2-MRed02 were assigned to bin 1 since their CDRs were essentially the same as to those of NRCoV2-1a/1d and NRCoV2-MRed04, respectively, with experimentally defined bins. Fig. 9G provides a schematic summary of binning results after further characterization. Unless specified otherwise, references to epitope bin numbers throughout the present disclosure refer to the bins identified in Fig.9F. The bin numbers provided in Fig.9E correspond to the bins shown in Fig.9G. [0068] Figure 10 shows the results of ELISA assessing the ability of monomeric VHHs in blocking (“neutralizing”) the binding of human ACE2 receptor (ACE2-Fc) to its SARS-CoV-2 S1-RBD ligand (i.e., S). A450 nm is a measure of blocking. VHH-72 VHH (Wrapp et al., 2020) and monomeric ACE2-H6 served as positive antibody controls, while toxin A-specific A20.1 VHH (Hussack et al., 2011) was a negative antibody control. “PBS” represents assays in which VHH was substituted with PBS and, similar to the A20.1 control, provides a reference binding signal for lack of any blocking (“min inhibition”). The “-ACE2-Fc” control represents an assay in which ACE2-Fc is omitted and provides a reference binding signal for 100% blocking (“max inhibition”). [0069] Figure 11 shows sensorgrams showing the ability of monomeric VHHs in blocking (“neutralizing”) the binding of ACE2 receptor to its ligand SARS-CoV-2 S. A tandem SPR in two different orientation formats were performed where injection of VHH (orientation #1) or ACE2 (orientation #2) at 20 – 40 × KD concentration (VHH) or 1 µM (ACE2) over sensor chip- immobilized S was followed by injection of VHH + ACE2 mix at the same VHH and ACE2 concentrations. Solid and dashed profiles represent binding results with the two orientation formats. “NRCoV2-02:ACE2” represents profiles for blocking (neutralizing) VHHs where the addition of the VHH or ACE2 results in no significant increase in binding over that achieved by the injection of the ACE2 or VHH over the antigen surface. “NRCoV2-11:ACE2” represents profiles for non-blocking (non-neutralizing VHHs where the addition of the VHH or ACE2 results in significant increase in binding over that achieved by the injection of the ACE2 or VHH over the antigen surface. RUs, representing binding differences between the first and second injection, were calculated from the sensorgrams and used to identify VHHs that block (neutralize) the binding of ACE2 receptor to its ligand S1-RBD. ACE2 is provided as an abbreviation for monomeric ACE2-H6. [0070] Figures 12A and 12B show the results of flow cytometry assessing the ability of monomeric VHHs in blocking (“neutralizing”) the binding of SARS-CoV-2 S to ACE2-expressing Vero E6 cells at 100 nM (Fig. 12A) or increasing (Fig. 12B) VHH concentrations. Fig. 12B provides plots showing inhibition of SARS-CoV-2 S binding to Vero E6 cells as a function of VHH concentration. The NRCoV2-1d, NRCoV2-02, NRCoV2-05, and NRCoV2-11 VHHs are S1-RBD, SR13, S1-NTD-specific. Monomeric ACE2 (ACE2-H6) serves as positive “antibody” control and reference, and VHH-72 VHH (Wrapp et al., 2020) is included as benchmark. “A20.1” and “PBS” represent negative control assays in which VHHs were replaced with C. difficile toxin A-specific A20.1 VHH (Hussack et al., 2011) and PBS, respectively. [0071] Figures 13A and 13B show virus-neutralizing potential of VHH-Fcs in flow cytometry- based surrogate virus neutralization assays. Fig.13A shows flow cytometry assessing the ability of bivalent VHH-Fcs in blocking (“neutralizing”) the binding of SARS-CoV-2 S to ACE2- expressing Vero E6 cells at 250 nM VHH-Fc concentrations. Fig. 13B shows flow cytometry assessing the ability of bivalent VHH-Fcs in blocking (“neutralizing”) the binding of SARS-CoV- 2 S to ACE2-expressing Vero E6 cells at increasing VHH-Fc concentrations. NRCoV2-1d, NRCoV2-02, NRCoV2-04, NRCoV2-05, NRCoV2-11, and NRCoV2-20 VHH-Fcs are S1-RBD- specific, while NRCoV2-SR01 and NRCoV2-SR13 VHH-Fcs are S1-NTD-specific. VHH-72 VHH- Fc (Wrapp et al., 2020) is included as a benchmark. “A20.1” and “PBS” represent negative control assays in which VHHs were replaced with C. difficile toxin A-specific A20.1 VHH (Hussack et al., 2011) and PBS, respectively. [0072] Figures 14A and 14B show the results of a VHH-Fc in vitro live-virus micro- neutralization assay. Antibody concentrations that gave 100% neutralization, i.e., MN100s, were used to rank the neutralizing potency of VHH-Fcs. A lower MN100 means a higher neutralization potency. VHH-72 (Wrapp et al., 2020) is included as benchmark. Fig.14A provides a plot showing the MN100s of bivalent VHH-Fcs. The inset shows MN100s of monomeric NRCoV2-02 and VHH- 72 VHHs. *The MN100 of NRCoV2-02 bivalent VHH-Fc is 0.01 nM, since its potency was not tested below the 0.01 nM concentration. Fig.14B provides a plot comparing the MN100s of bivalent VHH-Fcs to monovalent VHH-Fcs. Monovalent VHH-72-Fc did not show MN100 at the highest concentration tested (350 nM). In monovalent VHH-Fc constructs, one heavy chain displays an S- specific VHH, while the other displays a C. difficile toxin A-specific, mock VHH (A26.8) (Hussack et al., 2011). [0073] Figures 15A, 15B, 15C, 15D, and 15E show the results of VHH-Fc in vitro live-virus neutralization assay. Fig. 15A shows inhibition capability of S1-RBD-specific VHH-Fcs at high (312.5 nM) and low (2.5 nM) VHH-Fc concentrations. As expected, NRCoV2-08, NRCoV2-19 and NRCoV2-21 which showed no binding to spike protein-expressing CHO cells (CHO-S), do not neutralize either. VHH-72 (Wrapp et al., 2020) and C. difficile toxin A-specific VHH A20.1 (Hussack et al., 2011) are included as benchmark and negative control, respectively. Figs.15B-D provide representative examples showing inhibition capability of VHH-Fcs as a function of VHH- Fc concentration, for select S-RBD specific antibodies (Fig. 15B), S1-NTD-specific antibodies (Fig. 15C), and S2-specific antibodies (Fig. 15D). Antibody concentrations that gave 50% neutralization, i.e., IC50s, were calculated from graphs and used to rank the neutralizing potency of VHH-Fcs. Bin ud, epitope bin undetermined. Fig. 15E shows a summary of IC50 categorized based on subunit/domain specificity and epitope bin. A lower IC50 means a higher neutralization potency. VHH-72 is shown as open circle in bin 1. Bin ud, epitope bin undetermined. The line through the data points is the median. [0074] Figures 16A, 16B, 16C, and 16D show data on the stability of VHHs against aerosolization treatment. Fig. 16A shows SEC profiles of pre- vs post-aerosolized VHHs, for representative VHHs. NRCoV2-1d, NRCoV2-02 and NRCoV2-07 represent the vast majority of VHHs which were resistant to aerosolization-induced aggregation, showing a homogenously monomeric peak. In contrast, the VHH-72 benchmark forms a significant amount of soluble aggregates following aerosolization. NRCoV2-11 on the other hand represents the few VHHs that formed visible, precipitating aggregates reflected in significant reduction of their monomeric peak areas (compare monomeric peak for pre- vs post-aeosolized NRCoV2-11). Ve, elution volume. Fig. 16B summarizes the % recovery of all VHHs and Fig. 16C summarizes the % recovery of a subset of VHHs. % recovery represents the proportion of a VHH that remained monomerically soluble following aerosolization. The open circle in Fig.16B represents benchmark VHH-72. The line through the data points is the median. Fig.16D shows the results of ELISA assessing the effect of aerosolization on the functionality of VHHs by comparing the binding activity of pre- vs post- aerosolized VHHs against SARS-CoV-2 S. Essentially identical EC50s for pre- vs post-aerosolized VHHs clearly indicate aerosolization had no effect on the functional activity of VHHs. Pre, pre- aerosolized VHH; post, post-aerosolized VHH. [0075] Figure 17 provides the results of sandwich ELISA demonstrating the potential utility of VHHs in detecting/capturing SARS-CoV-2, SARS-CoV and related viruses, as well as their spike proteins. SARS-CoV-2 S, S1 and S1-RBD antigens were used as surrogates for viruses. Specific detection of S, S1 and S1-RBD was achieved using NRCoV2-02 VHH as the capture antibody and NRCoV2-1d, NRCoV2-02, NRCoV2-04, NRCoV2-07, or NRCoV2-11 VHH-Fcs as detecting antibodies. SC50 is the concentration of antigen that gives 50% binding and were calculated from graphs. [0076] Figure 18 shows an alignment of amino acid sequences of S-specific VHH antibodies described herein. [0077] Figure 19 shows an alignment of amino acid sequences of S1-NTD-specific VHH antibodies described herein. [0078] Figure 20 shows an alignment of amino acid sequences of S2-specific VHH antibodies described herein. [0079] Figure 21 shows an alignment of amino acid sequences of S1-RBD-specific VHH antibodies described herein. [0080] Figures 22A, 22B, 22C, and 22D show the results of efficacy tests of VHH-Fcs in hamsters challenged with SARS-CoV-2. Fig.22A shows lung viral load in VHH-Fc-treated (VHH- 72 benchmark, 1d, 05, MRed05, SR01, S2A3, 1d/MRed05, 1d/SR01) and control groups treated with PBS or isotype A20.1 VHH-Fc at 5 dpi. PFU, plaque-forming unit. Fig.22B shows the percent body weight change for antibody-treated and control groups. Fig. 22C shows the percent body weight change at 5 dpi. In Fig.22A and Fig.22C, treatment effects, assessed by one-way ANOVA with Dunnett’s multiple comparison post hoc test, were significant (*p<0.05, **p<0.01, ***p<0.001 or ****p<0.0001). Dunnett’s test was performed by comparing treatment groups against the isotype control. ns, not significant. Fig.22D shows a correlation curve of body weight change vs viral titer at 5 dpi. A strong negative correlation (r = -0.9436, p<0.0001) between body weight change and lung viral titer was observed. [0081] Figure 23 shows immunohistochemical demonstration of SARS-CoV-2 nucleocapsid (N) protein in the lungs of VHH-Fcs-treated animals. Untreated (PBS) and A20.1 isotype-treated animals showed strong viral N protein immunoreactivity which was mainly found in large multifocal patches of consolidated areas. Black arrow indicates the presence of viral N protein in bronchiolar epithelial cells. Omission of anti-nucleocapsid antibody eliminated the staining (Negative). Shown also is the absence of staining in healthy animals (Naïve). A marked reduction in viral N protein staining was seen in all lung tissues examined from VHH-Fc-treated animals (middle and bottom panels). While no staining was observed in 05, MRed05, 1d/SR01 and 1d/MRed05, small foci of viral N protein was detected in VHH-72, 1d, SR01 and S2A3. Representative images are shown from a single experiment. [0082] Figure 24 shows immunohistochemical detection of infiltrating macrophages in the lungs of VHH-Fc-treated animals. Untreated (PBS) and A20.1 isotype-treated animals showed an intense immune reaction to anti-Iba-1 antibody and an increased number of Iba-1-positive macrophagesin the consolidated areas. A substantial reduction in the number of Iba-1-positive macrophages was seen in the perivascular areas and pulmonary interstitium in the lungs of VHH-Fc-treated animals. Representative images are shown from a single experiment. [0083] Figure 25 shows immunohistochemical detection of T lymphocytes in the lungs of VHH- Fc-treated animals. Untreated (PBS) and A20.1 isotype-treated animals showed an increased number of T lymphocytes in the pulmonary interstitium. A dramatic decrease in the number of T lymphocytes was seen in the lungs of VHH-Fc-treated animals. Representative images are shown from a single experiment. [0084] Figure 26 shows immunohistochemical detection of apoptotic cells in the lungs of VHH- Fc-treated animals. Untreated (PBS) and A20.1 isotype-treated animals showed an increase in the number of TUNEL-positive cells with classical features of apoptotic cells in the pulmonary interstitium. The large grey frame in the corner of PBS panel shows the magnification of the region (small grey frame) in the lung parenchyma, scale bar = 50 µm. A marked reduction in the TUNEL- positive cells was seen in the lungs of NRCoV2-05- and NRCoV2-MRed05-treated animals. Black arrows indicate occasional TUNEL-positive cells. Representative images are shown from a single experiment. [0085] Figure 27 shows on-/off-rate maps summarizing VHH kinetic rate constants, kas and kds determined by SPR for the binding of VHHs to SARS-CoV S. [0086] Figures 28A and 28B show on-/off-rate maps summarizing VHH kinetic rate constants, kas and kds determined by SPR for the binding of VHHs to SARS-CoV-2 Alpha S (Fig.28A) and SARS-CoV-2 Beta S (Fig.28B). [0087] Figure 29 shows representative SPR sensorgrams showing single-cycle kinetics analysis of NRCoV2-02, NRCoV2-15 and NRCoV2-MRed05 binding to Wuhan, Alpha and Beta S (NRCoV2-02, NRCoV2-15) and RBD (NRCoV2-MRed05). [0088] Figure 30 shows a summary of IC50s obtained by live virus neutralization assays (LVNAs) for VHH-Fcs against Wuhan, Alpha, and Beta SARS-CoV-2 variants. The epitope bin numbers provided in Fig.30 correspond to the bins shown in Fig.9G. [0089] Figures 31A, 31B, 31C, and 31D show results from live virus neutralization assays assessing the ability of SARS-CoV-2 VHH-Fcs in blocking the infection of ACE2-expressing Vero E6 cells by SARS-CoV-2 Alpha (Fig. 31A and Fig. 31C) and Beta (Fig. 31B and Fig. 31D) variants at fixed (Fig. 31A and Fig. 31B) or varying (Fig. 31C and Fig. 31D) VHH-Fc concentrations. Inhibition assays shown in Fig.31A and Fig.31B were performed at 312, 12.5 or 0.5 nM VHH-Fc concentrations. IC50s calculated from graphs in Fig. 31C and Fig. 31D are recorded in Table 19. VHH-72 and C. difficile toxin A-specific VHH A20.1 are included as a benchmark and negative antibody control, respectively. The epitope bin numbers provided in Figs. 31C and 31D correspond to the bins shown in Fig.9G. [0090] Figure 32 shows in vivo stability and persistence of VHHs. Stability and persistence were determined by monitoring the concentration of a representative VHH-Fc (NRCoV2-1d) in hamster blood at various days post-injection by ELISA. VHH-72 VHH-Fc was used as the benchmark. DETAILED DESCRIPTION [0091] The following is a detailed description provided to aid those skilled in the art in practicing the present disclosure. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The terminology used in the description herein is for describing particular embodiments only and is not intended to be limiting of the disclosure. [0092] Terms defined below may have the meanings ascribed to them, unless specified otherwise. However, it should be understood that other meanings that are known or understood by those having ordinary skill in the art are also possible, and within the scope of the present disclosure. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. Definitions [0093] The “coronavirus spike polypeptide” or “coronavirus spike protein” (S) is the major coronavirus surface protein, and is a glycosylated homotrimer that binds to a host cell receptor and mediates coronavirus entry into a host cell. The coronavirus may be SARS-CoV-2, SARS-CoV, or another coronavirus. “SARS-CoV-2” may be used herein to refer to any strain or variant of the SARS-CoV-2 virus. Similarly, “SARS-CoV” may be used to refer to any strain or variant of the SARS-CoV virus. A SARS-CoV-2 variant is a strain of SARS-CoV-2 that comprises one or more mutations relative to the Wuhan strain of SARS-CoV-2. A variant may be, but need not be, a variant that has been designated as a variant of concern or a variant of interest by the World Health Organization. [0094] As used herein, the term “polypeptide” refers to a molecule comprising two or more amino acid residues linked by peptide bonds. A polypeptide may have primary, secondary, and/or tertiary structure. A “protein” comprises at least one polypeptide and may have primary, secondary, tertiary, and/or quaternary structure. The terms “polypeptide” and “protein” are often used interchangeably, and a polypeptide may be comprised by a protein. For example, a protein may be a homo- or hetero-multimer that comprises two or more polypeptides, or a protein may comprise a single polypeptide. A polypeptide or protein may include one or more post- translational modifications, such as, but not limited to, glycosylation, phosphorylation, lipidation, S-nitrosylation, N-acetylation, or methylation. [0095] As used herein, the term “fragment”, in the context of a polypeptide, refers to a portion of a polypeptide comprising a series of consecutive amino acid residues from a parent polypeptide. In a specific embodiment, the term “fragment” refers to an amino acid sequence of at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 consecutive amino acid residues from a parent polypeptide. In embodiments, a fragment may comprise an epitope or binding domain from a parent polypeptide. In embodiments, a fragment may be a biologically active fragment that retains one or more functional characteristics of a parent polypeptide. [0096] The term “antibody”, as used herein, refers to an antigen binding protein comprising at least a heavy chain variable region (VH) that binds a target epitope. The term antibody includes monoclonal antibodies comprising immunoglobulin heavy and light chain molecules, single heavy chain variable domain antibodies, and variants and derivatives thereof, including chimeric variants of monoclonal and single heavy chain variable domain antibodies. The antibody may be a naturally-occurring antibody, it may be obtained by manipulation of a naturally-occurring antibody, or it may be produced using recombinant methods. For example, an antibody may include, but is not limited to a Fv, single-chain Fv (scFv; a molecule consisting of VL and VH connected with a peptide linker), Fab, F(ab')2, single domain antibody (sdAb; an antibody composed of a single VL or VH), or a multivalent presentation of any of these. Antibodies such as those just described may require linker sequences, disulfide bonds, or other types of covalent bond to link different portions of the antibody. Those of skill in the art will be familiar with the requirements of the different types of antibodies and various approaches for their construction. [0097] In a non-limiting example, the antibody may be a single domain antibody derived from a naturally- occurring source. Heavy chain antibodies of camelid origin (Hamers-Casterman et al, 1993) lack light chains and thus their antigen binding sites consist of one domain, termed VHH. sdAbs have also been observed in shark and are termed VNAR (Nuttall et al, 2003). Other sdAbs may be engineered based on human Ig heavy and light chain sequences (Jespers et al, 2004; To et al, 2005). As used herein, the term “single domain antibody” includes single domain antibodies directly isolated from VH, VHH, VL, or VNAR reservoir of any origin through phage display or other technologies, single domain antibodies derived from the aforementioned single domain antibodies, recombinantly produced single domain antibodies, as well as single domain antibodies generated through further modification of such single domain antibodies by humanization, affinity maturation, stabilization, solubilization, camelization, or other methods of antibody engineering. Also encompassed by the disclosure are homologues, derivatives, or fragments that retain the antigen-binding function and specificity of the single domain antibody. [0098] Single domain antibodies possess desirable properties for antibody molecules, such as high thermostability, high detergent resistance, relatively high resistance to proteases (Dumoulin et al, 2002) and high production yield (Arbabi-Ghahroudi et al, 1997). They can also be engineered to have very high affinity by isolation from an immune library (Li et al, 2009) or by in vitro affinity maturation (Davies & Riechmann, 1996). Further modifications to increase stability, such as the introduction of non-canonical disulfide bonds (Hussack et al, 2011; Kim et al, 2012), may also be brought to a single domain antibody. [0099] A person of skill in the art would be well-acquainted with the structure of a single-domain antibody. A single domain antibody comprises a single immunoglobulin domain