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WO2025117384A1 - Anticorps dirigés contre la souche de l'hémagglutinine de la grippe largement neutralisants - Google Patents

Anticorps dirigés contre la souche de l'hémagglutinine de la grippe largement neutralisants Download PDF

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Publication number
WO2025117384A1
WO2025117384A1 PCT/US2024/057131 US2024057131W WO2025117384A1 WO 2025117384 A1 WO2025117384 A1 WO 2025117384A1 US 2024057131 W US2024057131 W US 2024057131W WO 2025117384 A1 WO2025117384 A1 WO 2025117384A1
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antibody
amino acid
antigen binding
seq
binding fragment
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Sarah Faith ANDREWS
Grace Emma MANTUS
Ankita Jayant CHOPDE
Adrian CREANGA
Rebecca Aileen GILLESPIE
Masaru Kanekiyo
Lauren Yvette-Marie COMINSKY
Julie Eva RAAB
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US Department of Health and Human Services
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1018—Orthomyxoviridae, e.g. influenza virus
    • 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
    • A61P31/16—Antivirals for RNA viruses for influenza or rhinoviruses
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • This relates to monoclonal antibodies and antigen binding fragments thereof that specifically bind to the stem region of influenza virus hemagglutinin (HA) and their use, for example, in methods of treating a subject with an influenza A infection, detecting influenza virus in a sample, and for selecting vaccines.
  • HA hemagglutinin
  • Sequence Listing is submitted as an XML file in the form of the file named “Sequence.xml” (58,709 bytes), which was created on November 13, 2024, which is incorporated by reference herein.
  • Influenza virus epidemics are typically associated with 290,000 to 640,000 deaths annually worldwide (luliano et al., Lancet 391, 1285-1300 (2016)).
  • H1N1, H3N2, and H2N2 influenza subtypes have caused pandemics in the past 100 years with increased mortality rates, including the 1918 H1N1 influenza pandemic, which was responsible for 20 million to 50 million deaths.
  • the high mutability of influenza virus and existence of ample animal reservoirs make the emergence of another pandemic highly likely.
  • a need remains for antibodies that target different epitopes on influenza virus proteins, such as the hemagglutinin (HA) protein, that can help to design better immunogens, and can be used therapeutically and prophylactically.
  • HA hemagglutinin
  • Monoclonal antibodies and antigen binding fragments thereof that specifically bind the stem region of HA of an influenza virus are disclosed herein.
  • the monoclonal antibodies and antigen binding fragments bind the HA of H3N2 influenza virus.
  • the monoclonal antibodies and antigen binding fragments bind the HA of H1N1 influenza virus.
  • the monoclonal antibodies and antigen binding fragments can bind multiple subtypes.
  • the monoclonal antibodies and antigen binding fragments can bind the HA of group 1 and group 2 influenza viruses.
  • an isolated monoclonal antibody including a heavy chain variable region and a light chain variable region comprising a heavy chain complementarity determining region (HCDR)l, a HCDR2, and a HCDR3 and a light chain complementarity determining region (LCDR)l, a LCDR2, and a LCDR3 of the VH and VL set forth as one of: a) SEQ ID NOs: 9 and 13, respectively (323-2019_c2328.144); b) SEQ ID NOs: 17 and 21, respectively (323-220-03JB05); c) SEQ ID NOs: 1 and 5, respectively (323-2001_c39.1); d) SEQ ID NOs: 65 and 69, respectively (315-53-1G08), e) SEQ ID NOs: 25 and 29, respectively (323-2007_cl 33.101); f) SEQ ID NOs: 33 and 37, respectively (321-205-1C09); g) SEQ ID NOs: 41 and 45, respectively (321-213
  • methods for preventing or treating influenza in a subject. These methods include administering to the subject a therapeutically effective amount of a disclosed antibody or antigen binding fragment, or a nucleic acid encoding the antibody or the antigen binding fragment.
  • methods for detecting an influenza virus infection in a subject.
  • the methods include contacting a biological sample from the subject with a disclosed monoclonal antibody or antigen binding fragment, and detecting antibody bound to the sample. The presence of antibody bound to the sample indicates that the subject has an influenza virus infection.
  • methods for identifying a protein as a vaccine candidate for preventing or treating an influenza virus infection.
  • the methods include contacting the protein with a disclosed monoclonal antibody or antigen binding fragment, under conditions sufficient to form an immune complex, and detecting the presence of an immune complex. The presence of the immune complex indicates that the protein is a vaccine candidate for an influenza virus infection.
  • FIG. 1 Broadly neutralizing monoclonal antibodies (mAbs) against group 1 and group 2 influenza virus subtypes.
  • mAbs 321 -2001 -c39.1, 315-53-1G08 and MEDI8852 (a previously described HA stemspecific mAb) were tested side-by-side for neutralization against a panel of eight influenza virus strains representing all subtypes known to infect humans. Shown is the microneutralization inhibitory concentration 80 (IC80) in Ltg/rnl for each mAb.
  • FIGS. 2A-2B Broadly neutralizing mAbs across H3N2 strains.
  • mAbs 323-2007_cl33.101, 323- 2019_c2328.144, 323-220-03JB05, 323-2001_c39.1, MEDI8852, and CR8020 were tested for neutralization against 22 H3N2 strains ranging from 1968 through 2021, one H10N8 strain, and two H7N9 strains.
  • FIG. 2A Graph showing the IC80 for each mAb. Each dot represents the IC80 for one H3N2 strain, and the lines and numbers above indicate the median IC80.
  • FIG. 2B Table listing the IC80 (jlg/ml) against seven of the H3N2 strains, the H10N8 strain, and the two H7N9 strains.
  • FIGS. 3A-3B Broadly neutralizing mAbs against group 1 subtypes.
  • mAbs 321-205-1C09, 321- 213-1 A07, MEDI8852, and CR6261 (a previously described HA stem-specific mAb) were tested against a panel of 15 H1N1 strains from 1943 to 2018, an H2N2 strain, an H5N1 strain, and a H6N1 strain.
  • FIG. 3A Graph showing the IC80 against the 15 H1N1 strains for each mAh. Each dot represents the IC80 for one H1N1 strain, and the lines and numbers above indicate the median IC80.
  • FIG. 3B Table listing the IC80 (pg/ml) of each mAb against all strains tested.
  • FIG. 4 Additional potent and broadly neutralizing mAbs against H1N1 strains.
  • the graph shows microneutralization IC80 against pandemic (A/Cal09) and pre-pandemic (A/NC99) H1N1 strains of multiple mAbs isolated from participants of the Hl stabilized stem clinical trial. Each line represents the IC80 of a given mAb against both H1N1 strains.
  • FIGS. 5A-5B Structure of H10 stem with glycan mutated residues highlighted, and illustrating the central and lower epitopes of the stem region of HA.
  • FIG. 5A Gly45 blocks the central epitope, and Gly34 blocks the lower epitope.
  • Unclear (gray) indicates mAbs that were blocked by both Gly34 and Gly45 or neither.
  • FIG. 5B Donut plot identifying proportion of mAbs that bound either Gly45 or Gly34 H10/H3 trimer.
  • FIGS. 6A-6G Lower epitope-reactive antibodies demonstrate greater neutralization breadth across H3N2 strains than central epitope -reactive antibodies.
  • FIG. 6B Spider plot of the mean ICso of central and lower epitope mAbs that showed neutralization against H3N2 strains tested. Non-neutralizing mAbs (ICso>25) were excluded from this analysis.
  • FIG. 6B Spider plot
  • nucleic acid and amino acid sequences listed herein are shown using standard letter abbreviations for nucleotide bases, and single letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand.
  • SEQ ID NO: 1 is the amino acid sequence of the heavy chain variable (V H ) domain of 323- 2001_c39.1.
  • SEQ ID NOs: 2, 3 and 4 are the amino acid sequences of the IMGT (IMMUNOGENETICS® information system) HCDR1, HCDR2, and HCDR3 of 323-2001_c39.1.
  • SEQ ID NO: 5 is the amino acid sequence of the light chain variable (VL) domain of 323- 2001_c39.1.
  • SEQ ID NOs: 6, 7 and 8 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR3 of 323-2001_c39.1.
  • SEQ ID NO: 9 is the amino acid sequence of the VH domain of 323-2019_c2328.144.
  • SEQ ID NOs: 10, 11 and 12 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 323-2019_c2328.144.
  • SEQ ID NO: 13 is the amino acid sequence of the V domain of 323-2019_c2328.144.
  • SEQ ID NOs: 14, 15 and 16 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR3 of 323-2019_c2328.144.
  • SEQ ID NO: 17 is the amino acid sequence of the VH domain of 323-220-03_lB05.
  • SEQ ID NOs: 18, 19 and 20 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 323-220-03_lB05.
  • SEQ ID NO: 21 is the amino acid sequence of the V domain of 323-220-03_lB05.
  • SEQ ID NOs: 22, 23 and 24 are the amino acid sequence of the IMGT LCDR1, LCDR2, and LCDR2 of 323-220-03_lB05.
  • SEQ ID NO: 25 is the amino acid sequence of the VH domain of 323-2007_cl33.101.
  • SEQ ID Nos: 26, 27, and 28 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 323-2007_cl33.101.
  • SEQ ID NO: 29 is the amino acid sequence of the VLdomain of 323-2007_cl 33.101.
  • SEQ ID NOs: 30, 31 and 32 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR2 of 323-2007_cl33.101.
  • SEQ ID NO: 33 is the amino acid sequence of the VH domain of 321-205-1C09.
  • SEQ ID NOs: 34, 35 and 36 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 321-205-1C09.
  • SEQ ID NO: 37 is the amino acid sequence of the VL domain of 321-205-1C09.
  • SEQ ID NOs: 38, 39 and 40 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR2 of 321-205-1C09.
  • SEQ ID NO: 41 is the amino acid sequence of the VH domain of 321-213-1A07.
  • SEQ ID NOs: 42, 43 and 44 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 321-213-1A07.
  • SEQ ID NO: 45 is the amino acid sequence of the V domain of 321-213-1A07.
  • SEQ ID NOs: 46, 47 and 48 are the amino acid sequences of the IMGT LCDR1, LCDR2, and
  • SEQ ID NO: 49 is the amino acid sequence of the VH domain of 321-205-1D01.
  • SEQ ID NOs: 50, 51 and 52 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 321-205-1D01.
  • SEQ ID NO: 53 is the amino acid sequence of the V domain of 321-205-1D01.
  • SEQ ID NOs: 54, 55 and 56 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR3 of 321-205-1D01.
  • SEQ ID NO: 57 is the amino acid sequence of the VH domain of 321-102-1E12.
  • SEQ ID NOs: 58, 59 and 60 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 321-102-1E12.
  • SEQ ID NO: 61 is the amino acid sequence of the VL domain of 321-102-1E12.
  • SEQ ID NOs: 62, 63, and 64 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR3 of 321-102-1E12.
  • SEQ ID NO: 65 is the amino acid sequence of the VH domain of 315-53-1GO8.
  • SEQ ID NOs: 66, 67, 68 are the amino acid sequences of the IMGT HCDR1, HCDR2, and HCDR3 of 315-53-1G08.
  • SEQ ID NO: 69 is the amino acid sequence of the VL domain of 315-53-1G08.
  • SEQ ID NOs: 70, 71 and 72 are the amino acid sequences of the IMGT LCDR1, LCDR2, and LCDR3 of 315-53-1G08.
  • mAbs monoclonal antibodies
  • antigen binding fragments that specifically bind to the stem region of influenza virus HA and their use, for example, in methods of treating a subject with an influenza A virus infection, and their use for detection of an influenza virus in a sample, and for selecting vaccines.
  • These antibodies neutralize several influenza virus subtypes, including within the circulating H1N1 and H3N2 subtypes.
  • a group of mAbs was isolated that bind to HA and neutralize influenza A virus. These antibodies confer protection against infection in both prophylactic and therapeutic settings.
  • the monoclonal antibodies and antigen binding fragments bind the HA of H3N2 influenza virus.
  • the monoclonal antibodies and antigen binding fragments bind the HA of H1N1 influenza virus.
  • the monoclonal antibodies and antigen binding fragments can bind multiple subtypes.
  • the monoclonal antibodies and antigen binding fragments can bind the HA of group 1 and group 2 influenza viruses. In some aspects, these antibodies and antigen binding fragments inhibit propagation in vitro of influenza A H1N1 and/or H3N2 virus.
  • an antigen includes singular or plural antigens and can be considered equivalent to the phrase “at least one antigen.”
  • the term “comprises” means “includes.” It is further to be understood that any and all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for descriptive purposes, unless otherwise indicated. Although many methods and materials similar or equivalent to those described herein can be used, particular suitable methods and materials are described herein. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. To facilitate review of the various aspects, the following explanations of terms are provided:
  • Administration The introduction of an agent, such as a disclosed antibody, into a subject by a chosen route.
  • Administration can be local or systemic.
  • the agent such as an antibody
  • exemplary routes of administration include, but are not limited to, oral, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), sublingual, rectal, transdermal (for example, topical), intranasal, vaginal, and inhalation routes.
  • Amino acid substitution The replacement of one amino acid in a polypeptide with a different amino acid.
  • Antibody and Antigen Binding Fragment An immunoglobulin, antigen-binding fragment, or derivative thereof, that specifically binds and recognizes an analyte (antigen) such as a HA protein, such as the stem region of the HA protein.
  • analyte such as a HA protein, such as the stem region of the HA protein.
  • antibody is used herein in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antigen binding fragments, so long as they exhibit the desired antigen-binding activity.
  • Non-limiting examples of antibodies include, for example, intact immunoglobulins and variants and fragments thereof that retain binding affinity for the antigen.
  • antigen binding fragments include but are not limited to Fv, Fab, Fab', Fab'-SH, F(ab') 2 ; diabodies; linear antibodies; single-chain antibody molecules e.g., scFv); and multispecific antibodies formed from antibody fragments.
  • Antibody fragments include antigen binding fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies (see, e.g., Kontermann and Diibel (Eds.), Antibody Engineering, Vols. 1-2, 2 nd ed., Springer-Verlag, 2010).
  • Antibodies also include genetically engineered forms such as chimeric antibodies (such as humanized murine antibodies) and heteroconjugate antibodies (such as bispecific antibodies).
  • An antibody may have one or more binding sites. If there is more than one binding site, the binding sites may be identical to one another or may be different. For instance, a naturally-occurring immunoglobulin has two identical binding sites, a single-chain antibody or Fab fragment has one binding site, while a bispecific or bifunctional antibody has two different binding sites.
  • immunoglobulin typically has heavy (H) chains and light (L) chains interconnected by disulfide bonds.
  • Immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable domain genes.
  • X lambda
  • K kappa
  • Each heavy and light chain contains a constant region (or constant domain) and a variable region (or variable domain).
  • the heavy and the light chain variable regions specifically bind the antigen.
  • VH refers to the variable region of an antibody heavy chain, including that of an antigen binding fragment, such as Fv, scFv, dsFv or Fab.
  • VL refers to the variable domain of an antibody light chain, including that of an Fv, scFv, dsFv or Fab.
  • the VH and VL contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs” (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, 5 th ed., NIH Publication No.
  • the sequences of the framework regions of different light or heavy chains are relatively conserved within a species.
  • the framework region of an antibody that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.
  • the CDRs are primarily responsible for binding to an epitope of an antigen.
  • the amino acid sequence boundaries of a given CDR can be readily determined using any of a number of well-known schemes, including those described by Kabat et al. (Sequences of Proteins of Immunological Interest, 5 th ed., NIH Publication No. 91-3242, Public Health Service, National Institutes of Health, U.S. Department of Health and Human Services, 1991; “Kabat” numbering scheme), Al-Lazikani et al., (“Standard conformations for the canonical structures of immunoglobulins,” J. Mol. Bio., 273(4):927-948, 1997; “Chothia” numbering scheme), and Lefranc et al. (“IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains,” Dev. Comp. Immunol., 2003;
  • the CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3 (from the N-terminus to C-terminus), and are also typically identified by the chain in which the particular CDR is located.
  • a VH CDR3 is the CDR3 from the VH of the antibody in which it is found
  • a VL CDR1 is the CDR1 from the V of the antibody in which it is found.
  • Light chain CDRs are sometimes referred to as LCDR1, LCDR2, and LCDR3.
  • Heavy chain CDRs are sometimes referred to as HCDR1, HCDR2, and HCDR3.
  • a disclosed antibody includes a heterologous constant domain.
  • the antibody can include a constant domain that is different from a native constant domain, such as a constant domain including one or more modifications (such as the “LS” mutation) to increase half-life.
  • a “monoclonal antibody” is an antibody obtained from a population of substantially homogeneous antibodies, that is, the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, for example, containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts.
  • polyclonal antibody preparations typically include different antibodies directed against different determinants (epitopes)
  • each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen.
  • the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies may be made by a variety of techniques, including but not limited to the hybridoma method, recombinant DNA methods, phage-display methods, and methods utilizing transgenic animals containing all or part of the human immunoglobulin loci, such methods and other exemplary methods for making monoclonal antibodies being described herein.
  • monoclonal antibodies are isolated from a subject.
  • Monoclonal antibodies can have conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions (see, for example, Greenfield (Ed.), Antibodies: A Laboratory Manual, 2 nd ed. New York: Cold Spring Harbor Laboratory Press, 2014.)
