WO2023156187A1 - High affinity antibodies against the sars-cov-2 receptor binding domain - Google Patents

High affinity antibodies against the sars-cov-2 receptor binding domain Download PDF

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Publication number
WO2023156187A1
WO2023156187A1 PCT/EP2023/052295 EP2023052295W WO2023156187A1 WO 2023156187 A1 WO2023156187 A1 WO 2023156187A1 EP 2023052295 W EP2023052295 W EP 2023052295W WO 2023156187 A1 WO2023156187 A1 WO 2023156187A1
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Prior art keywords
antibody
cov
sars
amino acid
block
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PCT/EP2023/052295
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French (fr)
Inventor
Hedda WARDEMANN
Rajagopal MURUGAN
Ralf Bartenschlager
Heeyoung Kim
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Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts
Universität Heidelberg
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Publication of WO2023156187A1 publication Critical patent/WO2023156187A1/en

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    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • C07K16/1003—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2 or Covid-19]
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6854—Immunoglobulins
    • G01N33/6857—Antibody fragments
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—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

  • the present invention concerns the field of therapeutic and diagnostic antibodies against SARS- CoV-2.
  • the invention relates to an antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10' 9 M.
  • the present invention further relates to a polynucleotide encoding the antibody of the invention, a vector or expression construct comprising said polynucleotide, a host cell comprising said polynucleotide, vector or expression construct, or a non-human transgenic organism comprising the polynucleotide, vector or expression construct of the invention.
  • the invention relates to a method for producing the antibody of the invention and to the use of the host cell of the invention for producing the antibody of the invention. Moreover, the present invention provides for using an antibody, a polynucleotide or a vector of the invention for treating and/or preventing a disease or condition or for using the antibody for diagnosing said disease or condition. Finally, the invention relates to a kit for diagnosing SARS- CoV-2 infection in a subject.
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • SARS-CoV-2 severe acute respiratory syndrome coronavirus 2
  • hACE2 human angiotensin-converting enzyme 2
  • SARS-CoV- 2 alpha variant B.1.1.7
  • SARS-CoV-2 beta variant B.1.1351
  • SARS-CoV-2 delta variant B.1.617.2
  • SARS-CoV-2 omicron variant B.1.1.529
  • BA.l, BA.2 and BA.3 omicron sub-variants
  • BA.5 subvariant BA.5.
  • the present invention relates to an antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10' 9 M.
  • the terms “have”, “comprise” or “include” are meant to have a nonlimiting meaning or a limiting meaning. Thus, having a limiting meaning these terms may refer to a situation in which, besides the feature introduced by these terms, no other features are present in an embodiment described, i.e. the terms have a limiting meaning in the sense of “consisting of’ or “essentially consisting of’. Having a non-limiting meaning, the terms refer to a situation where besides the feature introduced by these terms, one or more other features are present in an embodiment described.
  • the terms “preferably”, “more preferably”, “most preferably”, “particularly”, “more particularly”, “typically”, and “more typically” are used in conjunction with features in order to indicate that these features are preferred features, i.e. the terms shall indicate that alternative features may also be envisaged in accordance with the invention.
  • the term “at least one” as used herein means that one or more of the items referred to following the term may be used in accordance with the invention. For example, if the term indicates that at least one item shall be used this may be understood as one item or more than one item, i.e. two, three, four, five or any other number. Depending on the item the term refers to the skilled person understands as to what upper limit the term may refer, if any.
  • antibody refers to any polypeptide which comprises amino acid sequence stretches that are capable of forming a binding pocket that is sufficient for specific binding to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) as referred to herein.
  • an antibody may be, preferably, a monoclonal antibody, a single chain antibody, a chimeric antibody or any fragment or derivative of such antibodies being still capable of binding to the receptor binding domain (RBD) of SARS-CoV-2 spike protein specifically as referred to herein.
  • Fragments and derivatives comprised by the term antibody as used herein encompass a bispecific antibody, a synthetic antibody, a Fab, F(ab)2 Fv or scFv fragment or a chemically modified derivative of any of these antibodies.
  • Antibodies or fragments thereof in general, can be obtained by using methods which are described, e.g., in Harlow and Lane "Antibodies, A Laboratory Manual", CSH Press, Cold Spring Harbor, 1988.
  • Monoclonal antibodies can be prepared by the techniques which comprise the fusion of mouse myeloma cells to spleen cells derived from immunized mammals and, preferably, immunized mice.
  • Antibodies may also be produced recombinantly by techniques well known in the art.
  • the antibody of the present invention can be, preferably, generated by using the techniques described in the accompanying Examples below.
  • the antibody of the invention shall specifically bind to the receptor binding domain (RBD) of SARS-CoV-2 spike protein.
  • RBD receptor binding domain
  • the term “receptor binding domain (RBD)” as used herein refers to a region of the SARS-CoV-2 spike protein which is involved in binding of the said spike protein of the virus to the human Angiotensin Converting Enzyme (hACE)-2 receptor on host cells.
  • the RBD consists of amino acids 319 to 541 of the SARS-CoV-2 spike protein of WT SARS-CoV-2 (see preferably, BetaCoV/Wuhan/IVDC-HB-01/2019, accession ID: EPI ISL 402119; BetaCoV/Wuhan/IVDC-HB-04/2020, accession ID: EPI ISL 402120; BetaCoV/Wuhan/IVDC-HB-05/2019, accession ID: EPI ISL 402121). It will be understood that in virus variants of SARS-CoV-2, the position may differ due to the presence of one or more additional amino acids and/or deletions of one or more amino acids.
  • such variants shall also comprise a RBD which consists of amino acids corresponding to the amino acids of the RBD in WT SARS-CoV-2 at amino acid positions 319 to 541.
  • the spike protein is a glycoprotein that forms a homotrimer at the surface of SARS-CoV-2 (Wrapp et al, Science, 367: 1260-1263).
  • the RBD may be exhibited by each monomer in either a so-called “up” or a so -called “down” configuration.
  • SARS-CoV-2 spike protein The structure and amino acid composition of the SARS-CoV-2 spike protein is well known in the art, for WT SARS-CoV-2 as well as for various variants of the virus, such as SARS-CoV- 2 alpha variant (B. l.1.7), SARS-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
  • SARS-CoV- 2 alpha variant B. l.1.7
  • SARS-CoV-2 beta variant B.1.1351
  • SARS-CoV-2 delta variant B.1.617.2
  • SARS-CoV-2 omicron variant B.1.1.529
  • the phrase “specifically binds to” as used in accordance with the present invention means that the antibody shall not cross-react significantly with components or regions other than the RBD.
  • Cross-reactivity of an antibody as mentioned herein can be tested by the skilled person by various techniques including immunological technologies such as Western blotting, ELISA or RIA based assays or measuring of binding affinities using, e.g., surface plasmon resonance technology.
  • equilibrium dissociation constant (Kd) indicates the propensity for the antib ody/antigen (i.e. RBD) complex to dissociate into its free components, i.e. free antibody and free antigen.
  • the equilibrium dissociation constant (Kd) can be expressed as follows:
  • Kd [A] x * [B] y / [A x B y ] wherein [A x ], [B y ], and [A x B y ] are the concentrations of A, B and AB at the equilibrium, respectively.
  • the smaller the equilibrium dissociation constant the more tightly bound the ligand is, or the higher the affinity between ligand and protein.
  • an antibody with a picomolar equilibrium dissociation constant Kd in the range of 10' 12 M
  • Kd in the range of 10' 9 M
  • the binding of the antibody of the invention and the RBD shall be with an equilibrium dissociation constant (Kd) of less than 10' 9 M, preferably, between 10' 9 and IO' 10 M or, preferably, even less than IO' 10 M.
  • Kd equilibrium dissociation constant
  • the equilibrium dissociation constant referred to in accordance with the present invention can be determined by techniques well known in the art, preferably, it is to be determined using surface plasmon resonance described in the accompanying Examples, below.
  • the antibody according to the invention shall, preferably, comprise three complementary determining regions.
  • CDR complementary determining region
  • the term “complementary determining region (CDR)” as used herein refers to regions in the variable domains of the heavy and light chain of an antibody that define the binding affinity and specificity of the antibody. There are three CDRs for the heavy chain, CDR1-H, CDR2-H and CDR3-H, and three CDRs for the light chain, CDR1-L, CDR2-L, and CDR3-L.
  • Antibodies exhibiting binding to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10' 9 M preferably, have CDRs as listed in Table 1, below, or CDRs having an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of the SEQ ID NOs mentioned in Table 1 retaining binding to RBD with Kd of less than 10' 9
  • such antibodies are useful for the diagnostic and/or therapeutic purposes referred to herein.
  • the antibody of the invention comprises at least one heavy chain CDR said heavy chain CDR being
  • the antibody of the invention comprises a heavy chain CDR1, CDR2 and CDR3 selected from the aforementioned heavy chain CDRs.
  • the antibody of the invention comprises a heavy chain CDR1, CDR2 and CDR3 combination as referred to in the following Table 2:
  • the antibody of the present invention comprises at least one light chain CDR, said light chain CDR being
  • a light chain CDR2 having an amino acid sequence selected from the group consisting of: (a) an amino acid sequence as shown in any one of SEQ ID NOs: 8, 9, 81 to 83 and 84 to 88;
  • the antibody of the invention comprises a light chain CDR1, CDR2 and CDR3 selected from the aforementioned heavy chain CDRs.
  • the antibody of the invention comprises a light chain CDR1, CDR2 and CDR3 combination as referred to in the following Table 3:
  • the antibody of the invention comprises a heavy and light chain CDR1, CDR2 and CDR3 combination as referred to in the following Table 4: able 4:
  • such a variant amino acid sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to the concrete amino acid sequence identified by a SEQ ID No.
  • Sequence identity between two amino acid sequences as referred to herein, in general can be determined by alignment of two sequences either over the entire length of one of the sequences or within a comparison window. The percentage is calculated by determining the number of positions at which the identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
  • Optimal alignment and calculation of sequence identity can be done by using published techniques or methods codified in computer programs such as, for example, BLASTP, BLASTN or FASTA.
  • the percent sequence identity values are, preferably, calculated over the entire amino acid sequence.
  • a series of programs based on a variety of algorithms is available to the skilled worker for comparing different sequences. In this context, the algorithms of Needleman and Wunsch or Smith and Waterman give particularly reliable results.
  • the program PileUp or the programs Gap and BestFit which are part of the GCG software packet (Genetics Computer Group, US), may be used.
  • sequence identity values recited above in percent (%) are to be determined, in another aspect of the invention, using the program GAP over the entire sequence region with the following settings: Gap Weight: 50, Length Weight: 3, Average Match: 10.000 and Average Mismatch: 0.000, which, unless otherwise specified, shall always be used as standard settings for sequence alignments.
  • the CDR amino acid sequences which differs by at least one amino acid exchange, deletion and/or addition differs from the specific sequence shown in any one of the CDR SEQ ID numbers by at most 3, at most 2 or at most 1 amino acid. Said at most 3, at most 2 or at most 1 amino acid may be deleted exchange or added.
  • the antibody of the invention may further comprise amino acids or amino acid sequence from the frame work regions.
  • frame regions refer to amino acid sequences interposed between CDRs, i.e. to those portions of immunoglobulin light and heavy chain variable regions that are relatively conserved among different immunoglobulins in a single species.
  • the light and heavy chains of an immunoglobulin each have four FRs, designated FR1-L, FR2-L, FR3-L, FR4-L, and FR1-H, FR2-H, FR3-H, FR4-H, respectively. From N-terminal to C-terminal, light chain variable region and heavy chain variable region both typically have the following order of these elements: FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4.
  • an antibody according to the invention may also be a full-length antibody (i.e. antibodies comprising two heavy chains and two light chains).
  • the light chain includes two domains or regions, a variable domain (VL) and a constant domain (CL).
  • the heavy chain includes four domains, a variable domain (VH) and three constant domains (CHI, CH2 and CH3, collectively referred to as CH).
  • the variable regions of both light (VL) and heavy (VH) chains determine binding recognition and specificity to the antigen.
  • the constant region domains of the light (CL) and heavy (CH) chains confer important biological properties such as antibody chain association, secretion, trans-placental mobility, complement binding, and binding to Fc receptors (FcR).
  • the Fv fragment is the N- terminal part of the Fab fragment of an immunoglobulin and consists of the variable portions of one light chain and one heavy chain.
  • the specificity of the antibody resides in the structural complementarity between the antibody combining site and the antigenic determinant.
  • Antibody combining sites are made up of residues that are primarily from the hypervariable or complementarity determining regions. Occasionally, residues from non-hypervariable or framework regions (FR) influence the overall domain structure and hence the combining site.
  • the light chains of human antibodies generally are classified as kappa and lambda light chains, and each of these contains one variable region and one constant domain. Heavy chains are typically classified as mu, delta, gamma, alpha, or epsilon chains, and these define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
  • Human IgG has several subtypes, including, but not limited to, IgGl, lgG2, lgG3, and lgG4.
  • Human IgA subtypes include IgAl and lgA2.
  • the IgA isotypes contain four heavy chains and four light chains; the IgG and IgE isotypes contain two heavy chains and two light chains; and the IgM isotype contains ten or twelve heavy chains and ten or twelve light chains.