that retains the immunoglobulin fold; most notably, only three CDR/hypervariable loops form the antigen-binding site. However, and as would be understood by one of skill in the art, not all CDRs may be required for binding the antigen. For example, and without wishing to be limiting, one, two, or three of the CDRs may contribute to binding and recognition of the antigen by a single domain antibody. The CDRs of the single domain antibody or variable domain are referred to herein as CDR1, CDR2, and CDR3, and numbered as defined by Lefranc et al., 2003. [00100] As described herein, the amino acid sequence and structure of a heavy chain variable domain, including a VHH, can be considered—without however being limited thereto—to be comprised of four framework regions or ‘FR’, which are referred to in the art and herein as ‘Framework region 1’ or ‘FR1’; as ‘Framework region 2’ or ‘FR2’; as ‘Framework region 3’ or ‘FR3’; and as ‘Framework region 4’ or ‘FR4’, respectively; which framework regions are interrupted by three complementarity determining regions or ‘CDR s’, which are referred to in the art as ‘Complementarity Determining Region 1’ or ‘CDR1’; as ‘Complementarity Determining Region 2’ or ‘CDR2’; and as ‘Complementarity Determining Region 3’ or ‘CDR3’, respectively. CDRs described in the present disclosure have been defined using the IMGT numbering system (Lefranc et al, 2003). [00101] The term “binding” as used herein in the context of binding between an antibody, such as a VHH, and a coronavirus spike protein epitope as a target, refers to the process of a non-covalent interaction between molecules. Preferably, said binding is specific. The terms ‘specific’ or ‘specificity’ or grammatical variations thereof refer to the number of different types of antigens or their epitopes to which a particular antibody such as a VHH can bind. The specificity of an antibody, also referred to as “specific binding”, can be determined based on affinity. A specific antibody preferably has a binding affinity (Kd) for its epitope of less than 10 7 M, preferably less than 10 8 M. [00102] The term “affinity”, as used herein, refers to the strength of a binding reaction between a binding domain of an antibody and an epitope. It is the sum of the attractive and repulsive forces operating between the binding domain and the epitope. The term “affinity”, as used herein, refers to the equilibrium dissociation constant, Kd. [00103] The term “epitope” or “antigenic determinant”, as used herein, refers to a part of an antigen that is recognized by an antibody. The term epitope includes linear epitopes and conformational epitopes. A linear epitope is an epitope that is recognized by an antibody based on its primary structure, and a stretch of contiguous amino acids is sufficient for binding. A conformational epitope is based on 3-D surface features and shape and/or tertiary structure of the antigen. [00104] The term “neutralizing antibody”, as used herein, refers to an antibody that, when bound to an epitope, interferes with at least one of the steps leading to the release of a virus genome, such as a coronavirus genome, into a host cell. [00105] The term “subject”, as used herein, refers to an animal that is susceptible to infection by a coronavirus. The subject may be an animal that is susceptible to infection by a coronavirus that binds an ACE2 receptor, such as SARS-CoV-2 or SARS-CoV. The subject may be a human or non-human animal. Preferably the subject is a human or non-human mammal. Correspondingly, the ACE2 receptor may be a human ACE2 receptor or an animal ACE2 receptor. [00106] The term “administering”, as used herein, refers to the introduction into a subject of a therapeutic agent. Many administration routes are known in the art, and include, but are not limited to, parenteral (intravenous, intramuscular, and subcutaneous), oral, nasal, ocular, transmucosal (buccal, vaginal, and rectal), transdermal, and pulmonary administration. [00107] The terms “strong interaction” and “strong binding”, as used herein, refer to the presence of salt bridges and cation-pi interactions between amino acid residues, as is known to the skilled person. [00108] The terms “weak interaction” and “weak binding”, as used herein, refer to the presence of hydrogen bonds and non-bonded/hydrophobic interactions, as is known to the skilled person. [00109] The term "purified," as used herein, refers to a molecule, e.g. a polypeptide or protein that has been identified and substantially separated and/or recovered from the components of its natural environment. The term “isolated antibody”, as used herein, refers to an antibody that is substantially freed from other antibody molecules having different antigenic specificities. Further, a purified or isolated antibody may be substantially free of one or more other cellular and/or chemical substances. Absolute purity is not required for a molecule to be considered purified or isolated. [00110] The term “pharmaceutically acceptable”, as used herein, means generally regarded as safe when administered to humans. Preferably, as used herein, the term “pharmaceutically acceptable” is approved by a federal or state government regulatory agency for use in animals, more preferably in humans. The term “carrier” means a diluent, adjuvant, excipient, or vehicle with which a compound is formulated and/or administered. Such pharmaceutical carriers can be water and sterile liquids, such as petroleum, animal, vegetable or synthetically derived oils such as peanut oil, soybean oil, mineral oil, sesame oil. Water or saline solutions and aqueous dextrose and glycerol solutions are preferably used as carriers for injectable solutions. Suitable pharmaceutical carriers are, for example, described in “Remington (23rd edition), The Science and Practice of Pharmacy”. [00111] As used herein the term “linked” or “linkage” includes covalent and non-covalent linkage (bonding). As used herein, the term “linker” refers to a chemical group or molecule that can be used to join one molecule to another. An antibody may be linked to another molecule by a linker or an antibody may be directly linked (aka joined, fused, or bonded) to another molecule, without the use of a linker. Suitable linkers are known in the art and may be selected based on the chemical nature of the molecules being joined. Examples of linkers include peptide linkers and chemical cross-linkers. Peptide linkers may comprise a single amino acid residue or a plurality of amino acid residues. An antibody and a polypeptide may, for example, be linked by chemical conjugation, with or without the use of a linker, or produced as a fusion, for example by recombinant protein expression. [00112] As used herein the term “label” refers to a molecule or compound that can be used to label a molecule, such as an antibody, to allow detection of the molecule. Suitable labels will be known to one skilled in the art and include, but are not limited to, radioisotopes; enzymes, such as horse radish peroxidase (HRP) or calf intestinal alkaline phosphate (AP); fluorophores; antigen binding fragments from cleaved antibodies (Fabs); and colloidal gold. Covalent linkage is commonly used to link a label to a molecule of interest, however, non-covalent linkage is also possible, for example, when the label is a Fab. [00113] As used herein, the term “nucleic acid molecule” refers to any nucleic acid-containing molecule including, but not limited to, DNA, RNA, and DNA/RNA hybrids, in any form and/or conformation. The term encompasses nucleic acids that include any of the known base analogs of DNA and RNA. For example, single-stranded, double-stranded, nuclear, extranuclear, extracellular, and isolated nucleic acids are all contemplated. [00114] As used herein, the term “vector” refers to a synthetic nucleotide sequence used for manipulation of genetic material, including but not limited to cloning, subcloning, sequencing, or introduction of exogenous genetic material into cells, tissues or organisms. It is understood by one skilled in the art that vectors may contain synthetic DNA sequences, naturally occurring DNA sequences, or both. Examples of commonly used vectors include plasmids, viral vectors, cosmids, and artificial chromosomes. [00115] As used herein, the term “regulatory sequence” includes promoters, enhancers and other expression control elements, such as polyadenylation sequences, matrix attachment sites, insulator regions for expression of multiple genes on a single construct, ribosome entry/attachment sites, introns that are able to enhance expression, and silencers. Promoters may be cell-specific or tissue- specific to facilitate expression in a desired target. [00116] When referring to two nucleotide sequences, one being a regulatory sequence, the term “operably linked” is used herein to mean that the two sequences are associated in a manner that allows the regulatory sequence to affect expression of the other nucleotide sequence. It is not required that the operably-linked sequences be directly adjacent to one another with no intervening sequence(s). [00117] As used herein, the term “host cell” refers to a cell into which a nucleic acid molecule or vector may be introduced, for example to allow for replication of the nucleic acid molecule or vector by the host cell and/or to allow for expression of the nucleic acid molecule, or of a nucleic acid molecule comprised by the vector, by the host cell to produce a product of interest, such as an RNA or protein. In a specific embodiment, the nucleic acid molecule may encode an antibody as described herein, and introduction of the nucleic acid molecule into the host cell may allow the antibody to be expressed by the host cell. A host cell may be any suitable cell, such as a bacterial cell or eukaryotic cell. Commonly used host cells include E. coli, yeast, and mammalian cells, such as, but not limited to, Chinese hamster ovary (CHO) cells, mouse myeloma cells, and human embryonic kidney (HEK) cells. [00118] The term “treatment” and variations thereof, such as “treat” or “treating”, as used herein, refer to the administration of a therapeutic molecule or composition to a subject to reduce or eliminate one or more symptoms of an illness or disease in the subject and/or to reduce the duration of the illness or disease in the subject. [00119] The term “prevention” and variations thereof, such as “prevent” or “preventing”, as used herein, refer to the prophylactic administration of a therapeutic molecule or composition to a subject to prevent the occurrence of, or to reduce the severity of, an illness or disease in the subject. [00120] The term “sample” as used herein, refers to a sample in which a coronavirus presence is suspected or expected. For example, the sample may be a biological sample from a subject, such as, but not limited to, blood or a fraction thereof, saliva, cellular material, urine, or feces; a sample from a bioreactor; or an environmental sample. [00121] The term "sequence identity" as used herein refers to the percentage of sequence identity between two amino acid sequences or two nucleic acid sequences. To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g. gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e. % identity = (number of identical overlapping positions/total number of positions) x 100). In one embodiment, the two sequences are the same length. The determination of percent identity between two sequences can also be accomplished using a mathematical algorithm. One non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, modified as in Karlin and Altschul, 1993. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g. for score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the present disclosure. BLAST protein searches can be performed with the XBLAST program parameters set, e.g. to score-50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule of the present invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., 1997. Alternatively, PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g. of XBLAST and NBLAST) can be used (see, e.g. the NCBI website). Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted. [00122] As used herein the singular forms "a", "an", and "the" include plural references unless the context clearly dictates otherwise. [00123] The phrase "and/or", as used herein, should be understood to mean "either or both" of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with "and/or" should be construed in the same fashion, i.e., "one or more" of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the "and/or" clause, whether related or unrelated to those elements specifically identified. [00124] As used herein in the specification and in the claims, "or" should be understood to have the same meaning as "and/or" as defined above. For example, when separating items in a list, "or" or "and/or" shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as "only one of' or "exactly one of" or, when used in the claims, "consisting of" will refer to the inclusion of exactly one element of a number or list of elements. In general, the term "or" as used herein shall only be interpreted as indicating exclusive alternatives (i.e., "one or the other but not both") when preceded by terms of exclusivity, such as "either," "one of," "only one of," or "exactly one of." [00125] As used herein, all transitional phrases such as "comprising," "including," "carrying," "having," "containing," "involving," "holding," "composed of," and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases "consisting of” and "consisting essentially of” shall be closed or semi-closed transitional phrases, respectively. [00126] As used herein, the phrase "at least one," in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase "at least one" refers, whether related or unrelated to those elements specifically identified. Description [00127] The present disclosure relates to SARS-CoV-2 spike protein-specific antibodies and uses thereof. Provided are isolated or purified antibodies comprising complementarity determining region (CDR) 1, CDR2, and CDR3 sequences as outlined in Table 6. The antibodies described herein recognize a variety of spike protein epitopes in different subunit and domains of the coronavirus spike protein, specifically S2, the N-terminal domain of S1 (S1-NTD), and the receptor binding domain of S1 (S1-RBD). Within these subunits/domains, antibodies described herein recognize several different epitopes. Because of this epitopic diversity, antibodies described herein may be used in combination, for example for combination therapy, or as bi- specific or multi-specific antibodies. [00128] An antibody as described herein comprises an antigen binding portion of an antibody heavy chain, wherein the antigen binding portion comprises a first complementarity determining region (CDR1), a second complementarity determining region (CDR2), and a third complementarity determining region (CDR3), and wherein CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 20, SEQ ID NO: 64, and SEQ ID NO: 110; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 34, SEQ ID NO: 78, and SEQ ID NO: 124; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127; SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128; SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135. In an embodiment, the antibody comprises the amino acid sequence set forth in SEQ ID NO: 183, 184, 185, or 186. [00129] In an embodiment, an antibody as described herein comprises the amino acid sequence set forth in SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, or SEQ ID NO: 182. In another embodiment, the antibody comprises an amino acid sequence having at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, and/or SEQ ID NO: 182 and comprises CDR1, CDR2, and CDR3 sequences that, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 20, SEQ ID NO: 64, and SEQ ID NO: 110; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 34, SEQ ID NO: 78, and SEQ ID NO: 124; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127; SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128; SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135. [00130] Another embodiment is a nucleic acid molecule encoding an antibody as described herein. A further embodiment is a vector comprising the nucleic acid molecule. Optionally, the nucleic acid molecule may be operably linked to at least one promoter and/or regulatory element to enable expression in a host cell. A further embodiment is a host cell comprising the nucleic acid or vector. [00131] An antibody as described herein may be comprised within a composition. For example, the antibody may be comprised within a pharmaceutical composition that comprises a pharmaceutically acceptable carrier and/or diluent, the antibody may be linked to another molecule, or the antibody may be immobilized on a substrate. In an embodiment, the pharmaceutical composition may be for delivery by inhalation or nebulization. [00132] Antibodies and compositions as described herein may be used, or for use, to treat or prevent a coronavirus infection, including an infection caused by at least one coronavirus that specifically binds an ACE2 receptor. Antibodies as described herein may also be used in the manufacture of a medicament for prevention or treatment of a coronavirus infection. In a specific embodiment, the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV. Further provided is a method for prevention or treatment of a coronavirus infection comprising administering an antibody or composition as described herein to a subject in need thereof. In an embodiment, the administration is by inhalation or nebulization. [00133] Antibodies and compositions as described herein may also be used, or for use, to detect, quantify, and/or capture a coronavirus, a coronavirus spike polypeptide or a coronavirus spike polypeptide fragment. Further provided are methods for detecting, quantifying, and/or capturing a coronavirus, a coronavirus spike polypeptide or a coronavirus spike polypeptide fragment using an antibody or composition as described herein. In an embodiment, the coronavirus or spike polypeptide is a coronavirus or spike polypeptide that specifically binds an ACE2 receptor. The ACE2 receptor may be a human ACE2 receptor or an animal ACE2 receptor. In a specific embodiment, the coronavirus is SARS-CoV-2 or SARS-CoV, or the spike polypeptide or fragment thereof is from SARS-CoV-2 or SARS-CoV [00134] Several of the antibodies described herein have the characteristics of neutralizing antibodies, and some have been demonstrated to be cross-reactive with the spike protein of other coronaviruses, such as SARS-CoV and related coronaviruses that infect bats, pangolin, and civet, suggesting that antibodies described herein may be useful for binding the spike protein of more than one coronavirus; including coronaviruses that bind an ACE2 receptor, such as SARS-CoV-2 and SARS-CoV. Antibodies described herein have also been demonstrated to bind various SARS- CoV-2 spike protein variants, such as the Wuhan-Hu-1 variant that was first identified in China; the B.1.1.7 variant that was first identified in the United Kingdom (also referred to herein as the UK variant, or the Alpha variant); the B.1.352 variant that was first identified in South Africa (also referred to herein as the South Africa variant, or the Beta variant), the B.1.617.1 variant that was first detected in India (also referred to herein as Kappa); the B.1.617.2 variant that was first detected in India (also referred to herein as Delta); and the B.1.1.529 variant that was first detected in South Africa (also referred to herein as Omicron). [00135] Antibodies described herein may be linked to another molecule or substrate. For example, they may be linked to a detectable label to allow detection, quantification, and/or visualization; they may be linked to a molecule that extends antibody half-life, such as polyethylene glycol (PEG), Ig Fc, serum albumin, serum-albumin-specific antibody, serum- albumin-specific peptide, or Fc-specific peptides, proteins or antibodies; they may be