  • a “humanized” antibody or antigen binding fragment includes a human framework region and one or more CDRs from a non-human (such as a mouse, rat, or synthetic) antibody or antigen binding fragment.
  • the non-human antibody or antigen binding fragment providing the CDRs is termed a “donor,” and the human antibody or antigen binding fragment providing the framework is termed an “acceptor.”
  • all of the CDRs are from the donor immunoglobulin in a humanized immunoglobulin. Constant regions need not be present, but if they are, they can be substantially identical to human immunoglobulin constant regions, such as at least about 85-90%, such as about 95% or more identical.
  • all parts of a humanized antibody or antigen binding fragment, except possibly the CDRs are substantially identical to corresponding parts of natural human antibody sequences.
  • a “chimeric antibody” is an antibody which includes sequences derived from two different antibodies, which typically are of different species.
  • a chimeric antibody includes one or more CDRs and/or framework regions from one human antibody and CDRs and/or framework regions from another human antibody.
  • a “fully human antibody” or “human antibody” is an antibody which includes sequences from (or derived from) the human genome and does not include sequence from another species.
  • a human antibody includes CDRs, framework regions, and (if present) an Fc region from (or derived from) the human genome.
  • Human antibodies can be identified and isolated using technologies for creating antibodies based on sequences derived from the human genome, for example by phage display or using transgenic animals (see, e.g., Barbas et al. Phage display: A Laboratory Manuel. 1 st Ed. New York: Cold Spring Harbor Laboratory Press, 2004. Print.; Lonberg, Nat. Biotech., 23: 1117-1125, 2005; Lonenberg, Cun. Opin. Immunol., 20:450-459, 2008).
  • Antibody or antigen binding fragment that neutralizes an influenza virus An antibody or antigen binding fragment that specifically binds to an influenza antigen (such as the HA protein) in such a way as to inhibit a biological function associated with the influenza virus that inhibits infection.
  • the antibody can neutralize the activity of one or more influenza viruses.
  • an antibody or antigen binding fragment that neutralizes the influenza virus may interfere with the virus by binding it directly and limiting entry into cells.
  • an antibody may interfere with one or more post-attachment interactions of the pathogen with a receptor, for example, by interfering with viral entry using the receptor.
  • an antibody that is specific for an influenza virus neutralizes the infectious titer of this virus.
  • Biological sample A sample obtained from a subject. Biological samples include all clinical samples useful for detection of disease or infection in subjects, including, but not limited to, cells, tissues, and bodily fluids, such as blood, sputum, nasal swab, derivatives and fractions of blood (such as serum), cerebrospinal fluid, as well as biopsied or surgically removed tissue, for example tissues that are unfixed, frozen, or fixed in formalin or paraffin.
  • a biological sample is obtained from a subject having or suspected of having an influenza virus infection, such as, but not limited to, an influenza A virus infection.
  • Bispecific antibody A recombinant molecule composed of two different antigen binding domains that consequently binds to two different antigenic epitopes.
  • Bispecific antibodies include chemically or genetically linked molecules of two antigen-binding domains.
  • the antigen binding domains can be linked using a linker.
  • the antigen binding domains can be monoclonal antibodies, antigen-binding fragments (e.g., Fab, scFv), or combinations thereof.
  • a bispecific antibody can include one or more constant domains but does not necessarily include a constant domain.
  • Conditions sufficient to form an immune complex Conditions which allow an antibody or antigen binding fragment to bind to its cognate epitope to a detectably greater degree than, and/or to the substantial exclusion of, binding to substantially all other epitopes. Conditions sufficient to form an immune complex are dependent upon the format of the binding reaction and typically are those utilized in immunoassay protocols, or those conditions encountered in vivo. See Greenfield (Ed.), Antibodies: A Laboratory Manual, 2 nd ed. New York: Cold Spring Harbor Laboratory Press, 2014, for a description of immunoassay formats and conditions.
  • the conditions employed in the methods are “physiological conditions” which include reference to conditions (e.g., temperature, osmolarity, pH) that are typical inside a living mammal or a mammalian cell. While it is recognized that some organs are subject to extreme conditions, the intra-organismal and intracellular environment normally lies around pH 7 (e.g., from pH 6.0 to pH 8.0, more typically pH 6.5 to 7.5), contains water as the predominant solvent, and exists at a temperature above 0°C and below 50°C. Osmolarity is within the range that is supportive of cell viability and proliferation.
  • conditions e.g., temperature, osmolarity, pH
  • an immune complex can be detected through conventional methods, for instance immunohistochemistry (IHC), immunoprecipitation (IP), flow cytometry, immunofluorescence microscopy, ELISA, immunoblotting (for example, Western blot), magnetic resonance imaging (MRI), computed tomography (CT) scans, radiography, and affinity chromatography.
  • IHC immunohistochemistry
  • IP immunoprecipitation
  • IP flow cytometry
  • ELISA immunofluorescence microscopy
  • immunoblotting for example, Western blot
  • MRI magnetic resonance imaging
  • CT computed tomography
  • Conjugate A complex of two molecules linked together, for example, linked together by a covalent bond.
  • an antibody is linked to an effector molecule; for example, an antibody that specifically binds to HA, covalently linked to an effector molecule, such as a detectable label.
  • the linkage can be by chemical or recombinant means.
  • the linkage is chemical, wherein a reaction between the antibody moiety and the effector molecule has produced a covalent bond formed between the two molecules to form one molecule.
  • a peptide linker short peptide sequence
  • conjugates can be prepared from two molecules with separate functionalities, such as an antibody and an effector molecule, they are also sometimes referred to as “chimeric molecules.”
  • “Conservative” amino acid substitutions are those substitutions that do not substantially affect or decrease a function of a protein, such as the ability of the protein to interact with a target protein.
  • a HA-specific antibody can include up to 1, 2, 3, 4, 5, 6, 7, 8, 9, or up to 10 conservative substitutions compared to a reference antibody sequence and retain specific binding activity for HA protein binding, and/or influenza virus neutralization activity.
  • the term conservative variant also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid.
  • Non-conservative substitutions are those that reduce an activity or function of the antibody, such as the ability to specifically bind to HA, such as the stem region of HA. For instance, if an amino acid residue is essential for a function of the protein, even an otherwise conservative substitution may disrupt that activity. Thus, a conservative substitution does not alter the basic function of a protein of interest.
  • Placement in direct physical association includes both in solid and liquid form, which can take place either in vivo or in vitro.
  • Contacting includes contact between one molecule and another molecule, for example the amino acid on the surface of one polypeptide, such as an antigen, that contacts another polypeptide, such as an antibody.
  • Contacting can also include contacting a cell for example by placing an antibody in direct physical association with a cell.
  • Control A reference standard.
  • the control is a negative control, such as sample obtained from a healthy patient not infected with an influenza virus.
  • the control is a positive control, such as a tissue sample obtained from a patient diagnosed with an influenza virus infection.
  • the control is a historical control or standard reference value or range of values (such as a previously tested control sample, such as a group of patients with known prognosis or outcome, or group of samples that represent baseline or normal values).
  • a difference between a test sample and a control can be an increase or conversely a decrease.
  • the difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference.
  • a difference is an increase or decrease, relative to a control, of at least about 5%, such as at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, at least about 300%, at least about 350%, at least about 400%, or at least about 500%.
  • a “degenerate variant” refers to a polynucleotide encoding a polypeptide (such as an antibody heavy or light chain) that includes a sequence that is degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences encoding a peptide are included as long as the amino acid sequence of the peptide encoded by the nucleotide sequence is unchanged.
  • Detectable marker A detectable molecule (also known as a label) that is conjugated directly or indirectly to a second molecule, such as an antibody, to facilitate detection of the second molecule.
  • the detectable marker can be capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy or diagnostic imaging techniques (such as CT scans, MRIs, ultrasound, fiberoptic examination, and laparoscopic examination).
  • detectable markers include fluorophores, chemiluminescent agents, enzymatic linkages, radioactive isotopes and heavy metals or compounds (for example super paramagnetic iron oxide nanocrystals for detection by MRI).
  • Detecting To identify the existence, presence, or fact of something.
  • Effective amount A quantity of a specific substance sufficient to achieve a desired effect in a subject to whom the substance is administered. For instance, this can be the amount necessary to inhibit an influenza infection, such as an H INI or H3N2 influenza virus infection, or to measurably alter outward symptoms of such an infection.
  • an influenza infection such as an H INI or H3N2 influenza virus infection
  • a desired response is to inhibit or reduce or prevent an influenza virus infection.
  • the influenza virus infection does not need to be completely eliminated or reduced or prevented for the method to be effective.
  • administration of an effective amount can decrease the influenza virus infection (for example, as measured by infection of cells, or by number or percentage of subjects infected by the influenza virus), by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable influenza virus infection), as compared to a suitable control.
  • administering can reduce or inhibit infection (for example, as measured by infection of cells, or by number or percentage of subjects infected by the influenza virus or by an increase in the survival time of infected subjects, or reduction in symptoms associated with the infection), for example by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination or prevention of detectable infection), as compared to a suitable control.
  • infection for example, as measured by infection of cells, or by number or percentage of subjects infected by the influenza virus or by an increase in the survival time of infected subjects, or reduction in symptoms associated with the infection
  • the effective amount of an antibody or antigen binding fragment that specifically binds HA that is administered to a subject to inhibit infection will vary depending upon a number of factors associated with that subject, for example the overall health and/or weight of the subject.
  • An effective amount can be determined by varying the dosage and measuring the resulting response, such as, for example, a reduction in pathogen titer.
  • Effective amounts also can be determined through various in vitro, in vivo or in situ immunoassays.
  • an effective amount encompasses a fractional dose that contributes, optionally in combination with previous or subsequent administrations, to attaining an effective response.
  • an effective amount of an agent can be administered in a single dose, or in several doses, for example daily, during a course of treatment lasting several days or weeks. However, the effective amount can depend on the subject being treated, the severity and type of the condition being treated, and the manner of administration.
  • a unit dosage form of the agent can be packaged in an amount, or in multiples of the effective amount, for example, in a vial (e.g., with a pierceable lid) or syringe having sterile components.
  • Effector molecule A molecule intended to have or produce a desired effect; for example, a desired effect on a cell to which the effector molecule is targeted, or a detectable marker. Effector molecules can include, for example, polypeptides and small molecules. Some effector molecules may have or produce more than one desired effect.
  • Epitope An antigenic determinant. These are particular chemical groups or peptide sequences on a molecule that are antigenic, such that they elicit a specific immune response, for example, an epitope is the region of an antigen to which B and/or T cells respond. An antibody can bind to a particular antigenic epitope, such as an epitope on HA, such as the stem region of HA.
  • an encoding nucleic acid sequence can be expressed when its DNA is transcribed into RNA or an RNA fragment, which in some examples is processed to become mRNA.
  • An encoding nucleic acid sequence (such as a gene) may also be expressed when its mRNA is translated into an amino acid sequence, such as a protein or a protein fragment.
  • a heterologous gene is expressed when it is transcribed into an RNA.
  • a heterologous gene is expressed when its RNA is translated into an amino acid sequence. Regulation of expression can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein molecules after they are produced.
  • Expression Control Sequences Nucleic acid sequences that regulate the expression of a heterologous nucleic acid sequence to which it is operatively linked. Expression control sequences are operatively linked to a nucleic acid sequence when the expression control sequences control and regulate the transcription and, as appropriate, translation of the nucleic acid sequence.
  • expression control sequences can include appropriate promoters, enhancers, transcriptional terminators, a start codon (ATG) in front of a protein-encoding gene, splice signals for introns, maintenance of the correct reading frame of that gene to permit proper translation of mRNA and stop codons.
  • control sequences includes, at a minimum, components whose presence can influence expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Expression control sequences can include a promoter.
  • Expression vector A vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed.
  • An expression vector comprises sufficient cis- acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system.
  • Non-limiting examples of expression vectors include cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
  • a polynucleotide can be inserted into an expression vector that contains a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host.
  • the expression vector typically contains an origin of replication, a promoter, as well as specific nucleic acid sequences that allow phenotypic selection of the transformed cells.
  • Fc region The constant region of an antibody excluding the first heavy chain constant domain.
  • Fc region generally refers to the last two heavy chain constant domains of IgA, IgD, and IgG, and the last three heavy chain constant domains of IgE and IgM.
  • An Fc region may also include part or all of the flexible hinge N-terminal to these domains.
  • an Fc region may or may not include the tailpiece, and may or may not be bound by the J chain.
  • the Fc region is typically understood to include immunoglobulin domains Cy2 and Cy3 and optionally the lower part of the hinge between Cyl and Cy2.
  • the human IgG heavy chain Fc region is usually defined to include residues following C226 or P230 to the Fc carboxyl-terminus, wherein the numbering is according to EU numbering.
  • the Fc region includes immunoglobulin domains Ca2 and Ca3 and optionally the lower part of the hinge between Cal and Ca2.
  • Hemagglutinin An influenza virus surface glycoprotein that is a homotrimeric integral membrane glycoprotein. HA mediates binding of the virus particle to a host cell and subsequent entry of the virus into the host cell.
  • the nucleotide and amino acid sequences of numerous influenza HA proteins are known in the art and are publicly available, such as through the NCBI Influenza Virus Resource database (Bao et al., J Virol 82:596-601, 2008).
  • HA (along with NA) is one of the two major influenza virus antigenic determinants.
  • the three identical monomers that constitute HA are constructed into a central a helix coil; three spherical heads contain the sialic acid binding sites.
  • HA monomers are synthesized as precursors that are then glycosylated and cleaved into two smaller polypeptides: the HA1 and HA2 subunits.
  • Each HA monomer consists of a long, helical chain anchored in the membrane by HA2 and topped by a large HA1 globular head which contains the sialic acid receptor binding sites.
  • the HA2 protein chain facilitates membrane fusion; the C-terminal end of the protein is embedded in the viral membrane.
  • the stem, also known as the stalk, of HA is comprised of residues 18-59 and 292-520, including portions of HA1 and HA2 and anchors the HA protein into the viral lipid envelope.
  • the central and lower epitopes of the stem region of a group 2 HA are illustrated in FIG. 5A. In a group 1 HA the central epitope is the same as group 2, but the lower epitope is shifted lower.
  • An antibody that specifically binds an Hl subtype influenza virus does not delectably bind an influenza virus of another subtype, such as H2, H3, etc.
  • An antibody that binds HA can specifically bind to a single variant or all variants within a subtype.
  • Type A influenza viruses are further divided into Group 1 and Group 2. These Groups are further divided into subtypes, which refers to classification of a virus based on the sequence of its HA protein. Examples of subtypes are Hl, H2, H3, H4, H5, H6, H7, H8, H8, H10, Hll, H12, H13, H14, H15, H16, H17 and Hl 8.
  • Group 1 influenza subtypes are Hl, H2, H5, H6, H8, H9, Hll, H12, H13, H16, H17 and H18.
  • Group 2 influenza subtypes are H3, H4, H7, H10, H14, and H15.
  • Heterologous Originating from a different genetic source.
  • a nucleic acid molecule that is heterologous to a cell originated from a genetic source other than the cell in which it is expressed.
  • a heterologous nucleic acid molecule encoding a protein, such as an scFv is expressed in a cell, such as a mammalian cell.
  • Methods for introducing a heterologous nucleic acid molecule in a cell or organism are well known in the art, for example transformation with a nucleic acid, including electroporation, lipofection, particle gun acceleration, and homologous recombination.
  • Host cell Cells in which a vector can be propagated, and its DNA expressed.
  • the cell may be prokaryotic or eukaryotic.
  • the term also includes any progeny of the subject host cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, such progeny are included when the term “host cell” is used.
  • IgA A polypeptide belonging to the class of antibodies that are substantially encoded by a recognized immunoglobulin alpha gene. In humans, this class or isotype comprises IgAi and IgA2.
  • IgA antibodies can exist as monomers, polymers (referred to as plgA) of predominantly dimeric form, and secretory IgA.
  • the constant chain of wild-type IgA contains an 18-amino-acid extension at its C-terminus called the tail piece (tp).
  • Polymeric IgA is secreted by plasma cells with a 15-kDa peptide called the J chain linking two monomers of IgA through the conserved cysteine residue in the tail piece.
  • IgG A polypeptide belonging to the class or isotype of antibodies that are substantially encoded by a recognized immunoglobulin gamma gene. In humans, this class comprises IgGi, IgG , IgG ⁇ , and IgG i.
  • Immune complex The binding of antibody or antigen binding fragment (such as a scFv) to a soluble antigen forms an immune complex.
  • the formation of an immune complex can be detected through conventional methods, for instance immunohistochemistry, immunoprecipitation, flow cytometry, immunofluorescence microscopy, ELISA, immunoblotting (for example, Western blot), magnetic resonance imaging, CT scans, radiography, and affinity chromatography.
  • Influenza virus A segmented negative-strand RNA virus that belongs to the Orthomyxoviridae family. There are four types of influenza viruses, A, B, C and D. Influenza A viruses infect a wide variety of birds and mammals, including humans, horses, marine mammals, pigs, ferrets, and chickens.