  • Antibodies according to the invention may be IgG, IgE, IgD, IgA, or IgM immunoglobulins or fragments thereof.
  • a humanized antibody according to the invention refers to immunoglobulin chains or fragments thereof (such as Fab, Fab', F(ab)2, Fv, or other antigen binding sub-sequences of antibodies), which contain minimal sequence (but typically, still at least a portion) derived from non-human immunoglobulin.
  • humanized antibodies are human immunoglobulins (the recipient antibody) in which CDR residues of the recipient antibody are replaced by CDR residues from a non-human species immunoglobulin (the donor antibody) such as a mouse, rat or rabbit having the desired specificity, affinity and capacity.
  • the framework sequence of said antibody or fragment thereof may be a human consensus framework sequence.
  • humanized antibodies can comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and maximize antibody performance.
  • the humanized antibody will comprise substantially all of at least one, and typically at least two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region, typically that of a human immunoglobulin, which (e.g.
  • human immunoglobulin constant region may be modified (e.g. by mutations or glycol-engineering) to optimize one or more properties of such region and/or to improve the function of the (e.g. therapeutic) antibody, such as to increase or reduce Fc effector functions or to increase serum half-life.
  • a chimeric antibody according to the invention refers to an antibody whose light and/or heavy chain genes have been constructed, typically by genetic engineering, from immunoglobulin variable and constant regions which are identical to, or homologous to, corresponding sequences of different species, such as mouse and human.
  • variable region genes derive from a particular antibody class or subclass while the remainder of the chain derives from another antibody class or subclass of the same or a different species. It covers also fragments of such antibodies.
  • a typical therapeutic chimeric antibody is a hybrid protein composed of the variable or antigen-binding domain from a mouse antibody and the constant or effector domain from a human antibody, although other mammalian species may be used.
  • the antibody of the invention comprises a heavy chain having an amino acid sequence selected from the group consisting of:
  • said antibody preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
  • said antibody preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
  • the antibody of the invention comprises a light chain having an amino acid sequence selected from the group consisting of:
  • said antibody preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
  • the antibody of the present invention comprises a heavy and light chain combination as referred to in the following Table 5:
  • a variant amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from any of the aforementioned amino acid sequences shall still be capable of exhibiting essentially the same immunological properties as the concrete amino acid sequence identified by a SEQ ID No. More preferably, such a variant amino acid sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to the concrete amino acid sequence identified by a SEQ ID number.
  • the antibody of the invention and, in particular, those useful for therapeutic purposes as mentioned before, neutralizes SARS-CoV-2 in vitro with IC50 of at most 1.0 pg/ml, at most 0.1 pg/ml or at most 0.01 pg/ml.
  • Neutralization of SARS-CoV-2 in vitro as referred to herein can be tested in vitro by applying antibodies to be tested for neutralizing potential to SARS-CoV-2 virus preparations, adding this antibody- virus mixture to a culture of hACE2 expressing cells and determining infection of the hACE2 expressing cells. If said cells are infected SARS-CoV-2 will replicate in these cells, which can be measured by quantifying the amount of viral RNA or protein produced in these cells or by determining the degree of cell damage caused by virus replication in the inoculated cell culture, which is known in the field as plaque assay.
  • neutralization and neutralizing potential of an antibody can be tested as described in the accompanying Examples, below.
  • neutralizing potential of an antibody may also be determined by using a surrogate neutralization assay.
  • an enzyme-conjugated or labeled SARS-CoV-2 spike protein or RBD thereof may be applied to immobilized hACE2 in the presence of antibodies to be tested.
  • IC50 values as referred to above may be determined for a given antibody.
  • the antibody of the present invention typically, neutralizes a significant range of SARS-CoV-2 variants. More preferably, the antibody neutralizes at least two, at least three, at least four or at least five of the SARS- CoV-2 variants. Preferably, said antibody neutralizes at least two, at least three, at least four or at least five variants that are selected from the currently known SARS-CoV-2 variants, i.e.
  • WT wildtype SARS-CoV-2, SARS-CoV-2 alpha variant (B.l.1.7), SARS-CoV-2 beta variant (B.1.1351), SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
  • SARS-CoV-2 refers except as specified otherwise to the wildtype (WT) SARS-CoV-2 as well as to all variants thereof.
  • Variants of SARS-CoV-2 include all SARS-CoV-2 virus mutants that are derived from SARS-CoV-2 WT or any variant thereof by natural mutagenesis or which are artificially designed based on said SARS-CoV-2 WT or any mutant thereof.
  • SARS-CoV-2 is selected from the group consisting of: wildtype (WT) SARS-CoV-2, SARS- CoV-2 alpha variant (B. l.1.7), SARA-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
  • the antibody of the invention can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2.
  • the antibody of the present invention shall, preferably, block binding of at least one antibody that has been classified either as a Classi, Class2 or Class3 antibody (i.e. belonging into the group of antibodies of Classi, Class2 and Class3). It will be understood that there are antibodies that may block binding of more than one antibody of either one class or of different classes. Moreover, the antibody of the invention my also block binding of an antibody allocated to different classes. Blocking binding of an antibody belonging to Classi, Class2 and Class3 from binding to the RBD of WT SARS-CoV-2 can be determined by well-known techniques including those described in the Examples, below.
  • anti-SARS-CoV-2 antibodies can be generated which are capable of specifically binding to the RBD of the SARS-CoV-2 spike protein with high affinity. These antibodies are particularly useful for treating, preventing and/or diagnosing SARS-CoV-2 infection. Those antibodies that display a particularly high affinity and neutralizing capacity in terms of strength and range are particularly useful for the treatment and/or prevention of SARS-CoV-2 infection, although they may be used for diagnostic purposes as well. Those antibodies that exhibit a particular high affinity but less neutralizing capacity are particularly useful as diagnostic antibodies, although they may be useful for therapeutic and/or prophylactic purposes as well.
  • the antibodies of the invention are, furthermore, neutralizing antibodies for virus variants of concern such as the SARS-CoV-2 omicron variant.
  • the present invention further relates to a polynucleotide encoding the antibody of the invention.
  • polynucleotide refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids).
  • the term as used herein encompasses the sequence specified herein as well as the complementary or reverse- complementary sequence thereof.
  • the polynucleotide is RNA or DNA.
  • DNAs or RNAs with backbones modified for stability or for other reasons are also encompassed as polynucleotides.
  • DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples are also encompassed as polynucleotides. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. Every nucleic acid sequence herein that encodes a certain polypeptide of the invention may due to the degeneracy of the genetic code have silent variations. The degeneracy of the genetic code yields a large number of functionally identical polynucleotides that encode the same polypeptide.
  • the codons GCA, GCC, GCG and GCU all encode the amino acid alanine.
  • the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide.
  • Such nucleic acid variations are silent variations.
  • the polynucleotide of the invention shall encode the antibody of the invention, i.e. it shall comprise a nucleic acid sequences which encodes said antibody of the invention.
  • the polynucleotide of the present invention may comprise additional nucleic acid sequences.
  • the polynucleotide of the present invention may comprise in addition to an open reading frame further untranslated sequence at the 3’ and at the 5’ terminus of the coding gene region: at least 500, preferably 200, more preferably 100 nucleotides of the sequence upstream of the 5’ terminus of the coding region and at least 100, preferably 50, more preferably 20 nucleotides of the sequence downstream of the 3’ terminus of the coding gene region.
  • the polynucleotide of the present invention shall be provided, preferably, either as an isolated polynucleotide (i.e. purified or at least isolated from its natural context such as its natural gene locus) or in genetically modified or exogenously (i.e. artificially) manipulated form.
  • An isolated polynucleotide can, for example, comprise less than approximately 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in the genomic DNA of the cell from which the nucleic acid is derived.
  • the polynucleotide preferably, is provided in the form of double or single stranded molecule.
  • polynucleotide encompasses DNA, including cDNA and genomic DNA, or RNA polynucleotides.
  • polynucleotides including naturally occurring modified polynucleotides such as glycosylated or methylated polynucleotides or artificial modified ones such as biotinylated polynucleotides.
  • the present invention contemplates a vector or expression construct comprising the polynucleotide of the invention.
  • vector preferably, encompasses phage, plasmid, cosmids, viral vectors as well as artificial chromosomes, such as bacterial or yeast artificial chromosomes (YAC).
  • the vector encompassing the polynucleotide of the present invention preferably, further comprises selectable markers for propagation and/or selection in a host.
  • the vector may be incorporated into a host cell by various techniques well known in the art. If introduced into a host cell, the vector may reside in the cytoplasm or may be incorporated into the genome. In the latter case, it is to be understood that the vector may further comprise nucleic acid sequences which allow for homologous recombination or heterologous insertion.
  • Vectors can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques.
  • transformation and “transfection”, conjugation and transduction, as used in the present context, are intended to comprise a multiplicity of prior-art processes for introducing foreign nucleic acid (for example DNA) into a host cell, including calcium phosphate, rubidium chloride or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, f-mating, natural competence, carbon-based clusters, chemically mediated transfer, electroporation or particle bombardment.
  • Suitable methods for the transformation or transfection of host cells, including plant cells can be found in text books such as Sambrook et al.
  • the vector of the present invention is an expression vector.
  • an expression vector i.e. a vector which comprises the polynucleotide of the invention having the nucleic acid sequence operatively linked to an expression control sequence (also called “expression cassette”) allowing expression in prokaryotic or eukaryotic cells or isolated fractions thereof.
  • Suitable expression vectors are known in the art such as Okayama-Berg cDNA expression vector pcDVl (Pharmacia), pCDM8, pRc/CMV, pcDNAl, pcDNA3 (Invitrogene) or pSPORTl (GIBCO BRL). Further examples of typical fusion expression vectors are pGEX, pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ), where glutathione S transferase (GST), maltose E-binding protein and protein A, respectively, are fused with the recombinant target protein. Examples of suitable inducible non-fiision E.
  • coli expression vectors are, inter alia, pTrc and pET l id.
  • the tar-get gene expression of the pTrc vector is based on the transcription from a hybrid trp-lac fusion promoter by host RNA polymerase.
  • the target gene expression from the pET l id vector is based on the transcription of a T7-gnl0-lac fusion promoter, which is mediated by a co-expressed viral RNA polymerase (T7 gnl).
  • This viral polymerase is provided by the host strains BL21 (DE3) or HMS174 (DE3) from a resident lambda-prophage which harbors a T7 gnl gene under the transcriptional control of the lacUV 5 promoter.
  • vectors which are suitable in prokaryotic organisms are, for example, in E. coli, pLG338, pACYC184, the pBR series such as pBR322, the pUC series such as pUC18 or pUC19, the Ml Bmp series, pKC30, pRep4, pHSl, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-IIIl 13-B1, lambdagtl l or pBdCl, in Streptomyces plJlOl, plJ364, plJ702 or plJ361, in Bacillus pUBUO, pC194 or pBD214, in Corynebacterium pSA77 or pAJ667.
  • vectors for expression in the yeast S. cerevisiae comprise pYep Seel, pMFa, pJRY88 and pYES2 (Invitrogen Corporation, San Diego, CA).
  • Vectors and pro-cesses for the construction of vectors which are suitable for use in other fungi, such as the filamentous fungi comprise those which are described in detail in text books such as van den Hondel, C.A.M.J.J., & Punt, P.J. (1991) “Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of fungi, J.F. Peberdy et al., Ed., pp.
  • yeast vectors are, for example, pAG-1, YEp6, YEpl3 or pEMBLYe23.
  • the polynucleotides of the present invention can be also expressed in insect cells using baculovirus expression vectors.
  • Baculovirus vectors which are available for the expression of proteins in cultured insect cells, e.g., Sf9 cells, comprise the pAc series and the pVL series.
  • An integration vector refers to a DNA molecule, linear or circular, that can be incorporated, e.g., into a microorganism's genome, such as a bacteria’s genome, and provides for stable inheritance of a gene encoding a polypeptide of interest, such as the alcohol acyl transferase of the invention.
  • the integration vector generally comprises one or more segments comprising a gene sequence encoding a polypeptide of interest under the control of additional nucleic acid segments that provide for its transcription.
  • Such additional segments may include promoter and terminator sequences, and one or more segments that drive the incorporation of the gene of interest into the genome of the target cell, usually by the process of homologous recombination.
  • the integration vector will be one which can be transferred into the target cell, but which has a replicon which is nonfunctional in that organism. Integration of the segment comprising the gene of interest may be selected if an appropriate marker is included within that segment.
  • One or more nucleic acid sequences encoding appropriate signal peptides that are not naturally associated with a polypeptide to be expressed in a host cell of the invention can be incorporated into (expression) vectors.
  • a DNA sequence for a signal peptide leader can be fused in-frame to a nucleic acid of the invention so that the alcohol acyl transferase of the invention is initially translated as a fusion protein comprising the signal peptide.
  • the expressed polypeptide will be targeted differently.
  • a secretory signal peptide that is functional in the intended host cells for instance, enhances extracellular secretion of the expressed polypeptide.
  • Other signal peptides direct the expressed polypeptide to certain organelles, like the chloroplasts, mitochondria and peroxisomes.
  • the signal peptide can be cleaved from the polypeptide upon transportation to the intended organelle or from the cell. It is possible to provide a fusion of an additional peptide sequence at the amino or carboxyl terminal end of the polypeptide.