linked to a therapeutic molecule; they may be immobilized onto a substrate, such as a plastic surface, a magnetic bead or a protein sheet or bead; and/or they may be linked to a polypeptide. In a specific embodiment, antibodies described herein may be linked to an ACE2 polypeptide or a fragment thereof. [00136] Antibodies described herein may also be employed in various formats and combinations. For example, antibodies described herein may be monoparatropic or multiparatropic (including biparatropic), or monospecific or multispecific (including bispecific). Antibodies described herein may be in a monovalent format or in a multivalent format (including a bivalent format). Antibodies described herein that are specific for the same or different epitopes, or for the same or different spike protein subunit or domains, may be linked, for example to produce antibodies with different affinities and/or specificities. Further, antibodies described herein may be linked to one or more other antibodies or antibody fragments. In addition, antibodies described herein may be used individually or in combination. A combination may comprise any two or more antibodies described herein, or it may comprise at least one antibody described herein and another antibody. In some embodiments, the antibodies are VHH antibodies or VHH-Fc antibodies. [00137] Antibodies described herein may be useful for a variety of applications. For example, they may be useful for detecting the presence of a coronavirus or a coronavirus spike polypeptide or fragment thereof; for capturing a coronavirus or a coronavirus spike polypeptide or fragment thereof; for quantifying the amount of a coronavirus or a coronavirus spike polypeptide or fragment thereof in a sample; for treatment or prevention of a coronavirus infection; for diagnosing a coronavirus infection; for monitoring the production of a coronavirus spike protein or fragment thereof; for purification of a coronavirus spike protein or fragment thereof; for detecting the level of expression of a coronavirus spike protein or fragment thereof, and/or for quantifying the amount of a coronavirus. Antibodies described herein have been shown to be stable against aerosolization, indicating that they may be suitable for delivery to the lungs by inhalation or nebulization. Further, cross-reactive antibodies may have general applicability for the treatment, prevention, detection, quantification or capture of coronaviruses, in addition to SARS-CoV-2, or coronavirus spike polypeptides or fragments thereof from coronaviruses in addition to SARS-CoV-2. In specific embodiments, cross-reactive antibodies may be used to bind coronaviruses or coronavirus spike polypeptides that bind an ACE2 receptor, including fragments of such coronavirus spike polypeptides. [00138] Antibodies described herein may be classified based on the spike protein subunit or domain to which they bind. Nine antibodies were generated that bind to the S1-NTD domain, 24 antibodies were generated that bind to the S1-RBD domain, and 14 antibodies were generated that bind to the S2 subunit (see Tables 5 and 6). Neutralization assays, as described in the Examples, identified antibodies with neutralizing properties within each of these three groups. To the inventors’ knowledge, this is the first known observation of single domain antibodies neutralizing the SARS-CoV-2 virus by targeting a non-S1-RBD region of S, i.e., S1-NTD or S2. [00139] Within the three groups of antibodies identified above, further classification is possible based on epitope specificity, which was determined by epitope binning experiments (see Example 7). Preliminary results showed that antibodies binding to S1-NTD may be grouped into three epitope bins; antibodies binding S1-RBD may be grouped into six epitope bins, with some overlap between bins; and antibodies binding S2 may be grouped into five epitope bins (Fig.9F). Further characterization identified additional epitope bins, so that antibodies binding to S1-NTD may be grouped into four epitope bins; antibodies binding S1-RBD may be grouped into six epitope bins, with some overlap between bins; and antibodies binding S2 may be grouped into seven epitope bins (Fig.9G). [00140] Antibodies described herein may also be classified based on their pattern of cross- reactivity with different coronavirus spike proteins and/or spike protein variants, as shown in Figures 6A and 6B. Antibodies that recognize the same set of spike proteins and/or spike protein variants may be viewed as a single group. [00141] As demonstrated in the Examples, several of the antibodies described herein have substantially increased binding affinity in comparison to a benchmark VHH spike protein antibody, VHH-72 (Wrapp et al., 2020). Further, many of the antibodies described herein are demonstrated to outperform VHH-72 in neutralization assays, and some are demonstrated to be more broadly neutralizing than VHH-72. Additionally, some antibodies described herein are demonstrated to be more broadly cross-reactive than VHH-72. [00142] The antibodies described in the following examples may be modified, while still retaining antigen specificity. For example, changes may be introduced into the amino acid sequence of the framework regions, or the antibodies may be humanized. The antibodies may also be linked to other molecule(s). Antibodies and compositions resulting from such modifications are contemplated and encompassed by the present disclosure. Examples [00143] The following non-limiting examples are illustrative of the present disclosure and/or outline studies conducted pertaining to the present disclosure. [00144] Several coronavirus spike protein fragments (spike protein antigens) were used in the Examples described below. Table 1 provides a list of spike protein fragments used in these studies. [00145] Table 1. Coronavirus spike protein fragments used for library selection, binding and epitope study experiments Reference Accession describing
Figure imgf000042_0001
RBD/SD1 (aa319-591) b Wrapp et al., (Wuhan) QHD43416.1 NRC 6xHis 2020
Figure imgf000043_0001
t SARS-CoV S AAU04646.1 NRC F Galipeau et al., Cive 1 a b LAG-Dual Strep-6xHis 2021 na, not
Figure imgf000044_0001
applicable Example 1: Antigen Validation Introduction [00146] Prior to use in library selection (panning) experiments, four SARS-CoV-2 spike protein antigens (S, S1, S1-RBD, and S2, as described in Table 1) were validated for structural integrity and functionality in adsorbed/captured states on microtiter wells by standard ELISA. Unless stated otherwise, all spike protein fragments used in the following Examples were produced as described in Stuible et al., 2021. Materials and Methods [00147] Binding to cognate human angiotensin converting enzyme (ACE2) receptor [00148] ELISA was performed to determine if spike proteins were able to bind to human ACE2 when passively adsorbed (S, S1, S1-RBD and S2) or captured (S1, S1-RBD) on microtiter wells. For passive adsorption, wells of NUNC® Immulon 4 HBX MaxiSorp™ microtiter plates (Thermo Fisher, Cat#3855) were coated with 50 ng of SARS-CoV-2 spike proteins (S, S1, S2, S1-RBD) in 100 µL PBS overnight at 4°C. Following removal of protein solutions and three washes with PBST (PBS supplemented with 0.05% [v/v] Tween® 20), wells were blocked with PBSC (1% [w/v] casein [SIGMA, Cat#E3414] in PBS) at room temperature for 1 h. For capturing, in vivo biotinylated fragments harboring the AviTagTM (AviTag-S1, AviTag-S1-RBD) were diluted in PBS and added at 50 ng/well (100 µL) to pre-blocked Streptavidin Coated High Capacity Strip wells (Thermo Fisher, Cat#15501). After 1 h incubation at room temperature, wells were washed five times with PBST and incubated for an additional hour with 100 µL/well of 2-fold serially diluted ACE2-Fc (human ACE2 fused to human IgG1 Fc domain; ACROBiosystems, Cat#AC2- H5257) in PBSTC (PBS/0.2% casein/0.1% Tween® 20). Wells were washed five times and incubated for 1 h with 1 µg/mL HRP-conjugated goat anti-human IgG (SIGMA, Cat#A0170). Wells were washed 10 times and incubated with 100 µL peroxidase substrate solution (SeraCare, Cat#50-76-00) at room temperature for 15 min. Reactions were stopped by adding 50 µL 1 M H2SO4 to wells, and absorbance were subsequently measured at 450 nm using a Multiskan™ FC photometer (Thermo Fisher). [00149] Binding to cognate anti-spike protein polyclonal antibody [00150] The four spike antigens were passively adsorbed as described above. After blocking with PBSC, wells were emptied, washed five times and incubated at room temperature for 1 h with 100 µL of 1 µg/mL anti-SARS-CoV-2 spike rabbit polyclonal antibody (Sino Biologicals, Cat#40589- T62) in PBSCT. Following 10 washes with PBST, wells were incubated with 100 µL 1/2500 dilution (320 ng/mL) of goat anti-rabbit:HRP (Jackson Immunoresearch, Cat#111-035-144) in PBSCT for 1 h at room temperature. After 1 h incubation and final five washes with PBST, the peroxidase activity was determined as described above. Results and Discussion [00151] The passively adsorbed spike fragments, S, S1, S1-RBD, as well as the streptavidin- captured fragments, AviTag-S1-RBD and AviTag-S1, were found to bind to ACE2 with similarly high affinities (EC50 = 0.10 – 0.32 nM; Fig.1A, Table 2). As expected, the S2 subunit of the spike protein did not bind to ACE2. Additionally, as shown in Fig. 1B and Table 3, all four spike fragments in passively-adsorbed states (S, S1, S2, and S1-RBD), bound with high affinity (EC50 = 0.34 – 0.65 nM) to a polyclonal antibody known to be specific for SARS-CoV-2 spike protein; confirming the structural integrity/identity of the spike protein fragments. The ELISA data demonstrate that the various spike fragments tested should maintain their natural and intact structures in passively-adsorbed and captured states during panning experiments. [00152] Table 2: Binding affinity (EC50) of passively absorbed spike fragments and streptavidin- captured spike fragments to ACE2 Antigen S S1 S2 S1-RBD AviTag-S1-RBD AviTag-S1 “nb”
Figure imgf000046_0001
[00153] Table 3: Binding affinity (EC50) of passively absorbed spike fragments to a polyclonal antibody known to be specific for SARS-CoV-2 spike protein Antigen S S1 S2 S1-RBD
Figure imgf000046_0002
Example 2: Llama Immunization and Serum Analyses Introduction [00154] As described below, two llamas were immunized with SARS-CoV-2 S or S/S1-RBD to trigger the generation of a diverse pool of antibodies targeting manifold sites over the surface of S, and targeting the S1-RBD sub-domain of S which is used by the virus to start the process of host cell infection through interaction with the ACE2 receptor. Llama sera were assessed by ELISAs for generation of immune responses against SARS-CoV-2 spike proteins, and by flow cytometry surrogate neutralization assays for generation of neutralizing antibodies. Materials and Methods [00155] Llama immunization [00156] Immunizations were performed at Cedarlane Laboratories (Burlington, ON, Canada) and essentially as described (Hussack et al., 2011). One llama (Eva Green) was immunized with 100 g of S in 500 µL PBS combined with 500 µL of Freund’s complete adjuvant on day 0, followed by immunization with 70 g of S1-RBD (ACROBiosystems, Cat#SPD-S52H6) in Freund’s incomplete adjuvant on each of days 7, 14, and 21. Bleeds were taken at days 0, 21, and 28. A second llama (Maple Red) was immunized with 100 g of S in 500 µL PBS combined with 500 µL of Freund’s complete adjuvant on day 0, followed by immunization with 100 g of S mixed with Freund’s incomplete adjuvant on day 7, and immunization with 50 g of S mixed with Freund’s incomplete adjuvant on each of days 14 and 21. [00157] Serum ELISA [00158] Llama sera were tested for antigen-specific immune response by ELISA essentially as described (Hussack et al., 2011; Henry et al., 2016). Briefly, dilutions of sera in PBST were added to wells pre-coated with S, S1, S2 or S1-RBD. Negative antigen control wells were pre-coated with casein (100 µL of 1% v/w) or recombinant human dipeptidase 1 ectodomain, DPEP1 (50 ng/well; Sino Biological, Cat#13543-H08H). Following 1 h incubation at room temperature, wells were washed 10 times with PBST and incubated with HRP-conjugated polyclonal goat anti-llama IgG heavy and light chain antibody (Bethyl, Cat#A160-100P) for 1 h at room temperature. After 10 washes, the peroxidase activity was determined as described above. [00159] Serum surrogate neutralization assay by flow cytometry [00160] Trimeric SARS-CoV-2 S was chemically biotinylated using EZ-Link™ NHS-LC-LC- Biotin following manufacturer’s instructions (Thermo Fisher, Cat#21343). Vero E6 cells (ATCC, Cat#CRL-1586) were maintained according to ATCC protocols. Briefly, cells were grown to confluency in DMEM medium (Thermo Fisher, Cat#11965084) supplemented with 10% heat inactivated FBS (Thermo Fisher, Cat#10438034) and 2 mM GlutamaxTM (Thermofisher, Cat#35050061) at 37°C in a humidified 5% CO2 atmosphere in T75 flasks. For flow cytometry experiments, cells were harvested by AccutaseTM (Thermo Fisher, Cat#A111050) treatment, washed once by centrifugation, and resuspended at 1 106 cells/mL in PBSB (PBS containing 1% BSA) and 0.05% [v/v] sodium azide [SIGMA, Cat#S2002]). Cells were kept on ice until use. To determine the presence of neutralizing antibodies in the immune sera of llamas, 400 ng of chemically biotinylated trimeric SARS-CoV-2 S was mixed with 5 104 Vero E6 cells in the presence of 2-fold dilutions of sera (pre immune, day 21 and day 28 serum) in a final volume of 150 µL. Following 1 h of incubation on ice, cells were washed twice with PBSB by centrifugation for 5 min at 1200 rpm and then incubated for an additional hour with 50 µL of Streptavidin, R- Phycoerythrin Conjugate (SAPE, ThermoFisher, Cat# S866) at 250 ng/mL diluted in PBSB. After a final wash, cells were resuspended in 100 µL PBSB and data were acquired on a CytoFLEX® S flow cytometer (Beckman Coulter, Brea, CA) and analyzed by FlowJoTM software (FlowJo LLC, v10.6.2, Ashland, OR). Percent inhibition (neutralization) was calculated according to the following formula: % inhibition = 100 x [1 - (Fn - Fmin) / (Fmax - Fmin)], where, Fn is the measured fluorescence at any given competitor serum dilution, Fmin is the baseline fluorescence measured in the presence of cells and SAPE only, and Fmax is the maximum fluorescence, measured in the absence of competitor serum. Results and Discussion [00161] The results of ELISAs performed with pre-immune (day 0) and immune (day 21 and 28) sera demonstrate that both llamas generated a strong immune response against target immunogens S, S1, S2 and S1-RBD (Fig. 2A). Based on EC50 values, which indicate the strength of immune responses, Eva Green generated a stronger immune response, up to 10-fold stronger, than Maple Red consistently across all four spike fragments (Fig.2A; Table 4). Further, the immune responses were specific for SARS-CoV-2 antigens, as sera from day 0, 21 and 28 did not react with casein or DPEP1. Interestingly, one initial injection of S was enough to develop a strong, maximum immune response against S2 by Eva Green. Llama sera were also assessed by flow cytometry surrogate neutralization assays for generation of neutralizing antibodies, i.e., antibodies that block the interaction between the trimeric SARS-CoV-2 S and ACE2 displayed on the surface of Vero E6 cells. As shown in Fig. 2B and Table 5, inhibition serum titers of 3300 (Day 21) and 6200 (Day 28) reciprocal serum dilution (RSD) were obtained in the case of Eva Green sera whereas weaker inhibition serum titers, <200 (Day 21) and <400 RSD (Day 28), were obtained for Maple Red. [00162] Table 4. ELISA results summarizing day 0, 21 and 28 binding serum titers (EC50s) of Eva Green and Maple Red llamas against spike protein fragments S, S1, S2 and S1-RBD Llama Day Binding serum titer, EC50 (reciprocal serum dilution) S S1 S2 S1-RBD
Figure imgf000049_0001
[00163] Table 5. Flow cytometry-based surrogate virus neutralization assay results summarizing day 21 and 28 inhibition serum titers (IC50s) of Eva Green and Maple Red llamas using spike protein S as surrogate for the virus Llama Inhibition serum titer, IC50 (reciprocal serum dilution)
Figure imgf000049_0002
Example 3: Phage Display Library Construction, Selection and Screening Introduction [00164] Two libraries (Eva Green and Maple Red) were constructed and subjected to selection against spike protein fragments. Selection and screening efforts were aimed at isolating not only S1-RBD binders, but also S1-NTD and S2 binders, as recent findings indicate that in addition to S1-RBD binders, S1-NTD and S2 binders could also be neutralizing (Rogers et al., 2020; Ravichandran et al., 2020). To this end, two libraries were generated and were selected under six different conditions to maximize the number and epitopic diversity of hits against S1-RBD, S1- NTD and S2. After two rounds of selection, monoclonal phages ELISA and DNA sequencing were performed to identify antigen-specific hits. Materials and Methods [00165] Phage display library construction [00166] On day 28, 100 mL of blood from each of the two llamas was drawn and peripheral blood mononuclear cells (PBMCs) were purified by Ficoll® gradient at Cedarlane Laboratories (Burlington, ON, Canada). Two independent phage-displayed VH/VHH libraries were constructed from 5 × 107 PBMCs as described previously (Henry et al., 2016; Rossotti et al., 2015; Henry et al., 2015). Total RNA was extracted from PBMCs using TRIzol™ Plus RNA Purification Kit (Thermo Fisher, Cat#12183555) following manufacturer’s instructions and used to reverse transcribe cDNA with SuperScript™ IV VILO™ Master Mix supplemented with random hexamer (Thermofisher, Cat#SO142) and oligo (dT) (Thermofisher, Cat#AM5730G) primers. VH/VHH genes were amplified using semi-nested PCR and cloned into the phagemid vector pMED1, followed by transformation of E. coli TG1 to construct two libraries with sizes of 1 × 107 and 2 × 107 independent transformants for Eva Green and Maple Red, respectively. Both libraries showed an insert rate of 95%, as verified by DNA sequencing. Phage particles displaying the VHs/VHHs were rescued from E. coli cell libraries using M13K07 helper phage (New England Biolabs, Cat#N0315S) as described in Hussack et al., 2011 and used for selection experiments described below. [00167] Library selection and screening [00168] Library selections (pannings) and screenings were performed essentially as described (Hussack et al., 2011; Rossotti et al., 2015). Library selections were performed on microtiter wells under 6 different phage binding/elution conditions designated PI - P6. Briefly, for the phage binding step, library phages were diluted at 1 x 1011 colony-forming units (cfu)/mL in PBSBT [PBS supplemented with 1% [w/v] BSA and 0.05% Tween® 20] and incubated in antigen-coated microtiter wells for 2 h at 4°C. For PI - P4, phages were added to wells with passively-adsorbed S (10 pg/well; PI), passively-adsorbed S2 (10 pg/well; P2), streptavidin-captured biotinylated SI (0.5 pg/well; P3) and streptavidin-captured biotinylated Sl-RBD (0.5 pg/well; P4). For P5, phages were pre-absorbed on passively-adsorbed Sl-RBD wells (10 pg/well) for 1 h at 4°C and then the unbound phage in the solution was transferred to wells with streptavidin-captured biotinylated SI (0.5 pg/well) in the presence of non-biotinylated Sl-RBD competitor in solution (10 pg/well). Following the binding stage (PI - P5), wells were washed 10 times with PBST and bound phages were eluted by treatment with 100 mM glycine pH 2.2 for 10 min at room temperature, followed by immediate neutralization of phages with 2 M Tris. Similar to P4, in P6, phages were bound on streptavidin-captured biotinylated Sl-RBD but elution of bound phages were carried out competitively with 50 nM ACE2-Fc following the washing step. For all pannings, a small aliquot of eluted phage was used to determine their titer on LB-agar/ampicillin plates and the remaining were used for their subsequent amplification in E.coli TGI strain (Hussack et al., 2011). The amplified phages were used as input for the next round of selection as described above.