  • Influenza A viruses are categorized into subtypes based on the type of two proteins, hemagglutinin (HA) and neuraminidase (NA) that are on the surface of the viral envelope. Different influenza viruses encode for different HA and NA proteins. There are 18 different HA subtypes and 11 different NA subtypes, Hl through H18 and N1 through Ni l respectively.
  • influenza A viruses include but are not limited to: H1N1 (such as 1918 H1N1), H1N2, H1N7, H2N2 (such as 1957 H2N2), H2N1, H3N1, H3N2, H3N8, H4N8, H5N1, H5N2, H5N8, H5N9, H6N1, H6N2, H6N5, H7N1, H7N2, H7N3, H7N4, H7N7, H7N9, H8N4, H9N2, H10N1, H10N7, H10N8, Hl INI, H11N6, H12N5, H13N6, and H14N5.
  • H1N1 such as 1918 H1N1
  • H1N2, H1N7, H2N2 such as 1957 H2N2
  • influenza A viruses In animals, most influenza A viruses cause mild localized infections of the respiratory and intestinal tract. However, highly pathogenic influenza A strains, such as H5N1, cause systemic infections in poultry in which mortality may reach 100%.
  • Influenza A viruses that have caused disease in humans include the following subtypes: H1N1, H2N2, and H3N2. Other subtypes of viruses that have infected humans but are not transmitted from person to person are: H5N1 (bird flu), H6N1, H7N7, H1N2, H9N2, H7N2, H7N3, H10N7 and H10N8. There are different lineages of HA and NA within each subtype that are distinguished by amino acid sequence.
  • H1N1 viruses that circulated before 2009 and swine flu H1N1 viruses that have circulated amongst humans since 2009 represent different HA and NA lineages. Within each lineage, virus variants of different “clades” circulate in the population each winter. Antibodies to HA and NA are associated with resistance to influenza disease.
  • Inhibiting or treating a disease Inhibiting the full development of a disease or condition, for example, in a subject who is at risk for a disease such as an influenza virus infection. “Treatment” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition after it has begun to develop. The term “ameliorating,” with reference to a disease or pathological condition, refers to any observable beneficial effect of the treatment. Inhibiting a disease can include preventing or reducing the risk of the disease, such as preventing or reducing the risk of viral infection.
  • the beneficial effect can be evidenced, for example, by a delayed onset of clinical symptoms of the disease in a susceptible subject, a reduction in severity of some or all clinical symptoms of the disease, a slower progression of the disease, a reduction in the viral load, an improvement in the overall health or well-being of the subject, or by other parameters that are specific to the particular disease.
  • a “prophylactic” treatment is a treatment administered to a subject who does not exhibit signs of a disease or exhibits only early signs for the purpose of decreasing the risk of developing pathology.
  • reduces is a relative term, such that an agent reduces a disease or condition if the disease or condition is quantitatively diminished following administration of the agent, or if it is diminished following administration of the agent, as compared to a reference agent.
  • prevents does not necessarily mean that an agent completely eliminates the disease or condition, so long as at least one characteristic of the disease or condition is eliminated.
  • a composition that reduces or prevents an infection can, but does not necessarily completely, eliminate such an infection, so long as the infection is measurably diminished, for example, by at least about 50%, such as by at least about 70%, or about 80%, or even by about 90% the infection in the absence of the agent, or in comparison to a reference agent.
  • isolated A biological component (such as a nucleic acid, peptide, or protein, for example an antibody) that has been substantially separated, produced apart from, or purified away from other biological components in the cell of the organism in which the component naturally occurs, that is, other chromosomal and extra-chromosomal DNA and RNA, and proteins.
  • isolated nucleic acids, peptides and proteins include nucleic acids and proteins purified by standard purification methods.
  • the term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell, as well as chemically synthesized nucleic acids.
  • An isolated nucleic acid, peptide or protein, for example an antibody can be at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% pure.
  • Kabat position A position of a residue in an amino acid sequence that follows the numbering convention delineated by Kabat et al. (Sequences of Proteins of Immunological Interest, 5 th Edition, Department of Health and Human Services, Public Health Service, National Institutes of Health, Bethesda, NIH Publication No. 91-3242, 1991).
  • Linker A bi-functional molecule that can be used to link two molecules into one contiguous molecule, for example, to link a detectable marker to an antibody.
  • Non-limiting examples of peptide linkers include glycine-serine linkers.
  • conjugating can refer to making two molecules into one contiguous molecule; for example, linking two polypeptides into one contiguous polypeptide, or covalently attaching an effector molecule or detectable marker radionuclide or another molecule to a polypeptide, such as an scFv.
  • the linkage can be either by chemical or recombinant means.
  • “Chemical means” refers to a reaction between the antibody moiety and the effector molecule such that there is a covalent bond formed between the two molecules to form one molecule.
  • Nucleic acid (molecule or sequence): A deoxyribonucleotide or ribonucleotide polymer or combination thereof including without limitation, cDNA, mRNA, genomic DNA, and synthetic (such as chemically synthesized) DNA or RNA.
  • the nucleic acid can be double stranded (ds) or single stranded (ss). Where single stranded, the nucleic acid can be the sense strand or the antisense strand.
  • Nucleic acids can include natural nucleotides (such as A, T/U, C, and G), and can include analogs of natural nucleotides, such as labeled nucleotides.
  • cDNA refers to a DNA that is complementary or identical to an mRNA, in either single stranded or double stranded form.
  • Encoding refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom.
  • a gene encodes a protein if transcription and translation of mRNA produced by that gene produces the protein in a cell or other biological system.
  • coding strand the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings
  • non-coding strand used as the template for transcription
  • a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. Nucleotide sequences that encode proteins and RNA may include introns.
  • NA Neuraminidase
  • An influenza virus membrane glycoprotein An influenza virus membrane glycoprotein. NA is involved in the destruction of the cellular receptor for the viral HA by cleaving terminal sialic acid residues from carbohydrate moieties on the surfaces of infected cells. NA also cleaves sialic acid residues from viral proteins, preventing aggregation of viruses. NA (along with HA) is one of the two major influenza virus antigenic determinants. NA forms a tetramer comprised of four identical subunits (monomers) in vivo. As described under the term “influenza”, antibodies that inhibit NA activity prevent virus spread, thereby limiting the infectious process and reducing morbidity and mortality.
  • a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.
  • a promoter such as the CMV promoter
  • operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.
  • compositions and formulations suitable for pharmaceutical delivery of the disclosed agents are conventional. Remington: The Science and Practice of Pharmacy, 22 nd ed., London, UK: Pharmaceutical Press, 2013, describes compositions and formulations suitable for pharmaceutical delivery of the disclosed agents.
  • parenteral formulations usually include injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • injectable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • solid compositions e.g., powder, pill, tablet, or capsule forms
  • conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate.
  • compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, added preservatives (such as non-natural preservatives), and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
  • the pharmaceutically acceptable carrier is sterile and suitable for parenteral administration to a subject for example, by injection.
  • the active agent and pharmaceutically acceptable carrier are provided in a unit dosage form such as a pill or in a selected quantity in a vial. Unit dosage forms can include one dosage or multiple dosages (for example, in a vial from which metered dosages of the agents can selectively be dispensed).
  • Polypeptide A polymer in which the monomers are amino acid residues that are joined together through amide bonds. When the amino acids are alpha-amino acids, either the L-optical isomer or the D- optical isomer can be used, the L-isomers being preferred.
  • the terms “polypeptide” or “protein” as used herein are intended to encompass any amino acid sequence and include modified sequences such as glycoproteins.
  • a polypeptide includes both naturally occurring proteins, as well as those that are recombinantly or synthetically produced.
  • a polypeptide has an amino terminal (N-terminal) end and a carboxy-terminal end. In some aspects, the polypeptide is a disclosed antibody or a fragment thereof.
  • purified does not require absolute purity; rather, it is intended as a relative term.
  • a purified peptide preparation is one in which the peptide or protein (such as an antibody) is more enriched than the peptide or protein is in its natural environment within a cell.
  • a preparation is purified such that the protein or peptide represents at least 50% of the total peptide or protein content of the preparation.
  • a recombinant nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, for example, by genetic engineering techniques.
  • a recombinant protein is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence.
  • a recombinant protein is encoded by a heterologous (for example, recombinant) nucleic acid that has been introduced into a host cell, such as a bacterial or eukaryotic cell.
  • the nucleic acid can be introduced, for example, on an expression vector having signals capable of expressing the protein encoded by the introduced nucleic acid or the nucleic acid can be integrated into the host cell chromosome.
  • Sequence identity The identity between two or more nucleic acid sequences, or two or more amino acid sequences, is expressed in terms of the percentage identity between the sequences. Sequence identity can be measured in terms of percentage identity; the higher the percentage, the more identical the sequences. Homologs and variants of a VL or a VH of an antibody that specifically binds a target antigen are typically characterized by possession of at least about 75% sequence identity, for example at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full-length alignment with the amino acid sequence of interest.
  • Any suitable method may be used to align sequences for comparison.
  • programs and alignment algorithms are described in: Smith and Waterman, Adv. Appl. Math. 2(4) :482-489, 1981; Needleman and Wunsch, J. Mol. Biol. 48(3) :443-453, 1970; Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85(8):2444-2448, 1988; Higgins and Sharp, Gene, 73( l):237-244, 1988; Higgins and Sharp, Bioinformatics, 5(2):151-3, 1989; Corpet, Nucleic Acids Res. 16(22): 10881-10890, 1988; Huang et al.
  • the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is present in both sequences.
  • the percent sequence identity between the two sequences is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (such as 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100.
  • an antibody or antigen binding fragment refers to a binding reaction which determines the presence of a target protein in the presence of a heterogeneous population of proteins and other biologies.
  • an antibody binds preferentially to a particular target protein, peptide or polysaccharide (such as an antigen present on the surface of a pathogen, for example the stem region of HA and does not bind in a significant amount to other proteins present in the sample or subject.
  • the epitope may be present on the HA protein of more than one type of influenza virus, such that the antibody binds to HA on Hl and/or H2 influenza viruses, but does not bind to other proteins, such as proteins from other viruses or other proteins (non-HA) of influenza virus, such as NA.
  • Specific binding can be determined by standard methods. See Harlow & Lane, Antibodies, A Laboratory Manual, 2 nd ed., Cold Spring Harbor Publications, New York (2013), for a description of exemplary immunoassay formats and conditions that can be used to determine specific immunoreactivity.
  • KD refers to the dissociation constant for a given interaction, such as a polypeptide ligand interaction or an antibody antigen interaction.
  • KD refers to the concentration of the individual components of the bimolecular interaction divided by the concentration of the complex.
  • An antibody that specifically binds to an epitope on HA can bind molecules/agents including this domain, including viruses, substrate to which the protein is attached, or the protein in a biological specimen. It is, of course, recognized that a certain degree of non-specific interaction may occur between an antibody and a non-target. Typically, specific binding results in a much stronger association between the antibody and an HA protein than between the antibody other different influenza proteins (such as the NA protein) or from non-influenza virus proteins.
  • Specific binding typically results in greater than 2-fold, such as greater than 5-fold, greater than 10-fold, or greater than 100-fold increase in amount of bound antibody (per unit time) to a protein including the epitope or cell or tissue expressing the target epitope as compared to a protein or cell or tissue lacking this epitope.
  • Specific binding to a protein under such conditions requires an antibody that is selected for its specificity for a particular protein.
  • immunoassay formats are appropriate for selecting antibodies or other ligands specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with a protein.
  • Subject Living multi-cellular vertebrate organisms, a category that includes human and nonhuman mammals, such as non-human primates, pigs, camels, bats, sheep, cows, dogs, cats, rodents, and the like.
  • the subject is a human.
  • the subject is a bird, such as a chicken or turkey.
  • a subject is selected that is in need of inhibiting an influenza virus infection.
  • the subject is either uninfected and at risk of the influenza virus infection or is infected and in need of treatment.
  • a transformed cell is a cell into which a nucleic acid molecule has been introduced by molecular biology techniques.
  • transformed and the like encompasses all techniques by which a nucleic acid molecule might be introduced into such a cell, including transduction with viral vectors, transformation with plasmid vectors, and introduction of DNA by electroporation, lipofection, and particle gun acceleration.
  • Vector An entity containing a nucleic acid molecule (such as a DNA or RNA molecule) bearing a promoter(s) that is operationally linked to the coding sequence of a protein of interest and can express the coding sequence.
  • Non-limiting examples include a naked or packaged (lipid and/or protein) DNA, a naked or packaged RNA, a subcomponent of a virus or bacterium or another microorganism that may be replication-incompetent, or a virus or bacterium or other microorganism that may be replication-competent.
  • a vector is sometimes referred to as a construct.
  • Recombinant DNA vectors are vectors having recombinant DNA.
  • a vector can include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication.
  • a vector can also include one or more selectable marker genes and other genetic elements.
  • Viral vectors are recombinant nucleic acid vectors having at least some nucleic acid sequences derived from one or more viruses.
  • a viral vector comprises a nucleic acid molecule encoding a disclosed antibody or antigen binding fragment that specifically binds to HA and neutralizes the influenza virus.
  • the viral vector can be an adeno-associated virus (AAV) vector.
  • AAV adeno-associated virus
  • Isolated monoclonal antibodies and antigen binding fragments are provided that specifically bind HA of influenza virus, specifically the stem region of HA.
  • the monoclonal antibodies and antigen binding fragments specifically bind to HA and neutralize influenza virus.
  • the antibodies and antigen binding fragments can be fully human.
  • the disclosed antibodies and antigen binding fragments inhibit an influenza virus infection.
  • the disclosed antibodies inhibit an influenza virus infection in vivo, and can be administered prior to, or after, an infection with an influenza virus.
  • Multispecific antibodies, such as bispecific antibodies, including the variable domains of these antibodies are also provided.
  • compositions comprising the antibodies and antigen binding fragments and a pharmaceutically acceptable carrier.
  • the monoclonal antibody or antigen binding fragment binds the central epitope of the stem HA, see FIG. 5A. In other aspects, the monoclonal antibody or antigen binding fragment binds the lower epitope of the stem region of HA, see FIG. 5A.
  • Nucleic acids encoding the antibodies, antigen binding fragments, variable domains, and expression vectors comprising these nucleic acids are also provided.
  • the antibodies, antigen binding fragments, nucleic acid molecules, host cells, and compositions can be used for research, diagnostic, treatment and prophylactic purposes.
  • the disclosed antibodies and antigen binding fragments can be used to diagnose a subject with an influenza virus infection or can be administered to inhibit an influenza virus infection in a subject.
  • the presently disclosed mAbs, and antigen binding fragments thereof bind to HA and neutralize influenza A virus. These antibodies specifically bind the stem region of HA. In some aspects, the disclosed antibody, or antigen binding fragment, inhibits propagation in vitro of influenza A, such as H INI and/or H3N2 virus. In some aspects, the monoclonal antibodies and antigen binding fragments bind the HA of H3N2 influenza virus. In some aspects, the disclosed antibody, or antigen binding fragment, inhibits propagation in vitro of H3N2 influenza virus. In other aspects, the monoclonal antibodies and antigen binding fragments bind the HA of H1N1 influenza virus.
  • the disclosed antibody, or antigen binding fragment inhibits propagation in vitro of H INI influenza virus.
  • the monoclonal antibodies and antigen binding fragments can bind the HA of group 1 and group 2 influenza viruses, and thus are of use for treating these infections.
  • the antibodies, and antigen binding fragments confer protection against infection in both prophylactic and therapeutic settings.
  • the monoclonal antibodies and antigen binding fragments can bind multiple subtypes.
  • the monoclonal antibodies and antigen binding fragments can bind the HA of group 1 and group 2 influenza viruses.
  • the monoclonal antibody or antigen binding fragment binds the central epitope of the stem HA.
  • the monoclonal antibody or antigen binding fragment binds the lower epitope of the stem region of HA. See FIG. 5A.
  • H1N1 321- 205-1C09, 321-213-1A07, 321-205-1D01, 321-102 -E12
  • three of the mAbs have very high neutralization profiles against H3N2 strains (323-220-1B05, 323-2019_c2328.144, and 323- 2007_c 133.010).
  • Two mAbs exhibit a good neutralization profile across all subtypes known to have infected humans. These are Hl, H5, H2, H6, H9, H3, H10 and H7 (323-2001_c39.1, 53-1G08).
  • the monoclonal antibodies and antigen binding fragments can bind the HA of group 1 and group 2 influenza viruses.
  • the monoclonal antibody binds HA of an Hl, H2, H3, H4, H5, H6, H7, H8, H9, H10, Hl 1, H12, H13, H14, H15, H16, H17 or H18 subtype influenza virus.
  • the antibody or antigen binding fragment thereof binds HA of a Hl or H3 subtype influenza virus. Neutralization data is provided in the figures.
  • monoclonal antibodies refers to isolated monoclonal antibodies that include heavy and/or light chain variable domains (or antigen binding fragments thereof) comprising a CDR1, CDR2, and/or CDR3 with reference to the IMGT numbering scheme (unless the context indicates otherwise).
  • CDR numbering schemes such as the Kabat, Chothia or IMGT numbering schemes
  • the amino acid sequence and the CDRs of the heavy and light chain of the disclosed monoclonal antibody according to the IMGT numbering scheme are provided in the listing of sequences, but these are exemplary only.