  • gene construct refers to polynucleotides comprising the polynucleotide of the invention and additional functional nucleic acid sequences.
  • a gene construct according to the present invention is, preferably, a linear DNA molecule.
  • a gene construct in accordance with the present invention may be a targeting construct which allows for random or site- directed integration of the targeting construct into genomic DNA.
  • target constructs preferably, comprise DNA of sufficient length for either homologous or heterologous recombination as described in detail below. In both cases, the construct must be, preferably, integrity, with structures to control gene expression, such as a promoter, a site of transcription initiation, a site of polyadenylation, and a site of transcription termination.
  • a gene construct in accordance with the present invention may also be generated by using genomic modification techniques such as genome editing using the CRISPR/Cas technology.
  • the present invention provides a host cell comprising the polynucleotide of the invention or the vector or expression construct of the invention.
  • the host cell of the invention is capable of expressing the polypeptide of the invention comprised in the vector or gene construct of the invention.
  • the host cell is, typically transformed or transduced with said vector or gene construct such that the polypeptide of the invention can be expressed from the vector or gene construct.
  • the transformed vector or gene construct may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host cell genome as specified elsewhere herein in more detail.
  • a host cell according to the invention may be produced based on standard genetic and molecular biology techniques that are generally known in the art, e.g., as described in standard text books such as Sambrook, J., and Russell, D.W.
  • said host cell is a bacterial cell, a fungal cell, an animal cell or a plant cell.
  • Bacterial cells may be gram-positive or gram-negative bacterial cells.
  • Preferred bacterial cells may be selected from the genera Escherichia, Klebsiella, Helicobacter, Bacillus, Lactobacillus, Streptococcus, Amycolatopsis, Rhodobacter, Pseudomonas, Paracoccus, Lactococcus or Pantoea.
  • useful gram positive bacterial host cells may be Bacillus alkalophius, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus Jautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, Bacillus thuringiensis, Streptomyces spheroides, Streptomyces thermoviolaceus, Streptomyces lividans, Streptomyces murinus, Streptoverticillum verticillium ssp.
  • Rhodobacter sphaeroides Rhodomonas palustri, or Streptococcus lactis.
  • useful gram negative bacterial host cells may be Escherichia coli, Pseudomonas sp., preferably, Pseudomonas purrocinia, Pseudomonas fluorescens, Rhodobacter capsulatus, Rhodobacter sphaeroides, Paracoccus carotinifaciens, Paracoccus zeaxanthinifaciens or Pantoea ananatis.
  • Preferred fungal host cells may be Aspergillus, Fusarium, Trichoderma, Yeast, Pichia, or Saccharomyces host cells.
  • Yeast as used herein includes ascosporogenous yeast, basidiosporogenous yeast, and yeast belonging to the Blastomycetes.
  • Preferred animal host cells may comprise mammalian host cells, avian host cells, reptilian host cells or insect host cells.
  • Preferred animal host cells are HeLa cells, HEK293T, F or E cells, U20S cells, A549 cells, HT1080 cells, CAD cells, P19 cells, NIH3T3 cells, L929 cells, N2a cells, CHO cells, MCF-7 cells, Y79 cells, SO-Rb50 cells, HepG2 cells, DUKX-X11 cells, J558L cells or BHK cells.
  • Preferred plant host cells comprise tobacco, rice, wheat, pea or tomato cells.
  • the present invention relates to a non-human transgenic organism comprising the polynucleotide of the invention or the vector or expression construct of the invention.
  • non-human transgenic organism refers to an organism which has been genetically modified in order to comprise the polynucleotide, vector or gene construct of the present invention. Said genetic modification may be the result of any kind of homologous or heterologous recombination event, mutagenesis or gene editing process. Accordingly, the transgenic non-human organism shall differ from its non-transgenic counterpart in that it comprises the non-naturally occurring (i.e. heterologous) polynucleotide, vector or gene construct in its genome.
  • Non-human organisms envisaged as transgenic non-human organisms in accordance with the present invention are, preferably, multi-cellular organisms, such as an animal, plant, multi-cellular fungi or algae.
  • said non-human organism is an animal or a plant.
  • Preferred animals are mammals, in particular, laboratory animals such as rodents, e.g., mice, rats, rabbits or the like, or farming animals such as sheep, goat, cows, horses or the like.
  • Preferred plants are crop plants or vegetables, in particular, selected from the group consisting of tobacco, rice, wheat, pea and tomato. Methods for the production of transgenic non-human organisms are well known in the art; see, standard text books, e.g. Lee-Yoon Low et al., Transgenic Plants: Gene constructs, vector and transformation method. 2018. DOI.10.5772/intechopen.79369; Pinkert, C. A. (ed.) 1994.
  • the present invention also provides a method for producing the antibody of the invention comprising (i) expressing the polynucleotide or the vector of the invention in a host cell and (ii) obtaining the said antibody from said host cell.
  • the term “producing” as used herein refers to the process of recombinant production of the antibody in a host cell.
  • the manufacture may also comprise further steps such as purifying the produced antibody or formulating the antibody or purified antibody as a pharmaceutical composition. Accordingly, the aforementioned method of the present invention may consist of the aforementioned steps or may comprise further additional steps.
  • Expressing the polynucleotide or the vector of the invention in a host cell may, for example, also include the step of generating the polynucleotide or vector of the invention as well as the step of introducing said polynucleotide or vector into the host cell.
  • Generating the polynucleotide of the invention or the vector comprising it may, e.g., also comprise the step of generating a polynucleotide sequence encoding the antibody of the invention on the basis of sequences for antibodies obtained from B-cells.
  • said B- cells are obtained from patients which have successfully survived an infection by SARS-CoV- 2 or subjects that have been successfully vaccinated.
  • generating the polynucleotide sequence may comprise the following steps: (a) Single cell sorting was performed on bait+ memory B cells; (b) Ig gene amplification and sequencing (Murugan et al., 2015 Eur J Immunol.
  • polynucleotoide or vector generated as described before into a host cell for expression can be done by all techniques available in the art, including salt-based transfection, lipofection, electroporation, injection, viral transfection techniques and the like.
  • the polynucleotide or vector may be stably integrated into the genome of the host cell or may be transiently present.
  • Obtaining the antibody from the host cell can be achieved by purifying or partially purifying the antibody from the host cells or host cell culture.
  • various techniques may be used including precipitation, filtration, ultra-filtration, extraction, chromatography techniques such as ion-exchange-, affinity- and/or size exclusion chromatography, HPLC or electrophoresis.
  • chromatography techniques such as ion-exchange-, affinity- and/or size exclusion chromatography, HPLC or electrophoresis.
  • the skilled person is well aware of how an antibody may be purified in order to provide it in isolated form. Preferred techniques are those described in the accompanying Examples below.
  • the invention relates to the use of the host cell of the invention for producing the antibody of the invention.
  • the host cell of the present invention may, typically, be cultured under suitable conditions and for time sufficient for expression of the polynucleotide or vector of the invention such that the antibody will be produced.
  • the antibody may be obtained from a host cell culture as described elsewhere herein.
  • the present invention relates to an antibody, a polynucleotide or a vector as defined herein above in accordance with the invention for use in treating and/or preventing a disease or condition.
  • the disease or condition referred to herein is associated with SARS-CoV- 2 infection in a subject.
  • the antibody, polynucleotide or vector according to the present invention may be formulated as a medicament for use in in treating and/or preventing a disease or condition.
  • a medicament is, preferably, for topical or systemic administration.
  • a medicament will be administered intra-muscularly or subcutaneously.
  • the medicament may be administered by other routes as well.
  • aerosol formulations or sprays applying medicament in the respiratory systems such as the nasal tract or the lung are also conceivable.
  • the medicament is, preferably, administered in conventional dosage forms prepared by combining the ingredients with standard pharmaceutical carriers according to conventional procedures. These procedures may involve mixing or dissolving the ingredients as appropriate to the desired preparation.
  • a solution is envisaged for the medicament.
  • the form and character of the pharmaceutical acceptable carrier is dictated by the amount of active ingredient with which it is to be combined, the route of administration and other well-known variables.
  • a carrier must be acceptable in the sense of being compatible with the other ingredients of the formulation and being not deleterious to the recipient thereof.
  • the pharmaceutical carrier employed may include a solid, a gel, or a liquid. Examples for solid carriers are lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like.
  • liquid carriers are phosphate buffered saline solution, syrup, oil, water, emulsions, various types of wetting agents, are distilled water, physiological saline, Ringer's solutions, dextrose solution, and Hank's solution, and the like.
  • the carrier may include time delay material well known to the art, such as glyceryl mono-stearate or glyceryl distearate alone or with a wax.
  • liposomal carriers or genetically engineered viruses may be considered as well.
  • a genetically engineered virus may be administered that produces the antibody of the invention over a long period within an organism to be treated.
  • suitable carriers comprise those mentioned above and others well known in the art, see, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pennsylvania.
  • the medicament may also include other carriers, adjuvants, or non-toxic, non-therapeutic, non-immunogenic stabilizers and the like. It is to be understood that the formulation of a medicament takes place under GMP standardized conditions or the like in order to ensure quality, pharmaceutical security, and effectiveness of the medicament.
  • a therapeutically effective dosage of the antibody or polynucleotide of the invention refers to an amount to be used in medicament.
  • a therapeutically effective dosage is an amount of the antibody or polynucleotide that prevents, ameliorates or treats the symptoms accompanying a disease or condition referred to in this specification.
  • Therapeutic efficacy and toxicity of the compound can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio between therapeutic and toxic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50.
  • the dosage regimen will be determined by the attending physician and other clinical factors.
  • dosages for any one patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. Progress can be monitored by periodic assessment.
  • the medicament referred to herein is administered at least once in order to treat or ameliorate or prevent a disease or condition recited in this specification. However, the said medicament may be administered more than one time.
  • treating refers to any improvement, cure or amelioration of the disease or condition as referred to herein. It will be understood that treatment may not occur in 100% of the subjects to which the antibody has been administered. The term, however, requires that the treatment occurs in a statistically significant portion of subjects (e.g. a cohort in a cohort study). Whether a portion is statistically significant can be determined without further ado by a person skilled in the art using various well-known statistic evaluation tools, e.g., determination of confidence intervals, p-value determination, Student's t-test, Mann-Whitney-U test etc. Details are found in Dowdy and Wearden, Statistics for Research, John Wiley & Sons, New York 1983. Preferred confidence intervals are at least 90%, at least 95%, at least 97%, at least 98% or at least 99 %. The p-values are, preferably, 0.05, 0.01, 0.005, 0.001, or 0.0001.
  • prevention window refers to significantly reducing the likelihood with which the disease or condition develops in a subject within a defined window (prevention window) starting from the administration of the antibody onwards.
  • the prevention window is within 1 to 5 days, within 1 to 3 weeks, within 1 to 3 months or within 3 to 6 months or 3 to 12 months.
  • the preventive window may, dependent on the kind of medicament, also be several years up to the entire life time.
  • the prevention window depends on the amount of antibody, polynucleotide or vector which is administered and the applied dosage regimen.
  • suitable prevention windows can be determined by the clinician based on the amount of antibody or polynucleotide to be administered and the dosage regimen to be applied without further ado.
  • prevention may not occur in 100% of the subjects to which the antibody has been administered.
  • the term requires that the prevention occurs in a statistically significant portion of subjects (e.g. a cohort in a cohort study). Whether a portion is statistically significant can be determined without further ado by a person skilled in the art using various well-known statistic evaluation tools, e.g., determination of confidence intervals, p-value determination, Student's t-test, Mann-Whitney-U test etc. Details are described elsewhere herein.
  • disease or condition referred to herein is associated with SARS-CoV-2 infection in a subject” refers to any disease or condition resulting directly or indirectly from an infection by SARS-CoV-2.
  • the disease referred to herein is Covid 19.
  • the term also encompasses any symptom associated with SARS-CoV-2 infection. Typically, such symptoms may be fever, cough, headache, fatigue, breathing difficulties, loss of smell, and loss of taste, respiratory failure, or multi-organ dysfunction.
  • the present invention also relates to a composition
  • a composition comprising (i) an antibody as defined herein above and can block at least one of the antibodies belonging to Classi, Class2 and Class3 and hACE2 from binding to WT SARS-CoV-2 RBD and (ii) an antibody as defined herein above and can block at least one of the antibodies belonging to Classi, Class2 and Class3 but not hACE2 from binding to the RBD of WT SARS-CoV-2 RBD for use in treating and/or preventing a disease or condition.
  • the present invention also relates to an antibody as defined herein above in accordance with the present invention for use in diagnosing SARS-CoV-2 infection.
  • diagnosing means assessing whether a subject has been infected by SARS-CoV-2, or not. Alternatively, the term also encompasses determining the virus load of an infected subject, i.e. the amount of virus present in said subject or a sample thereof. As will be understood by those skilled in the art, such an assessment is usually not intended to be correct for 100% of the subjects to be diagnosed. The term, however, requires that the assessment is correct for a statistically significant portion of the subjects (e.g. a cohort in a cohort study).
  • Whether a portion is statistically significant can be determined without further ado by the person skilled in the art using various well known statistic evaluation tools, e.g., determination of confidence intervals, p-value determination, Student's t-test, Mann- Whitney test etc..