[00169] After two rounds of selection, 16 (Eva Green) or 12 (Maple Red) colonies from each of the PI - P6 selections were screened for antigen binding by monoclonal phage ELISA against S, SI, S2 and Sl-RBD. Individual colonies from eluted-phage titer plates were grown in 96 deep well plates in 0.5 mL 2YT media/100 pg/mL-carbenicillin/1 % (w/v) glucose at 37°C and 250 rpm to an OD600 of 0.5. Then, 1010 cfu M13K07 helper phage was added to each well and incubation continued for another 30 min under the same conditions. Cells were subsequently pelleted by centrifugation, the supernatant was discarded and the bacterial pellets were resuspended in 500 pL 2YT/100 pg/mL carbencillin/50 pg/mL kanamycin and incubated overnight at 28°C. Next day, phage supernatants were recovered by centrifugation, diluted 3-fold in PBSTC and used in subsequent screening assays by ELISA. To this end, antigens were coated onto microtiter wells at 50 ng/well overnight at 4°C. Next day, plates were blocked with PBSC, washed five times with PBSTC, and 100 pL of phage supernatants prepared above were added to wells, followed by incubation for 1 h at room temperature in an orbital shaking platform. After 10 washes, binding of phages was detected by adding 100 µL/well of anti-M13:HRP (Santa Cruz, Cat#SC-53004HRP) at 40 ng/mL in PBSTC and incubating as above. After 10 washes, the peroxidase activity was determined as described previously. Following confirmation of success of library panning as determined by monoclonal phages ELISA, a total of 1200 individual clones ( 100 clones per panning strategy; 600 clones per library) were colony-PCRed and subsequently sequenced, resulting in the identification of 35 (Eva Green) and 12 (Maple Red) potential spike-specific VHH antibodies. Results and Discussion [00170] Eva Green and Maple Red libraries were constructed with functional sizes (library sizes corrected for insert rate) of ~1 x 107 and ~2 x 107, respectively. Two rounds of selection under six different panning conditions (P1 – P6) were subsequently performed for both libraries. To confirm the success of selection in enriching for binders, samples of 12-16 clones per panning condition were tested for binding against S, S1, S2 and S1-RBD by phage ELISA. The frequent occurrence of positive clones determined by monoclonal phage ELISA confirmed selections efficiently enriched for binders. Specificity patterns observed, i.e., binding against S vs S1 vs. S2 vs S1-RBD, in sample sets reflected the selection strategy as well as the immunization strategy (Eva Green was immunized with S once but predominantly [three times] with S1-RBD). In P3, P4 and P6, as expected based on the selection strategy, essentially all binders were S1-RBD specific. For Maple Red, the immunization with the whole spike S generated a strong bias against non-S1-RBD- specific antibodies, an observation recently seen with patients recovered from SARS-CoV-2 natural infection (Rogers et al., 2020) and rabbits immunized with SARS-CoV-2 S (Ravichandran et al.. 2020). Panning against S (P1) essentially produced S2 binders as opposed to S1-RBD binders seen in the case of Eva Green library. Additionally, in contrast to what was observed in the case of the Eva Green, for the Maple Red P3 strategy, where panning was performed against S1, half of the binders tested were specific for non-S1-RBD region of S1. Nonetheless when selections were specifically directed towards S1-RBD binders, as in the P4 and P6 selection strategies, all tested binders were S1-RBD specific. Additionally, the P5 strategy almost exclusively selected for VHHs specific to non-RBD region of the S1 subunit. In summary, the immunization strategy was a key determinant of the outcome of in vivo generated VHHs with respect to spike subunit/domain specificity, and in vitro directed selection strategies effectively yielded intended binding specificities. Subsequently, a larger number of clones, >600 clones per library, were screened by DNA sequencing to obtain a large pool of potential binders. The unique sequences were subjected to binding validation, as described below. Example 4: VHH Cloning/Expression in E. coli, Stability/Affinity Validation and Cross- Reactivity Studies Introduction [00171] Hits identified by monoclonal phage ELISA and DNA sequencing were cloned into the expression vector pMRo.BAP.H6 (Rossotti et al., 2019), produced as His6-tagged VHHs in the periplasmic space of E. coli BL21(DE3) and purified by immobilized metal-ion affinity chromatography (IMAC). VHHs were subsequently validated for binding and further explored for cross-reactivity soluble ELISA against SARS-CoV-2, SARS-CoV and MERS-CoV spike proteins. Additionally, VHHs were validated for aggregation resistance by size exclusion chromatography (SEC) and thermostability by circular dichroism Tm measurement assays. Lead VHHs were produced in mammalian cells in fusion with human IgG1 Fc and were subsequently tested in a comprehensive cross-reactivity ELISA against a collection of various coronavirus spike proteins (S). Materials and Methods [00172] DNA sequence analysis and VHH production in E. coli [00173] Colonies were analyzed by DNA sequencing and identified VHH sequences were aligned using IMGT system. VHHs were subsequently cloned into pET expression vector (Novagen, Madison, WI) for their production in BL21(DE3) E.coli as monomeric soluble protein (Rosotti et al., 2019). Briefly, individual colonies were cultured overnight in 10 mL of LB supplemented with 50 µg/mL of kanamycin (LB/Kan) at 37°C and 250 rpm. After 16 h, cultures were added to 250 mL LB/Kan and grown to an OD600 of 0.6. Expression of VHHs was induced with 10 µM of IPTG (isopropyl -D-1-thiogalactopyranoside) overnight at 28°C and 250 rpm. The following day, bacterial pellets were harvested by centrifugation at 6,000 rpm for 15 min at 4°C and VH/VHHs were extracted by sonication and purified by IMAC as described previously (Rosotti et al., 2019). In addition, for ELISA (see below), a small fraction was biotinylated by incubating 1 mg of purified VHHs with 10 µM of ATP (Alfa Aesar, Cat#CAAAJ61125-09), 100 µM of D-(+)-biotin (VWR, Cat#97061-446) and a bacterial cell extract overexpressing E.coli BirA as described previously (Rossotti et al., 2015b). The same procedure was followed to produce a biotinylated VHH-72 benchmark VHH (Wrapp et al., 2020), a SARS-CoV spike protein-specific VHH that cross-reacts with the SARS-CoV-2 spike protein receptor binding domain. [00174] VHH binding validation and preliminary cross-reactivity studies by ELISA [00175] Binding validation studies were performed with S1-RBD-specific clones. Briefly, microtiter well plates were coated with 50 ng/well SARS-CoV-2 S1-RBD in 100 µL PBS overnight at 4 . Plates were blocked with PBSC for 1 h at room temperature, then washed five times with PBST and incubated with decreasing concentrations of biotinylated VHHs. After 1 h incubation, plates were washed 10 times with PBST and binding of VHHs was probed using HRP- streptavidin (Jackson ImmunoResearch, Cat#016-030-084). Finally, plates were washed 10 times with PBST and peroxidase activity was determined as described above. [00176] Stability determinations by size exclusion chromatography (SEC) and circular dichroism [00177] Purified VHHs were subjected to SEC to validate their aggregation resistance. Briefly, 2 mg of each affinity purified VHH was injected into Superdex™ 75 GL column (Cytiva) connected to an ÄKTA FPLC protein purification system (Cytiva) as previously described (Henry et al., 2017). PBS was used as running buffer at 0.8 mL/min. Fractions corresponding to the monomeric peak were pooled and stored at 4°C until use. To determine thermostability, VHH Tms were measured by circular dichroism as previously described (Henry et al., 2017). Ellipticity of VHHs were determined at 200 µg/mL VHH concentrations and 205 nm wavelength in 100 mM sodium phosphate buffer, pH 7.4. Ellipticity measurements were normalized to percentage scale and Tms were determined from plot of % folded vs temperature and fitting the data to a Boltzmann distribution. [00178] Production of VHHs in mammalian cells in fusion with human IgG1 Fc [00179] Codon-optimized genes for bivalent VHH-Fcs were synthesized (GenScript). For heterodimeric monovalent VHH-Fcs, VHH genes were PCR amplified as described previously and cloned into pTT5-hIgG1Fc between the genes for human VH leader sequence and the human IgG1 hinge/Fc sequences, using NarI/HindIII restriction sites. Bivalent VHH-Fcs were produced by transient transfection of HEK293-6E cells followed by protein A affinity chromatography as previously described (Rosotti et al., 2019). Heterodimeric monovalent VHH-Fcs were produced by co-transfection of HEK293-6E cells with two pTT5 vectors, one encoding for a 6xHis-tagged heavy chain (VHH1-hinge-CH2-CH3-His6), the other for a non-tagged heavy chain of a different VHH (VHH2-hinge-CH2-CH3). The heterodimeric antibodies were purified by sequential protein A affinity chromatography and IMAC. For IMAC, antibodies were eluted using a linear 0 - 0.5 M imidazole gradient over 20 column volumes to separate species bearing one 6×His tag (heterodimeric, monovalent) from those bearing two 6×His tags (homodimeric, bivalent). Proteins were buffer exchanged using Amicon® Ultra-15 Centrifugal Filter Units (Millipore, Cat#UFC905024) with phosphate-buffered saline (PBS), pH 7.4. The same procedure was applied for the generation of the reference bio-VHH-72 and VHH-72-Fc using the sequence published by Wrapp et al., 2020. The sequence of the VHH was ordered as GeneBlock (IDT DNA) flanked by SfiI sites for cloning into pMRo.BAP.H6, and NarI/HindIII for cloning into pTT5-hIgG1Fc. Protein purity was evaluated by SDS-PAGE using 4–20% Mini-PROTEAN® TGX Stain-Free™ Gels (Bio-Rad, Cat#17000435). [00180] VHH-Fc comprehensive cross-reactivity studies by ELISA [00181] Recombinant coronavirus spike proteins S (Table 1) were coated overnight onto NUNC® MaxiSorp™ 4BX plates (Thermo Fisher) at 50 ng/well in 100 µL of PBS, pH 7.4. The next day, plates were blocked with 200 µL PBSC for 1 h at room temperature, then washed five times with PBST and incubated at room temperature for 1 h on rocking platform at 80 rpm with 1 µg/mL VHH-Fc diluted in PBSTC. Plates were washed five times with PBSTC and binding of VHH-Fcs was detected using 1 µg/mL HRP-conjugated goat anti-human IgG. Finally plates were washed five times and peroxidase (HRP) activity was measured as described above. Results and Discussion [00182] A total of ~1200 colonies were analyzed by DNA sequencing. Forty seven potential VHH binders were identified from the two libraries (35 from the Eva Green and 12 from the Maple Red library) by phage ELISA and DNA sequencing, with the vast majority (35 VHHs) coming from the Eva Green library (Tables 6 and 7). Some VHHs may be clonally related due to their high sequence identity in their CDRs. Examples include NRCoV2-1a, NRCoV2-1c and NRCoV2-1d from the Eva Green library (Table 6) and NRCoV2-MRed02 and NRCoV2-MRed04 from the Maple Red library (Table 7). VHH hits were cloned in E. coli, confirmed by DNA sequencing, and expressed and purified by IMAC. Following expression of VHHs, the binding of a sample set of VHHs was validated by ELISA. Affinities, expressed as EC50s, were high, ranging from 0.4 to 7.2 nM (data not shown). VHHs were also tested for aggregation resistance and stability, and cross-reactivity. [00183] Aggregation resistance and stability are desirable attributes of biotherapeutics, as they affect both efficacy and manufacturability. By size exclusion chromatography, all VHHs tested were found to be aggregation resistant (Figs.4A and 4B), except for NRCoV2-08, which showed some degree of aggregation The VHHs were also tested for thermal stability and found to be highly thermostable. With the exception of NRCoV2-11, which had a relatively lower Tm of 60.4°C, the remaining 25 VHHs tested had Tms higher than 65°C, with a Tm range and median of 65.5 – 79.8°C and 70.4°C, respectively (Figs.5A and 5B). Many VHHs had Tms that were higher than that of the VHH-72 benchmark (73.0°C). VHHs with antigen binding activity were produced as monomeric and dimeric VHH-Fcs for subsequent binding and neutralization assays. The schematic formats of these fusion molecules are depicted in Fig.3. [00184] The results of cross-reactivity studies using SARS-CoV-2 variants and various coronaviruses are shown in Fig.6A and 6B. Initial experiments showed that for the UK (Alpha) and South Africa (Beta) variants of SARS-CoV-2, eight out of nine S1-NTD-specific VHHs tested were cross-reactive to both variants (Fig.6A). In the case of S1-RBD-specific VHHs, 15/20 cross- reacted to both variants and an additional four cross-reacted with the UK variant. Only one (NRCoV2-08) VHH was not cross-reactive at all. Additionally, one S1-NTD-specific VHH, six S1- RBD-specfic and eight S2-specific VHHs cross-reacted with SARS-CoV. Many antibodies also cross-reacted with pangolin CoV, with fewer, but still significant, numbers cross-reacting to SARS-like CoV W1V1, bat SARS-like CoV and civet SARS-CoV with similar cross-reactivity patterns. None of the antibodies tested cross-reacted with Swine deltaCoV, Avian IBV, hedgehog CoV HKU31, Bat CoV HKU9, Bat 229E-related CoV, bat CoV 512, human MERS betaCoV Jordan, human CoV-NL63, Human CoV-OC43 or human CoV-HKU1. [00185] In a subsequent experiment (results shown in Fig. 6B), VHHs were examined for cross- reactivity to a collection of spike glycoproteins from various coronavirus genera and SARS-CoV- 2 variants by ELISA (Fig. 6B) and SPR (Tables 11 and 12), many VHH-Fcs cross-reacted with the S protein from variants Alpha, Beta, Gamma, Delta and Kappa (B.1.617.1; Variant Being Monitored [VBM]). The exceptions were: 1) RBD-specific VHHs NRCoV2-02/ NRCoV2-05 did not cross-react with Beta and Gamma and NRCoV2-04/ NRCoV2-14/ NRCoV2-15, did not cross- react with Kappa and 2) S2-specific VHHs NRCoV2-MRed18 and NRCoV2-MRed19 did not cross-react with Kappa. All nine NTD-specific VHHs cross-reacted with all variants tested. Additionally, many VHHs cross-reacted with pangolin CoV, with fewer cross-reacting to SARS- CoV, SARS-like CoV WIV1, bat SARS-like CoV and civet SARS CoV. These viruses, including variants, are all of the Betacoronavirus Sarbecovirus subgenus. None of the antibodies tested cross- reacted with the remaining 11 non-Sarbecovirus Betacoronavirus, or with Alphacoronavirus, Deltacoronavirus or Gammacoronavirus. 29 VHHs cross-reacted with the Omicron variant (Fig. 6B). The broadly cross-reactive antibodies included VHHs targeting all three regions of the S protein (RBD, NTD, S2). The most broadly cross-reactive VHHs recognizing 10 – 12 viruses, including SARS-CoV-2 variants, were two NTD binders (NRCoV2-SR01, NRCoV2-SR02), six RBD binders (NRCoV2-1d, NRCoV2-07, NRCoV2-11, NRCoV2-12, NRCoV2-20, NRCoV2- MRed04) and six S2 binders (NRCoV2-S2F3, NRCoV2-S2G3, NRCoV2-S2G4, NRCoV2- MRed18, NRCoV2-MRed19, NRCoV2-MRed20). The VHH-72 benchmark was also broadly cross-reactive. The panel of VHHs had similar cross-reactivity profiles to human ACE2, except that ACE2 did not bind civet SARS-CoV S and, unsurprisingly, bound HCoV-NL63 S. [00186] When tested by SPR against SARS-CoV, 12 out of 14 ELISA-positive VHHs cross- reacted with SARS-CoV S, most with comparably high affinities (Table 11. Seven of these VHHs were S2-specific, four were RBD-specific and one was NTD-specific. Against the Alpha and Beta variants, the SPR cross-reactivity data, performed with 37 VHHs, were consistent with ELISA, except for NRCoV2-04 and NRCoV2-14, which were negative or very weak for binding to the Beta variant by SPR (Tables 11 and 12). All 37 VHHs tested bound the Alpha variant S protein, and 34 were also cross-reactive to the Beta variant S protein (Figs.28A (Alpha) and 28B (Beta); Fig.29; Table 11; Table 12). Thirteen out of 17 RBD-specific VHHs bound all three variants with similar affinities, except for VHHs NRCoV2-10, NRCoV2-15 and NRCoV2-17 which bound to the Beta variant with 40 – 50-fold weaker affinity; the remaining four that did not bind the Beta variant showed cross-reactivity with the Alpha variant with similar (NRCoV2-04, NRCoV2-14) or reduced (~5-fold [NRCoV2-05] and ~20-fold [NRCoV2-02]) affinity relative to the Wuhan variant. All NTD-specific and S2-specific VHHs cross-reacted with the three variants with essentially the same or similar affinities. [00187] The cross-reactivity of the VHHs and VHH-Fcs is significant, as it is believed that the progenitor of SARS-CoV was generated by recombination among bat SARS-like coronaviruses that spread to humans via civet cat as an intermediate host (Zheng et al, 2020). Further, most new emerging viruses are derived from strains circulating in zoonotic reservoirs. Antibodies that can cross-react against a variety of animal and human coronaviruses have potential to be used for detection and/or treatment of emerging coronavirus outbreaks.