  • a monoclonal antibody that includes the heavy and light chain CDRs of any one of the antibodies described herein. In some aspects, a monoclonal antibody is provided that includes the heavy and light chain variable regions of any one of the antibodies described herein.
  • amino acid sequences of the VH, VL, HCDRs, and LCDRs are provided in the table below.
  • the antibody or antigen binding fragment is based on or derived from the 323- 2001_c39.1 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the central epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 323-2001_c39.1 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an Hl, H5, H2, H6, H9, H3, H10 and H7 influenza virus.
  • the influenza virus an is HINT, H5N1, H2N2, H6N1, H9N2, H3N2, H10N8, H7N9.
  • the influenza virus can be an H1N1 influenza virus.
  • the influenza virus can be an H3N2 influenza virus.
  • the antibody or antigen binding fragment comprises a Vn and aVL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 323-2001_c39.1 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the monoclonal antibody binds Hl, H5, H2, H6, H9, H3, H10 and H7 influenza viruses.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 1, and specifically binds to HA and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 5, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a V independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 1 and 5, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 2, 3, and 4, respectively, and/or a V L comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 6, 7 (GAS), and 8, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 2, 3, and 4, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 6, 7 (GAS), and 8 respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 1, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 1, and wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 5, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 5, and the antibody or antigen binding fragment specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 1 and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 5, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the amino acid sequences set forth as SEQ ID NOs: 1 and 5, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication.
  • the antibody or antigen binding fragment is based on or derived from the 323- 2019_c2328.144 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the lower epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a V H and a VL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 323-2019_c2328.144 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H3N2 influenza virus.
  • the influenza virus can be an H10N8 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 9, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 13, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a V L independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 9 and 13, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 10, 11, and 12, respectively, and/or a V comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 14, 15 (RNY) and 16, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 10, 11, and 12, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 14, 15 (RNY) and 16, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 9, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 9, and wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 13, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 13, and the antibody or antigen binding fragment specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 9, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 13, and specifically binds to HA.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the amino acid sequences set forth as SEQ ID NOs: 9 and 13, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication.
  • the antibody or antigen binding fragment is based on or derived from the 323-220- O3_1BO5 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the lower epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a V H and a V L comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 323-220-03_lB05 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H3N2 influenza virus.
  • the influenza virus can be an H10N8 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 17, and specifically binds to HA and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 21, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 17 and 21, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 18, 19, and 20, respectively, and/or a V comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 22, 23 (GAS), and 24, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 18, 19, and 20, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 22, 23 (GAS), and 24, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 17, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 17, and wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 21, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 21, and specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 17, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 21, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the amino acid sequences set forth as SEQ ID NOs: 17 and 21, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication. d. Monoclonal antibody 323-2007_cl33.101
  • the antibody or antigen binding fragment is based on or derived from the 323- 2007_cl33.101 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the lower epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 323-2007_cl33.101 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H3N2 influenza virus.
  • the influenza virus can be an H10N8 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 25, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a V comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 29, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 25 and 29, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 26, 27, and 28, respectively, and/or a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 30, 31 (RAS), and 32, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 26, 27, and 28, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 30, 31 (RAS), and 32, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 25, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 25, and wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 29, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 29, and the antibody or antigen binding fragment specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 25, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 29, and specifically binds to HA and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a V H and a V L comprising the amino acid sequences set forth as SEQ ID NOs: 25 and 29, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication.
  • the antibody or antigen binding fragment is based on or derived from the 321-205- 1C09 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the central epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a V H and a V L comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 321-205-1C09 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H INI, H5N1, H2N2, H6N1, or an H9N2 influenza virus. In other aspects, the influenza virus can be an H1N1 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 33, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 37, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a V independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 33 and 37, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 34, 35, and 36, respectively, and/or a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 38, 39 (GVS), and 40, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 34, 35, and 36, respectively
  • VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 38, 39 (GVS), and 40, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 34, 35, and 36, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 38, 39 (GVS), and 40, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 33, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 33, and wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 37, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 37, and specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 33, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 37, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a V H and a V L comprising the amino acid sequences set forth as SEQ ID NOs: 33 and 37, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication. f. Monoclonal antibody 32I-213-1A07
  • the antibody or antigen binding fragment is based on or derived from the 321-213- 1 A07 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the central epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a V H and a V L comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 321-213-1A07 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H INI, H5N1, H2N2, H6N1, or an H9N2 influenza virus. In other aspects, the influenza virus can be an H1N1 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 41, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 45, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a V independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 41 and 45, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 42, 43, and 44, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 46, 47 (GAS), and 48, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 41, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 41, and wherein the VL comprises an amino acid sequence at least 90% identical to SEQ ID NO: 45, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 45, and specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 41, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 45, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a V comprising the amino acid sequences set forth as SEQ ID NOs: 41 and 45, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication.
  • the antibody or antigen binding fragment is based on or derived from the 321-205- 1D01 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds a lower epitope of the stem HA.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 321-205-1D01 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H1N1 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 49, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 53, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 49 and 53, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 50, 51, and 52, respectively, and/or a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 54, 55 (EVT), and 56, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 50, 51, and 52, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 54, 55 (EVT), and 56, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 49, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 49, and wherein the V L comprises an amino acid sequence at least 90% identical to SEQ ID NO: 53, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 53, and specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 49, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 53, and specifically binds to HA, and inhibits an influenza virus, such as an H3N2 influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a V comprising the amino acid sequences set forth as SEQ ID NOs: 49 and 53, respectively, and specifically binds to HA, and inhibits an influenza virus,
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication. h. Monoclonal antibody 321-102-1E12
  • the antibody or antigen binding fragment is based on or derived from the 321-102- 1E12 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the lower epitope of the stem HA.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 321-102-1E12 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • the influenza virus can be an H1N1, H5N1, H2N2, H6N1, or an H9N2 influenza virus. In other aspects, the influenza virus can be an H1N1 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 57, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 61, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 57 and 61, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 58, 59, and 60, respectively, and/or a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 62, 63 (DAS), and 64, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 58, 59, and 60, respectively
  • VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 62, 63 (DAS), and 64, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a V H comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 58, 59, and 60, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 62, 63 (DAS), and 64, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 57, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 57, and wherein the V comprises an amino acid sequence at least 90% identical to SEQ ID NO: 61, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 61, and specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 57, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 61, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a V H and a V L comprising the amino acid sequences set forth as SEQ ID NOs: 57 and 61, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication. i. Monoclonal antibody 315-53-1G08
  • the antibody or antigen binding fragment is based on or derived from the 315-53- 1G08 antibody, and specifically binds to HA, such as the stem region of HA, and inhibits an influenza virus.
  • the monoclonal antibody or antigen binding fragment binds the central epitope of the stem HA, see FIG. 5A.
  • the antibody or antigen binding fragment comprises a Viiand a VL comprising the HCDR1, the HCDR2, the HCDR3, the LCDR1, the LCDR2, and/or the LCDR3, respectively (for example, according to IMGT, Kabat or Chothia), of the 315-53- 1G08 antibody, and specifically binds to HA, and inhibits an influenza virus.
  • influenza virus can be an Hl, H5, H2, H6, H9, H3, H10 and H7 influenza virus.
  • influenza virus an is H1N1, H5N1, H2N2, H6N1, H9N2, H3N2, H10N8, H7N9.
  • influenza virus can be an H1N1 influenza virus.
  • influenza virus can be an H3N2 influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 65, and specifically binds to HA and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a V comprising an amino acid sequence at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence set forth as SEQ ID NO: 69, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL independently comprising amino acid sequences at least 90% (such as at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequences set forth as SEQ ID NOs: 65 and 69, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 66, 67 and 68 respectively, and/or a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 70, 71 (ATS), and 72, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH comprising a HCDR1, a HCDR2, and a HCDR3 as set forth as SEQ ID NOs: 66, 67, and 68, respectively, a VL comprising a LCDR1, a LCDR2, and a LCDR3 as set forth as SEQ ID NOs: 70, 71 (ATS), and 72, respectively, wherein the VH comprises an amino acid sequence at least 90% identical to SEQ ID NO: 65, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 65, and wherein the V L comprises an amino acid sequence at least 90% identical to SEQ ID NO: 69, such as 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 69, and the antibody or antigen binding fragment specifically binds to HA, and inhibits an influenza virus.
  • variations due to sequence identity fall outside the CDRs.
  • the antibody or antigen binding fragment comprises a VH comprising the amino acid sequence set forth as SEQ ID NO: 65 and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VL comprising the amino acid sequence set forth as SEQ ID NO: 69, and specifically binds to HA, and inhibits an influenza virus.
  • the antibody or antigen binding fragment comprises a VH and a VL comprising the amino acid sequences set forth as SEQ ID NOs: 65 and 69, respectively, and specifically binds to HA, and inhibits an influenza virus.
  • the disclosed antibodies and antigen binding fragments inhibit viral entry and/or replication. j. Additional antibodies
  • antibodies that bind to an epitope of interest can be identified based on their ability to cross-compete (for example, to competitively inhibit the binding of, in a statistically significant manner) with the antibodies provided herein in binding assays. In other examples, antibodies that bind to an epitope of interest can be identified based on their ability to cross-compete (for example, to competitively inhibit the binding of, in a statistically significant manner) with the one or more of the antibodies provided herein in binding assays.
  • Human antibodies that bind to the same epitope on HA, to which the disclosed antibodies bind can be produced using any suitable method.
  • Such antibodies may be prepared, for example, by administering an immunogen to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigenic challenge.
  • Such animals typically contain all or a portion of the human immunoglobulin loci, which replace the endogenous immunoglobulin loci, or which are present extrachromosomally or integrated randomly into the animal's chromosomes. In such transgenic mice, the endogenous immunoglobulin loci have generally been inactivated.
  • Additional human antibodies that bind to the same epitope can also be made by hybridoma-based methods.
  • Human myeloma and mouse-human heteromyeloma cell lines for the production of human monoclonal antibodies have been described. (See, e.g., Kozbor J. Immunol., 133: 3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987); and Boerner et al., J. Immunol., 147: 86 (1991).) Human antibodies generated via human B- cell hybridoma technology are also described in Li et ah, Proc. Natl. Acad. Sci.
  • Antibodies and antigen binding fragments that specifically bind to the same epitope can also be isolated by screening combinatorial libraries for antibodies with the desired binding characteristics. For example, by generating phage display libraries and screening such libraries for antibodies possessing the desired binding characteristics. Such methods are reviewed, e.g., in Hoogenboom et al. in Methods in Molecular Biology 178: 1-37 (O'Brien et al., ed., Human Press, Totowa, N.J., 2001) and further described, e.g., in the McCafferty et al., Nature 348:552-554; Clackson et al., Nature 352: 624-628 (1991); Marks et al., J. Mol. Biol.
  • repertoires of VH and VL genes are separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be screened for antigen-binding phage as described in Winter et al., Ann. Rev. Immunol., 12: 433-455 (1994).
  • Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments.
  • scFv single-chain Fv
  • Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas.
  • naive repertoire can be cloned (e.g., from human) to provide a single source of antibodies to a wide range of non-self and also self- antigens without any immunization as described by Griffiths et ah, EMBO J, 12: 725-734 (1993).
  • naive libraries can also be made synthetically by cloning unrearranged V-gene segments from stem cells and using PCR primers containing random sequence to encode the highly variable CDR3 regions and to accomplish rearrangement in vitro, as described by Hoogenboom and Winter, J. Mol. Biol., 227: 381-388 (1992).
  • Patent publications describing human antibody phage libraries include, for example: U.S. Pat. No.
  • An antibody or antigen binding fragment of the antibodies disclosed herein can be a human antibody or fragment thereof. Chimeric antibodies are also provided.
  • the antibody or antigen binding fragment can include any suitable framework region, such as (but not limited to) a human framework region from another source, or an optimized framework region.
  • a heterologous framework region such as, but not limited to a mouse or monkey framework region, can be included in the heavy or light chain of the antibodies.
  • the antibody can be of any isotype.
  • the antibody can be, for example, an IgA, IgM or an IgG antibody, such as IgGi IgG2, IgGs, or IgG4.
  • the class of an antibody that specifically binds to HA can be switched with another.
  • a nucleic acid molecule encoding VL or VH is isolated such that it does not include any nucleic acid sequences encoding the constant region of the light or heavy chain, respectively.
  • a nucleic acid molecule encoding VL or VH is then operatively linked to a nucleic acid sequence encoding a CL or CH from a different class of immunoglobulin molecule.
  • an antibody that specifically binds the spike protein, that was originally IgG may be class switched to an IgA. Class switching can be used to convert one IgG subclass to another, such as from IgGi to IgG . IgG ⁇ or IgG4.
  • the disclosed antibodies are oligomers of antibodies, such as dimers, trimers, tetramers, pentamers, hexamers, heptamers, octamers and so on.
  • the antibody or antigen binding fragment can be derivatized or linked to another molecule (such as another peptide or protein).
  • the antibody or antigen binding fragment is derivatized such that the binding to HA is not affected adversely by the derivatization or labeling.
  • the antibody or antigen binding fragment can be functionally linked (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another antibody (for example, a bi-specific antibody or a diabody), a detectable marker, an effector molecule, or a protein or peptide that can mediate association of the antibody or antibody portion with another molecule (such as a streptavidin core region or a polyhistidine tag).
  • the antibody or antigen binding fragment specifically binds HA with an affinity (e.g., measured as KD) of no more than 1.0 x 10' 8 M, no more than 5.0 x 10' 8 M, no more than 1.0 x 10' 9 M, no more than 5.0 x 10' 9 M, no more than 1.0 x 10' 10 M, no more than 5.0 x 10' 10 M, or no more than 1.0 x 10’ 11 M.
  • K D can be measured, for example, by a radiolabeled antigen binding assay (RIA) performed with the Fab version of an antibody of interest and its antigen.
  • RIA radiolabeled antigen binding assay
  • solution binding affinity of Fabs for antigen is measured by equilibrating Fab with a minimal concentration of ( 125 I)-labeled antigen in the presence of a titration series of unlabeled antigen, then capturing bound antigen with an anti-Fab antibody- coated plate (see, e.g., Chen et al., J. Mol. Biol. 293(4): 865-881, 1999).
  • MICROTITER® multi-well plates (Thermo Scientific) are coated overnight with 5 pg/ml of a capturing anti-Fab antibody (Cappel Labs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked with 2% (w/v) bovine serum albumin in PBS for two to five hours at room temperature (approximately 23° C.).
  • a non-adsorbent plate NUNCTM Catalog #269620
  • 100 pM or 26 pM [ 125 I]-antigen are mixed with serial dilutions of a Fab of interest (e.g., consistent with assessment of the anti-VEGF antibody, Fab- 12, in Presta et al., Cancer Res.
  • the Fab of interest is then incubated overnight; however, the incubation may continue for a longer period (e.g., about 65 hours) to ensure that equilibrium is reached. Thereafter, the mixtures are transferred to the capture plate for incubation at room temperature (e.g., for one hour). The solution is then removed, and the plate washed eight times with 0.1% polysorbate 20 (TWEEN-20®) in PBS. When the plates have dried, 150 pl/well of scintillant (MICROSCINTTM-20; PerkinElmer) is added, and the plates are counted on a TOPCOUNTTM gamma counter (PerkinElmer) for ten minutes. Concentrations of each Fab that give less than or equal to 20% of maximal binding are chosen for use in competitive binding assays.
  • KD can be measured using surface plasmon resonance assays using a BIACORE®- 2000 or a BIACORE®-3000 (BIAcore, Inc., Piscataway, N.J.) at 25°C with immobilized antigen CM5 chips at -10 response units (RU).
  • CM5 carboxymethylated dextran biosensor chips
  • EDC N-ethyl-N'-(3-dimethylaminopropyl)-carbodiimide hydrochloride
  • NHS N- hydroxysuccinimide
  • Antigen is diluted with 10 mM sodium acetate, pH 4.8, to 5 pg/ml ( ⁇ 0.2 pM) before injection at a flow rate of 5 1/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1 M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05% polysorbate 20 (TWEEN-20TM) surfactant (PBST) at 25° C at a flow rate of approximately 25 1/min.
  • TWEEN-20TM polysorbate 20
  • association rates (k on ) and dissociation rates (k O ff) are calculated using a simple one-to-one Langmuir binding model (BIACORE® Evaluation Software version 3.2) by simultaneously fitting the association and dissociation sensorgrams.
  • the equilibrium dissociation constant (KD) is calculated as the ratio k O ff/kon. See, e.g., Chen et al., J. Mol. Biol. 293:865-881 (1999).
  • a multispecific antibody, or a bispecific antibody such as a dual variable domain antibody (DVD-IGTM) is provided that comprises an antibody or antigen binding fragment that specifically binds HA, as provided herein.
  • any suitable method can be used to design and produce a bispecific antibody, such as crosslinking two or more antibodies, antigen binding fragments (such as scFvs) of the same type or of different types.
  • Exemplary methods of making multispecific antibodies, such as bispecific antibodies include those described in PCT Pub. No. WO2013/163427, which is incorporated by reference herein in its entirety.