  • the present invention also relates to the use of the antibody of the invention for determining the presence of SARS-CoV-2 in a non-diagnostic sample.
  • non-diagnostic sample refers to any sample from the environment that is not used for the diagnosis of a SARS-CoV-2 infection.
  • samples may be samples of gaseous samples such as air or liquid samples.
  • gaseous samples may be investigated for the presence or absence of SARS-CoV-2 when monitoring and evaluating the indoor quality of air, the efficacy of air filtration systems, the quality of gaseous products and the like.
  • Liquid samples may be investigated for the presence or absence of SARS-CoV-2 in order to monitor the distribution of the virus, e.g., by assessing its presence or absence in waste waters, the quality of liquids, the quality of water in the environment or drinking water and the like.
  • the present invention also relates to a method for diagnosing SARS-CoV-2 infection in a subject suspected to be infected by said SARS-CoV-2 comprising the steps of a) contacting the antibody of the invention with a sample of said subject; and b) determining binding of SARS-CoV-2 to said antibody, whereby the SARS- CoV-2 infection is to be diagnosed.
  • subject as used herein relates to animals, preferably mammals, and, more preferably, humans.
  • the subject according to the present invention shall be a subject suffering from or suspected to suffer from SARS-CoV-2 infection.
  • a subject shows already symptoms associated with SARS-CoV-2 infection or has been in contact with one or more other subjects known to suffer from SARS-CoV-2 infection and, thus, is at risk of being infected as well.
  • sample refers to a sample of a body fluid, to a sample of separated cells or to a sample from a tissue or an organ.
  • Samples of body fluids can be obtained by well-known techniques and include, preferably, samples of blood, plasma, serum, urine, saliva or exhausted air more preferably, samples of blood, plasma or serum.
  • Tissue or organ samples may be obtained from any potentially infected tissue or organ by, e.g., biopsy or surface scratching.
  • contacting means that the sample of the subject is brought into physical proximity to the antibody of the invention such that SARS-CoV-2 viruses comprised in the sample may be bound by said antibody. Contacting is typically carried out under conditions and for a time sufficient to allow for specific binding of the antibody to a SARS- CoV-2 virus.
  • the skilled person is well aware of how to choose suitable conditions and how long those conditions shall be applied. Preferred conditions are also described in the accompanying Examples, below.
  • the formation of a complex between the antibody of the invention and the virus may be determined by a secondary antibody capable of generating a detectable signal upon binding.
  • the virus upon binding to the antibody may release a component from said antibody which upon release generated a detectable signal.
  • the aforementioned principles may be realized by assays that are carried out in solution using beads comprising the antibody or the invention or can be carried out on test stripes that comprise the antibody of the invention in immobilized form.
  • the formation of the complex between the antibody and the virus may be determined by measuring differences in physical or chemical properties of the antibody with and without virus bound thereto.
  • Various formats for electrochemical assays are known to the person skilled in the art.
  • the aforementioned method may be used qualitatively, i.e. an infection will be diagnosed, or quantitatively, i.e. the virus load during an infection will be diagnosed. For the latter case, it will be understood that the determined amount of viruses may be compared to a reference in order to determine the virus load.
  • the present invention also relates to a method for determining SARS-CoV-2 in a nondiagnostic sample comprising the steps of: a) contacting the antibody of the invention with said sample; and b) determining binding of SARS-CoV-2 to said antibody, whereby the presence of SARS-CoV-2 is to be determined.
  • determining refers to determining the presence, absence or amount of SARS-CoV-2 in the non-diagnostic sample. Thus, the term typically encompasses qualitative determination as well as quantitative determination. The skilled artisan is well aware of how quantification of SARS-CoV-2 can be made in the context of a quantitative determination and how suitable calibration measures can be provided.
  • the invention relates to a kit for diagnosing SARS-CoV-2 infection in a subject comprising the antibody of the invention and detection reagents for determining binding of SARS-CoV-2 to said antibody.
  • kit refers to a collection of components as referred to before required for diagnosing SARS-CoV-2 infection in a subject.
  • the components of the kit are provided in separate containers or within a single container.
  • the kit shall in addition to the antibody of the invention also comprise detection reagents for binding of SARS-CoV-2 to said antibody. These reagents may include components that may generate a detectable signal upon binding of the antibody of the invention to the SARS-CoV-2. Moreover, such reagents may encompass any washing or buffer solutions required for determining binding.
  • the container also typically comprises instructions for diagnosing SARS-CoV-2 infection in a subject. These instructions may be in the form of a manual or may be provided by a computer program code.
  • the invention relates to a kit for determining SARS-CoV-2 in a non-diagnostic sample comprising the antibody of the invention and detection reagents for determining binding of SARS-CoV-2 to said antibody.
  • Embodiment 1 An antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10' 9 M.
  • Embodiment 2 The antibody of embodiment 1, wherein said antibody neutralizes SARS-CoV-
  • IC50 of at most 1.0 pg/ml, at most 0.1 pg/ml or at most 0.01 pg/ml.
  • Embodiment 3 The antibody of embodiment 1 to 2, wherein said SARS-CoV-2 is selected from the group consisting of wildtype (WT) SARS-CoV-2, SARS-CoV-2 alpha variant (B.1.1.7), SARA-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2), and SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
  • WT wildtype
  • SARS-CoV-2 SARS-CoV-2 alpha variant
  • SARA-CoV-2 beta variant B.1.1351
  • SARS-CoV-2 delta variant B.1.617.2
  • SARS-CoV-2 omicron variant B.1.1.529
  • Embodiment 4 The antibody of any one of embodiments 1 to 3, wherein the said antibody can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2.
  • Embodiment 5 The antibody of any one of embodiments 1 to 4, wherein said antibody comprises at least one heavy chain CDR said heavy chain CDR being
  • Embodiment 6 The antibody of any one of embodiments 1 to 5, wherein said antibody comprises at least one light chain CDR, said light chain CDR being
  • a light chain CDR2 having an amino acid sequence selected from the group consisting of: (a) an amino acid sequence as shown in any one of SEQ ID NOs: 8, 9, 81 to 83 and 84 to 88;
  • Embodiment 7 The antibody of any one of embodiments 1 to 6, wherein said antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of:
  • Embodiment 8 The antibody of any one of embodiments 1 to 7, wherein said antibody comprises a light chain having an amino acid sequence selected from the group consisting of:
  • said antibody preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
  • said antibody preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
  • Embodiment 9 A polynucleotide encoding the antibody of any one of embodiments 1 to 8.
  • Embodiment 10 The polynucleotide of embodiment 9, wherein said polynucleotide is RNA or DNA.
  • Embodiment 11 A vector or expression construct comprising the polynucleotide of embodiment 9 or 10.
  • Embodiment 12 A host cell comprising the polynucleotide of embodiment 9 or 10 or the vector or expression construct of embodiment 11.
  • Embodiment 13 The host cell of claim 12, wherein said host cell is a bacterial cell, a fungal cell, an animal cell or a plant cell.
  • Embodiment 14 A non-human transgenic organism comprising the polynucleotide of embodiment 9 or 10 or the vector or expression construct of embodiment 11.
  • Embodiment 15 The non-human transgenic organism of embodiment 14, wherein said organism is an animal or a plant.
  • Embodiment 16 A method for producing the antibody of any one of embodiments 1 to 8 comprising (i) expressing the polynucleotide of embodiment 9 or 10 or the vector of embodiment 11 in a host cell and (ii) obtaining the said antibody from said host cell.
  • Embodiment 17 Use of the host cell of embodiment 12 or 13 for producing the antibody of any one of embodiments 1 to 8.
  • Embodiment 18 An antibody as defined in any one of embodiments 1 to 8, a polynucleotide as defined in embodiment 9 or 10 or a vector as defined in embodiment 11 for use in treating and/or preventing a disease or condition.
  • Embodiment 19 The antibody, polynucleotide or vector of embodiment 18, wherein said disease or condition is associated with SARS-CoV-2 infection in a subject.
  • Embodiment 20 A composition comprising (i) an antibody as defined in any one of embodiments 1 to 8 and can block at least one antibody belonging to Classi, Class2 or Class3 and hACE2 from binding to WT SARS-CoV-2 RBD and (ii) an antibody as defined in any one of embodiments 1 to 8 and can block at least one antibody belonging to Classi, Class2 or Class3 but not hACE2 from binding to the RBD of WT SARS-CoV-2 RBD for use in treating and/or preventing a disease or condition.
  • Embodiment 21 The antibody, polynucleotide or vector of embodiment 20, wherein said disease or condition is associated with SARS-CoV-2 infection in a subject.
  • Embodiment 22 An antibody as defined in any one of embodiments 1 to 8 for use in diagnosing SARS-CoV-2 infection.
  • Embodiment 23 Use of an antibody as defined in any one of embodiments 1 to 8 for determining SARS-CoV-2 in a non-diagnostic sample.
  • Embodiment 24 A method for diagnosing SARS-CoV-2 infection in a subject suspected to be infected by said SARS-CoV-2 comprising the steps of: a) contacting the antibody of any one of embodiments 1 to 8 with a sample of said subject; and b) determining binding of SARS-CoV-2 to said antibody, whereby the S ARS-CoV- 2 infection is to be diagnosed.
  • Embodiment 25 A method for determining SARS-CoV-2 in a non-diagnostic sample comprising the steps of: a) contacting the antibody of any one of embodiments 1 to 8 with said sample; and b) determining binding of SARS-CoV-2 to said antibody, whereby the SARS- CoV-2 is to be determined.
  • Embodiment 26 A kit for diagnosing SARS-CoV-2 infection in a subject comprising the antibody of any one of embodiments 1 to 8 and detection reagents for determining binding of SARS-CoV-2 to said antibody.
  • Embodiment 27 A kit for determining SARS-CoV-2 in a non-diagnostic sample comprising the antibody of any one of embodiments 1 to 8 and detection reagents for determining binding of SARS-CoV-2 to said antibody.
  • Figure 1 Antibody binding to spike protein and RBD detected in ELISA. Binding of reactive antibodies to spike and RBD is comparable to positive controls. Area under the binding curve (AUC) was calculated for each antibody. Out of 263 mAbs, 113 showed binding to spike protein and/or RBD based on our cut-off AUC. A) Spike, B) RBD, C) AUC Spike, D) AUC RBD.
  • Figure 2 Majority of spike binding antibodies (58%) target RBD while a considerable proportion (29%) of antibodies target epitopes in Spike other than RBD.13% of antibodies with weak binding to RBD may recognize hidden (inaccessible) epitopes of the trimeric spike protein.
  • FIG. 3 Antibodies with high affinity to RBD can be identified.
  • RBD reactive antibodies show a range of affinities (10‘ 5 M to IO' 10 M). Affinity measurement using the same method allowed for a direct comparison to the published antibodies including antibodies in clinical use.
  • Antibodies with comparable affinity (10‘ 7 - 10' 9 M) to or even higher affinity ( ⁇ 10' 9 M) than the published antibodies were identified.
  • RBD binding antibodies show efficient in vitro SARS-CoV-2 neutralization. mAbs that bind to the epitopes in spike protein other than RBD do not show virus neutralization. The majority of RBD-binding antibodies show, however, no neutralizing capacity. 19% of RBD- binding antibodies show various degree of virus neutralization (IC50 ⁇ 1.0 ug/ml).
  • Figure 5 High antibody affinity critical but not sufficient for virus neutralization. Virusneutralizing antibodies show affinities of 10' 7 M or lower (IC50 ⁇ 1.0 ug/ml). 27% and 23% of antibodies with affinity less 10' 7 M and 10' 9 M, respectively, show virus neutralization. The majority of high affinity anti-RBD antibodies do not neutralize virus and therefore target nonneutralizing epitopes. The potency of the antibodies depends on their affinity (the higher the better) and epitope specificity. The data demonstrate that high affinity alone is not enough.
  • Figure 7 Distribution of the antibodies found in the present studies to different classes. High affine antibodies are often enriched in Classl/2, S309 or none (not yet defined). High affinity is often associated with low kinetic off rate - sign of efficient selection in the germinal center driven B cell response. Rare class antibody with high affinity such as Class2/3 has high kinetic on rate and good off rate.
  • Figure 8 Antibodies with distinct binding profile differ in blocking hACE2 binding to RBD. Majority of Classl/2, 1/2/3, 1/3, 1/3/4, 1/4 antibodies block hACE2 binding to WT RBD, suggesting their epitope overlaps with the hACE2 interaction site in RBD. Antibodies belonging to Classi, 4, S309 and none class do not block hACE2 binding to WT RBD, suggesting they do not bind to receptor binding motif (RBM) in RBD.
  • RBM receptor binding motif
  • Figure 9 Virus neutralization limited to antibodies with a few distinct binding profiles. High affine antibodies in Classl/2, Classl/2/3 and Class2/3 show efficient virus neutralization - protective epitopes. High affinity in antibodies with other binding profiles such as S309 and none classes does not result in virus neutralization - non-protective epitopes
  • Neutralizing antibodies may or may not block hACE2 binding to RBD.
  • SPR hACE2 interaction with RBD upon binding to mAbl was measured. All Classl/2 mAbs block hACE2 interaction with RBD, while Class2/3 mAb does not. This suggests Classl/2 and Class2/3 antibodies neutralize virus by binding to different epitopes.