Figure imgf000059_0001
Figure imgf000060_0001
, 4 e k P i p
Figure imgf000061_0001
Example 5: Binding characteristics of VHHs and VHH-Fcs: Surface Plasmon Resonance (SPR) and ELISA Binding Studies Introduction [00190] Binding of anti-SARS-CoV-2 VHHs against various SARS-CoV-2 spike protein fragments (Wuhan) was assayed using SPR and ELISA to determine their affinity and domain/sub- domain specificity. Binding of VHHs against SARS-CoV, SARS-CoV-2 UK (Alpha) variant and SARS-CoV-2 South African (Beta) variant spike protein S was also carried out to determine their virus cross-reactivity patterns. Materials and Methods [00191] Affinity/specificity determination of VHHs against SARS-CoV spike (S), SARS-CoV-2 spike (S) and SARS-CoV-2 spike fragments by SPR [00192] Standard SPR techniques were used for binding studies. All SPR assays were performed on a BiacoreTM T200 instrument (Cytiva) at 25°C with HBS-EP running buffer (10 mM HEPES, 150 mM NaCl, 3 mM EDTA, 0.005 % [v/v] Tween® 20, pH 7.4) and CM5 sensor chips (Cytiva). Prior to SPR analyses all analytes in flow (VHHs, ACE2 receptor) were SEC-purified on a SuperdexTM 75 Increase 10/300 GL column (Cytiva) in HBS-EP buffer at a flow rate of 0.8 mL/min to obtain monomeric proteins. SARS-CoV spike (S), SARS-CoV-2 spike trimer (S) and various SARS-CoV-2 spike fragments were immobilized on CM5 sensor chips through standard amine coupling (10 mM acetate buffer, pH 4.0; Cytiva). On the first sensor chip, 1983 response units (RUs) of SARS-CoV spike (Sino Biologicals, Cat# 40634-V08B), 843 RUs of SARS-CoV- 2 S1-RBD fused to human Fc (S1-RBD-Fc) and 972 RUs of EGFR (irrelevant control surface) were immobilized. On a second sensor chip, 2346 RUs of SARS-CoV-2 S, 1141 RUs of SARS- CoV-2 S1 subunit and 1028 RUs of SARS-CoV-2 S2 subunit were immobilized. The theoretical maximum binding response for VHHs binding to these surfaces ranged from 224 – 262 RUs. An ethanolamine blocked surface on each sensor chip served as a reference. Single cycle kinetics was used to determine VHH and ACE2 binding kinetics and affinities. VHHs at various concentration ranges (from 0.25 – 4 nM to 125 – 2000 nM) were flowed over all surfaces at a flow rate of 40 µL/min with 180 s of contact time and 600 s of dissociation time. Surfaces were regenerated with a 12 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 100 µL/min. Injection of EGFR-specific VHH EK2 served as a negative control for the SARS-CoV and SARS-CoV-2 surfaces and as a positive control for the EGFR surface. The ACE2 affinity was determined using similar conditions by flowing a range of monomeric ACE2 concentrations (31.53 – 500 nM). All affinities were calculated by fitting reference flow cell-subtracted data to a 1:1 interaction model using BIAevaluation Software v3.0 (Cytiva). [00193] For VHH 12 and MRed05, VHH-Fc formats were used in SPR experiments. Approximately 200 RUs of VHH-Fcs (2 µg/mL) were captured on goat anti-human IgG surfaces (4000 RUs, Jackson ImmunoResearch, Cat#109-005-098) at a flow rate of 10 µL/min for 30 s. A range of SEC-purified RBD fragments (Table 1; SARS-CoV, Wuhan, Alpha and Beta) at 0.62 – 10 nM were flowed over the captured VHH-Fc at a flow rate of 40 µL/min with 180 s of contact time and 300 s of dissociation. Surfaces were regenerated with a 120 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 50 µL/min. Affinities were calculated from reference flow cell subtracted sensorgrams as described above. [00194] Domain specificity determination of VHHs by ELISA. [00195] VHHs that bound to the S1 subunit but not its S1-RBD domain in SPR assays, were further examined by ELISA to determine if they were binding to the S1-NTD domain of S1. Briefly, S, S1, S1-NTD and S1-RBD were coated onto NUNC® MaxiSorp™ 4BX plates (Thermo Fisher) at 100 ng/well in 100 µL PBS, pH 7.4. The next day, plates were blocked with 200 µL PBSC for 1 h at room temperature, then washed five times with PBST and incubated with fixed (13 nM) or decreasing concentrations of VHH-Fcs diluted in PBSTC. After 1 h, plates were washed 10 times with PBSTC and binding of VHH-Fc fusions was detected by incubating wells with 100 µL of 1 µg/mL HRP-conjugated goat anti-human IgG. Finally, plates were washed 10 times with PBST and peroxidase activity was determined as described above. EC50s for the binding of VHH- Fcs to S and S fragments were obtained from the plot of A450 nm (binding) vs VHH-Fc concentration. S1-NTD covering amino acids 16-305 of SARS-CoV-2 S (GenBank accession number: QHD43416.1) was expressed in CHO cells. [00196] Affinity/specificity determination of VHHs against spike protein S from SARS-CoV-2 Wuhan, UK (Alpha) and South African (Beta) variants by SPR [00197] Affinity and specificity of VHHs against spike protein S from SARS-CoV-2 Wuhan, UK and South African variants by SPR was determined essentially as described above. Results and Discussion [00198] VHHs were tested by SPR against SARS-CoV-2 S, S1, S1-RBD and S2 to determine their affinity and domain/sub-domain specificity. Binding data are presented in Fig. 6C, Figs. 7A-B, Table 8 and Table 9. In SPR binding assays, NRCoV2-SR01, NRCoV2-SR02, NRCoV2-SR03, NRCoV2-SR04, NRCoV2-SR13, NRCoV2-SR16, NRCoV2-MRed03, NRCoV2-MRed06 and NRCoV2-MRed07 bound to the S1 subunit but not to its S1-RBD domain. Subsequent ELISAs performed against SARS-CoV-2 S, S1, S1-NTD and S1-RBD showed these VHHs were S1-NTD- specific (Figs. 6D and 6E and Table 10). VHHs displayed high affinity towards their target (i.e., S) with the vast majority having KDs in the range of single-digit-nM to pM. Three clusters of VHHs based on domain/subdomain specificity were identified: (i) S1-RBD-specific VHHs; (ii) S1-NTD- spepcfic VHHs; and (iii) S2-specific VHHs (Fig.7A). [00199] As for the S1-RBD-specific VHHs, with the exception of NRCoV2-06, which had an affinity of 223 nM (Table 11), the remaining 16 cluster members displayed high affinities ranging from 0.02 - 10 nM, all vastly outperforming the benchmark VHH-72 VHH, which had a KD of 86.2 nM. Nine VHHs were S1-NTD-specific and, similar to S1-RBD-specific VHHs, displayed high affinities (KDs) in the range of 0.1 – 5.2 nM. Lastly, 11 VHHs were S2 subunit-specific, with similarly high affinities (KDs) ranging from 0.09 – 12.8 nM. [00200] VHHs were tested against SARS-CoV (S) in SPR assays for quantitative determination of cross-reactivity. VHHs were first screened for cross-reactivity at fixed concentrations. Twelve out of 37 VHHs screened showed cross-reactivity to SARS-CoV S. These 12 VHHs were subsequently subjected to comprehensive binding analysis against both SARS-CoV S and SARS- CoV-2 S at multiple VHH concentrations. The SPR cross-reactivity results, which agreed with those from ELISAs, are presented in Fig.27 and Table 11. Seven out of the 12 VHHs tested were S2-specific, four were S1-RBD-specific and one was S1-NTD-specific. NRCoV2-MRed04 showed weak binding to SARS-CoV S compared to SARS-CoV-2 S (300 nM for SARS-CoV S vs 1 nM for SARS-CoV-2 S), but the remaining VHHs cross-reacted with high/comparable affinities to both SARS-CoV-2 S and SARS-CoV S. NRCoV2-07, NRCoV2-12, NRCoV2-MRed18, NRCoV2-MRed19 and NRCoV2-MRed20 cross-reacted with SARS-CoV S with relatively lower affinities in comparison to SARS-CoV-2 S, but nonetheless with high absolute affinities in the low nanomolar KD range. The S1-NTD-specific VHH, NRCoV2-SR01, cross-reacted with SARS-CoV S with high affinity (0.15 nM for SARS-CoV S vs 0.56 nM for SARS-CoV-2 S); one S1-RBD- specific VHH, NRCoV2-11, cross-reacted with SARS-CoV S with very high affinity (0.014 nM for SARS-CoV S vs 0.018 nM for SARS-CoV-2 S); and four S2-specific VHHs demonstrated high, comparable affinities to SARS-CoV and SARS-CoV-2 S in the single-digit-nM to pM KD range. [00201] Against the Alpha and Beta variants, SPR cross-reactivity data performed with 37 VHHs, were consistent with ELISA, except for NRCoV2-04 and NRCoV2-14 which were negative or very weak for binding to the Beta variant by SPR. All 37 VHHs tested bound the Alpha variant S protein, 34 of which were also cross-reactive to the Beta variant S protein (Fig.28A, Fig.28B and Table 12). Thirteen out of 17 RBD-specific VHHs bound all three variants with similar affinities, except for VHHs NRCoV2-10, NRCoV2-15 and NRCoV2-17 which bound to the Beta variant with 40 – 50-fold weaker affinity; the remaining four that did not bind the Beta variant showed cross- reactivity with the Alpha variant with similar (NRCoV2-04, NRCoV2-14) or reduced (~5-fold [NRCoV2-05] and ~20-fold [NRCoV2-02]) affinity relative to the Wuhan variant. All NTD- specific and S2-specific VHHs cross-reacted with the three variants with essentially the same or similar affinities.
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Figure imgf000066_0001
Figure imgf000067_0001
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Figure imgf000068_0001
Figure imgf000069_0001
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Figure imgf000070_0001
Figure imgf000070_0002
[00206] Table 12. SPR affinity (KD) of VHHs against trimeric spikes protein S from the Wuhan- Hu-1 (Wuhan), UK B.1.1.7 (Alpha) and South Africa B.1.351 (Beta) SARS-CoV-2 variants Subun KD (nM) VHH/ACE2 it/domain specificity/epitope bin Wuhan Alpha Beta
Figure imgf000072_0001
NRCoV2-S2F3 3.03 +4 +4 NRC V2 MR d18 603 129 648
Figure imgf000073_0001
, p g p p p p shown in Fig.9G. Example 6: Cell Binding Assays by Flow Cytometry Introduction [00207] In the previous Examples, lead VHHs were shown to be binding to SARS-CoV-2 S in its purified form. In this Example, it was confirmed whether the VHHs also bind to SARS-CoV-2 S in its more natural context, i.e., displayed on the cell membrane of CHO cells. Materials and Methods [00208] A stable Chinese hamster ovary (CHO) cell line CHOBRI TM/55E1 (Stuible et al., 2021) overexpressing SARS-CoV-2 S (CHO-S) was grown in BalanCD™ CHO Growth A medium (Irvine Scientific) supplemented with 50 µM of methionine sulfoximine (MSX) at 120 rpm and 37°C in a humidified 5% CO2 atmosphere. When the cell count reached 2 x 106/mL, the expression of the membrane anchored SARS-CoV-2 trimeric spike protein (SmT1, described in Stuible et al, 2021) was induced by adding cumate at 2 µg/mL. Expression was carried out for 48 h at 32 C. For flow cytometry experiments, cells were harvested by centrifugation and resuspended at 1 x 106 cells/mL in PBSB (1% PBS containing 1% BSA and 0.05 [v/v] sodium azide). Cells were kept on ice until use. Serially, three-fold dilutions of VHH-Fcs were prepared in V-Bottom 96-well microtest plates (Globe Scientific, Cat# 120130) and mixed with 50 µL of CHO-S cells. Plates were incubated for 1 h on ice, washed twice with PBSB by centrifugation 5 min at 1200 rpm and then incubated for an additional hour with 50 µL of R-Phycoerythrin AffiniPure F(ab') Fragment Goat Anti-Human IgG (Jackson Immunoresearch, Cat#109-116-170) at 250 ng/mL diluted in PBSB. After a final wash, cells were resuspended in 100 µL PBSB and data were acquired on a Beckman Culter CytoFlex S and analyzed by FlowJo™ (FlowJo LLC, v10.6.2, Ashland). Results and Discussion [00209] Interestingly, four VHH-Fcs (NRCoV2-08, NRCoV2-19, NRCoV2-21, NRCoV2-S202) which bound to SARS-CoV-2 S in purified form did not bind to SARS-CoV-2 S-displaying target cells. The remaining 41 VHH-Fcs, however, bound to cells in a dose dependent manner (Fig.8A- B; Table 13). Aside from NRCoV2-03 which had a modest apparent affinity (EC50app) of ~ 80 nM, the remaining 18 S1-RBD-specific VHH-Fcs bound to S-displaying CHO-S cells with high affinities (EC50 range: 0.3 – 8.1 nM; EC50 median: 1 nM). For S1-NTD-binders, excluding the outlier NRCoV2-MRed07 (EC50 = 132 nM), the apparent EC50s for the remaining VHHs were also high (range: 1.2 – 15.1 nM; median: 7 nM). Similarly, affinities for S2-specific VHH-Fcs were also high (EC50 range: 0.1 – 6.5; EC50 median: 1 nM). VHH-72 benchmark with an EC50 of 0.2 nM ranked amongst the strongest S1-RBD-specific binders. [00210] Table 13. Summary of VHH-Fc bindings to SARS-CoV-2 S expressing CHO-S cells S1-RBD-specific S1-NTD-specific S2-specific x
Figure imgf000074_0001
NRCoV2- 1.3 280 NRCoV2- 10 44 MRed18 0.9 10205
Figure imgf000075_0001
Example 7: Epitope Studies Introduction [00211] Western blotting experiments were performed to determine if VHHs bind to conformational or linear epitopes. Additionally, competitive sandwich ELISA as well as SPR were performed to differentiate VHHs with respect to recognizing non-overlapping epitopes. Materials and Methods [00212] Epitope typing by sodium dodecyl sulphate-polyacrylamide gel electrophoresis/western blotting (SDS-PAGE/WB) [00213] A standard SDS-PAGE/WB was performed to detect the binding of VHHs to nitrocellulose-immobilized, denatured SARS-CoV-2 S. Briefly, 10 µg/lane of S was run on 4–20% Mini-PROTEAN® TGX Stain-Free™ Protein Gels (Bio-Rad, Cat# 4568081), transferred to nitrocellulose (Sigma, Cat#GE10600002) and blocked with 1% PBSC overnight at 4 . Then, 0.5- cm nitrocellulose strips containing the denatured S were placed on Mini Incubation Trays (Bio- Rad, Cat#1703902) and incubated with 1 mL of 1 µg/mL VHH-Fcs or biotinylated VHHs (VHH- BAP-His6). After 1 h incubation at room temperature, strips were washed 10 times with PBST and the binding of VHH-Fcs or biotinylated VHHs to denatured S was probed, respectively, by incubating strips with 1 mL of 100 ng/mL anti-human Ig Fc antibody-peroxidase conjugate or streptavidin-peroxidase conjugate (Jackson ImmunoResearch, Cat#016-030-084) at room temperature for 1 h. Finally, strips were washed 10 times with PBST and peroxidase activity was detected using chemiluminescent reagent (SuperSignalTM West Pico PLUS Chemiluminescent Substrate, ThermoFisher, Cat#34580). Images of developed strips were acquired on Molecular Imager® Gel Doc™ XR System (Bio-Rad, Cat#1708195EDU). [00214] Epitope binning by SPR [00215] Standard SPR techniques were used for binding studies. All SPR assays were performed on a BiacoreTM T200 instrument (Cytiva) at 25°C with HBS-EP running buffer (10 mM HEPES, 150 mM NaCl, 3 mM EDTA, 0.005 % [v/v] Tween® 20, pH 7.4) and CM5 sensor chips (Cytiva). Prior to SPR analyses all analytes in flow (VHHs, ACE2 receptor) were SEC-purified on a Superdex® 75 Increase 10/300 GL column (Cytiva) in HBS-EP buffer at a flow rate of 0.8 mL/min to obtain monomeric proteins. VHH epitope binning was performed by SPR dual injection experiments on the SARS-CoV-2 S at a flow rate of 40 µL/min in HBS-EP buffer. Dual injections consisted of injection of VHH1 (at 50 – 100 × KD concentration) for 150 s, followed by immediate injection of a mixture of VHH1 + VHH2 (both at 50 – 100 × KD concentration) for 150 s. The opposite orientation was also performed (VHH2 followed by VHH2 + VHH1) (Fig.9C). Surfaces were regenerated using a 12 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 100 µL/min. All pairwise combinations of VHHs were analyzed and distinct or overlapping epitope bins determined. [00216] Epitope binning by ELISA [00217] The pairwise ability of VHHs to bind to their antigen in a sandwich ELISA format was evaluated as described previously (Rosotti et al., 2015a; Delfin-Riela et al., 2020), (Fig. 9D). Briefly, a matrix of 14 wells (row) 23 wells (column) was generated using six NUNC® MaxiSorp™ 4BX plates (Thermo Fisher) and coated overnight at 4°C with 4 µg/mL streptavidin (Jackson ImmunoResearch, Cat#016-000-113) in 100 µL PBS, pH 7.4. Wells were blocked with 200 µL PBSC for 1 h at room temperature and then biotinylated VHHs (10 µg/mL in 100 µL PBSCT) were captured in each row (same VHH in each row; 14 rows for a total of 14 VHHs) for 1 h at room temperature. Wells were washed 5 times with PBST and incubated with 100 ng/mL of SARS-CoV-2 S1 diluted in PBSCT for 1 h. Wells were washed and each column was incubated with the pairing, VHH-Fcs/ACE2-Fc at 1 µg/mL used as detector antibodies (same VHH-Fc in each column; 23 column for a total of 22 VHH-Fcs and ACE2-Fc). The binding of VHH-Fcs/ACE2-Fc to S1 was detected using 100 µL 1 µg/mL HRP-conjugated goat anti-human IgG (SIGMA, Cat#A0170). Finally, plates were washed 10 times with PBST and peroxidase activity was determined as described above. The same procedure was carried out performing a matrix of 17 well (row) x 20 wells (column) as shown in Fig.9E. Results and Discussion [00218] To determine whether VHHs recognize conformational