  • Non-limiting examples of suitable crosslinkers include those that are heterobifunctional, having two distinctly reactive groups separated by an appropriate spacer (such as m- maleimidobenzoyl-N-hydroxysuccinimide ester) or homobifunctional (such as disuccinimidyl suberate).
  • the multispecific antibody such as the bispecific antibody, includes a disclosed antibody that specifically binds HA, or an antigen binding fragment thereof, and an antibody or antigen binding fragment thereof that specifically binds NA, see for example, PCT Application No. PCT/US2023/071194.
  • two or more of the disclosed monoclonal antibodies that specifically bind HA are included in the multispecific antibody.
  • the multi-specific antibody may have any suitable format that allows for binding to HA by the antibody or antigen binding fragment as provided herein.
  • Bispecific single chain antibodies can be encoded by a single nucleic acid molecule. Non-limiting examples of bispecific single chain antibodies, as well as methods of constructing such antibodies are provided in U.S. Pat. Nos. 8,076,459, 8,017,748, 8,007,796, 7,919,089, 7,820,166, 7,635,472, 7,575,923, 7,435,549, 7,332,168, 7,323,440, 7,235,641, 7,229,760, 7,112,324, 6,723,538. Additional examples of bispecific single chain antibodies can be found in PCT application No.
  • a scFv molecule can be fused to one of the VL-CL (L) or VH- CH1 chains, e.g., to produce a bibody one scFv is fused to the C-term of a Fab chain.
  • the bispecific tetravalent immunoglobulin known as the dual variable domain immunoglobulin or DVD-immunoglobulin molecule is disclosed in Wu et ah, Mabs 1:339-47, 2019.
  • a DVD-immunoglobulin molecule includes two heavy chains and two light chains. Unlike IgG, however, both heavy and light chains of a DVD-immunoglobulin molecule contain an additional variable domain (VD) connected via a linker sequence at the N-termini of the VH and VL of an existing monoclonal antibody (mAb). Thus, when the heavy and the light chains combine, the resulting DVD-immunoglobulin molecule contains four antigen recognition sites, see Jakob et al., Mabs 5: 358-363, 2013, see Fig. 1 for schematic and space-filling diagrams. A DVD-immunoglobulin molecule functions to bind two different antigens on each DFab simultaneously.
  • VD variable domain
  • mAb monoclonal antibody
  • VD1 The outermost or N-terminal variable domain is termed VD1 and the innermost variable domain is termed VD2; the VD2 is proximal to the C-terminal CHI or CL.
  • VD1 The outermost or N-terminal variable domain
  • VD2 the innermost variable domain is termed VD2; the VD2 is proximal to the C-terminal CHI or CL.
  • VD1 The outermost or N-terminal variable domain
  • VD2 the innermost variable domain
  • DVD- immunoglobulin molecules can be manufactured and purified to homogeneity in large quantities, have pharmacological properties similar to those of a conventional IgGi, and show in vivo efficacy. Any of the disclosed monoclonal antibodies can be included in a DVD-immunoglobulin format.
  • Combinations of antibodies and antigen binding fragments that can be used in a muti-specific, antibody, such as a bispecific antibody include, but are not limited to: a) 323-2019_c2328.144 and 321-205- 1C09; b) 321-205-1C09 and 321-205- 1D01 ; c) 323-2019_c2328.144 and 315-53-1G08.
  • a multi-specific antibody, such as a bispecific antibody includes 323-2019_c2328.144 and 321-205-1C09, or antigen binding fragments thereof.
  • a multi- specific antibody, such as a bispecific antibody includes 321-205-1C09 and 321-205-1D01, or antigen binding fragments thereof.
  • a multispecific antibody, such as a bispecific antibody includes 323-2019_c2328.144 and 315-53-1G08, or antigen binding fragments thereof.
  • Antigen binding fragments are encompassed by the present disclosure, such as Fab, F(ab')i, and Fv which include a heavy chain and V and specifically bind HA. These antibody fragments retain the ability to selectively bind with the antigen and are “antigen-binding” fragments.
  • Non-limiting examples of such fragments include:
  • Fab the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;
  • the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain;
  • (Fab')2 the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction
  • F(ab')2 is a dimer of two Fab’ fragments held together by two disulfide bonds
  • Fv a genetically engineered fragment containing the VL and VL expressed as two chains:
  • Single chain antibody such as scFv
  • scFv Single chain antibody
  • Single chain antibody defined as a genetically engineered molecule containing the VH and the VL linked by a suitable polypeptide linker as a genetically fused single chain molecule
  • a suitable polypeptide linker as a genetically fused single chain molecule
  • a dimer of a single chain antibody defined as a dimer of a scFV. This has also been termed a “miniantibody.”
  • Any suitable method of producing the above-discussed antigen binding fragments may be used. Non-limiting examples are provided in Harlow and Lane, Antibodies: A Laboratory Manual, 2 nd , Cold Spring Harbor Laboratory, New York, 2013.
  • Antigen binding fragments can be prepared by proteolytic hydrolysis of the antibody or by expression in a host cell (such as an E. coli cell) of DNA encoding the fragment. Antigen binding fragments can also be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antigen binding fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab')2. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab' monovalent fragments.
  • cleaving antibodies such as separation of heavy chains to form monovalent lightheavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.
  • amino acid sequence variants of the antibodies provided herein are provided.
  • Amino acid sequence variants of an antibody may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the antibody VH domain and/or V domain, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., antigen-binding.
  • variants having one or more amino acid substitutions are provided.
  • Sites of interest for substitutional mutagenesis include the CDRs and the framework regions.
  • Amino acid substitutions may be introduced into an antibody of interest and the products screened for a desired activity, e.g., retained/improved antigen binding, decreased immunogenicity, or improved ADCC or CDC.
  • the variants typically retain amino acid residues necessary for correct folding and stabilizing between the VH and the VL regions and will retain the charge characteristics of the residues in order to preserve the low pl and low toxicity of the molecules.
  • Amino acid substitutions can be made in the V H and the VL regions to increase yield. In some aspects, the amino acid substitutions are not in the CDRs of the antibody.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 1.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 5.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 9.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 13.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 17.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 21.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 25.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 29.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 33.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 37.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 41.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 45.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 49.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 53.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 57.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 61.
  • the heavy chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 65.
  • the light chain of the antibody comprises up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) compared to the amino acid sequence set forth as one of SEQ ID NO: 69.
  • the antibody or antigen binding fragment can include up to 10 (such as up to 1, up to 2, up to 3, up to 4, up to 5, up to 6, up to 7, up to 8, or up to 9) amino acid substitutions (such as conservative amino acid substitutions) in the framework regions of the heavy chain of the antibody/bispecific antibody, or the light chain of the antibody/bispecific antibody, or the heavy and light chains of the antibody/bispecific antibody, compared to known framework regions, or compared to the framework regions of the antibody, and maintain the specific binding activity for the epitope of HA.
  • the amino acid substitutions re not in the CDRs of the antibody.
  • substitutions, insertions, or deletions may occur within one or more CDRs so long as such alterations do not substantially reduce the ability of the antibody to bind antigen.
  • conservative alterations e.g., conservative substitutions as provided herein
  • each CDR either is unaltered, or contains no more than one, two or three amino acid substitutions.
  • only the framework residues are modified so the CDRs are unchanged.
  • VH amino acid sequence is one of SEQ ID NOs: 1, 9, 17, 25, 33, 41, 49, 57, or 65.
  • VL amino acid sequence is one of SEQ ID NOs: 5, 13, 21, 29, 37, 45, 53, 61, or 69.
  • an antibody disclosed herein, an antigen binding fragment, or bispecific antibody is altered to increase or decrease the extent to which the antibody or antigen binding fragment is glycosylated. Addition or deletion of glycosylation sites may be conveniently accomplished by altering the amino acid sequence such that one or more glycosylation sites is created or removed.
  • the carbohydrate attached thereto may be altered.
  • Native antibodies produced by mammalian cells typically comprise a branched, biantennary oligosaccharide that is generally attached by an N-linkage to Asn297 of the CEE domain of the Fc region. See, e.g., Wright et al. Trends Biotechnol. 15(l):26-32, 1997.
  • the oligosaccharide may include various carbohydrates, e.g., mannose, N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as a fucose attached to a GlcNAc in the “stem” of the biantennary oligosaccharide structure.
  • modifications of the oligosaccharide in an antibody may be made in order to create antibody variants with certain improved properties.
  • variants having a carbohydrate structure that lacks fucose attached (directly or indirectly) to an Fc region.
  • the amount of fucose in such antibody may be from 1% to 80%, from 1% to 65%, from 5% to 65% or from 20% to 40%.
  • the amount of fucose is determined by calculating the average amount of fucose within the sugar chain at Asn297, relative to the sum of all glycostructures attached to Asn 297 e.g., complex, hybrid and high mannose structures) as measured by MALDI-TOF mass spectrometry, as described in WO 2008/077546, for example.
  • Asn297 refers to the asparagine residue located at about position 297 in the Fc region; however, Asn297 may also be located about ⁇ 3 amino acids upstream or downstream of position 297, i.e. , between positions 294 and 300, due to minor sequence variations in antibodies. Such fucosylation variants may have improved ADCC function. See, e.g., US Patent Publication Nos. US 2003/0157108 (Presta, L.); US 2004/0093621 (Kyowa Hakko Kogyo Co., Ltd).
  • Examples of publications related to “defucosylated” or “fucose-deficient” antibody variants include: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US 2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO 2005/035586; WO 2005/035778;
  • knockout cell lines such as alpha- 1,6-fucosyltransferase gene, FUT8, knockout CHO cells (see, e.g., Yamane-Ohnuki et al., BiotechnoL Bioeng., 87(5): 614-622, 2004; Kanda et al., BiotechnoL Bioeng., 94(4):680-688, 2006; and W02003/085107).
  • Antibody variants are further provided with bisected oligosaccharides, e.g., in which a biantennary oligosaccharide attached to the Fc region of the antibody is bisected by GlcNAc. Such antibody variants may have reduced fucosylation and/or improved ADCC function. Examples of such antibody variants are described, e.g., in WO 2003/011878 (Jean-Mairet etaL) U.S. Pat. No. 6,602,684 (Umana etal.); and US 2005/0123546 (Umana et al.). Antibody variants with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such antibody variants may have improved CDC function. Such antibody variants are described, e.g., in PCT Publication Nos. WO 1997/30087; WO 1998/58964; and WO 1999/22764.
  • the constant region of the antibody comprises one or more amino acid substitutions to optimize in vivo half-life of the antibody.
  • the serum half-life of IgG Abs is regulated by the neonatal Fc receptor (FcRn).
  • the antibody comprises an amino acid substitution that increases binding to the FcRn.
  • Non-limiting examples of such substitutions include substitutions at IgG constant regions T250Q and M428L (see, e.g., Hinton et aL, J Immunol., 176(l):346-356, 2006); M428L and N434S (the “LS” mutation, see, e.g., Zalevsky, et al., Nature BiotechnoL, 28(2): 157-159, 2010); N434A (see, e.g., Petkova et aL, Int. Immunol., 18( 12): 1759- 1769, 2006); T307A, E380A, and N434A (see, e.g., Petkova et al., Int.
  • the disclosed antibodies and antigen binding fragments can be linked to or comprise an Fc polypeptide including any of the substitutions listed above, for example, the Fc polypeptide can include the M428L and N434S substitutions.
  • an antibody provided herein may be further modified to contain additional nonproteinaceous moieties.
  • the moieties suitable for derivatization of the antibody include but are not limited to water soluble polymers.
  • water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-l,3-dioxolane, poly-1, 3,6- trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol,
  • PEG
  • Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water.
  • the polymer may be of any molecular weight, and may be branched or unbranched.
  • the number of polymers attached to the antibody may vary, and if more than one polymer is attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the antibody derivative will be used in an application under defined conditions, etc.
  • the antibodies, antigen binding fragments, and bispecific antibodies that specifically bind to HA, as disclosed herein, can be conjugated to an agent, such as an effector molecule or detectable marker. Both covalent and noncovalent attachment means may be used.
  • agent such as an effector molecule or detectable marker.
  • Various effector molecules and detectable markers can be used, including (but not limited to) toxins and radioactive agents such as 125 I, 32 P, 14 C, 3 H and 35 S and other labels, target moieties, enzymes and ligands, etc.
  • toxins and radioactive agents such as 125 I, 32 P, 14 C, 3 H and 35 S and other labels, target moieties, enzymes and ligands, etc.
  • the choice of a particular effector molecule or detectable marker depends on the particular target molecule or cell, and the desired biological effect.
  • the procedure for attaching a detectable marker to an antibody, antigen binding fragment, or bispecific antibody varies according to the chemical structure of the effector.
  • Polypeptides typically contain a variety of functional groups, such as carboxyl (-COOH), free amine (-NH 2 ) or sulfhydryl (-SH) groups, which are available for reaction with a suitable functional group on a polypeptide to result in the binding of the effector molecule or detectable marker.
  • the antibody, antigen binding fragment, or bispecific antibody is derivatized to expose or attach additional reactive functional groups.
  • the derivatization may involve attachment of any suitable linker molecule.
  • the linker is capable of forming covalent bonds to both the antibody or antigen binding fragment and to the effector molecule or detectable marker.
  • Suitable linkers include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers.
  • the linkers may be joined to the constituent amino acids through their side chains (such as through a disulfide linkage to cysteine) or the alpha carbon, or through the amino, and/or carboxyl groups of the terminal amino acids.
  • a suitable method for attaching a given agent to an antibody or antigen binding fragment or bispecific antibody can be determined.
  • the antibody, antigen binding fragment or bispecific antibody can be conjugated with a detectable marker; for example, a detectable marker capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy or diagnostic imaging techniques (such as CT, computed axial tomography (CAT), MRI, magnetic resonance tomography (MTR), ultrasound, fiberoptic examination, and laparoscopic examination).
  • detectable markers include fluorophores, chemiluminescent agents, enzymatic linkages, radioactive isotopes and heavy metals or compounds (for example super paramagnetic iron oxide nanocrystals for detection by MRI).
  • useful detectable markers include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, 5- dimethylamine-l-napthalenesulfonyl chloride, phycoerythrin, lanthanide phosphors and the like.
  • Bioluminescent markers are also of use, such as luciferase, green fluorescent protein (GFP), and yellow fluorescent protein (YFP).
  • GFP green fluorescent protein
  • YFP yellow fluorescent protein
  • An antibody, antigen binding fragment, or bispecific antibody can also be conjugated with enzymes that are useful for detection, such as horseradish peroxidase, 0- galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like.
  • an antibody or antigen binding fragment When an antibody or antigen binding fragment is conjugated with a detectable enzyme, it can be detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present, the addition of hydrogen peroxide and diaminobenzidine leads to a colored reaction product, which is visually detectable.
  • An antibody, antigen binding fragment, or bispecific antibody may also be conjugated with biotin, and detected through indirect measurement of avidin or streptavidin binding. It should be noted that the avidin itself can be conjugated with an enzyme or a fluorescent label.
  • the antibody, antigen binding fragment or bispecific antibody can be conjugated with a paramagnetic agent, such as gadolinium. Paramagnetic agents such as superparamagnetic iron oxide are also of use as labels. Antibodies can also be conjugated with lanthanides (such as europium and dysprosium), and manganese. An antibody, antigen binding fragment, or bispecific antibody may also be labeled with a predetermined polypeptide epitope recognized by a secondary reporter (such as leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags).
  • a secondary reporter such as leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags.
  • the antibody, antigen binding fragment or bispecific antibody can also be conjugated with a radiolabeled amino acid, for example, for diagnostic purposes.
  • the radiolabel may be used to detect an influenza virus by radiography, emission spectra, or other diagnostic techniques.
  • labels for polypeptides include, but are not limited to, the following radioisotopes: 3 H, 14 C, 35 S, 90 Y, " m Tc, 11 'In, 125 I, 131 I.
  • the radiolabels may be detected, for example, using photographic film or scintillation counters, fluorescent markers may be detected using a photodetector to detect emitted illumination.
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • the average number of detectable marker moieties per antibody, antigen binding fragment, or bispecific antibody in a conjugate can range, for example, from 1 to 20 moieties per antibody or antigen binding fragment.
  • the average number of effector molecules or detectable marker moieties per antibody or antigen binding fragment in a conjugate range from about 1 to about 2, from about 1 to about 3, about 1 to about 8; from about 2 to about 6; from about 3 to about 5; or from about 3 to about 4.
  • the loading (for example, effector molecule per antibody ratio) of a conjugate may be controlled in different ways, for example, by: (i) limiting the molar excess of effector molecule-linker intermediate or linker reagent relative to antibody, (ii) limiting the conjugation reaction time or temperature, (iii) partial or limiting reducing conditions for cysteine thiol modification, (iv) engineering by recombinant techniques the amino acid sequence of the antibody such that the number and position of cysteine residues is modified for control of the number or position of linker-effector molecule attachments.