  • Figure 11 Some of Classl/2 and Class2/3 antibodies have non-overlapping epitopes in RBD. Three Classl/2 antibodies and one Class2/3 antibody were tested against each other to block binding to RBD. Two of three Classl/2 antibodies did not block Class2/3 antibody from binding to RBD. Classl/2/3 mAb (2939) blocks Class2/3 (3279) but not Classl/2 (1255) mAbs from binding to RBD.
  • Figure 12 Antibodies with non-overlapping epitopes show synergy in virus neutralization. High affinity binding to non-overlapping epitopes by mAbs 3279 and 1255 translates into more efficient virus neutralization when used in cocktail compared to on their own. Starting concentration was 10 pg/ml for all mABs.
  • FIG. 13 High affine antibodies show broad VoC virus neutralization. High affine antibodies belonging to Classl/2 and Class2/3 show high neutralization capacity against three Variants of Concern (VoCs) tested. High affine antibodies with S309 profile show specific neutralization against alpha variant but not against WT or other variants.
  • VoCs Variants of Concern
  • Figure 14 General trend in loss of antibody affinity to Omicron variant RBD. Only three control mAbs (S309, REGN10933 and CR3022) have measurable binding to Omicron RBD, while the rest lost binding completely. mAbs from this study show increased, similar, decreased or complete loss in affinity to Omicron RBD compared to WT RBD.
  • Non-neutralizing antibody classes retain high affinity to Omicron RBD. High affinity in antibodies with binding profiles such as S309 does not result in WT virus neutralization. Majority of the mAbs belonging to the non-neutralizing antibody classes bind to Omicron RBD with similar or higher affinity in comparison to WT RBD.
  • Figure 16 Neutralizing antibody classes bind to Omicron RBD with reduced affinity. High affine antibodies in Classl/2, Classl/2/3 and Class2/3 show efficient WT virus neutralization. Majority of the mAbs belonging to the three classes bind to Omicron RBD with reduced affinity in comparison to WT RBD. mAbs 1255 in Classl/2 and 2939 in Classl/2/3 retain higher binding to Omicron RBD compared to other antibodies of the respective classes.
  • Figure 17 Two high affine mAbs bind to Omicron RBD without blocking each other.
  • High affine antibodies (1255 and 2939) can both bind to WT and Omicron RBD without blocking each other - suggesting they bind non-overlapping epitopes.
  • Figure 18 Two high affine mAbs differ in blocking hACE2 binding to Omicron RBD. 1255 blocks whereas 2939 does not block hACE2 interaction with both WT and Omicron RBD, indicating the difference in their binding site overlap with hACE2 interaction site.
  • Figure 19 mAbs from this study compared to currently used antibodies in clinics.
  • Figure 20 2939 and 1255 show high Omicron variant neutralization capacity.
  • mAh 2939 show better Omicron neutralization than therapeutically used mAh S309 - VIR Biotechnology (Sotrovimab).
  • Given antibodies were mixed with defined amounts of SARS-CoV-2 virus particles and after 30 minutes, the mixture was added to VeroE6 cells. After 24 hours, SARS- CoV-2 replication in the inoculated cells was measured by fixing the cells and immunostaining of the viral nucleocapsid protein.
  • dosedependent neutralization capacity expressed as IC50 value, was calculated by non-linear regression sigmoidal dose response analysis using the GraphPad Prism 7 software package.
  • Figure 21 Virus neutralizing capacity may differ between variants. mAbs that do not neutralize WT virus show weak neutralizing capacity of the Omicron variant. Inhibition values of these mAbs (IC50 values) are still lower than those of antibodies 1255 and 2939.
  • Figure 22 Virus neutralization using mAb S309; upper curve omicron, middle curve delta, lower curve WT (strain H2P4, Steuten 2021).
  • Plasmids encoding His-tagged versions of full length spike protein and RBD were kindly provided by Florian Krammer (Amanat et al., 2020 Nat Med 26, 1033-1036). Spike and RBD proteins were recombinantly expressed in HEK293F cells (Thermo Fischer Scientific) and purified using affinity column chromatography. Using commercially available kits, RBD was biotinylated and spike was labelled with A647 and both proteins were used as baits to detect antigen reactive memory B cells in FACS.
  • PBMCs from hospitalized patients and convalescent donors were incubated with 0.125 ug/ml of biotinylated RBD and 0.5 ug/ml of spike_A647 along with the following mouse anti-human antibodies at the noted dilutions: CD19-Brilliant Violet 786 (BV786) (SJ25C1) at 1: 10, CD27-phycoerythrin (M-T271) at 1:5, IgG- BV510(G18-145) at 1 :20, CD138-BV421 (MI15) at 1 :20, IgD-allophycocyanin (APC)-H7 (IA6-2) at 1 :20 and CD38-BV605 (HB7) at 1 :20.
  • BV786 CD19-Brilliant Violet 786
  • M-T271 CD27-phycoerythrin
  • MI15 IgG- BV510(G18-145)
  • HB7 CD38-BV605
  • Ig genes from single B cells were amplified as matrix PCR approach as previously described (Murugan et al., 2015 Eur J Immunol. 45(9):2698-700). In brief, reverse transcription was performed using random hexamers and the resulting complementary DNA was used as template to amplify IGH, IGK and IGL genes with barcoded primer matrix in the second PCR. Pooled and purified amplicons were ligated with adaptors and sequenced using Illumina MiSeq 2x300 bp paired end sequencing. The sequence reads were further analyzed using sciReptor to obtain and integrate Ig gene information of heavy and light genes with flow cytometry index data (Imkeller et al., 2016 BMC Bioinformatics 17, 67). Single cells with paired and functional Ig genes on both loci were used for analysis.
  • Antibodies of different isotypes with preference for IgG, encoded by germline and somatically mutated Ig genes were selected for cloning and recombinant expression as described previously (Tiller et al., 2008, J Immunol Methods. 329(1-2): 112-124).
  • Ig gene specific primers tagged with restriction enzyme binding sites were used to amplify heavy and light chain genes and clone them into the corresponding expression vectors (IgG, Igk and IgA).
  • Vectors containing successfully cloned heavy and light genes were cotransfected into HEK293F cells (Thermo Fischer Scientific) and recombinant monoclonal antibodies were expressed.
  • Antibody binding to spike protein and recombinant RBD fragments was investigated by ELISA.
  • High binding 384-well plates were coated with 2 ng/ pl spike protein or 4 ng/ pl RBD in PBS. 25 pl/ well of the respective solution was added and incubated over night at 4 °C. The next day, ELISA plates were washed thrice with 0.05 % Tween in PBS (PBS-T) using the Tecan plate washer and blocked with 1 % BSA in PBS for 1 h at RT.
  • Four dilutions of each antibody supernatant in PBS were prepared in a 1 :4 serial dilution with an initial concentration of 4 pg/ ml.
  • PBS and the monoclonal antibody mGO53 were used as negative control while the monoclonal antibodies CR3022 and S309 were used as positive controls.
  • ELISA plates were washed three times with PBS-T and samples were loaded onto the plates. 15 pl/ well of diluted antibodies was added to the plates and incubated for 2 h at RT. ELISA plates were washed thrice with PBS-T. HRP-conjugated anti-human IgG-Fcy (Jackson ImmunoResearch) was diluted 1 : 1000 in blocking buffer, loaded onto the ELISA plate (15 pl/ well) and incubated for 1 h at RT.
  • ELIS As were developed using 20 pl/ well of 1 : 1000 dilution H2O2 in ABTS solution. Absorbance was measured at 405 nm every 2 min in a total of 20 min using Tecan MIOOOPro plate reader. Reactivity of the antibodies was assessed by calculating the area under the curve (AUC) of the absorbance measured of the four dilutions using GraphPad Prism 8.
  • AUC area under the binding curve
  • SPR Surface Plasmon Resonance
  • a serial dilution of RBD was performed in SPR running buffer and the following concentrations were injected into both the flow cells: 0 nM, 12.4 nM, 37.0 nM, 111.1 nM, 333.3 nM and 1000 nM using a flow rate of 30 pl/ min. Dissociation and association took place at 25 °C for 60 s and 180 s, respectively. Between the injections of different sample antibodies, flow cells were regenerated using 10 mM glycine in HC1. Data was analyzed using a 1 : 1 binding model or steady-state kinetic analysis using Biacore T200 software V2.0.
  • RBD reactive antibodies showed broad range of affinity to RBD (10‘ 5 M to IO' 10 M). Affinity measurement using the same method allowed for a direct comparison to the published antibodies including antibodies in clinical use. Antibodies with comparable affinity (10‘ 7 - 10' 9 M) to or even higher affinity ( ⁇ 10' 9 M) than the published antibodies were identified.
  • SARS-CoV-2 WT isolated H2P4, Steuten 2021
  • B.l.1.7 alpha
  • B.1.351 beta
  • B.1.617.2 delta
  • B.1.1.529.1 omicron
  • SARS-CoV-2 WT B.
  • B.1.351 (beta) and B.1.617.2 (delta) variant were amplified in VeroE6 cells and virus titers of stocks were determined by plaque assay and Tissue Culture Infectious Dose (TCID) 50 assay in VeroE6 cells.
  • TCID 50 assay To avoid rapid cell culture adaptation, stocks of the B.1.1.5291 (omicron) variant were produced in Calu-3 cells and titers were determined in VeroE6 cells using TCID 50 assay.
  • monoclonal antibodies were diluted 1 :3 for 10 steps with a test range from 0.5 ng/ml to 10 pg/ml and were incubated with 6xl0 4 TCID 50 of SARS-CoV-2 WT, B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta) and the B.1.1.529.1 (omicron) variant.
  • 6xl0 4 TCID 50 of SARS-CoV-2 WT B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta) and the B.1.1.529.1 (omicron) variant.
  • Virus replication was determined by immunostaining for the viral nucleocapsid protein using an incell ELISA.
  • IC50 inhibitory concentration 50
  • Virus neutralization was observed only among the antibodies that bound to the RBD, but not to the other epitopes in spike. Antibodies with better neutralizing capacity compared to the published antibodies were identified. Indeed, the virus neutralizing capacity was observed only among antibodies with high affinity. (RBD Kd ⁇ 10-7 M). Nevertheless, only 27% and 23% of antibodies with RBD Kd ⁇ 10-7M and RBD Kd ⁇ 10-9M, respectively, neutralized the virus. This suggests the potency of antibodies depends on both epitope specificity and high affinity. Refer to Fig. 4 and 5.
  • Example 4 Antibody binding region in RBD elucidated by a blocking assay using published antibodies with known epitopes and hACE2
  • antibodies are grouped into different classes. Antibodies of the same class do not necessarily target the same epitope or bind in the same mode.
  • the class categories are not absolute, i.e. antibodies can belong to more than one class depending on the exact target epitope.
  • an assay was developed to measure their capacity in blocking previously reported antibodies with known epitopes/classes from binding to RBD.
  • Blocking assay was performed using Biacore T200 system and Biacore sensor chip CM5.
  • a flow cell was immobilized with anti-human IgG antibodies using human antibody capture kit by following manufacturer’s instructions.
  • Sample antibody (mAbl) was captured in the flow cell at 20 pg/ml, followed by the capture mGO53 at 100 pg/ml.
  • Stabilization of the flow cell was performed by SPR running buffer at 10 pl/ min flow rate for 5 min.
  • injection ofRBD at 1 pM was immediately followed by an injection of 20 pg/ml mAb2 using dual injection option.
  • Binding values were calculated by measuring the difference in response units before and after the injection of mAb2 and subtracting the background binding as measured by performing the same steps while injecting the running buffer instead ofRBD. Between the injections of different sample antibodies, flow cell was regenerated using 3 M MgC12. Data was analyzed using using Biacore T200 software V2.0.
  • Blocking of binding to hACE2 was also investigated. Blocking assay was performed using Biacore T200 system and Biacore sensor chip CM5. A flow cell was immobilized with antihuman IgG antibodies using human antibody capture kit by following manufacturer’s instructions. Sample antibody (mAbl) was captured in the flow cell at 20 pg/ml, followed by stabilization of the flow cell by SPR running buffer at 10 pl/ min flow rate for 5 min. To measure binding, injection ofRBD at 1 pM was immediately followed by an injection of 200 nM hACE2 using dual injection option. Binding values were calculated by measuring the difference in response units before and after the injection of hACE2 and subtracting the background binding as measured by performing the same steps while injecting the running buffer instead ofRBD. Between the injections of different sample antibodies, flow cell was regenerated using 3 M MgC12. Data was analyzed using using using Biacore T200 software V2.0.
  • Classl/2 and Class2/3 antibodies neutralize virus by binding to different, nonoverlapping epitopes (Fig. 10).
  • Three Classl/2 antibodies and one Class2/3 antibody were tested against each other to block binding to RBD.
  • Two of three Classl/2 antibodies did not block Class2/3 antibody from binding to RBD.
  • Classl/2/3 mAb (2939) blocks Class2/3 (3279) but not Classl/2 (1255) mAbs from binding to RBD (Fig. 11).