or linear epitopes, they were subjected to binding analysis against SARS-CoV-2 S by denaturing, SDS-PAGE/Western blot. As shown in Fig. 9A using the monomeric VHHs as probe, three out of 26 VHHs tested bound to denatured S, indicating they were recognizing linear epitopes, while the remaining VHHs appeared to be conformational epitope-specific based on their lack of significant binding to denatures S. In assays where VHH-Fc was used instead of VHH, 15 out of 37 VHH-Fcs tested were determined to bind to linear epitopes (Fig. 9B). These linear epitope-specific VHHs give the option of virus detection against denatured S by robust diagnostic techniques such as SDS-PAGE/Western blot, where the additional molecular weight information provided by the SDS-PAGE would serve as a second, confirmatory piece of information to eliminate/reduce false positives obtained by binding data alone. [00219] To identify the number of distinct (non-overlapping) epitopes, VHHs were subjected to epitope binning experiments by SPR and sandwich ELISA. In SPR epitope binning assays, the first VHH (“VHH1”) was flowed over a spike protein-immobilized sensorchip and allowed to saturate its epitope, followed by the addition of the second, VHH2 applied as a mixture of VHH1 + VHH2 to keep the VHH1 epitope saturated during the binding of VHH2. Assays were performed in a second orientation as well to cross-confirm results: VHH2 + (VHH2+ VHH1). Fig.9C (left panel) exemplifies a VHH pair (NRCoV2-02/NRCoV2-05) binding to an overlapping epitope, hence belonging to the same epitope bin, as the addition of the second VHH does not result in any increased binding (i.e., increase in RU) over that obtained for the addition of the first VHH. Fig. 9C (right panel), on the other hand, exemplifies a VHH pair (NRCoV2-02/NRCoV2-07) binding to non-overlapping epitopes, hence belonging to different epitope bins, as the addition of the second VHH results in significant increase in binding over that already achieved by the addition of the first VHH. SPR assays were performed with combination pairs of nine VHHs, including VHH- 72 against S1-RBD, six VHHs against S1 and 10 VHHs against S2. A conceptually similar assay to SPR was performed for 14 more S1-RBD-specific VHHs by a sandwich ELISA to further expand on epitope bins identified by SPR for the S1-RBD-specific VHHs (Figs.9D (initial results) and 9E (further results)). The sandwich ELISA allowed for the rapid identification of antibody pairs that simultaneously bound to the antigen, hence to non-overlapping epitopes. ACE2 and the benchmark VHH, VHH-72, were also included in the epitope binning experiments. The ELISA experiments confirmed the results of epitope binning by SPR, expanded the number of binders within each epitope bin, and identified new epitope bins. The epitope binning results obtained by SPR and ELISA are summarized in Figs. 9F (initial results), 9G (further results) and Table 14. Initial binning results identified 14 non-overlapping/partially overlapping bins: six for S1-RBD-specific VHHs, three for S1-NTD-specific VHHs and five for S2-specific VHHs. Benchmark VHH-72 binned with S1-RBD-specific VHHs NRCoV2-1a/1c/1d, NRCoV2-07, NRCoV2-12, NRCoV2-18, NRCoV2-20, MRed02 and NRCov2-MRed04. Thirteen out of 22 RBD-specific VHHs tested, binned with ACE2 (Fig. 9F). Further characterization led to the identification of 17 non- overlapping/partially overlapping bins: six for S1-RBD-specific VHHs, four for S1-NTD-specific VHHs and seven for S2-specific VHHs (as shown in Fig.9G). e 0 0 0 0
Figure imgf000079_0001
Figure imgf000080_0001
Example 8: Surrogate Virus Neutralization Assays Introduction [00221] Surrogate neutralization assays were performed to identify potential neutralizing VHHs/VHH-Fcs, i.e., VHHs/VHH-Fcs inhibiting SARS-CoV-2 viruses from entering host cells. Three different surrogate assays were performed: ELISA, SPR and flow cytometry. In ELISA and SPR, ACE2 and SARS-CoV-2 S acted as surrogates for an ACE2-containing host cell and an S- containing invading virus, respectively. In flow cytometry assays, which were performed directly against the host cell (Vero E6), S1-RBD or S served as surrogate virus. Antibodies that interfered with the binding of spike fragment proteins to ACE2 in the surrogate assays were considered to be neutralizing antibodies. Materials and Methods [00222] ACE2 competition assay by ELISA [00223] Wells of NUNC® MaxiSorp™ microtiter plates (Thermo Fisher) were coated overnight at 4°C with 50 ng/well of S in 100 µL PBS, pH 7.4. Next day, plates were blocked with 250 µL PBSC for 1 h at room temperature. For ACE2/VHH competition binding to SARS-CoV-2 S, 50 µL of ACE2-Fc (ACROBiosystems, Cat#AC2-H5257) at 400 ng/mL was mixed with 50 µL of VHH at 1 µM, and then transferred to SARS-CoV-2 S coated microtiter plate wells. After 1 h incubation at room temperature, plates were washed 10 times with PBST and the ACE2-Fc binding was detected using 1 µg/mL goat anti-human IgG (Fc specific) peroxidase antibody (SIGMA, Cat# A0170) in 100 µL PBSCT. After 10 washes with PBST, the peroxidase activity was determined as described above. [00224] ACE2 competition assay by SPR [00225] Standard SPR techniques were used for binding studies. All SPR assays were performed on a BiacoreTM T200 instrument (Cytiva) at 25°C with HBS-EP running buffer (10 mM HEPES, 150 mM NaCl, 3 mM EDTA, 0.005 % [v/v] Tween® 20, pH 7.4) and CM5 sensor chips (Cytiva). Prior to SPR analyses, all analytes in flow (VHHs, ACE2 receptor) were SEC-purified on a SuperdexTM 75 Increase 10/300 GL column (Cytiva) in HBS-EP buffer at a flow rate of 0.8 mL/min to obtain monomeric proteins. VHHs were analyzed for their ability to block the SARS- CoV-2 spike trimer (S) interaction with ACE2 using SPR dual injection experiments. VHHs and ACE2 were flowed over the SARS-CoV-2 S surface at 40 µL/min in HBS-EP buffer. Dual injections consisted of injection of ACE2 (1 µM) for 150 s, followed by immediate injection of a mixture of ACE2 (1 µM) + VHH (at 20 – 40 × KD concentration) for 150 s. The opposite orientation was also performed (VHH followed by VHH + ACE2). Surfaces were regenerated using a 12 s pulse of 10 mM glycine, pH 1.5, at a flow rate of 100 µL/min. All pairwise combinations of VHHs and ACE2 were analyzed. VHHs that competed with ACE2 for SARS-CoV-2 spike trimer binding showed no increase in binding response during the second injection. Conversely, a binding response was seen during the second injection for VHHs that did not compete with ACE2. [00226] ACE2 competition assay by flow cytometry [00227] Experiments were performed essentially as described in Example 2. Briefly, 400 ng of chemically biotinylated trimeric SARS-CoV-2 S was mixed with 5 104 Vero E6 cells in the presence of decreasing concentrations of VHHs or VHH-Fcs in a final volume of 150 µL. Following 1 h incubation on ice, cells were washed twice with PBSB by centrifugation at 1200 rpm for 5 min and then incubated for an additional hour with 50 µL Streptavidin, R-Phycoerythrin Conjugate (SAPE, ThermoFisher, Cat#S866) at 250 ng/mL diluted in PBSB. After a final wash, cells were resuspended in 100 µL PBSB and data were acquired on a CytoFlexTM S flow cytometer (Beckman Culter) and analyzed by FlowJoTM (FlowJo LLC, v10.6.2, Ashland, OR). As an internal reference for competition experiments, a competition assay with recombinant human ACE2-His6 in lieu of VHH was also included. A20.1, a C. difficile toxin A-specific VHH (Hussack et al., 2011) was used as negative control VHH. Percent inhibition (neutralization) was calculated according to the following formula: % inhibition = 100 x [1 - (Fn - Fmin) / (Fmax - Fmin)], where, Fn is the measured fluorescence at any given competitor VHH concentration, Fmin is the background fluorescence measured in the presence of cells and SAPE only, and Fmax is the maximum fluorescence, measured in the absence of VHH competitor. Results and Discussion [00228] Initially, a total of 26 VHHs (14 S1-RBD-specific, 6 S1-NTD-specific and 6 S2-specific) were subjected to competitive ELISA, to identify those that are neutralizing, i.e., reduce the binding of ACE2-Fc to S. As shown in Fig.10, the majority of S1-RBD binders were significantly neutralizing, with NRCoV2-1d, NRCoV2-02, NRCoV2-05 and NRCoV2-07 displaying essentially 100% inhibition and outperforming the VHH-72 benchmark. Two of the S1-NTD- specific VHHs (NRCoV2-SR01, NRCoV2-SR02) showed significant neutralization, with NRCoV2-SR02 essentially neutralizing at 100%. None of the S2 binders showed significant neutralizing activity. A conceptually similar assay to ELISA was performed by a competitive SPR. The results are shown in Fig. 11 and Table 16. The four lead neutralizers identified by ELISA, i.e., NRCoV2-01d, NRCoV2-02, NRCoV2-05 and NRCoV2-07, were confirmed by SPR to be complete neutralizers (‘blockers”). NRCoV2-14, NRCoV2-15, NRCoV2-18 and NRCoV2-20 showed partial neutralization (“+/-“; Table 16). The remaining VHHs tested were judged to be non-neutralizing. Although the ELISA and SPR results agreed in the case of the majority of VHHs, there was some disagreement. For example, while NRCoV2-SR02, NRCoV2-06, NRCoV2-10, and NRCoV2-11 were neutralizing by ELISA, they were not found to be neutralizing by SPR. Conversely, NRCoV2-20 was judged to be somewhat neutralizing by SPR, but non-neutralizing by ELISA. [00229] Finally, a quantitative surrogate neutralization assay was performed by flow cytometry, where antibodies were assessed based on their ability to block the interaction of trimeric SARS- CoV-2 S with ACE2 on the surface of Vero E6 cells (African green monkey kidney cells). (Vero E6 cells are known to be highly susceptible to infection by SARS-CoV-2 and SARS-CoV.) Both monomeric VHHs and bivalent VHH-Fcs were assessed. IC50s, IC99s and Imax% values, measures of potency and efficacy were used to rank neutralizing antibodies. A preliminary screen performed at a single concentration with S1-RBD-, S1-NTD- and S2-specfic VHHs showed that many of the S1-RBD-specific VHHs were potent neutralizers (Fig. 12A). Assays were also performed at multiple VHH concentrations allowing determination of IC50s and Imax% values (Fig.12B; Table 17). The Imax% for NRCoV2-SR13 was too low to warrant a reliable IC50 determination for this VHH. In agreement with the preliminary results, all of the neutralizers were S1-RBD-specific with many exhibiting high neutralization potencies and efficacies. In particular, NRCoV2-1d, NRCoV2-02, NRCoV2-05 and NRCoV2-07 led others with IC50/ Imax% values of 8.6 nM/72%, 5.1 nM/100%, 9.5 nM/97%, and 7.5 nM/86%, respectively. A second group of VHHs, including NRCoV2-10, NRCoV2-14, NRCoV2-15, NRCoV2-18, NRCoV2-20 and NRCoV2-MRed04 were also potent/efficacious neutralizers (Table 17). All of these antibodies outperformed the benchmark VHH-72, which had a far higher IC50 (59 nM). NRCoV2-11 and NRCoV2-17 although showing high potencies (IC50s of 16.8 nM and 9.4 nM, respectively), had weak efficacies (Imax% values of 20% and 18%, respectively). None of the S1-NTD or S2 binders was neutralizing. The results obtained by flow cytometry correlated well with those obtained by ELISA and SPR. [00230] To increase the neutralization potency and efficacy of the VHHs, they were reformatted as bivalent VHH-Fcs. The increase in size (from 16 kDa VHH to 80 kDa VHH-Fc) as well as avidity (from monovalent VHH to bivalent VHH-Fc) could sterically hinder the binding of S to ACE2 and increase VHHs’ apparent affinity leading to their improved neutralization potency and efficacy. Thus, VHH-Fcs were generated and tested in flow cytometry surrogate neutralization assays as described above. The majority of VHH-Fcs demonstrated high potencies and efficacies (Figs.13A- B; Table 17). Reformatting had a significant effect on the neutralization potencies/efficacies of VHHs. As for S1-RBD-specific VHHs, reformatting imparted neutralization capability to NRCoV2-04, and significantly improved the neutralization potency/efficacy of NRCoV2-11, NRCoV2-14, NRCoV2-15, NRCoV2-17, and NRCoV2-18, as well as the VHH-72 benchmark. The potency and efficacy of NRCoV2-1d, NRCoV2-02, NRCoV2-05 and NRCoV2-07 were not essentially affected with reformatting, except for NRCoV2-1d whose Imax% was increased from 72% (VHH) to 89% (VHH-Fc). Reformatting had a more profound effect on S1-NTD-specific VHHs, transforming six VHHs (NRCoV2-SR01, NRCoV2-SR02, NRCoV2-SR03, NRCoV2- SR04, NRCoV2-SR16, and NRCoV2-MRed07) into neutralizing antibodies, with some displaying strong potencies/efficacies (NRCoV2-SR01, NRCoV2-SR02, and NRCoV2-SR13). As for S2- specfic VHH-Fcs, none was found to be neutralizing. Based on IC99/Imax% values, many VHH-Fcs outperformed the VHH-72 benchmark. These included S1-RBD-specific VHH-Fcs NRCoV2-1a, NRCoV2-1d, NRCoV2-02, NRCoV2-05, NRCoV2-07, NRCoV2-11, NRCoV2-11a, NRCoV2- 12, NRCoV2-14, NRCoV2-15, NRCoV2-17, NRCoV2-20, NRCoV2-MRed04, NRCoV2- MRed05 and the S1-NTD-specific VHH-Fcs NRCoV2-SR02 and NRCoV2-SR03. [00231] The surrogate neutralization assays were then extended to variants Alpha, Beta, Gamma, Delta, Kappa and Omicron using all of the RBD-specific and a subset of NTD-specific VHH-Fcs (Table 15). In this assay Wuhan was included and performed again as an internal reference. Several observations were made. First, for cross-neutralizing VHHs, the IC50s across variants did not change significantly. Second, while all Wuhan neutralizers also remained Alpha neutralizers, some lost their capability to inhibit Beta, Gamma, Delta and Kappa with variable cross- neutralizing patterns. In particular, with respect to the RBD-specific VHHs, the cross-neutralization profiles for Beta vs Gamma and Delta vs Kappa were identical, which is likely reflective of the key escape mutations in these variants (K417N, E484K and N501Y for Beta vs K417T, E484K and N501Y for Gamma; L452R and T478K for Delta vs L452R and E484Q for Kappa). Third, and importantly, 12 out of 20 VHH-Fcs (10 RBD-specific, two NTD-specific) were Delta neutralizers, nine of which (eight RBD-specific, one NTD-specific) neutralized across all variants. Fourth, the majority of these nine pan-neutralizers (six RBD-specific, one NTD-specific) also neutralized SARS-CoV. Fifth, Omicron mutations had a major impact on antibodies targeting bin 1, from which only NRCoV2-12 and 20 were able to neutralize with comparable potency to Wuhan or the other variants tested. The neutralization ability of the benchmark VHH-72 was abolished by Omicron mutations. Antibodies from bin 2/3/4 were able to neutralize Omicron with comparable IC50 to Wuhan, except for NRCoV-2-02/05 and MRed05, which were negative. NRCoV2-11 (anti- RBD) and SR01 (anti-NTD) were also efficient, achieving neutralization as potent as was observed against Wuhan spike protein. From the list of antibodies tested NRCoV2-12, -20, -11 and -SR01 are the leads, showing efficient pan-neutralization against the SARS-CoV-2 variants generated so far, and outperforming the benchmark VHH-72. [00232] Table 15: Flow cytometry SVNAs against SARS-CoV-2 variants and SARS-CoV SVNA IC50 (nM) SARS-CoV-2 S VHH-Fc SARS-CoV S
Figure imgf000085_0001
VHH-72 5.6 10.6 5.1 3.3 10.5 8.5 - 7.8
Figure imgf000085_0002
3,4 17 8.6 10.6 26.4 214 - - 3.4 - 10 8.8 11.3 10.8 21.8 - - 4.3 -
Figure imgf000086_0001
7,9,10 SR13 7.7 22.4 - 16.5 - 12.2 - 15
Figure imgf000086_0002
-e c a f
Figure imgf000087_0001
Figure imgf000088_0001
[00234] Table 17: Neutralization capabilities of SARS-CoV-2-specific VHHs/VHH-Fcs obtained by surrogate virus neutralization flow cytometry assays against SARS-CoV-2 S (Wuhan) VHH/ACE2-H6 2 V H-Fc/ACE2-Fc2 Domain/ H VHH/ACE2 bd i 3 3 3 3 3 3
Figure imgf000089_0001
NRCoV2-S2A4 S2 - - - - - - NRCoV2-S2F3 S2 - - - - - - app
Figure imgf000090_0001