  • Nucleic acid molecules (for example, cDNA or RNA molecules) encoding the amino acid sequences of antibodies, antigen binding fragments, bispecific antibodies, and conjugates that specifically bind to HA, as disclosed herein, are provided. Nucleic acids encoding these molecules can readily be produced using the amino acid sequences provided herein (such as the CDR sequences and V H and V L sequences), sequences available in the art (such as framework or constant region sequences), and the genetic code. In several aspects, nucleic acid molecules can encode the VH, the VL, or both the VH and VL (for example in a bicistronic expression vector) of a disclosed antibody or antigen binding fragment. In some aspects, the nucleic acid molecules encode an scFv. In several aspects, the nucleic acid molecules can be expressed in a host cell (such as a mammalian cell) to produce a disclosed antibody or antigen binding fragment. Nucleic acid molecules encoding an scFv are provided.
  • the genetic code can be used to construct a variety of functionally equivalent nucleic acid sequences, such as nucleic acids which differ in their sequence, but which encode the same antibody sequence, or encode a conjugate or fusion protein including the V L and/or V H nucleic acid sequence.
  • an isolated nucleic acid molecule encodes the VH of a disclosed antibody.
  • the nucleic acid molecule encodes the VL of a disclosed antibody.
  • the nucleic acid molecule can encode a bi-specific antibody, such as in DVD- immunoglobulin format.
  • Nucleic acid molecules encoding the antibodies, antigen binding fragments, bispecific antibodies, and conjugates that specifically bind to HA can be prepared by any suitable method including, for example, cloning of appropriate sequences or by direct chemical synthesis by standard methods. Chemical synthesis produces a single stranded oligonucleotide. This can be converted into double stranded DNA by hybridization with a complementary sequence or by polymerization with a DNA polymerase using the single strand as a template.
  • Exemplary nucleic acids can be prepared by cloning techniques. Examples of appropriate cloning and sequencing techniques can be found, for example, in Green and Sambrook (Molecular Cloning: A Laboratory Manual, 4 th ed., New York: Cold Spring Harbor Laboratory Press, 2012) and Ausubel et al. (Eds.) (Current Protocols in Molecular Biology, New York: John Wiley and Sons, including supplements).
  • Nucleic acids can also be prepared by amplification methods.
  • Amplification methods include the polymerase chain reaction (PCR), the ligase chain reaction (LCR), the transcription-based amplification system (TAS), and the self-sustained sequence replication system (3SR).
  • PCR polymerase chain reaction
  • LCR ligase chain reaction
  • TAS transcription-based amplification system
  • 3SR self-sustained sequence replication system
  • the nucleic acid molecules can be expressed in a recombinantly engineered cell such as bacteria, plant, yeast, insect and mammalian cells.
  • the antibodies, antigen binding fragments, and conjugates can be expressed as individual proteins including the VH and/or V (linked to an effector molecule or detectable marker as needed) or can be expressed as a fusion protein. Any suitable method of expressing and purifying antibodies and antigen binding fragments may be used; non-limiting examples are provided in Al-Rubeai (Ed.), Antibody Expression and Production, Dordrecht; New York: Springer, 2011).
  • An immunoadhesin can also be expressed.
  • nucleic acids encoding a VH and VL, and immunoadhesin are provided.
  • the nucleic acid sequences can optionally encode a leader sequence.
  • the VH- and Vi -encoding DNA fragments can be operatively linked to another fragment encoding a flexible linker, e.g., encoding the amino acid sequence (Gly SerE, such that the VH and V L sequences can be expressed as a contiguous single -chain protein, with the V L and V H domains joined by the flexible linker (see, e.g., Bird et al., Science, 242(4877) :423-426, 1988; Huston et al., Proc. Natl. Acad. Sci.
  • a flexible linker e.g., encoding the amino acid sequence (Gly SerE, such that the VH and V L sequences can be expressed as a contiguous single -chain protein, with the V L and V H domains joined by the flexible linker (see, e.g., Bird et al., Science, 242(4877) :423-426, 1988; Huston et al., Proc. Nat
  • cleavage site can be included in a linker, such as a furin cleavage site.
  • the single chain antibody may be monovalent if only a single V H and V L are used, bivalent if two VH and VL are used, or polyvalent if more than two VH and V are used. Bispecific or polyvalent antibodies may be generated that bind specifically to HA and another antigen.
  • the encoded VH and VL optionally can include a furin cleavage site between the V H and V L domains.
  • Linkers can also be encoded, such as when the nucleic acid molecule encodes a bi-specific antibody in DVD-IGTM format.
  • One or more DNA sequences encoding the antibodies, antigen binding fragments, bispecific antibodies, or conjugates can be expressed in vitro by DNA transfer into a suitable host cell.
  • the cell may be prokaryotic or eukaryotic.
  • Numerous expression systems available for expression of proteins including E. coli, other bacterial hosts, yeast, and various higher eukaryotic cells such as the COS, CHO, HeLa and myeloma cell lines, can be used to express the disclosed antibodies and antigen binding fragments. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host may be used.
  • Hybridomas expressing the antibodies of interest are also encompassed by this disclosure.
  • nucleic acids encoding the antibodies, antigen binding fragments, and bispecific antibodies (such as DVD-immunoglobulin antibodies) described herein can be achieved by operably linking the DNA or cDNA to a promoter (which is either constitutive or inducible), followed by incorporation into an expression cassette.
  • the promoter can be any promoter of interest, including a cytomegalovirus promoter.
  • an enhancer such as a cytomegalovirus enhancer, is included in the construct.
  • the cassettes can be suitable for replication and integration in either prokaryotes or eukaryotes. Typical expression cassettes contain specific sequences useful for regulation of the expression of the DNA encoding the protein.
  • the expression cassettes can include appropriate promoters, enhancers, transcription and translation terminators, initiation sequences, a start codon (i.e., ATG) in front of a proteinencoding gene, splicing signals for introns, sequences for the maintenance of the correct reading frame of that gene to permit proper translation of mRNA, and stop codons.
  • the vector can encode a selectable marker, such as a marker encoding drug resistance (for example, ampicillin or tetracycline resistance).
  • expression cassettes which contain, for example, a strong promoter to direct transcription, a ribosome binding site for translational initiation (e.g., internal ribosomal binding sequences), and a transcription/translation terminator.
  • a strong promoter to direct transcription e.g., a ribosome binding site for translational initiation (e.g., internal ribosomal binding sequences), and a transcription/translation terminator.
  • this can include a promoter such as the T7, trp, lac, or lambda promoters, a ribosome binding site, and preferably a transcription termination signal.
  • control sequences can include a promoter and/or an enhancer derived from, for example, an immunoglobulin gene, HTLV, SV40 or cytomegalovirus, and a polyadenylation sequence, and can further include splice donor and/or acceptor sequences (for example, CMV and/or HTLV splice acceptor and donor sequences).
  • the cassettes can be transferred into the chosen host cell by any suitable method such as transformation or electroporation for E. coli and calcium phosphate treatment, electroporation or lipofection for mammalian cells. Cells transformed by the cassettes can be selected by resistance to antibiotics conferred by genes contained in the cassettes, such as the amp, gpt, neo and hyg genes.
  • Modifications can be made to a nucleic acid encoding a polypeptide described herein without diminishing its biological activity. Some modifications can be made to facilitate the cloning, expression, or incorporation of the targeting molecule into a fusion protein. Such modifications include, for example, termination codons, sequences to create conveniently located restriction sites, and sequences to add a methionine at the amino terminus to provide an initiation site, or additional amino acids (such as poly His) to aid in purification steps.
  • the antibodies, antigen binding fragments, bispecific antibodies, and conjugates can be purified according to standard procedures in the art, including ammonium sulfate precipitation, affinity columns, column chromatography, and the like (see, generally, Simpson et al. (Eds.), Basic methods in Protein Purification and Analysis: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press, 2009).
  • the antibodies, antigen binding fragment, and conjugates need not be 100% pure.
  • the polypeptides should be substantially free of endotoxin.
  • Methods are disclosed herein for the prevention or treatment of an influenza virus infection.
  • Prevention and treatment can include inhibition of infection with influenza A viruses.
  • the methods can include administering to a subject a therapeutically effective amount of a monoclonal antibody, an antigen binding fragment thereof, or a bispecific antibody, as disclosed above, or a nucleic acid encoding the antibody or antigen binding fragment.
  • the methods include contacting a cell with an effective amount of a monoclonal antibody, or antigen binding fragment thereof, that specifically binds HA.
  • the influenza viruses include, but are not limited to, circulating H1N1 and/or H3N2 viruses, related influenza viruses, any naturally emerging or engineered influenza viruses that contain similar HA proteins.
  • influenza virus can be a H1N1, H5N1, H2N2, H6N1, H9N2, H3N2, H10N8, or an H7N9 influenza virus.
  • the disclosed method can be used to inhibit an H1N1 infection in a subject.
  • the disclosed method can be used to inhibit an H3N2 infection in a subject.
  • the subject is a human or other mammal.
  • the subject is a bird, such as a chicken or turkey.
  • the methods include selecting a subject has an infection with an influenza virus for treatment.
  • the method can include selecting a subject who has an infection with an influenza virus for treatment.
  • a subject is selected that has an H3N2 infection.
  • a subject is selected that has an H1N1 infection.
  • a subject is selected that has an H5N1, H2N2, H6N1, H9N2, H10N8, or an H7N9 influenza virus infection.
  • the disclosed method can be used to inhibit an H1N1 infection in a subject.
  • the disclosed method can be used to inhibit an H3N2 infection in a subject. All of these subjects can be treated using the disclosed methods.
  • the disclosed antibodies, antigen binding fragments and nucleic acids can be used as emergency prophylaxis to protect individuals in the proximity of a developing influenza outbreak, or when encountering an increased risk of exposure.
  • the methods can include selecting a subject at risk of exposure to influenza virus, such as a subject that is at particular risk, such as the elderly, a pediatric subject, an immunocompromised individual, a pregnant person, a person with heart disease or a health care worker.
  • the method includes administering an antibody, an antigen-binding fragment thereof, or a bispecific antibody that specifically binds HA.
  • the method can also include administering to the subject a nucleic acid molecule encoding the antibody, antigen binding fragment, or bispecific antibody.
  • the method can include selecting a subject with an influenza virus infection.
  • the influenza virus infection does not need to be completely eliminated for the composition to be effective.
  • the symptoms of the viral infection can be reduced, such as fever, cough, upper respiratory symptoms, and/or lower respiratory symptoms.
  • the duration of symptoms is reduced by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or 100%, as compared to the duration of symptoms in the absence of the composition.
  • a composition can decrease the infection in a population by a desired amount, for example by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or 100%, as compared to the rate of infection in the absence of the composition.
  • a composition in some examples decreases viral titer by at least 10%, at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or 100% in a subject compared to in the absence of treatment.
  • administration of the antibody, antigen binding fragment, bispecific antibody results in a reduction in the establishment of a virus infection and/or reducing subsequent disease progression in a subject.
  • a reduction in the establishment of an infection, and/or a reduction in subsequent disease progression can encompass a statistically significant reduction in viral activity and/or replication.
  • methods are disclosed for treating a subject with an existing influenza virus infection. In other aspects, methods are disclosed for preventing an influenza virus infection.
  • these methods include administering to the subject a therapeutically effective amount of an antibody, antigen binding fragment thereof, or specific antibody, or a nucleic acid encoding the antibody, antigen binding fragment, or bispecific antibody, thereby preventing or treating the viral infection.
  • the method can prevent, delay or reduce symptoms of an influenza virus infection, such as fever, vomiting, body ache, sore throat, coughing, nasal congestion, headache, and fatigue.
  • the influenza virus is an H1N1 or an H3N2 influenza virus.
  • the influenza virus can be a H5N1, H2N2, H6N1, H9N2, H3N2, H10N8, or an H7N9 influenza virus.
  • a therapeutically effective amount of an antibody, antigen binding fragment, or bispecific antibody (or the nucleic acid encoding the antibody, antigen binding fragment or bispecific antibody) that specifically binds HA will depend upon the severity of the disease and/or infection and the general state of the patient's health.
  • a therapeutically effective amount of the antibody can provide either subjective relief of a symptom(s) or an objectively identifiable improvement as noted by the clinician or other qualified observer.
  • These compositions can be administered in conjunction with another therapeutic agent, either simultaneously or sequentially.
  • the antibody, antigen binding fragment, or nucleic acid encoding the antibody or antigen binding fragment can be combined with additional anti-viral therapy.
  • the subject is also administered an effective amount of an additional agent, such as anti-viral agent.
  • the methods can include administration of one on more additional agents known in the art.
  • the method can include administering a neuraminidase inhibitor (such as oseltamivir, or zanamivir).
  • the method can include administering to the subject a therapeutically effective amount of an M2 inhibitor, such as amantadine and/or rimantadine.
  • the method can include administering to the subject a therapeutically effective amount of peramivir.
  • the subject can be hydrated and administered balancing electrolytes.
  • the subject can be administered intravenous immunoglobulins.
  • influenza protein can be an H1N1, H1N2, H3N2, H5N1, H6N1, H7N2, H7N3, H7N7, H7N9, H9N2, H10N7 or H10N8 influenza A virus protein or can be an influenza B virus protein.
  • influenza protein can be an H1N1, H3N2, H2N2, H5N1 or H7N9 influenza virus protein.
  • the influenza virus protein can be a NA or a HA.
  • the influenza virus protein can be NA of an Nl, N2, N3, N4, N5, N6, N7, N8, N9, N10 or Ni l subtype influenza virus, or the HA of any influenza A subtype, such as Hl, H3, H2, H5, H7, H10, H9, or H6.
  • a bispecific antibody can also be utilized.
  • the subject can be administered a therapeutically effective amount of more than one antibody, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 antibodies with specificity for different influenza virus proteins.
  • the subject can be administered a therapeutically effective amount of one or more antibodies that bind HA.
  • Combinations of the antibodies disclosed herein are also of use.
  • the disclosed antibodies can also be administered with an effective amount of an antibody that specifically binds NA.
  • the subject can be administered a therapeutically effective amount of one or more additional antibodies or antigen binding fragments that specifically binds either NA or HA of a specific influenza A virus, such as H1N1, H1N2, H2N2, H3N2, H5N1, H6N1, H7N2, H7N3, H7N7, H7N9, H9N2, H10N7 or H10N8.
  • a specific influenza A virus such as H1N1, H1N2, H2N2, H3N2, H5N1, H6N1, H7N2, H7N3, H7N7, H7N9, H9N2, H10N7 or H10N8.
  • the subject can also be administered a therapeutically effective amount of an antibody or antigen binding fragment that specifically binds HA (or NA) of H INI or a therapeutically effective amount of an antibody or antigen binding fragment that specifically binds HA (or NA) of H5N1, or a therapeutically effective amount of an antibody or antigen binding fragment that specifically binds HA (or NA) of H7N9 or H3N2 influenza virus.
  • the subject can be administered 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 additional antibodies or antigen binding fragments that specifically bind an influenza virus protein.
  • the antibodies can be administered in one or more pharmaceutical compositions.
  • the antibodies can be administered in a single pharmaceutical composition.
  • pharmaceutical compositions are provided herein that include the disclosed antibodies and/or antigen binding fragments and additional antibodies that specifically bind an influenza virus protein.
  • compositions including the antibody, antigen binding fragment, bispecific antibody, or nucleic acid encoding the antibody, antigen binding fragment, or bispecific antibody that are disclosed herein, are administered depending on the dosage and frequency as required and tolerated by the patient.
  • the composition should provide a sufficient quantity to effectively treat the patient.
  • the dosage can be administered once but may be applied periodically until either a therapeutic result is achieved or until side effects warrant discontinuation of therapy.
  • a dose of the antibody is infused for thirty minutes every other day.
  • about one to about ten doses can be administered, such as three or six doses can be administered every other day.
  • a continuous infusion is administered for about five to about ten days.
  • the subject can be treated at regular intervals, such as daily, until a desired therapeutic result is achieved.
  • the dose is sufficient to treat or ameliorate symptoms or signs of disease without producing unacceptable toxicity to the patient.
  • compositions include one or more of the antibody or antigen binding fragment that specifically binds HA and nucleic acids encoding these antibodies (and antigen binding fragments and bispecific antibodies) that are disclosed herein in a carrier.
  • the compositions can include antibodies or antigen binding fragments that specifically bind an influenza virus protein.
  • Compositions are provided that include one or more antibodies, antigen binding fragments, bispecific antibodies, conjugates, or nucleic acid molecules encoding such molecules, that are disclosed herein in a pharmaceutically acceptable carrier.
  • the composition comprises two, three, four or more antibodies, antigen binding fragments, or bispecific antibodies that specifically bind HA.
  • compositions are useful, for example, for the inhibition or detection of an influenza virus infection, such as an H1N1 and/or an H3N2 infection.
  • the composition includes one or more of the antibodies disclosed herein, or an antigen binding fragment thereof, or a bispecific antibody thereof.
  • the composition comprises two, three, four or more antibodies that specifically bind HA.
  • the compositions are useful, for example, for the inhibition or detection of an influenza virus infection, such as an H1N1 and/or an H3N2 infection.
  • compositions can be prepared in unit dosage forms, such as in a kit, for administration to a subject.
  • the amount and timing of administration are at the discretion of the administering physician to achieve the desired purposes.
  • the antibody, antigen binding fragment, bispecific antibody, conjugate, or nucleic acid molecule encoding such molecules can be formulated for systemic or local administration.
  • the, antigen binding fragment, bispecific antibody, conjugate, or nucleic acid molecule encoding such molecules is formulated for parenteral administration, such as intravenous administration.