  • Antibodies with non-overlapping epitopes show synergy in virus neutralization, e.g., high affinity binding to non-overlapping epitopes by mAbs 3279 and 1255 translates into more efficient virus neutralization when used in cocktail compared to on their own (Fig. 12).
  • High affine antibodies belonging to Classl/2 and Class2/3 show high neutralization capacity against three Variants of Concern (VoCs) tested.
  • High affine antibodies with S309 profile show specific neutralization against alpha variant but not against WT or other variants (Fig. 13).
  • Omicron RBD has a particular high number of mutations (15 aa) compared to the WT RBD.
  • Affinity for SARS-CoV-2 omicron variant was investigated next.
  • SPR based assay was performed to determine affinity of RBD-binding antibodies using Biacore T200 system and Biacore sensor chip CM5.
  • Two flow cells were immobilized with anti-human Fab antibodies using human Fab capture kit by following manufacturer’s instructions.
  • Antibody samples (40 pg/ ml) as well as the negative control mGO53 (40 pg/ ml) were captured in the sample and reference flow cells, respectively. Stabilization of both flow cells was performed by SPR running buffer at 10 pl/ min flow rate for 10 min.
  • a serial dilution of Omicron RBD was performed in SPR running buffer and the following concentrations were injected into both the flow cells: 0 nM, 12.4 nM, 37.0 nM, 111.1 nM, 333.3 nM and 1000 nM using a flow rate of 30 pl/ min.
  • High affine antibodies were independently tested at 0 nM, 3 nM, 9.2 nM, 27.7 nM, 83.3 nM and 250 nM of Omicron RBD. Dissociation and association took place at 25 °C for 60 s and 180 s, respectively.
  • flow cells were regenerated using 10 mM glycine in HC1. Data was analyzed using a 1 : 1 binding model or steady-state kinetic analysis using Biacore T200 software V2.0.
  • mAbs 1255 in Classl/2 and 2939 in Classl/2/3 retain higher binding to Omicron RBD compared to other antibodies of the respective classes.
  • High affine antibodies (1255 and 2939) can both bind to WT and Omicron RBD without blocking each other - suggesting they bind non-overlapping epitopes (Fig. 17). It was further found that 1255 blocks whereas 2939 does not block hACE2 interaction with both WT and Omicron RBD, indicating the difference in their binding site overlap with hACE2 interaction site (Fig. 18).
  • Antibodies 2939 and 1255 show high Omicron variant neutralization capacity. Moreover, mAb 2939 show better Omicron neutralization than therapeutically used mAb S309 - VIR Biotechnology (Sotrovimab) (Fig. 19 and 20).
  • mAbs that do not neutralize WT virus show weak neutralizing capacity to Omicron variant virus. Inhibition values of these mAbs are still lower than 1255 and 2939 - suggesting the epitopes targeted by 1255 and 2939 are promising for protective vaccine responses (Fig. 21).
  • Classl/2 (1255) and Class2/3 (3279) antibodies show broad neutralization and could be considered for therapeutic purposes or diagnostic purposes.
  • Table 6 EC50 values (in pg/ml) of selected antibodies for SARS-CoV-2 variants; NC: not calculated. Cited literature

Abstract

The present invention concerns the field of therapeutic and diagnostic antibodies against SARS-CoV-2. Specifically, the invention relates to an antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10-9 M. The present invention further relates to a polynucleotide encoding the antibody of the invention, a vector or expression construct comprising said polynucleotide, a host cell comprising said polynucleotide, vector or expression construct, or a non-human transgenic organism comprising the polynucleotide, vector or expression construct of the invention. Yet, the invention relates to a method for producing the antibody of the invention and to the use of the host cell of the invention for producing the antibody of the invention. Moreover, the preset invention provides for using an antibody, a polynucleotide or a vector of the invention for treating and/or preventing a disease or condition or for using the antibody for diagnosing said disease or condition. Finally, the invention relates to a kit for diagnosing SARS-CoV-2 infection in a subject.

Description

High affinity antibodies against the SARS-CoV-2 receptor binding domain
The present invention concerns the field of therapeutic and diagnostic antibodies against SARS- CoV-2. Specifically, the invention relates to an antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10'9 M. The present invention further relates to a polynucleotide encoding the antibody of the invention, a vector or expression construct comprising said polynucleotide, a host cell comprising said polynucleotide, vector or expression construct, or a non-human transgenic organism comprising the polynucleotide, vector or expression construct of the invention. Yet, the invention relates to a method for producing the antibody of the invention and to the use of the host cell of the invention for producing the antibody of the invention. Moreover, the present invention provides for using an antibody, a polynucleotide or a vector of the invention for treating and/or preventing a disease or condition or for using the antibody for diagnosing said disease or condition. Finally, the invention relates to a kit for diagnosing SARS- CoV-2 infection in a subject.
In 2020, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the Covid- 19 disease has become a pandemic due to its high transmissibility and deadly outcome. The infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of Spike protein to host receptor, primarily human angiotensin-converting enzyme 2 (hACE2). Upon binding, fusion of viral and host membranes occurs allowing the virus to enter the host cell and start viral replication.
There have been some reports on neutralizing antibodies. Those antibodies typically bind to the receptor binding domain of the Spike protein and thereby inhibit binding to hACE2 and, thus, finally entering of the virus into the host cell (Asamow 2021, Cell 184, 3192-3204; Sharma 2021, Proteins. 2021; 1—11; WO2021/1207433). The antibodies reported so far, however, have affinities in the nano-molar range.
While antibodies that block this interaction are in emergency use as early Covid- 19 therapies, precise determinants of neutralization potency remain unknown.
There is a present need to develop further anti-SARS-CoV-2 antibodies having higher affinities and increased neutralization potential in terms of strength and range in order to efficiently and reliably treat and prevent as well as diagnose SARS-CoV-2 infections. This is even more important given the fact that the global pandemic is producing constantly novel viral variants of concern. As of today, there have been reports for multiple variants, including: SARS-CoV- 2 alpha variant (B.1.1.7), SARS-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including the currently known omicron sub-variants BA.l, BA.2 and BA.3, in a preferred embodiment further including subvariant BA.5.
The technical problem underlying the present invention may be seen as the provision of means and methods for complying with the aforementioned needs. The technical problem is solved by the embodiments characterized in the claims and herein below.
Thus, the present invention relates to an antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10'9 M.
It is to be understood that in the specification and in the claims, “a” or “an” can mean one or more of the items referred to in the following depending upon the context in which it is used. Thus, for example, reference to “an” item can mean that at least one item can be utilized.
As used in the following, the terms “have”, “comprise” or “include” are meant to have a nonlimiting meaning or a limiting meaning. Thus, having a limiting meaning these terms may refer to a situation in which, besides the feature introduced by these terms, no other features are present in an embodiment described, i.e. the terms have a limiting meaning in the sense of “consisting of’ or “essentially consisting of’. Having a non-limiting meaning, the terms refer to a situation where besides the feature introduced by these terms, one or more other features are present in an embodiment described.
Further, as used in the following, the terms “preferably”, “more preferably”, “most preferably”, "particularly", "more particularly", “typically”, and “more typically” are used in conjunction with features in order to indicate that these features are preferred features, i.e. the terms shall indicate that alternative features may also be envisaged in accordance with the invention.
Further, it will be understood that the term “at least one” as used herein means that one or more of the items referred to following the term may be used in accordance with the invention. For example, if the term indicates that at least one item shall be used this may be understood as one item or more than one item, i.e. two, three, four, five or any other number. Depending on the item the term refers to the skilled person understands as to what upper limit the term may refer, if any.
The term “antibody” as used herein refers to any polypeptide which comprises amino acid sequence stretches that are capable of forming a binding pocket that is sufficient for specific binding to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) as referred to herein. Such an antibody may be, preferably, a monoclonal antibody, a single chain antibody, a chimeric antibody or any fragment or derivative of such antibodies being still capable of binding to the receptor binding domain (RBD) of SARS-CoV-2 spike protein specifically as referred to herein. Fragments and derivatives comprised by the term antibody as used herein encompass a bispecific antibody, a synthetic antibody, a Fab, F(ab)2 Fv or scFv fragment or a chemically modified derivative of any of these antibodies. Antibodies or fragments thereof, in general, can be obtained by using methods which are described, e.g., in Harlow and Lane "Antibodies, A Laboratory Manual", CSH Press, Cold Spring Harbor, 1988. Monoclonal antibodies can be prepared by the techniques which comprise the fusion of mouse myeloma cells to spleen cells derived from immunized mammals and, preferably, immunized mice. Antibodies may also be produced recombinantly by techniques well known in the art. The antibody of the present invention can be, preferably, generated by using the techniques described in the accompanying Examples below.
The antibody of the invention shall specifically bind to the receptor binding domain (RBD) of SARS-CoV-2 spike protein. The term “receptor binding domain (RBD)” as used herein refers to a region of the SARS-CoV-2 spike protein which is involved in binding of the said spike protein of the virus to the human Angiotensin Converting Enzyme (hACE)-2 receptor on host cells. The RBD consists of amino acids 319 to 541 of the SARS-CoV-2 spike protein of WT SARS-CoV-2 (see preferably, BetaCoV/Wuhan/IVDC-HB-01/2019, accession ID: EPI ISL 402119; BetaCoV/Wuhan/IVDC-HB-04/2020, accession ID: EPI ISL 402120; BetaCoV/Wuhan/IVDC-HB-05/2019, accession ID: EPI ISL 402121). It will be understood that in virus variants of SARS-CoV-2, the position may differ due to the presence of one or more additional amino acids and/or deletions of one or more amino acids. Typically, such variants, however, shall also comprise a RBD which consists of amino acids corresponding to the amino acids of the RBD in WT SARS-CoV-2 at amino acid positions 319 to 541. The spike protein is a glycoprotein that forms a homotrimer at the surface of SARS-CoV-2 (Wrapp et al, Science, 367: 1260-1263). In the trimeric structure of the spike protein, the RBD may be exhibited by each monomer in either a so-called “up” or a so -called “down” configuration. The structure and amino acid composition of the SARS-CoV-2 spike protein is well known in the art, for WT SARS-CoV-2 as well as for various variants of the virus, such as SARS-CoV- 2 alpha variant (B. l.1.7), SARS-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
The phrase “specifically binds to” as used in accordance with the present invention means that the antibody shall not cross-react significantly with components or regions other than the RBD. Cross-reactivity of an antibody as mentioned herein can be tested by the skilled person by various techniques including immunological technologies such as Western blotting, ELISA or RIA based assays or measuring of binding affinities using, e.g., surface plasmon resonance technology.
The term “equilibrium dissociation constant (Kd)” as used herein indicates the propensity for the antib ody/antigen (i.e. RBD) complex to dissociate into its free components, i.e. free antibody and free antigen. The equilibrium dissociation constant (Kd) can be expressed as follows:
Kd = [A]x * [B]y / [AxBy] wherein [Ax], [By], and [AxBy] are the concentrations of A, B and AB at the equilibrium, respectively. Thus, the smaller the equilibrium dissociation constant, the more tightly bound the ligand is, or the higher the affinity between ligand and protein. For example, an antibody with a picomolar equilibrium dissociation constant (Kd in the range of 10'12M) binds more tightly to a particular antigen than an antibody with a nanomolar equilibrium dissociation constant (Kd in the range of 10'9M). The binding of the antibody of the invention and the RBD shall be with an equilibrium dissociation constant (Kd) of less than 10'9 M, preferably, between 10'9 and IO'10 M or, preferably, even less than IO'10 M. The equilibrium dissociation constant referred to in accordance with the present invention can be determined by techniques well known in the art, preferably, it is to be determined using surface plasmon resonance described in the accompanying Examples, below.
The antibody according to the invention shall, preferably, comprise three complementary determining regions. The term “complementary determining region (CDR)” as used herein refers to regions in the variable domains of the heavy and light chain of an antibody that define the binding affinity and specificity of the antibody. There are three CDRs for the heavy chain, CDR1-H, CDR2-H and CDR3-H, and three CDRs for the light chain, CDR1-L, CDR2-L, and CDR3-L. Antibodies exhibiting binding to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10'9 M, preferably, have CDRs as listed in Table 1, below, or CDRs having an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of the SEQ ID NOs mentioned in Table 1 retaining binding to RBD with Kd of less than 10'9
M. Preferably, such antibodies are useful for the diagnostic and/or therapeutic purposes referred to herein.
able 1: High affinity SARS-CoV-2 RBD antibodies
Figure imgf000007_0001
Figure imgf000008_0001
Particular preferred antibodies for therapeutic purposes are described in the following.
Preferably, the antibody of the invention comprises at least one heavy chain CDR said heavy chain CDR being
(I) a heavy chain CDR1 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 1, 16 to 23 and 24 to 30;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 16 to 23 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1, 24 to 30 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; (II) a heavy chain CDR2 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 2, 3, 31 to 38 and 39 to 47;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 2 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 3 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 31 to 38 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 39 to 47 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; or
(III) a heavy chain CDR3 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 4, 5, 48 to 55 and 56 to 65; (b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 4 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 5 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 48 to 55 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 56 to 65 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
Preferably, the antibody of the invention comprises a heavy chain CDR1, CDR2 and CDR3 selected from the aforementioned heavy chain CDRs.