eric ACE2. 3IC50, concentration of VHH/VHH/Fc giving 50% neutralization; IC99, concentration of VHH/VHH/Fc giving 99% neutralization; Imax%, maximal inhibitory effect; IC50, IC99 and Imax% values were extracted from graphs exemplified in Figs. 12B and Figs. 13B. Dash indicate VHH/VHH-Fc does not neutralize the interaction between Vero E6 cell-displayed ACE2 and soluble S. 4ICs cannot be determined with certainty due to low Imax% values. nd, not determined, due to lack of sufficient quantities and/or neutralization as VHH-Fc. Example 9: Live-Virus Neutralization Assays Introduction [00235] VHH-Fcs were subjected to authentic-virus neutralizations assays, i.e., micro- neutralization assays, to identify those that neutralized infection of host cells by the invading SARS-CoV-2 virus. Materials and Methods Authentic-virus neutralizations assays [00236] Neutralization activity of antibodies to SARS-CoV-2 was determined with the microneutralization assay. In brief, antibody (VHH-Fc and VHH) stocks were prepared at 1 mg/mL in PBS and sterilized by passing through 0.22 µM filters.1:5 serial dilutions of 50 µg/mL of each antibody was carried out in DMEM, high glucose media supplemented with 1 mM sodium pyruvate, 1mM non-essential amino acids, 100 U/ml penicillin-streptomycin, and 1% heat- inactivated fetal bovine serum. SARS-CoV-2 (strain SARS-CoV-2/Canada/VIDO-01/2020) was incubated at 250 pfu with antibody dilution in 1:1 ratio at 37oC for 1 h. Vero E6 cells seeded in 96-well plates were infected with virus/antibody mix and incubated at 37oC in humidified/5% CO2 incubator for 72 hours post-infection (hpi). Cells were then fixed in 10% formaldehyde overnight and virus infection was detected with mouse anti-SARS-CoV-2 nucleocapsid antibody (R&D Systems, clone #1035111) and counterstained with rabbit anti-mouse IgG-HRP (Rockland Inc.). Colorimetric development was obtained with o-phenylenediamine dihydrochloride peroxidate substrate (Sigma-Aldrich) and detected on Biotek Synergy H1 plate reader at 490 nm. IC50 was determined from non-linear regression on GraphPad Prism 9. For determining neutralization potencies by measuring cytopathic effect (CPE), infected Vero E6 cells were incubated at 37 for 96 h until the virus-only control wells had nearly 100% CPE (cell-only controls were also included). Neutralization was scored by MN100, lowest antibody concentration that gave no CPE, i.e., 100% neutralization. Assays were performed in technical duplicates. [00237] Results and Discussion [00238] A select set of lead VHH-Fcs were subjected to preliminary authentic-virus micro- neutralization assays to assess their SARS-CoV-2 virus-neutralizing activity. These included five S1-RBD-specific VHHs and two S1-NTD-specfic VHHs. Neutralization was scored by MN100, the lowest antibody concentration that gave no cytopathic effect (100% neutralization). Results are shown in Figs. 14A-B and Table 18. All VHH-Fcs demonstrated significant neutralization capabilities, with MN100s ranging from 6.25 nM (lowest neutralization capability) to 0.01 nM (highest neutralization capability). The most potent neutralizers were amongst the S1-RBD binders: NRCoV2-02 (MN100 0.01 nM); NRCoV2-1d (MN100 0.25 nM); NRCoV2-04 and NRCoV2-07 (MN1001.25 nM); NRCoV2-03 (MN1006.25 nM). NRCoV2-02 and NRCoV2-1d were far more potent neutralizers than the benchmark (VHH-72), by five- and 125-fold, respectively. S1-NTD binders had MN100s of 6.25 nM (NRCoV2-SR01, NRCoV2-SR02). The lead antibody, NRCoV2-02 also outperformed the benchmark in VHH format by 125-fold (Fig.14A inset). To explore the contribution of bivalency to the neutralization potency of VHH-Fcs, monovalent VHH-Fc versions of select VHH-Fcs were generated. Based on MN100 values, neutralization potencies were decreased by five-fold for NRCoV2-SR01, 25-fold for NRCoV2-1d and NRCoV2- 07 and more than 125-fold for NRCoV2-02, with their conversion from bivalent to monovalent VHH-Fcs, demonstrating the sizable contribution of bivalency to their neutralization potency. In the case of NRCoV2-02, the identical MN100 for its monovalent VHH and monovalent VHH-Fc versions indicates that the observed dramatic increase in neutralization potency in going from VHH to bivalent VHH-Fc was likely due solely to an increase in valency, not size (steric hindrance). The loss of bivalency also had drastic effect on VHH-72, rendering it non-neutralizing at the highest concentration tested. [00239] A more comprehensive authentic neutralization assay was performed to determine the IC50 of VHH-Fcs (Fig. 15 A-D; Table 19). Most potent neutralizers were amongst the S1-RBD binders with 17 out of 20 VHH-Fcs tested being neutralizing. The most potent VHH-Fcs recognized epitopes 2/3/4 and had IC50s of 0.0008- 3.1 nM (Fig.15E and Fig.30; Table 19). The leads were NRCoV-05 (IC500.0008 nM) followed closely by NRCoV-02 (IC500.12 nM) and NRCoV2-MRed 05 (IC500.17 nM). VHH-Fcs recognizing epitope 1 showed intermediate potencies with IC50s of 1.94 – 9.6 nM, with VHH-72 (belonging to the same bin 1) having similar IC50 (8.46 nM). VHH- Fcs recognizing epitope 5 and 6 showed IC50s of 9.96 – 76 nM. As for S1-NTD-specific VHH, six out of nine VHH-Fcs tested were neutralizing, with the lead VHH-Fcs having IC50s of 9.42, 14.31 and 54.2 nM. The remaining two had IC50s in the high nM - micromolar range. Out of 13 S2- specific VHH-Fcs tested, three, NRCoV2-S2A3, NRCoV2-S2G3 and NRCoV2-S2G4, were neutralizing with IC50s from 12.2 nM for S2A3 to high nM - micromolar range for S2G3 and S2G4. These belonged to three different epitope bins. Nine VHH-Fcs outperformed the VHH-72 benchmark by 2.5 – 10,000-fold. In particular, the NRCoV2-05, NRCoV2-02 and NRCoV2- MRed05 leads showed 10,000-fold, 70-fold and 50-fold higher potency than VHH-72, respectively. We provide the first examples of single domain antibodies that neutralize the SARS-CoV-2 virus by targeting the non-S1-RBD region of S, i.e., S1-NTD and S2. [00240] The live virus neutralization assays were then extended to include Alpha and Beta variants. With the exception of VHH-Fc NRCoV2-06, all remaining 16 RBD-specific Wuhan neutralizers maintained their ability to neutralize Alpha (Table 19, Fig. 30, Fig. 31A, and Fig. 31C). Interestingly, many VHHs from across different epitope bins showed improved IC50s by as high as 15-fold. Except for NRCoV2-05, which despite showing a reduced potency towards the Alpha variant (~40-fold) still exhibited the highest potency of all against the variant, the remaining VHHs demonstrated comparable potencies. Of the 16 Wuhan/Alpha neutralizers, 13 also neutralized the Beta variant (Fig.31B and Fig.31D), with the majority (10 of 13) demonstrating comparable potencies and two (NRCoV2-14 and NRCoV2-17) showing reductions (~10-fold). Although from the most potent bin (2/3/4), NRCoV2-02, NRCoV2-04 and NRCoV2-05, consistent with the cross-reactivity data (Fig. 6B), were completely abrogated presumably by the Beta mutations in the RBD (K417N, E484K, N501Y), several others including NRCoV2-MRed05, NRCoV2-10 and NRCov2-15 did retain their high neutralizing potencies against both Alpha and Beta variants. A similar trend was observed for the NTD-specific neutralizing VHHs: against the Alpha variant, potencies either remained essentially the same as those for the Wuhan variant or improved, while against the Beta variant, potencies diminished (Fig. 30 and Figs. 31 A-D). Nonetheless, NRCoV2-SR01 and NRCoV2-SR16 maintained respectable neutralization potencies against Beta. The potencies of S2-specific neutralizers (S2A3, S2G3, S2G4) were also decreased with variants. However, the lead NRCoV2-S2A3 still maintained comparable potencies across all three variants (IC50 of 12.2 nM, 31 nM and 54 nM for Wuhan, Alpha and Beta [Table 19]). Collectively, the neutralization profiles across Wuhan, Alpha and Beta variants were consistent with cross-reactivity profiles (Fig. 6B). Based on the cross-reactivity (Fig. 6B) and surrogate cross-neutralization data (Table 15), it is likely that many VHHs would also neutralize the Gamma, Kappa, Delta, and Omicron variants in live virus neutralization assays. [00241] Table 18: Neutralization capabilities (MN100) of SARS-CoV-2-specific VHH-Fcs obtained by authentic-virus (aka live virus) neutralization assays Do 2 V main/subunit MN100 HH (nM)
Figure imgf000093_0001
NRCoV2-07 x S1-RBD x null 31.25 A26.8 1VHH-72 ben SARS-CoV-2 S (Wrapp et al.
Figure imgf000094_0001
tive control VHH (Hussack et al., 2011).2MN100 is the lowest antibody concentration that gave no cytopathic effect (100% neutralization). Dash indicate VHH-Fc does not neutralize SARS-CoV-2 virus at the highest VHH-Fc concentration used. MN100 values were used to construct Fig.14A-B graphs.3The MN100 of monovalent VHH-72 and NRCoV2-02 VHHs were 156.25 and 1.25 nM, respectively. [00242] Table 19: Neutralization capabilities (IC50) of SARS-CoV-2-specific VHH-Fcs obtained by authentic-virus (aka live virus) neutralization assays Epitope LVNA IC50 (nM)
Figure imgf000094_0002
NTD specific V H 1VH
Figure imgf000095_0001
H-72 benchmark is a SARS-CoV S-specific VHH that cross-reacts with SARS-CoV-2 S (Wrapp et al., 2020); A20.1 is C. difficile toxin A-specific negative control VHH (Hussack et al., 2011. Epitope bin numbers correspond to the bins shown in Fig.9G. Example 10: Stability of VHHs against Aerosolization Introduction [00243] One effective therapeutic approach against COVID-19 might be the direct delivery of aerosolized antibodies to the nasal and lung epithelia by inhalation. VHHs in particular, are advantageously fit for such administration approach due to their high stability and robustness. Since aerosolization could compromise the structural integrity and function of antibodies that lack sufficient stability, such as mAbs (Detalle et al., 2016; Respaud et al., 2015), the effect of aerosolization on the stability of VHHs was tested. Materials and Methods [00244] Aerosolization studies [00245] Prior to aerosolization, 4 mg of each VHH was purified by size-exclusion chromatography using a Superdex™ 75 GL column (Cytiva) and PBS as running buffer, as described above. Protein fractions corresponding to the chromatogram’s monomeric peak were pooled, quantified and the concentration adjusted to 0.5 mg/mL. One mL of each VHH was subsequently aerosolized at room temperature with a portable mesh nebulizer (AeroNeb® Solo, Aerogen, Galway, Ireland), which produces 3.4- m particles. Aerosolized VHHs were collected into 15 mL Round-Bottom Polypropylene test tubes (Falcon, Cat#C352059) for 5 min to allow condensation and were subsequently quantified and kept at 4 C until use. Then 200 µL aliquots of pre- and post- aerosolized VHHs were subjected to SEC to obtain chromatogram profiles. Additionally, condensed VHHs were closely monitored for the formation of any visible aggregates, and in cases where aggregate formation was observed, aggregates were removed by centrifugation prior to concentration determination, SEC analysis and ELISA. % soluble aggregate was determined as the proportion of a VHH that gave elution volumes (Ves) smaller than that of the monomeric VHH fraction. % recovery was determined as the proportion of a VHH that remained monomerically soluble following aerosolization. [00246] To assess the effect of aerosolization on the functionality of VHHs, the activities of post- aerosolized VHHs were determined by ELISA and compared to those for pre-aerosolized VHHs. To perform ELISA, S1-Fc (ACRO Biosystems, Cat#S1N-C5255) was diluted in PBS to 500 ng/mL, and 100 µL/well were coated overnight at 4°C. The next day, plates were washed with PBST and blocked with 200 µL PBSC for 1 h at room temperature. After five washes with PBST, serial dilutions of the pre- and post- aerosolized VHHs were added to wells and incubated for 1 h at room temperature. Then plates were washed 10 times with PBST and binding of VHHs to S1- Fc was detected with rabbit anti-6xHis Tag antibody HRP Conjugate (Bethyl, Cat#A190-114P), diluted at 10 ng/mL in PBST and added at 100 µL/well. Finally, after 1 h incubation at room temperature, peroxidase activity was detected as described previously. Results and Discussion [00247] VHHs including the benchmark VHH-72 were examined for their aggregation resistance/stability against aerosolization. For a few VHHs, e.g., NRCoV2-MRed20, NRCoV2- S2A4, as well as the VHH-72 benchmark, aerosolization induced some soluble aggregation formation as determined by SEC (Fig. 16A; Table 20). Several VHHs, e.g., NRCoV2-11, NRCoV2-SR03, formed visible aggregates, which led to their reduced % recovery (Fig. 16A-C; Table 20). However, the majority of VHHs (20 out of 30 VHHs tested) were highly stable against aerosolization, that is, they did not form any soluble or visible aggregates and demonstrated high % recovery upon aerosolization treatment. Examples include NRCoV2-1c/1d, NRCoV2-02, NRCoV2-07, NRCoV2-17, NRCoV2-18 and NRCoV2-20. High % recovery indicates these VHHs advantageously lack non-specific binding to nebulizer surfaces. For therapeutic VHHs, this is expected to translate to a more effective drug delivery to the site of viral infection. Several VHHs, i.e., NRCoV2-04, NRCoV2-14, NRCoV2-15, NRCoV2-SR04 and NRCoV2-MRed04, while forming some visible aggregates, still showed a good % recovery upon aerosolization (52 – 69 %). To assess the effect of aerosolization on the functionality of VHHs, the activities (EC50s) of post- aerosolized VHHs were determined by ELISA and compared to those for pre-aerosolized VHHs. ELISAs were performed on a sample of four VHHs: NRCoV2-1d, NRCoV2-02, NRCoV2-07 and NRCoV2-11 (Fig. 16D). Comparison of EC50s for post-aerosolized VHHs vs pre-aerosolized VHHs demonstrated that aerosolization did not compromise the functionality of VHHs (Fig.16D; Table 21). [00248] Table 20: Stability of VHHs against aerosolization 2 Reco Soluble aggregates (%) H very P P Soluble Visible es
Figure imgf000097_0001
NRCoV2-11 24 6 5 -1 Yes NRCoV2-14 55 6 6 0 Yes ed
Figure imgf000098_0001
as te proporton o a VH tat gave euton voumes (Ves) sma er t an tat o te monomerc VHH fraction.3 Soluble agg. = “Post-aerosolization” – “Pre-aerosolization”. [00249] Table 21. Affinities (EC50s) of pre-aerosolized (“Pre”) vs post-aerosolized (“Post”) VHHs EC (nM) V H 50 H t
Figure imgf000098_0002
Example 11: VHHs for Diagnosis and Capture of SARS-CoV-2 Introduction [00250] VHHs described herein are promising diagnostic/capture agents against SARS-CoV-2, SARS-CoV and related viruses as well as their spike proteins. To explore the use of these VHHs as capture agents, four of the VHHs were tested in sandwich ELISA for their diagnostic/capturing capability against SARS-CoV-2. Materials and Methods Sandwich ELISA [00251] NUNC® MaxiSorp™ 4 HBX plates (Thermo Fisher) were coated overnight at 4°C with 4 µg/mL streptavidin (Jackson ImmunoResearch, Cat#016-000-113) in 100 µL PBS, pH 7.4. Wells were blocked with 200 µL PBSC for 1 h at room temperature followed by capturing biotinylated NRCoV2-02 VHH (10 µg/mL in 100 µL PBSCT) for 1 h at room temperature. Wells were washed five times with PBST and incubated with variable concentrations of SARS-CoV-2 S, S1 or S1-RBD diluted in PBSCT for 1 h. Well were washed and incubated with detecting VHH- Fcs at 1 µg/mL. The binding of VHH-Fcs to spike protein fragments was probed using 100 µL 1 µg/mL HRP-conjugated goat anti-human IgG (SIGMA, Cat#A0170). Finally, plates were washed 10 times with PBST and peroxidase activity was determined as described above. Results and Discussion [00252] To provide proof of concept for the utility of the VHHs as detecting / capturing agents against SARS-CoV-2, SARS-CoV and related viruses, sandwich ELISAs were performed with four VHHs using SARS-CoV-2 spike protein fragments as surrogates for the virus. Wells were coated with NRCoV2-02 VHH as the capturing antibody, followed by the capture of antigens S, S1, or S1-RBD added at variable concentrations. Then a second, VHH-Fc that binds to a non- overlapping epitope in relation to NRCoV2-02 was added as the detecting antibody followed by the addition of a HRP-conjugated probing antibody binding to the detecting antibody. The different VHH-Fcs tested as detecting antibodies were: NRCoV2-1d, NRCoV2-04, NRCoV2-07, and NRCoV2-11. Very low SC50 values were obtained in ELISA assays (Fig. 17, Table 22). In addition, limit of detection values as low as 0.08 ng/mL (8 picogram) spike protein could be detected with confidence (Table 23). These results indicate that the VHHs are promising virus detecting / capturing agents. [00253] Table 22: SC50 values obtained in ELISA assays SC50 (ng/mL) S S1 S1-RBD
Figure imgf000100_0002
[00254] Table 23: Limit of detection (ng/mL) NRCoV2-1d NRCoV2-04 NRCoV2-07 NRCoV2-11 14 41 14 14
Figure imgf000100_0001