  • the antibody, antigen binding fragment, bispecific antibody, or conjugate thereof in the composition is at least 70% (such as at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%) pure.
  • the composition contains less than 10% (such as less than 5%, less than 4%, less than 3%, less than 2%, less than 1%, less than 0.5%, or even less) of macromolecular contaminants, such as other mammalian (e.g., human) proteins.
  • compositions for administration can include a solution of the antibody, antigen binding fragment, bispecific antibody, conjugate, or nucleic acid molecule encoding such molecules, dissolved in a pharmaceutically acceptable carrier, such as an aqueous carrier.
  • a pharmaceutically acceptable carrier such as an aqueous carrier.
  • aqueous carriers can be used, for example, buffered saline and the like. These solutions are sterile and generally free of undesirable matter.
  • These compositions may be sterilized by any suitable technique.
  • the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
  • concentration of antibody in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the subject’s needs.
  • compositions can be prepared in unit dosage forms for administration to a subject.
  • the amount and timing of administration are at the discretion of the treating physician to achieve the desired purposes.
  • the antibody, antigen binding fragment, bispecific antibody, and/or nucleic acid can be formulated for systemic or local administration.
  • the antibody and/or nucleic acid is formulated for parenteral administration, such as intravenous administration.
  • administration is intramuscular.
  • Compositions also can be formulated for intranasal administration as a liquid or an aerosol.
  • the antibody can be administered to the respiratory tract by using a nebulizer.
  • Active ingredients can also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • macroemulsions for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • liposomes containing the immunogens or antibodies can be prepared by such methods as described in Epstein et al., Proc. Natl. Acad. Sci.
  • Liposomes with enhanced circulation time are disclosed in U.S. Pat. No. 5,013,556.
  • the reverse-phase evaporation method can be used with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE).
  • PEG-PE PEG-derivatized phosphatidylethanolamine
  • Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter.
  • Polypeptides such as antibodies or antibody fragments can be conjugated to the liposomes as described, for example, in Martin et al., J. Biol. Chem., 257:286-288 (1982) via a disulfide interchange reaction.
  • compositions for administration can include a solution of the antibody that specifically binds HA, or an antigen binding fragment thereof, or a bispecific antibody, dissolved in a pharmaceutically acceptable carrier, such as an aqueous carrier.
  • a pharmaceutically acceptable carrier such as an aqueous carrier.
  • aqueous carriers can be used, for example, buffered saline and the like.
  • These compositions may be sterilized by conventional, well known sterilization techniques.
  • the compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
  • concentration of antibodies, antigen binding fragments, or bispecific antibodies in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the subject’s needs. In some aspects, administration is intravenous.
  • Controlled-release parenteral formulations can be made as implants, oily injections, or as particulate systems.
  • Particulate systems include microspheres, microparticles, microcapsules, nanocapsules, nanospheres, and nanoparticles.
  • Microcapsules contain the therapeutic protein, such as a cytotoxin or a drug, as a central core. In microspheres the therapeutic is dispersed throughout the particle.
  • Particles, microspheres, and microcapsules smaller than about 1 pm are generally referred to as nanoparticles, nanospheres, and nanocapsules, respectively.
  • Capillaries have a diameter of approximately 5 pm so that only nanoparticles are administered intravenously.
  • Microparticles are typically around 100 pm in diameter and are administered subcutaneously or intramuscularly. See, for example, Kreuter, J., Colloidal Drug Delivery Systems, J. Kreuter, ed., Marcel Dekker, Inc., New York, NY, pp. 219-342 (1994); and Tice & Tabibi, Treatise on Controlled Drug Delivery, A. Kydonieus, ed., Marcel Dekker, Inc. New York, NY, pp. 315-339, (1992).
  • Polymers can be used for ion-controlled release of the antibody compositions disclosed herein.
  • Various degradable and nondegradable polymeric matrices for use in controlled drug delivery are known in the art (Langer, Accounts Chem. Res. 26:537-542, 1993).
  • the block copolymer, polaxamer 407 exists as a viscous yet mobile liquid at low temperatures but forms a semisolid gel at body temperature. It has been shown to be an effective vehicle for formulation and sustained delivery of recombinant interleukin-2 and urease (Johnston et al., Pharm. Res. 9:425-434, 1992; and Pec et al., J. Parent. Sci. Tech. 44(2) :58-65, 1990).
  • hydroxyapatite has been used as a microcarrier for controlled release of proteins (Ijntema et al., Int. J. Pharm. 112:215-224, 1994).
  • liposomes are used for controlled release as well as drug targeting of the lipid-capsulated drug (Betageri et al., Liposome Drug Delivery Systems, Technomic Publishing Co., Inc., Lancaster, PA (1993)).
  • Numerous additional systems for controlled delivery of therapeutic proteins are known (see U.S. Patent No. 5,055,303; U.S. Patent No. 5,188,837; U.S. Patent No. 4,235,871; U.S. Patent No. 4,501,728; U.S. Patent No.
  • a typical pharmaceutical composition for intravenous administration includes about 0.1 to 10 mg/kg of antibody (or antigen binding fragment) per day, or 0.5 to 15 mg/kg of antibody per day. Dosages from 0.1 up to about 100 mg/kg per subject per day may be used, particularly if the agent is administered to a secluded site and not into the circulatory or lymph system, such as into a body cavity or into a lumen of an organ. Exemplary doses include 1 to 10 mg/kg, such as 2 to 8 mg/kg, such as 3 to 6 mg/kg. Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remington's Pharmaceutical Science, 19th ed., Mack Publishing Company, Easton, PA (1995).
  • Antibodies, antigen binding fragments, and bispecific antibodies may be provided in lyophilized form and rehydrated with sterile water before administration, although they are also provided in sterile solutions of known concentration.
  • the antibody (antigen binding fragment, or bispecific antibody) solution is then added to an infusion bag containing 0.9% sodium chloride, USP, and typically administered at a dosage of from 0.1 to 50 mg/kg or 0.5 to 15 mg/kg of body weight.
  • Exemplary doses include 1 to 10 mg/kg, such as 2 to 8 mg/kg, such as 3 to 6 mg/kg.
  • Antibodies, antigen binding fragments thereof, and bispecific antibodies can be administered by intravenous infusion. Doses of the antibody, antigen binding fragment, or bispecific antibody vary, but generally range between about 0.5 mg/kg to about 50 mg/kg, such as a dose of about 1 mg/kg, about 5 mg/kg, about 10 mg/kg, about 20 mg/kg, about 30 mg/kg, about 40 mg/kg, or about 50 mg/kg. In some aspects, the dose of the antibody, antigen binding fragment or bispecific antibody can be from about 0.5 mg/kg to about 5 mg/kg, such as a dose of about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg or about 5 mg/kg.
  • the antibody, antigen binding fragment, or bispecific antibody is administered according to a dosing schedule determined by a medical practitioner. In some examples, the antibody, antigen binding fragment or bispecific antibody is administered weekly, every two weeks, every three weeks or every four weeks.
  • a therapeutically effective amount of a nucleic acid encoding the antibody, an antigen binding fragment thereof, or bispecific antibody can be administered to a subject in need thereof.
  • One approach to administration of nucleic acids is direct immunization with plasmid DNA, such as with a mammalian expression plasmid.
  • the nucleotide sequence encoding the antibody or fragment thereof can be placed under the control of a promoter to increase expression of the molecule.
  • Immunization by nucleic acid constructs is well known in the art and taught, for example, in U.S. Patent No. 5,643,578, and U.S. Patent No. 5,593,972 and U.S. Patent No. 5,817,637.
  • U.S. Patent No. 5,880,103 describes several methods of delivery of nucleic acids to an organism. The methods include liposomal delivery of the nucleic acids.
  • an antibody, antigen binding fragment thereof, or bispecific antibody can also be expressed by attenuated viral hosts or vectors or bacterial vectors, which can be administered to a subject.
  • Recombinant vaccinia virus, adeno-associated virus (AAV), herpes virus, retrovirus, cytomegalovirus, poxvirus or other viral vectors can be used to express the antibody.
  • vaccinia vectors are described in U.S. Patent No. 4,722,848.
  • BCG Bacillus Calmette Guerin provides another vector for expression of the disclosed antibodies (see Stover, Nature 351:456-460, 1991).
  • a nucleic acid encoding the antibody, an antigen binding fragment, or bispecific antibody is introduced directly into cells.
  • the nucleic acid can be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad’s HELIOSTM Gene Gun.
  • the nucleic acids can be “naked,” consisting of plasmids under control of a strong promoter.
  • the DNA is injected into muscle, although it can also be injected directly into other sites.
  • Dosages for injection are usually around 0.5 mg/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Patent No. 5,589,466).
  • a subject is administered DNA or RNA encoding a disclosed antibody, antigen binding fragment, or bispecific antibody, to provide in vivo antibody production, for example using the cellular machinery of the subject.
  • Any suitable method of nucleic acid administration may be used; nonlimiting examples are provided in U.S. Patent No. 5,643,578, U.S. Patent No. 5,593,972 and U.S. Patent No. 5,817,637.
  • U.S. Patent No. 5,880,103 describes several methods of delivery of nucleic acids encoding proteins to an organism.
  • One approach to administration of nucleic acids is direct administration with plasmid DNA, such as with a mammalian expression plasmid.
  • the nucleotide sequence encoding the disclosed antibody, antigen binding fragments thereof, or bispecific antibody can be placed under the control of a promoter to increase expression.
  • the methods include liposomal delivery of the nucleic acids. Such methods can be applied to the production of an antibody, or antigen binding fragments thereof.
  • a disclosed antibody or antigen binding fragment is expressed in a subject using the pVRC8400 vector (described in Barouch et al., J. Virol., 79(14), 8828-8834, 2005, which is incorporated by reference herein).
  • a subject (such as a human subject at risk of an influenza virus infection or having an influenza virus infection) can be administered an effective amount of an AAV viral vector that comprises one or more nucleic acid molecules encoding a disclosed antibody, antigen binding fragment, or bispecific antibody.
  • the AAV viral vector is designed for expression of the nucleic acid molecules encoding a disclosed antibody, antigen binding fragment, or bispecific antibody, and administration of the effective amount of the AAV viral vector to the subject leads to expression of an effective amount of the antibody, antigen binding fragment, or bispecific antibody in the subject.
  • AAV viral vectors that can be used to express a disclosed antibody, antigen binding fragment, or bispecific antibody in a subject include those provided in Johnson et al., Nat. Med., 15(8) :901-906, 2009 and Gardner et al., Nature, 519(7541):87-91, 2015, each of which is incorporated by reference herein in its entirety.
  • a nucleic acid encoding a disclosed antibody, antigen binding fragment, or bispecific antibody is introduced directly into tissue.
  • the nucleic acid can be loaded onto gold microspheres by standard methods and introduced into the skin by a device such as Bio-Rad’s HELIOSTM Gene Gun.
  • the nucleic acids can be “naked,” consisting of plasmids under control of a strong promoter.
  • the DNA is injected into muscle, although it can also be injected directly into other sites.
  • Dosages for injection are usually around 0.5 pg/kg to about 50 mg/kg, and typically are about 0.005 mg/kg to about 5 mg/kg (see, e.g., U.S. Patent No. 5,589,466).
  • Single or multiple administrations of a composition including a disclosed antibody, antigen binding fragment, or bispecific antibody, conjugate, or nucleic acid molecule encoding such molecules can be administered depending on the dosage and frequency as required and tolerated by the patient.
  • the dosage can be administered once but may be applied periodically until either a desired result is achieved or until side effects warrant discontinuation of therapy. Generally, the dose is sufficient to inhibit an influenza virus infection without producing unacceptable toxicity to the patient.
  • Data obtained from cell culture assays and animal studies can be used to formulate a range of dosage for use in humans.
  • the dosage normally lies within a range of circulating concentrations that include the ED50, with little or minimal toxicity.
  • the dosage can vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the effective dose can be determined from cell culture assays and animal studies.
  • the antibody, antigen binding fragment, bispecific antibody or nucleic acid molecule encoding such molecules, or a composition including such molecules is administered by a single subcutaneous, intravenous, intra-arterial, intraperitoneal, intramuscular, intradermal or intrathecal injection once a day.
  • the antibody, antigen binding fragment, bispecific antibody, conjugate, or nucleic acid molecule encoding such molecules, or a composition including such molecules can also be administered by direct injection at or near the site of disease.
  • a further method of administration is by osmotic pump e.g., an Alzet pump) or mini-pump (e.g..
  • an Alzet mini-osmotic pump which allows for controlled, continuous and/or slow-release delivery of the antibody, antigen binding fragment, conjugate, or nucleic acid molecule encoding such molecules, or a composition including such molecules, over a pre-determined period.
  • the osmotic pump or mini-pump can be implanted subcutaneously, or near a target site.
  • a typical composition for intravenous administration comprises about 0.01 to about 30 mg/kg of antibody, antigen binding fragment, bispecific antibody, or conjugate per subject per day (or the corresponding dose of a conjugate including the antibody or antigen binding fragment).
  • Any suitable method may be used for preparing administrable compositions; non-limiting examples are provided in such publications as Remington: The Science and Practice of Pharmacy, 22 nd ed., London, UK: Pharmaceutical Press, 2013.
  • the composition can be a liquid formulation including one or more antibodies, antigen binding fragments, or bispecific antibodies, in a concentration range from about 0.1 mg/ml to about 20 mg/ml, or from about 0.5 mg/ml to about 20 mg/ml, or from about 1 mg/ml to about 20 mg/ml, or from about 0.1 mg/ml to about 10 mg/ml, or from about 0.5 mg/ml to about 10 mg/ml, or from about 1 mg/ml to about 10 mg/ml.
  • influenza virus can be a H1N1, H5N1, H2N2, H6N1, H9N2, H3N2, H10N8, or an H7N9 influenza virus.
  • influenza virus can be an H1N1 influenza virus.
  • influenza virus can be an H3N2 influenza virus.
  • Biological samples include sections of tissues, for example, frozen sections taken for histological purposes, tissue from biopsies, autopsies and pathology specimens.
  • Bio samples also include body fluids, such as blood, serum, plasma, sputum, tears, saliva, spinal fluid, nasopharyngeal secretions or urine, or stool.
  • the sample can be a nasal wash, a throat swab, nasal swab, or a lung aspirate.
  • the sample is an environmental sample.
  • influenza virus can be a H1N1, H5N1, H2N2, H6N1, H9N2, H3N2, H10N8, or an H7N9 influenza virus.
  • influenza virus can be an H1N 1 influenza virus.
  • influenza virus can be an H3N2 influenza virus.
  • the presence of the influenza virus is detected in a sample suspected of containing the virus, wherein the method includes contacting the sample with an antibody disclosed herein, or an antigen binding fragment thereof, and determining binding of the antibody or antigen binding fragment to the virus in the sample. In these methods, binding of the antibody or antigen binding fragment to virus in the sample is indicative of the presence of the virus in the sample.
  • the sample is a biological sample. The binding of the antibody or antigen binding fragment can be quantitated.
  • influenza virus There are four genera of influenza virus (A, B, C and D), three of which (A, B and C) infect humans. Influenza A viruses are classified based on the viral surface proteins HA and NA.
  • HA subtypes Eighteen HA subtypes (or serotypes) and eleven NA subtypes of influenza A virus have been identified.
  • Specific influenza strain isolates can be identified by a standard nomenclature specifying virus type, geographical location where first isolated, sequential number of isolation, year of isolation, and HA and NA subtype.
  • the serotypes that are known to have been associated with deaths are H1N1, H1N2, H2N2, H3N2, H5N1, H5N6, H7N7, H7N9, H9N2, and H10N8.
  • the presently disclosed antibodies and antigen binding fragments specifically bind HA, and can be used to detect Hl, H2, H5, H6, H9, H3, H10 AND H7 influenza subtypes.
  • the disclosed methods include determining the HA subtype of the influenza virus.
  • the method includes contacting the sample with an antibody disclosed herein that specifically binds HA and determining binding of the antibody to the virus in the sample.
  • binding of the antibody to virus in the sample is indicative of the presence of an influenza virus in the sample.
  • the sample is a biological sample. In other aspects, the sample is an environmental sample.
  • the methods can also include contacting the sample with an antibody or antigen binding fragment thereof that specifically binds HA of an influenza virus and determining binding of the antibody to the virus in the sample.
  • binding of the antibody to virus in the sample is indicative of the presence of a particular subtype of influenza virus.
  • a method for detecting an influenza virus infection in a subject provides a method for detecting an influenza virus in a biological sample, wherein the method includes contacting a biological sample with the antibody or antigen binding fragment that specifically binds HA of influenza virus, specifically the antibodies and antigen binding fragments disclosed herein, under conditions conducive to the formation of an immune complex, and detecting the immune complex, to detect the presence of the HA polypeptide in the biological sample.
  • detection of the HA polypeptide in the sample detects or confirms a diagnosis of an influenza virus infection.
  • an antibody fragment such as an Fv fragment, a Fab, or any of the antigen binding fragments disclosed above, can be utilized in the disclosed methods.
  • the amount of influenza virus can be quantitated by methods known in the art.
  • the detection of HA of influenza virus can be achieved, for example, by contacting a sample to be tested, optionally along with a control sample, with the antibody (or antigen binding fragment) under conditions that allow for formation of a complex between the antibody or antigen binding fragment and the virus. Complex formation is then detected (e.g., using an ELISA).