More preferably, the antibody of the invention comprises a heavy chain CDR1, CDR2 and CDR3 combination as referred to in the following Table 2:
Table 2:
Figure imgf000012_0001
Preferably, the antibody of the present invention comprises at least one light chain CDR, said light chain CDR being
(I) a light chain CDR1 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 6, 7, 66 to 71 and 72 to 80;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 6 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 RBD and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 7 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 RBD and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 66 to 71 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD ofWT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 69, 72 to 80 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(II) a light chain CDR2 having an amino acid sequence selected from the group consisting of: (a) an amino acid sequence as shown in any one of SEQ ID NOs: 8, 9, 81 to 83 and 84 to 88;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 8 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 9 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 9, 81 to 83 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 82, 84 to 88 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; or
(III) a light chain CDR3 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 10, 11, 89 to 96 and 97 to 105;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 10 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 11 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 89 to 96 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 97 to 105 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
Preferably, the antibody of the invention comprises a light chain CDR1, CDR2 and CDR3 selected from the aforementioned heavy chain CDRs.
More preferably, the antibody of the invention comprises a light chain CDR1, CDR2 and CDR3 combination as referred to in the following Table 3:
Figure imgf000015_0001
Figure imgf000016_0001
More preferably, the antibody of the invention comprises a heavy and light chain CDR1, CDR2 and CDR3 combination as referred to in the following Table 4: able 4:
Figure imgf000017_0001
Figure imgf000018_0001
It will be understood that a variant amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from any of the aforementioned amino acid sequences shall still be capable of exhibiting essentially the same immunological properties as the concrete amino acid sequence identified by a SEQ ID number.
More preferably, such a variant amino acid sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to the concrete amino acid sequence identified by a SEQ ID No. Sequence identity between two amino acid sequences as referred to herein, in general, can be determined by alignment of two sequences either over the entire length of one of the sequences or within a comparison window. The percentage is calculated by determining the number of positions at which the identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment and calculation of sequence identity can be done by using published techniques or methods codified in computer programs such as, for example, BLASTP, BLASTN or FASTA. The percent sequence identity values are, preferably, calculated over the entire amino acid sequence. A series of programs based on a variety of algorithms is available to the skilled worker for comparing different sequences. In this context, the algorithms of Needleman and Wunsch or Smith and Waterman give particularly reliable results. To carry out the sequence alignments, the program PileUp or the programs Gap and BestFit, which are part of the GCG software packet (Genetics Computer Group, US), may be used. The sequence identity values recited above in percent (%) are to be determined, in another aspect of the invention, using the program GAP over the entire sequence region with the following settings: Gap Weight: 50, Length Weight: 3, Average Match: 10.000 and Average Mismatch: 0.000, which, unless otherwise specified, shall always be used as standard settings for sequence alignments.
In the case of the aforementioned variants of CDR sequences it is, however, preferably envisaged that the CDR amino acid sequences which differs by at least one amino acid exchange, deletion and/or addition differs from the specific sequence shown in any one of the CDR SEQ ID numbers by at most 3, at most 2 or at most 1 amino acid. Said at most 3, at most 2 or at most 1 amino acid may be deleted exchange or added.
Depending on the antibody type envisaged, the antibody of the invention may further comprise amino acids or amino acid sequence from the frame work regions. The term "framework regions" (FRs) refer to amino acid sequences interposed between CDRs, i.e. to those portions of immunoglobulin light and heavy chain variable regions that are relatively conserved among different immunoglobulins in a single species. The light and heavy chains of an immunoglobulin each have four FRs, designated FR1-L, FR2-L, FR3-L, FR4-L, and FR1-H, FR2-H, FR3-H, FR4-H, respectively. From N-terminal to C-terminal, light chain variable region and heavy chain variable region both typically have the following order of these elements: FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4.
Numbering systems have been established for assigning numbers to amino acids that occupy positions in each of above domains. Complementarity determining regions and framework regions of a given antibody can be identified using the Kabat system.. However, the CDRs can also be redefined according to an alternative nomenclature scheme based on IMGT definition (Lefranc 2003). Typically, CDR and FWR sequences are given herein according to the IMGT system in the IgBlast version 1.13.0.
An antibody according to the invention may also be a full-length antibody (i.e. antibodies comprising two heavy chains and two light chains). In such a case, the light chain includes two domains or regions, a variable domain (VL) and a constant domain (CL). The heavy chain includes four domains, a variable domain (VH) and three constant domains (CHI, CH2 and CH3, collectively referred to as CH). The variable regions of both light (VL) and heavy (VH) chains determine binding recognition and specificity to the antigen. The constant region domains of the light (CL) and heavy (CH) chains confer important biological properties such as antibody chain association, secretion, trans-placental mobility, complement binding, and binding to Fc receptors (FcR). It will be understood that there may be modifications such as mutations reducing FcR binding that may be introduced into the antibody of the invention to increase half-life and/or to reduce or improve effector functions. The Fv fragment is the N- terminal part of the Fab fragment of an immunoglobulin and consists of the variable portions of one light chain and one heavy chain. The specificity of the antibody resides in the structural complementarity between the antibody combining site and the antigenic determinant. Antibody combining sites are made up of residues that are primarily from the hypervariable or complementarity determining regions. Occasionally, residues from non-hypervariable or framework regions (FR) influence the overall domain structure and hence the combining site. The light chains of human antibodies generally are classified as kappa and lambda light chains, and each of these contains one variable region and one constant domain. Heavy chains are typically classified as mu, delta, gamma, alpha, or epsilon chains, and these define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively. Human IgG has several subtypes, including, but not limited to, IgGl, lgG2, lgG3, and lgG4. Human IgA subtypes include IgAl and lgA2. In humans, the IgA isotypes contain four heavy chains and four light chains; the IgG and IgE isotypes contain two heavy chains and two light chains; and the IgM isotype contains ten or twelve heavy chains and ten or twelve light chains. Antibodies according to the invention may be IgG, IgE, IgD, IgA, or IgM immunoglobulins or fragments thereof.
A humanized antibody according to the invention refers to immunoglobulin chains or fragments thereof (such as Fab, Fab', F(ab)2, Fv, or other antigen binding sub-sequences of antibodies), which contain minimal sequence (but typically, still at least a portion) derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (the recipient antibody) in which CDR residues of the recipient antibody are replaced by CDR residues from a non-human species immunoglobulin (the donor antibody) such as a mouse, rat or rabbit having the desired specificity, affinity and capacity. As such, at least a portion of the framework sequence of said antibody or fragment thereof may be a human consensus framework sequence. In some instances, Fv framework residues of the human immunoglobulin need to be replaced by the corresponding non-human residues to increase specificity or affinity. Furthermore, humanized antibodies can comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and maximize antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically at least two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region, typically that of a human immunoglobulin, which (e.g. human) immunoglobulin constant region may be modified (e.g. by mutations or glycol-engineering) to optimize one or more properties of such region and/or to improve the function of the (e.g. therapeutic) antibody, such as to increase or reduce Fc effector functions or to increase serum half-life.
A chimeric antibody according to the invention refers to an antibody whose light and/or heavy chain genes have been constructed, typically by genetic engineering, from immunoglobulin variable and constant regions which are identical to, or homologous to, corresponding sequences of different species, such as mouse and human. Alternatively, variable region genes derive from a particular antibody class or subclass while the remainder of the chain derives from another antibody class or subclass of the same or a different species. It covers also fragments of such antibodies. For example, a typical therapeutic chimeric antibody is a hybrid protein composed of the variable or antigen-binding domain from a mouse antibody and the constant or effector domain from a human antibody, although other mammalian species may be used. Preferably, the antibody of the invention comprises a heavy chain having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 12, 13, 106 to 123;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
12 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
13 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 106 to 113 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 114 to 123 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
Preferably, the antibody of the invention comprises a light chain having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 14, 15 124 to 141;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
14 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 15 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 124 to 131 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 132 to 141 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
More preferably, the antibody of the present invention comprises a heavy and light chain combination as referred to in the following Table 5:
Table 5:
Figure imgf000023_0001
Figure imgf000024_0001
It will be understood that a variant amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from any of the aforementioned amino acid sequences shall still be capable of exhibiting essentially the same immunological properties as the concrete amino acid sequence identified by a SEQ ID No. More preferably, such a variant amino acid sequence is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to the concrete amino acid sequence identified by a SEQ ID number. Preferably, the antibody of the invention and, in particular, those useful for therapeutic purposes as mentioned before, neutralizes SARS-CoV-2 in vitro with IC50 of at most 1.0 pg/ml, at most 0.1 pg/ml or at most 0.01 pg/ml.
Neutralization of SARS-CoV-2 in vitro as referred to herein can be tested in vitro by applying antibodies to be tested for neutralizing potential to SARS-CoV-2 virus preparations, adding this antibody- virus mixture to a culture of hACE2 expressing cells and determining infection of the hACE2 expressing cells. If said cells are infected SARS-CoV-2 will replicate in these cells, which can be measured by quantifying the amount of viral RNA or protein produced in these cells or by determining the degree of cell damage caused by virus replication in the inoculated cell culture, which is known in the field as plaque assay. If the antibody to be tested has neutralizing potential, the hACE2 expressing cells will be protected from infection and thus, do not produce viral RNA or protein or be protected from damage and cell death. Preferably, neutralization and neutralizing potential of an antibody can be tested as described in the accompanying Examples, below. Also preferably, neutralizing potential of an antibody may also be determined by using a surrogate neutralization assay. To this end, an enzyme-conjugated or labeled SARS-CoV-2 spike protein or RBD thereof may be applied to immobilized hACE2 in the presence of antibodies to be tested. If no binding to hACE2 or significantly reduced binding - as measured by the enzymatic activity or presence of the label - occurs in the presence of the antibodies, this will be an indicator for the neutralizing potential of said antibodies. Using the aforementioned examples of in vitro tests for the neutralizing potential of an antibody by testing the antibody of the invention, IC50 values as referred to above may be determined for a given antibody.
In addition to the aforementioned strength of neutralization, the antibody of the present invention, typically, neutralizes a significant range of SARS-CoV-2 variants. More preferably, the antibody neutralizes at least two, at least three, at least four or at least five of the SARS- CoV-2 variants. Preferably, said antibody neutralizes at least two, at least three, at least four or at least five variants that are selected from the currently known SARS-CoV-2 variants, i.e. wildtype (WT) SARS-CoV-2, SARS-CoV-2 alpha variant (B.l.1.7), SARS-CoV-2 beta variant (B.1.1351), SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
The term “SARS-CoV-2” as used herein refers except as specified otherwise to the wildtype (WT) SARS-CoV-2 as well as to all variants thereof. Variants of SARS-CoV-2 include all SARS-CoV-2 virus mutants that are derived from SARS-CoV-2 WT or any variant thereof by natural mutagenesis or which are artificially designed based on said SARS-CoV-2 WT or any mutant thereof. In particular encompassed are the variants of concern and, more preferably, SARS-CoV-2 is selected from the group consisting of: wildtype (WT) SARS-CoV-2, SARS- CoV-2 alpha variant (B. l.1.7), SARA-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2) or SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
Preferably, the antibody of the invention can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2.
Existing antibodies that bind to RBD have been classified based on their putative epitope region on RBD into different classes (Barnes 2020, Nature 588, 682-687). The antibody of the present invention shall, preferably, block binding of at least one antibody that has been classified either as a Classi, Class2 or Class3 antibody (i.e. belonging into the group of antibodies of Classi, Class2 and Class3). It will be understood that there are antibodies that may block binding of more than one antibody of either one class or of different classes. Moreover, the antibody of the invention my also block binding of an antibody allocated to different classes. Blocking binding of an antibody belonging to Classi, Class2 and Class3 from binding to the RBD of WT SARS-CoV-2 can be determined by well-known techniques including those described in the Examples, below.
Advantageously, it has been found in accordance with the studies underlying the present invention that anti-SARS-CoV-2 antibodies can be generated which are capable of specifically binding to the RBD of the SARS-CoV-2 spike protein with high affinity. These antibodies are particularly useful for treating, preventing and/or diagnosing SARS-CoV-2 infection. Those antibodies that display a particularly high affinity and neutralizing capacity in terms of strength and range are particularly useful for the treatment and/or prevention of SARS-CoV-2 infection, although they may be used for diagnostic purposes as well. Those antibodies that exhibit a particular high affinity but less neutralizing capacity are particularly useful as diagnostic antibodies, although they may be useful for therapeutic and/or prophylactic purposes as well. The antibodies of the invention are, furthermore, neutralizing antibodies for virus variants of concern such as the SARS-CoV-2 omicron variant.
Thanks to the present invention, therapy and diagnosis of SARS-CoV-2 associated diseases and disorders and, in particular, Covid- 19 may greatly benefit.
The explanations and definitions made above shall apply mutatis mutandis for all other embodiments described herein except if specified otherwise. The present invention further relates to a polynucleotide encoding the antibody of the invention.
The term “polynucleotide” as used in accordance with the present invention refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids). The term as used herein encompasses the sequence specified herein as well as the complementary or reverse- complementary sequence thereof. Preferably, the polynucleotide is RNA or DNA. The term also encompasses DNAs or RNAs with backbones modified for stability or for other reasons. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are also encompassed as polynucleotides. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. Every nucleic acid sequence herein that encodes a certain polypeptide of the invention may due to the degeneracy of the genetic code have silent variations. The degeneracy of the genetic code yields a large number of functionally identical polynucleotides that encode the same polypeptide. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are silent variations.