Example 12: In vivo therapeutic efficacy of VHH-Fcs [00255] Before testing VHH-Fcs in hamsters for in vivo efficacy, they were assessed for in vivo stability and persistence. NRCov2-1d VHH-Fc was chosen as a representative VHH and VHH-72 VHH-Fc, whose modified/enhanced version is currently in a phase 1 clinical trial, was included as a reference. Hamsters were injected intraperitoneally (IP) with 1 mg of each antibody and serum antibody concentration was monitored for up to four days by ELISA. Significant and comparable VHH-Fc concentrations were present in the hamster sera for both 1d and VHH-72 VHH-Fcs on days 1 and 4 post injection (Fig. 32), indicating that VHH-Fcs would have the required serum stability and persistence in vivo for the duration of the animal studies. [00256] The in vivo therapeutic efficacy of VHH-Fcs which were neutralizing by live virus neutralization assay was then assessed in a hamster model of SARS-CoV-2 infection. Five VHH- Fcs were selected to cover a wide range of important attributes including in vitro neutralization potencies and breadth, epitope bin, subunit/domain specificity and cross-reactivity pattern. These included three RBD-specific (1d, 05, MRed05), one NTD-specific (SR01) and one S2-specific (S2A3) VHH-Fcs. Cocktails of two VHH-Fcs were also included to explore synergy between the antibody pairs recognizing distinct epitopes within the RBD (1d/MRed05) or RBD and NTD (1d/SR01). [00257] Hamsters were administered IP with 1 mg of VHH-Fcs 24 h prior to intranasal challenge with SARS-CoV-2 Wuhan isolate. Daily weight change and clinical symptoms were monitored. At 5 dpi, lungs were collected to determine viral titers. Viral titer decrease and reversal of weight loss in antibody treated versus control animals were taken as measures of antibody efficacy. Animals treated with RBD binders 1d, 05, and MRed05 showed reduced lung viral burden by three, five and six orders of magnitude, respectively, relative to PBS or VHH-Fc isotype controls, with 05 and MRed05 reducing viral burden to below detectable levels (Fig. 22A). The RBD-specific VHH-72 benchmark caused a mean viral decrease of four orders of magnitude. The NTD binder SR01, and interestingly, the S2 binder S2A3, were also effective neutralizers, decreasing mean viral titers by four and three orders of magnitude, respectively. Both 1d/SR01 and 1d/MRed05 cocktails decreased viral titers by 6 orders of magnitude to undetectable levels of virus infection. While it was not possible to unravel potential synergies for 1d/MRed05, as MRed05 alone displayed essentially the same efficacy as the 1d/MRed05 combination, it was apparent that the 1d/SR01 combination benefited from synergy, decreasing viral titers by a further 2 - 3 orders of magnitude to undetectable levels, relative to 1d or SR01 alone. Moreover, in accordance with the viral titer decreases, a gradual reversal of weight loss in infected animals was observed with antibody treatment starting on 2 dpi (Figs. 22B and 22C). A strong negative correlation (r = -0.9436; p <0.0001) was observed between weight change and viral titer at 5 dpi (Fig.22D). [00258] Subsequent immunohistochemistry studies corroborated the viral titer and weight change results. First, in agreement with the viral titer observations, substantial viral antigen (nucleocapsid) reductions in hamster lungs were observed with antibody treatments (Fig.23; compare non-treated PBS and isotype controls to treated profiles). Although, small foci of viral antigen expression were detected in VHH-72-, 1d-, SR01- and S2A3-treated animals, none were detected in 05-, MRed05- , 1d/SR01- and 1d/MRed05-treated animals. Second, SARS-CoV-2 infection is characterized by an overt inflammatory response in the respiratory tract accompanied by an increased infiltration of inflammatory immune cells, e.g., macrophages and T lymphocytes, in the lung parenchyma 70. As expected, this was the case for the non-treated PBS and isotype control groups. In contrast, we observed a substantial reduction of macrophages and T lymphocytes infiltrate in lung parenchyma with antibody treatment (Figs.24, 25). The most dramatic decreases in the number of macrophages and T lymphocytes were seen with 05, MRed05, 1d/MRed05 and 1d/SR01 treatments. Interestingly, a reduction in inflammatory responses was also associated with a decrease in the number of apoptotic cells in antibody-treated animals (Fig.26). Altogether, the viral titer, weight change and immunohistochemistry results consistently demonstrate that a single dose of several of the VHH-Fcs reduced viral burden, immune cell infiltration and apoptosis in the lungs of infected hamsters. [00259] The preceding examples have been provided to illustrate various aspects of the disclosure and are non-limiting. The scope of the claims is not limited to specific details provided in the examples; rather the claims are to be given the broadest interpretation consistent with the teachings of the disclosure as a whole. [00260] Table 24: List of sequences described in the specification SEQ ID Sequence Seq. Antibody(ies) ce
Figure imgf000102_0001
15 GSTSGRNT CDR1 NRCoV2-15 16 GSPFSQLA CDR1 NRCoV2-17 3 5 2 4 6 7 1 8 9 0 2 5
Figure imgf000103_0001
53 ISRSGTTT CDR2 NRCoV2-08 54 ISSRGIS CDR2 NRCoV2-10 2 4 3 5 6 7 1 8 9 0 2 5
Figure imgf000104_0001
93 TKGPDLYYFGSGYSD CDR3 NRCoV2-02 94 NIYGPTYSTRRNEY CDR3 NRCoV2-03 2 4 3 5 6 7 1 8 9
Figure imgf000105_0001
133 AAKPPFYGSGTYSTPRAYLY CDR3 NRCoV2-MRed20 134 NAREFTGFDY CDR3 NRCoV2-MRed22 5
Figure imgf000106_0001
QLQLQESGGGLVQPGGSLTLSCAASGNTFSRSNMHWY 146 RQAPGAQREWVAAISSRGISTYAYSAKGRFTISRDNAKN VHH NRCoV2-10
Figure imgf000107_0001
EVQLVQSGGGSVQAGGSLRLSCVASGFTFDNYAIGWF 157 RQAPGKEREGVSCISGNGGVTIYADSVKGRFTISRDNA VHH NRCoV2-SR01
Figure imgf000108_0001
QVQLVQSGGGSVQAGGSLRLSCAASGSTFGIFLMGWR 168 RQAPGKQRELVAHITSGGATNYADSVKGRFTISRDNAK VHH NRCoV2-S2G3 2 3 4 5 6 7 1 8
Figure imgf000109_0001
EVQLVESGGGLVQPGGSLRLSCAASTIIFKGQTMGWF 179 RQAPGNERELVATMTTSGSANYADSVKGRFTISRDNEK VHH NRCoV2-MRed19 0 2 5 ce s, n in
Figure imgf000110_0001
X at position 35 is Ala, Glu, Gly, His, Asn, or Ser X at position 36 is Trp or Tyr X t iti n 37 i Ph Hi Ar V l Tr r Tr
Figure imgf000111_0001
X at position 82 is Ala or Thr X at position 83 is Phe, Ile, Leu, Thr, or Val X t iti n 85 i Ar r Thr
Figure imgf000112_0001
X at position 124 is Phe, Gly, Ile, Leu, Gln, Ser, Tyr, or absent X t iti n 125 i Al C A Gl Pr Ar Sr ce ic nt
Figure imgf000113_0001
X at position 47 is Phe, Gly, Leu, or Pro X at position 48 is Ala or Val X t iti n 49 i Al r Sr
Figure imgf000114_0001
X at position 118 is Ala, Gly, Leu, Met, Pro, Ser, Trp, or absent X t iti n 119 i Gln Al Gl Pr Ar r b nt ce Hs, n in
Figure imgf000115_0001
X at position 60 is Met, Arg, Ser, or absent X at position 61 is Ala, Ser, Thr, or Trp X t iti n 62 i A Gln Ph Ar Sr r Thr
Figure imgf000116_0001
X at position 124 is Cys, Phe, His, Ile, Lys, Pro, Arg, Ser, or Tyr X t iti n 125 i A Gln L Mt An Sr Thr ce ic nt
Figure imgf000117_0001
X at position 53 is Asp, Glu, Cys, Phe, His, Ser, Thr, Val, or Tyr X t iti n 54 i Hi L L r V l
Figure imgf000118_0001
X at position 107 is Asp, Ala, Arg, Ser, Val, Tyr, or absent X t iti n 108 i C Ph L L S r T r r ing
Figure imgf000119_0001
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Claims

WHAT IS CLAIMED IS: 1. An isolated or purified antibody that specifically recognizes at least one coronavirus spike polypeptide, wherein the antibody comprises an antigen binding portion of an antibody heavy chain, wherein the antigen binding portion comprises a first complementarity determining region (CDR1), a second complementarity determining region (CDR2), and a third complementarity determining region (CDR3), and wherein CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 1, SEQ ID NO: 45, and SEQ ID NO: 90; SEQ ID NO: 2, SEQ ID NO: 45, and SEQ ID NO: 91; SEQ ID NO: 1, SEQ ID NO: 46, and SEQ ID NO: 92; SEQ ID NO: 3, SEQ ID NO: 47, and SEQ ID NO: 93; SEQ ID NO: 4, SEQ ID NO: 48, and SEQ ID NO: 94; SEQ ID NO: 5, SEQ ID NO: 49, and SEQ ID NO: 95; SEQ ID NO: 6, SEQ ID NO: 50, and SEQ ID NO: 96; SEQ ID NO: 7, SEQ ID NO: 51, and SEQ ID NO: 97; SEQ ID NO: 8, SEQ ID NO: 52, and SEQ ID NO: 98; SEQ ID NO: 9, SEQ ID NO: 53, and SEQ ID NO: 99; SEQ ID NO: 10, SEQ ID NO: 54, and SEQ ID NO: 100; SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 12, SEQ ID NO: 56, and SEQ ID NO: 102; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 14, SEQ ID NO: 58, and SEQ ID NO: 104; SEQ ID NO: 15, SEQ ID NO: 59, and SEQ ID NO: 105; SEQ ID NO: 16, SEQ ID NO: 60, and SEQ ID NO: 106; SEQ ID NO: 17, SEQ ID NO: 61, and SEQ ID NO: 107; SEQ ID NO: 18, SEQ ID NO: 62, and SEQ ID NO: 108; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; SEQ ID NO: 20, SEQ ID NO: 64, and SEQ ID NO: 110; SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111; SEQ ID NO: 22, SEQ ID NO: 66, and SEQ ID NO: 112; SEQ ID NO: 23, SEQ ID NO: 67, and SEQ ID NO: 113; SEQ ID NO: 24, SEQ ID NO: 68, and SEQ ID NO: 114; SEQ ID NO: 25, SEQ ID NO: 69, and SEQ ID NO: 115; SEQ ID NO: 26, SEQ ID NO: 70, and SEQ ID NO: 116; SEQ ID NO: 27, SEQ ID NO: 71, and SEQ ID NO: 117; SEQ ID NO: 28, SEQ ID NO: 72, and SEQ ID NO: 118; SEQ ID NO: 29, SEQ ID NO: 73, and SEQ ID NO: 119; SEQ ID NO: 30, SEQ ID NO: 74, and SEQ ID NO: 120; SEQ ID NO: 31, SEQ ID NO: 75, and SEQ ID NO: 121; SEQ ID NO: 32, SEQ ID NO: 76, and SEQ ID NO: 122; SEQ ID NO: 33, SEQ ID NO: 77, and SEQ ID NO: 123; SEQ ID NO: 34, SEQ ID NO: 78, and SEQ ID NO: 124; SEQ ID NO: 35, SEQ ID NO: 79, and SEQ ID NO: 125; SEQ ID NO: 36, SEQ ID NO: 80, and SEQ ID NO: 125; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 126; SEQ ID NO: 20, SEQ ID NO: 81, and SEQ ID NO: 127; SEQ ID NO: 37, SEQ ID NO: 82, and SEQ ID NO: 128; SEQ ID NO: 38, SEQ ID NO: 83, and SEQ ID NO: 129; SEQ ID NO: 39, SEQ ID NO: 84, and SEQ ID NO: 130; SEQ ID NO: 40, SEQ ID NO: 85, and SEQ ID NO: 131; SEQ ID NO: 41, SEQ ID NO: 86, and SEQ ID NO: 132; SEQ ID NO: 42, SEQ ID NO: 87, and SEQ ID NO: 133; SEQ ID NO: 43, SEQ ID NO: 88, and SEQ ID NO: 134; or SEQ ID NO: 44, SEQ ID NO: 89, and SEQ ID NO: 135.
2. The antibody of claim 1, wherein the antibody is a neutralizing antibody and wherein CDR1, CDR2, and CDR3, respectively, comprise the amino acid sequence set forth in: SEQ ID NO: 11, SEQ ID NO: 55, and SEQ ID NO: 101; SEQ ID NO: 13, SEQ ID NO: 57, and SEQ ID NO: 103; SEQ ID NO: 19, SEQ ID NO: 63, and SEQ ID NO: 109; or SEQ ID NO: 21, SEQ ID NO: 65, and SEQ ID NO: 111.
3. The antibody of claim 1, wherein the antibody comprises the amino acid sequence set forth in SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, or SEQ ID NO: 186.
4. The antibody of claim 1, wherein the antibody comprises the amino acid sequence set forth in SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, or SEQ ID NO: 182, or an amino acid sequence having at least 75% sequence identity to the full length of the amino acid sequence set forth in SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, or SEQ ID NO: 182.
5. The antibody of any one of claims 1 to 4, wherein the antibody is a single domain antibody.
6. The antibody of claim 5, wherein the antibody is a VHH.
7. The antibody of any one of claims 1 to 6, wherein the antibody is of camelid origin.
8. The antibody of any one of claims 1 to 7, wherein the antibody is in a multivalent display format.
9. The antibody of claim 8, wherein the antibody is linked to an Fc fragment.
10. The antibody of claim 9, wherein the antibody is in a bivalent display format.
11. A nucleic acid molecule encoding an antibody as described in any one of claims 1 to 10.
12. A vector comprising the nucleic acid molecule of claim 11.
13. The vector of claim 12, wherein the nucleic acid molecule is operably linked to at least one promoter and/or regulatory element to enable expression in a host cell.
14. A host cell comprising the vector of claim 12 or 13.
15. A pharmaceutical composition comprising at least one antibody as defined in any one of claims 1 to 10 and a pharmaceutically acceptable carrier and/or diluent.
16. The pharmaceutical composition of claim 15, wherein the composition is for delivery by inhalation or nebulization.
17. A composition comprising at least one antibody as defined in any one of claims 1 to 10 linked to another molecule.
18. The composition of claim 17, wherein the other molecule is a label or polypeptide.
19. The composition of claim 17, wherein the other molecule is an ACE2 polypeptide or a fragment thereof.
20. A composition comprising at least one antibody as defined in any one of claims 1 to 10 immobilized on a substrate.
21. Use of the antibody of any one of claims 1 to 10 or the composition of any one of claims 15 to 19 to treat or detect a coronavirus infection.
22. The use of claim 21, wherein the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
23. The use of claim 21 or 22, wherein the coronavirus infection is caused by SARS-CoV-2 and/or SARS-CoV.
24. Use of the antibody of any one of claims 1 to 10 or the composition of any one of claims 15 to 20 to detect, quantify and/or capture a coronavirus; or to detect, quantify and/or capture a coronavirus spike polypeptide or fragment thereof.
25. The use of claim 24, wherein the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
26. The use of claim 25, wherein the coronavirus is SARS-CoV-2 or SARS-CoV.
27. A method for treating or preventing a coronavirus infection, the method comprising administering at least one antibody as defined in any one of claims 1 to 10 or a composition as defined in any one of claims 15 to 19 to a subject in need thereof.
28. The method of claim 27, wherein the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
29. The method of claim 27 or 276, wherein the coronavirus infection is caused by SARS- CoV-2 and/or SARS-CoV.
30. The method of any one of claims 27 to 29, wherein the administration is by inhalation or nebulization.
31. A method for detecting the presence of a coronavirus or a coronavirus spike polypeptide or fragment thereof in a sample, the method comprising exposing the sample to at least one antibody as defined in any one of claims 1 to 10 or a composition as defined in any one of claims 15 to 20 and assaying for specific binding between the at least one antibody and the sample, wherein specific binding indicates a presence of the at least one coronavirus or coronavirus spike polypeptide or fragment thereof in the sample.
32. A method for capturing a coronavirus or a coronavirus spike polypeptide or fragment thereof from a sample, the method comprising exposing the sample to the composition as defined in claim 20.
33. The method of claim 31 or 32, wherein the coronavirus is a coronavirus that specifically binds an ACE2 receptor or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
34. The method of any one of claims 31 to 33, wherein the coronavirus is SARS-CoV-2 or SARS-CoV, or the coronavirus spike polypeptide or fragment thereof is a SARS-CoV-2 or SARS- CoV coronavirus spike polypeptide or fragment thereof.
35. The antibody of any one of claims 1 to 10 or the composition of any one of claims 15 to 19 for use to detect or treat a coronavirus infection.
36. The antibody of claim 35, wherein the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
37. The antibody of claim 35 or 36, wherein the at least one coronavirus is SARS-CoV-2 and/or SARS-CoV.
38. The antibody of any one of claims 1 to 10 or the composition of any one of claims 15 to 19 for use to detect, quantify and/or capture a coronavirus; or to detect, quantify and/or capture a coronavirus spike polypeptide or fragment thereof.
39. The antibody of claim 38, wherein the coronavirus is a coronavirus that specifically binds an ACE2 receptor, or the coronavirus spike polypeptide is a coronavirus spike polypeptide that specifically binds an ACE2 receptor.
40. The antibody of claim 38 or 39, wherein the coronavirus is SARS-CoV-2 or SARS-CoV or the coronavirus spike polypeptide or fragment thereof is a SARS-CoV-2 or SARS-CoV spike polypeptide or fragment thereof.
41. Use of the antibody of any one of claims 1 to 10 in the manufacture of a medicament for prevention or treatment of a coronavirus infection.
42. The use of claim 41, wherein the coronavirus infection is caused by at least one coronavirus that specifically binds an ACE2 receptor.
43. The use of claim 42, wherein the at least one coronavirus is SARS-CoV-2 and/or SARS- CoV.
44. The use of any one of claims 41 to 43, wherein the medicament is for delivery by inhalation or nebulization.
45. An antibody cocktail composition comprising two or more of the antibodies as defined in any one of claims 1 to 10.
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