  • complex is detected in both samples and any statistically significant difference in the formation of complexes between the samples is indicative of the presence of influenza virus in the test sample.
  • the control is a standard value.
  • the control is the binding of the monoclonal antibody or antigen binding fragment to a control sample comprising a known quantity of HA protein.
  • the control can also be the binding of the monoclonal antibody or antigen binding fragment to a control sample from a subject known not to have an influenza virus infection.
  • the disclosed antibodies are used to test vaccines.
  • a vaccine composition can induce HA inhibiting antibodies, such as, but not limited to, inhibition of HA of H INI or H3N2 influenza viruses.
  • a method for testing a vaccine includes contacting a sample containing the vaccine, such as an HA polypeptide, or a recombinant attenuated virus, with the antibody (or antigen binding fragment) under conditions conducive to the formation of an immune complex, and detecting the immune complex.
  • the detection of the immune complex confirms the vaccine will be effective.
  • the detection of the immune complex in the sample indicates that the vaccine component, such as such as an HA antigen assumes a conformation capable of inducing neutralizing antibodies.
  • an antibody is directly labeled with a detectable label.
  • the antibody (or antigen binding fragment) that binds HA (the first antibody) is unlabeled and a second antibody or other molecule that can bind the antibody that binds HA is utilized.
  • a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody.
  • the first antibody is a human IgG
  • the secondary antibody may be an anti-human-IgG.
  • Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.
  • Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase.
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin.
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin.
  • a non-limiting exemplary luminescent material is luminol; a non-limiting exemplary a magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include 125 I, 131 I, 35 S or 3 H.
  • the antibodies can be directly labeled.
  • a second antibody is used that that specifically binds a disclosed isolated monoclonal antibody or antigen binding fragment to form an immune complex and detecting the binding of the second antibody.
  • Kits for detecting HA will typically comprise an antibody (or antigen binding fragment) that specifically binds HA, for example, any of the antibodies or antigen binding fragments disclosed herein.
  • an antibody fragment such as an Fv fragment or a Fab is included in the kit.
  • the antibody is labeled (for example, with a fluorescent, radioactive, or an enzymatic label).
  • kits in one aspect, includes instructional materials disclosing means of use.
  • the instructional materials may be written, in an electronic form (such as a computer diskette or compact disk) or may be visual (such as video files).
  • the kits may also include additional components to facilitate the particular application for which the kit is designed.
  • the kit may additionally contain means of detecting a label (such as enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a secondary antibody, or the like).
  • the kits may additionally include buffers and other reagents routinely used for the practice of a particular method. Such kits and appropriate contents are well known to those of skill in the art.
  • the diagnostic kit comprises an immunoassay.
  • the method of detecting HA in a biological sample generally includes the steps of contacting the biological sample with an antibody or antigen binding fragment which specifically binds, under immunologically reactive conditions, to HA.
  • the antibody is allowed to specifically bind under immunologically reactive conditions to form an immune complex, and the presence of the immune complex (bound antibody) is detected directly or indirectly.
  • Methods for detection and quantification of HA are disclosed above.
  • Example 1 Isolation and characterization of antibodies that specifically bind the stem region of influenza virus HA
  • HA stem-directed mAbs were used to detect and single-cell sort B cells expressing B cell receptors able to bind HA stem.
  • the immunoglobulin genes coding for the paired antibody heavy and light chain were then PCR amplified and sequenced from each sorted B cell. After analyzing the sequences, a subset of paired heavy and light chain immunoglobulin genes was selected to clone into expression vectors and were expressed as monoclonal antibodies (mAbs) in transiently transfected 293F cells. These mAbs were then tested for binding to the HA stem region and the ectodomain of several different influenza subtypes.
  • FIG. 1 Shown in FIG. 1 is microneutralization data for select mAbs divided according to their breadth across group 1 and group 2 influenza virus subtypes and that bind the central stem epitope.
  • mAbs 321-2001- c39.1, 315-53-1G08 and MEDI8852 were tested side-by-side for neutralization against a panel of eight influenza virus strains representing all subtypes known to infect humans.
  • the microneutralization inhibitory concentration 80 (IC80) in Ltg/rnl is listed for each mAb.
  • FIG. 2A is a graph wherein the IC80 is plotted for each mAb. Each dot represents the IC80 for one H3N2 strain with the lines and numbers above indicating the median IC80.
  • FIG. 2B shows the IC80 (Jlg/ml) against seven of the H3N2 strains, the H10N8 strain, and the two H7N9 strains.
  • FIG. 3A shows the IC80 against the 15 H1N1 strains for each mAb. Each dot represents the IC80 for one H1N1 strain, and the lines and numbers above indicate the median IC80.
  • FIG. 3B provides the IC80 tug/ml ) of each mAb against all strains tested.
  • FIG. 4 provides data for additional potent and broadly neutralizing antibodies disclosed herein.
  • Microneutralization IC80 against pandemic (A/Cal09) and pre-pandemic (A/NC99) H1N1 strains of multiple mAbs isolated from participants of the Hl stabilized stem clinical trial are shown in FIG. 4.
  • each line represents the IC80 of a given mAb against both H1N1 strains.
  • Four antibodies are specifically shown (321-205-1D01, 321-102-1E12, 321-213-1A07, and 321-205-1C09). This data can be compared to the data in FIGS. 3A-3B.
  • 321-205-1C09 and 321-213-1A07 described in Figure 3A-3B bind the central HA stem epitope.
  • the additional two mAbs 321-102-1E12 and 321-205-1D01 have a similar microneutralization IC80 but bind a separate, lower epitope of the HA stem.
  • bispecific antibodies are prepared: a) 323-2019_c2328 + 321-205-1C09 (potent H3N2 + potent H1N1) b) 321-205-1C09 + 321-205-1D01 (both potent H1N1 neutralizers but bind different epitopes on the HA stem) c) 323-2019_c2328 + 315-53- 1G08 (potent H3N2 + broadly neutralizing mAb)
  • the presently disclosed monoclonal antibodies, antigen binding fragments, and bispecific antibodies are tested in a mouse model of an influenza virus infection.
  • HA expression Expi293 cells (Thermo Fisher Catalog #A14527) were transfected with HA plasmids using EXPIFECTAMINETM (Thermo Fisher) and incubated for 4 to 5 days at 37°C. Cell supernatants were then harvested and loaded onto a column with Ni Sepharose excel (Cytiva) and purified by gravity flow. The HA protein was eluted from the column with 50mM Tris-HCl pH 8, 500mM NaCl containing 300 mM imidazole. It was then concentrated and further purified on a SUPERDEXTM Increase 200 10/300 GL size exclusion column (Cytiva) in PBS.
  • HA probes were made by either incubating biotinylated HAs with fluorescently conjugated streptavidin molecules at a 4:1 molar ratio or by directly conjugating unbiotinylated HAs to fluorophores according to the manufacturer’ s protocol (ThermoFisher Scientific).
  • Single-Cell 1g Amplification and Ig sequence analysis Reverse transcription was performed on single-sorted cells and multiplexed polymerase chain reaction (PCR) was used to amplify immunoglobulin heavy and light chain genes as described previously (Whittle et al., J Virol 88, 4047-4057 (2014)). PCR products were Sanger sequenced by Genewiz. (Tiller et al., J Immunol Methods 329, 112-124 (2008)).
  • RNA sequencing Single-Cell RNA sequencing (RNAseq) and Ig sequence analysis: cDNA from bulk-sorted plasmablasts was made using the lOx Genomics CHROMIUMTM Next GEM Single Cell 5’ Kit v2 per the manufacturer’s instructions. V(D)J genes were then amplified, and libraries made for next generation sequencing using the v2 10X Genomics B cell receptor amplification and library preparation kits according to the manufacturer’s instructions. V(D)J libraries were sequenced on a Novaseq (Illumina) targeting at least 10,000 reads per cell. The base call files (BCL) generated by the Novaseq sequencer were converted to paired- end reads and samples were demultiplexed using bcl2fastq version 2.20 and Cell Ranger version 3.0.2.
  • BCL base call files
  • Monoclonal antibodies were purified from the cell supernatant using sepharose Protein A (Pierce). To produce Fabs for kinetics, the mAbs were cleaved by LysC enzyme (1:2000 w/w) (New England BioLabs) at room temperature overnight. The enzymatic digestion was stopped by protease inhibitor (Roche). The digestion mixture was then passed through a protein A or protein G column to separate the Fc fragment from the Fab.
  • High-Throughput SPR Kinetics (see FIG. 6D): High throughput SPR capture kinetic experiments were performed on a Carterra LSA system, using an SAHC30M sensor chip in a 384-ligand array format. Chip surface was primed with run buffer (HBST-Carterra), and conditioned using 50mM NaOH (Carterra), IM NaCl (Teknova), and lOmM Glycine pH2 (Carterra). A capture lawn was prepared using a 15ug/mL of Human Fab-kappa Kinetics Biotin and Human Fab-lambda Kinetics Biotin conjugate mix (ThermoScientifc) for 10 minutes, followed by lOmM Glycine pH2 wash to determine capture lawn viability.
  • fragment antibodies were diluted fourfold (200nM, 50nM, 12.5nM, 3.125nM) in HBST+0.5mg/mL BSA (HBST+BSA) running buffer and printed onto the capture lawn for seven minutes, followed by a baseline injection of running buffer (HBST+BSA).
  • Antigens of interest (Port Chalmers/1/1973, Indiana/ 10/2011, Switzerland/9715293/2013, Darwin/6/2021), in a twofold dilution series (200nM-0nM), were sequentially injected onto the chip surface. For each concentration, the antigen was injected for five minutes (association phase), followed by HBST+BSA running buffer injection for fifteen minutes (dissociation phase).
  • R3 influenza viruses were used for the microneutralization assay. The procedure for rescue and propagation of these viruses is described in detail elsewhere (Creanga et al., Nat Commun 12, 1722 (2021)). Briefly, R3 APB1 viruses (i.e., H1N1, H3N2, H10N8) have the PB1 coding region replaced with TdKatushka2S reporter gene linked with a nuclear localization signal at the C-terminus (Tdkatushka2S-NLS).
  • Influenza viruses H7N9 were prepared as rewired replication-reporter restricted (R4 APB1) viruses in which HA coding region is inserted between PB1 genomic packaging signals, whereas Tdkatushka2S-NLS reporter gene is inserted between HA genomic packaging signals.
  • Influenza virus H5N1 was prepared as R3 AHA in which the reporter was inserted in the HA segment between the genomic packaging sequences and the virus was propagated in MDCK cell line stably expressing HA of A/Vietnam/ 1203/2004 (PMID 33741916).
  • the reverse genetics plasmids or full- length sequences of HA, NA and reporter segments found in R3/R4 APB 1 viruses can be made available upon request.
  • A/WSN/1933 H1N1 influenza virus i.e., PB2, PA, NP, M and NS
  • R3/R4 APB 1 viruses are rescued by reverse genetics in 293 cells stably expressing PB1 of A/WSN/1933 and they are propagated in MDCK-SIAT1 cells stably expressing PB1 of A/WSN/1933 (MDCK-SIAT-PB1 cell line).
  • each virus stock is titrated to determine the linear range between the virus dilution and the number of infected cells: 90 uL of 2-fold serial dilutions of the virus stock prepared in Opti-MEM are mixed with 30 pL MDCK-SIAT-PB1 cells (8xl0 A 5 cells/mL) and transferred in a 384-well plate in quadruplicate (25 pL/well). Plates were incubated for 18-26 h at 37°C with 5% CO2 humidified atmosphere. After incubation, fluorescent cells were imaged and counted by using a Celigo Image Cytometer (Nexcelom) with a customized red filter for detecting TdKatushka2 fluorescence. A virus dilution that resulted in 500-2000 fluorescent cells per well (linear range of the titration curve) was chosen for the neutralization assay.
  • the concentration at which there was >50% neutralization compared to the no antibody control is reported.
  • the limit of detection for this assay is 10 pg/mE.
  • a 7-point neutralization curve was plotted against antibody for each sample, and a four-parameter nonlinear fit was generated using Prism (GraphPad) to estimate the 50% (IC50, pg/mL) or 80% (IC80, pg/mL) inhibitory concentrations.
  • the limit of detection of the assay is 25 pg/mL and takes into account the antibody dilution after admixing with virus at 1 : 1 ratio.
  • mice Female DBA/2J mice, 6-8 weeks old, were purchased from Jackson Laboratories (Bar Harbor, ME). Upon arrival, mice were housed in standard microisolator caging at ABSL-2, five per cage. Preliminary studies established an LD50 of 207 pfu.
  • Example 4 Identification of two distinct epitopes (central and lower) that elicit an immune response from group 2 antibodies
  • Residues predicted to be important for binding of either central or lower epitope-reactive antibodies were identified and a glycan was introduced at each identified position (FIG. 5A).
  • residue 45 on HA2 was important for binding of antibodies to the central region of the stem (Andrews et al., Sci Transl Med 15, eade4976 (2023)).
  • Structural analysis of CR8043 suggested that the HA2 position 34 on the group 2 stem could be an important residue for antibodies targeting this lower stem epitope (Friesen et al., Proc Natl Acad Sci U S A 111, 445- 450 (2014)).
  • H-SPR High throughput surface plasmon resonance
  • MEDI8852 a central epitope targeted mAb that has been tested as an influenza therapeutic was also administered (Kallewaard et al., Cell 166, 596-608 (2016); Ali et al., Antimicrob Agents Chemother 62 (2016); Mallory et al., Biologicals 50, 81-86 (2017)), and CR8020, a lower epitope targeted mAh that has previously shown limited protection of mice against H3N2 and H7N9 challenge (FIG. 6E) (Ekiert et al., Science 333, 843-850 (2011)).
  • mAbs were administered at 10, 1, 0.5 or 0.1 mg kg' 1 48 hours prior to lethal challenge with a mouse- adapted H3N2 (A/Switzerland/9715293/2013) (McMahon et al., Proc Natl Acad Sci U SA 119, e2206333119 (2022)). Although all of the mAbs were at least partially protective at high doses (10 mg kg 1 and 1 mg kg' 1 ), both lower epitope targeted mAbs remained significantly more protective against lethal challenge than VRC01 at both 0.5 mg kg 1 (P ⁇ 0.01) and 0.1 mg kg 1 (P ⁇ 0.05) doses (FIG. 6F).
  • MEDI8552 was significantly protective at 0.5 mg kg 1 (P ⁇ 0.05) but not 0.1 mg kg 1 (P > 0.05) as compared with VRC01, and the central epitope targeted mAh isolated from this study was not significantly (P > 0.05) more protective at either 0.5 or 0.1 mg kg 1 (FIG. 6F).
  • MEDI8852 the most broadly reactive and potent central epitope targeting HA stem mAb published, was tested for its efficacy in preventing seasonal influenza infection after passive transfer in healthy adults (NCT05567783). Study results indicated that, though it did not prevent influenza infection, it did reduce the incidence of fever, supporting the idea that stem-directed mAbs could provide some protection against severe disease in vulnerable populations (Tan et al., Clin Infect Dis (2024)).
  • MEDI8852 also has a reduced ability to neutralize group 2 subtypes compared with group 1 (Paules et al., J Infect Dis 216, 356-365 (2017); Kallewaard et al., Cell 166, 596-608 (2016)) and that may have contributed to its lower efficacy against preventing influenza infection in a season when H3N2 infections dominated (2022-23 season).
  • group 1 Paules et al., J Infect Dis 216, 356-365 (2017); Kallewaard et al., Cell 166, 596-608 (2016)
  • This study demonstrated that antibodies targeting the lower epitope more potently neutralize recent H3N2 strains than central epitope-reactive antibodies, and two of these lower epitope-reactive antibodies outperformed MEDI8852 at low doses in protecting mice against seasonal H3 infection.
  • Central epitope targeted mAbs also had very limited ability to neutralize swine-origin variant H3N2 (A/Indiana/10/2011), whereas the lower epitope -targeted mAbs showed no reduction in their ability to neutralize this H3 strain of pandemic potential.
  • This greater overall breadth of neutralization for lower epitope targeted mAbs against H3N2 strains demonstrates an advantage of eliciting a diverse repertoire of stem-specific B cells outside of the broadly reactive central epitope.
  • targeting the lower epitope can provide better protection against both seasonal drifting H3 and novel animal-origin pandemic H3 and H10 viral strains.

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Abstract

Sont divulgués des anticorps monoclonaux et des fragments de liaison à l'antigène qui se lient spécifiquement à la région souche de l'hémagglutinine (HA) du virus de la grippe A. Selon certains aspects, ces anticorps et fragments de liaison à l'antigène sont utilisés dans des méthodes de traitement d'un sujet atteint d'une infection par le virus de la grippe A. Dans d'autres aspects, ces anticorps et fragments de liaison à l'antigène et anticorps bispécifiques sont utilisés pour la détection d'un virus de la grippe dans un échantillon, ainsi que pour la sélection de vaccins contre le virus de la grippe.
PCT/US2024/057131 2023-12-01 2024-11-22 Anticorps dirigés contre la souche de l'hémagglutinine de la grippe largement neutralisants Pending WO2025117384A1 (fr)

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