The polynucleotide of the invention shall encode the antibody of the invention, i.e. it shall comprise a nucleic acid sequences which encodes said antibody of the invention. In addition, the polynucleotide of the present invention may comprise additional nucleic acid sequences. Preferably, the polynucleotide of the present invention may comprise in addition to an open reading frame further untranslated sequence at the 3’ and at the 5’ terminus of the coding gene region: at least 500, preferably 200, more preferably 100 nucleotides of the sequence upstream of the 5’ terminus of the coding region and at least 100, preferably 50, more preferably 20 nucleotides of the sequence downstream of the 3’ terminus of the coding gene region.
The polynucleotide of the present invention shall be provided, preferably, either as an isolated polynucleotide (i.e. purified or at least isolated from its natural context such as its natural gene locus) or in genetically modified or exogenously (i.e. artificially) manipulated form. An isolated polynucleotide can, for example, comprise less than approximately 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in the genomic DNA of the cell from which the nucleic acid is derived. The polynucleotide, preferably, is provided in the form of double or single stranded molecule. It will be understood that the present invention by referring to any of the aforementioned polynucleotides of the invention also refers to complementary or reverse complementary strands of the specific sequences or variants there-of referred to before. The polynucleotide encompasses DNA, including cDNA and genomic DNA, or RNA polynucleotides.
Moreover, comprised are also chemically modified polynucleotides including naturally occurring modified polynucleotides such as glycosylated or methylated polynucleotides or artificial modified ones such as biotinylated polynucleotides.
The present invention contemplates a vector or expression construct comprising the polynucleotide of the invention.
The term “vector”, preferably, encompasses phage, plasmid, cosmids, viral vectors as well as artificial chromosomes, such as bacterial or yeast artificial chromosomes (YAC). The vector encompassing the polynucleotide of the present invention, preferably, further comprises selectable markers for propagation and/or selection in a host. The vector may be incorporated into a host cell by various techniques well known in the art. If introduced into a host cell, the vector may reside in the cytoplasm or may be incorporated into the genome. In the latter case, it is to be understood that the vector may further comprise nucleic acid sequences which allow for homologous recombination or heterologous insertion. Vectors can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. The terms “transformation” and “transfection”, conjugation and transduction, as used in the present context, are intended to comprise a multiplicity of prior-art processes for introducing foreign nucleic acid (for example DNA) into a host cell, including calcium phosphate, rubidium chloride or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, f-mating, natural competence, carbon-based clusters, chemically mediated transfer, electroporation or particle bombardment. Suitable methods for the transformation or transfection of host cells, including plant cells, can be found in text books such as Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989). Alternatively, a plasmid vector may be introduced by heat shock or electroporation techniques. Should the vector be a virus, it may be packaged in vitro using an appropriate packaging cell line prior to application to host cells. Preferably, the vector of the present invention is an expression vector. In such an expression vector, i.e. a vector which comprises the polynucleotide of the invention having the nucleic acid sequence operatively linked to an expression control sequence (also called “expression cassette”) allowing expression in prokaryotic or eukaryotic cells or isolated fractions thereof. Suitable expression vectors are known in the art such as Okayama-Berg cDNA expression vector pcDVl (Pharmacia), pCDM8, pRc/CMV, pcDNAl, pcDNA3 (Invitrogene) or pSPORTl (GIBCO BRL). Further examples of typical fusion expression vectors are pGEX, pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ), where glutathione S transferase (GST), maltose E-binding protein and protein A, respectively, are fused with the recombinant target protein. Examples of suitable inducible non-fiision E. coli expression vectors are, inter alia, pTrc and pET l id. The tar-get gene expression of the pTrc vector is based on the transcription from a hybrid trp-lac fusion promoter by host RNA polymerase. The target gene expression from the pET l id vector is based on the transcription of a T7-gnl0-lac fusion promoter, which is mediated by a co-expressed viral RNA polymerase (T7 gnl). This viral polymerase is provided by the host strains BL21 (DE3) or HMS174 (DE3) from a resident lambda-prophage which harbors a T7 gnl gene under the transcriptional control of the lacUV 5 promoter. The skilled worker is familiar with other vectors which are suitable in prokaryotic organisms; these vectors are, for example, in E. coli, pLG338, pACYC184, the pBR series such as pBR322, the pUC series such as pUC18 or pUC19, the Ml Bmp series, pKC30, pRep4, pHSl, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-IIIl 13-B1, lambdagtl l or pBdCl, in Streptomyces plJlOl, plJ364, plJ702 or plJ361, in Bacillus pUBUO, pC194 or pBD214, in Corynebacterium pSA77 or pAJ667. Examples of vectors for expression in the yeast S. cerevisiae comprise pYep Seel, pMFa, pJRY88 and pYES2 (Invitrogen Corporation, San Diego, CA). Vectors and pro-cesses for the construction of vectors which are suitable for use in other fungi, such as the filamentous fungi, comprise those which are described in detail in text books such as van den Hondel, C.A.M.J.J., & Punt, P.J. (1991) “Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of fungi, J.F. Peberdy et al., Ed., pp. 1-28, Cambridge University Press: Cambridge, or in: More Gene Manipulations in Fungi (J.W. Bennett & L.L. Lasure, Ed., pp. 396-428: Academic Press: San Diego). Further suitable yeast vectors are, for example, pAG-1, YEp6, YEpl3 or pEMBLYe23. As an alternative, the polynucleotides of the present invention can be also expressed in insect cells using baculovirus expression vectors. Baculovirus vectors which are available for the expression of proteins in cultured insect cells, e.g., Sf9 cells, comprise the pAc series and the pVL series.
Yet the vector may be an integration vector. An integration vector refers to a DNA molecule, linear or circular, that can be incorporated, e.g., into a microorganism's genome, such as a bacteria’s genome, and provides for stable inheritance of a gene encoding a polypeptide of interest, such as the alcohol acyl transferase of the invention. The integration vector generally comprises one or more segments comprising a gene sequence encoding a polypeptide of interest under the control of additional nucleic acid segments that provide for its transcription.
Such additional segments may include promoter and terminator sequences, and one or more segments that drive the incorporation of the gene of interest into the genome of the target cell, usually by the process of homologous recombination. Typically, the integration vector will be one which can be transferred into the target cell, but which has a replicon which is nonfunctional in that organism. Integration of the segment comprising the gene of interest may be selected if an appropriate marker is included within that segment. One or more nucleic acid sequences encoding appropriate signal peptides that are not naturally associated with a polypeptide to be expressed in a host cell of the invention can be incorporated into (expression) vectors. For example, a DNA sequence for a signal peptide leader can be fused in-frame to a nucleic acid of the invention so that the alcohol acyl transferase of the invention is initially translated as a fusion protein comprising the signal peptide. Depending on the nature of the signal peptide, the expressed polypeptide will be targeted differently. A secretory signal peptide that is functional in the intended host cells, for instance, enhances extracellular secretion of the expressed polypeptide. Other signal peptides direct the expressed polypeptide to certain organelles, like the chloroplasts, mitochondria and peroxisomes. The signal peptide can be cleaved from the polypeptide upon transportation to the intended organelle or from the cell. It is possible to provide a fusion of an additional peptide sequence at the amino or carboxyl terminal end of the polypeptide.
The term “gene construct” as used herein refers to polynucleotides comprising the polynucleotide of the invention and additional functional nucleic acid sequences. A gene construct according to the present invention is, preferably, a linear DNA molecule. Typically, a gene construct in accordance with the present invention may be a targeting construct which allows for random or site- directed integration of the targeting construct into genomic DNA. Such target constructs, preferably, comprise DNA of sufficient length for either homologous or heterologous recombination as described in detail below. In both cases, the construct must be, preferably, impeccable, with structures to control gene expression, such as a promoter, a site of transcription initiation, a site of polyadenylation, and a site of transcription termination. Moreover, it will be understood that a gene construct in accordance with the present invention may also be generated by using genomic modification techniques such as genome editing using the CRISPR/Cas technology. Yet, the present invention provides a host cell comprising the polynucleotide of the invention or the vector or expression construct of the invention.
The host cell of the invention is capable of expressing the polypeptide of the invention comprised in the vector or gene construct of the invention. The host cell is, typically transformed or transduced with said vector or gene construct such that the polypeptide of the invention can be expressed from the vector or gene construct. The transformed vector or gene construct may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host cell genome as specified elsewhere herein in more detail. A host cell according to the invention may be produced based on standard genetic and molecular biology techniques that are generally known in the art, e.g., as described in standard text books such as Sambrook, J., and Russell, D.W. "Molecular Cloning: A Laboratory Manual" 3d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, (2001); and F.M. Ausubel et al, eds., "Current protocols in molecular biology", John Wiley and Sons, Inc., New York (1987), and later supplements thereto.
Preferably, said host cell is a bacterial cell, a fungal cell, an animal cell or a plant cell.
Bacterial cells may be gram-positive or gram-negative bacterial cells. Preferred bacterial cells may be selected from the genera Escherichia, Klebsiella, Helicobacter, Bacillus, Lactobacillus, Streptococcus, Amycolatopsis, Rhodobacter, Pseudomonas, Paracoccus, Lactococcus or Pantoea. More preferably, useful gram positive bacterial host cells may be Bacillus alkalophius, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus Jautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, Bacillus thuringiensis, Streptomyces spheroides, Streptomyces thermoviolaceus, Streptomyces lividans, Streptomyces murinus, Streptoverticillum verticillium ssp. verticillium. Rhodobacter sphaeroides, Rhodomonas palustri, or Streptococcus lactis. Also more preferably, useful gram negative bacterial host cells may be Escherichia coli, Pseudomonas sp., preferably, Pseudomonas purrocinia, Pseudomonas fluorescens, Rhodobacter capsulatus, Rhodobacter sphaeroides, Paracoccus carotinifaciens, Paracoccus zeaxanthinifaciens or Pantoea ananatis.
Preferred fungal host cells may be Aspergillus, Fusarium, Trichoderma, Yeast, Pichia, or Saccharomyces host cells. Yeast as used herein includes ascosporogenous yeast, basidiosporogenous yeast, and yeast belonging to the Blastomycetes. Preferred animal host cells may comprise mammalian host cells, avian host cells, reptilian host cells or insect host cells. Preferred animal host cells are HeLa cells, HEK293T, F or E cells, U20S cells, A549 cells, HT1080 cells, CAD cells, P19 cells, NIH3T3 cells, L929 cells, N2a cells, CHO cells, MCF-7 cells, Y79 cells, SO-Rb50 cells, HepG2 cells, DUKX-X11 cells, J558L cells or BHK cells.
Preferred plant host cells comprise tobacco, rice, wheat, pea or tomato cells.
The present invention relates to a non-human transgenic organism comprising the polynucleotide of the invention or the vector or expression construct of the invention.
The term “non-human transgenic organism” as used herein refers to an organism which has been genetically modified in order to comprise the polynucleotide, vector or gene construct of the present invention. Said genetic modification may be the result of any kind of homologous or heterologous recombination event, mutagenesis or gene editing process. Accordingly, the transgenic non-human organism shall differ from its non-transgenic counterpart in that it comprises the non-naturally occurring (i.e. heterologous) polynucleotide, vector or gene construct in its genome. Non-human organisms envisaged as transgenic non-human organisms in accordance with the present invention are, preferably, multi-cellular organisms, such as an animal, plant, multi-cellular fungi or algae. Preferably, said non-human organism is an animal or a plant. Preferred animals are mammals, in particular, laboratory animals such as rodents, e.g., mice, rats, rabbits or the like, or farming animals such as sheep, goat, cows, horses or the like. Preferred plants are crop plants or vegetables, in particular, selected from the group consisting of tobacco, rice, wheat, pea and tomato. Methods for the production of transgenic non-human organisms are well known in the art; see, standard text books, e.g. Lee-Yoon Low et al., Transgenic Plants: Gene constructs, vector and transformation method. 2018. DOI.10.5772/intechopen.79369; Pinkert, C. A. (ed.) 1994. Transgenic animal technology: A laboratory handbook. Academic Press, Inc., San Diedo, Calif.; Monastersky G. M. and Robl, J. M. (ed.) (1995) Strategies in Transgenic Animal Science. ASM Press. Washington D.C); Sambrook, loc.cit, Ausubel, loc.cit).
The present invention also provides a method for producing the antibody of the invention comprising (i) expressing the polynucleotide or the vector of the invention in a host cell and (ii) obtaining the said antibody from said host cell.
The term “producing” as used herein refers to the process of recombinant production of the antibody in a host cell. The manufacture may also comprise further steps such as purifying the produced antibody or formulating the antibody or purified antibody as a pharmaceutical composition. Accordingly, the aforementioned method of the present invention may consist of the aforementioned steps or may comprise further additional steps.
Expressing the polynucleotide or the vector of the invention in a host cell may, for example, also include the step of generating the polynucleotide or vector of the invention as well as the step of introducing said polynucleotide or vector into the host cell.
Generating the polynucleotide of the invention or the vector comprising it may, e.g., also comprise the step of generating a polynucleotide sequence encoding the antibody of the invention on the basis of sequences for antibodies obtained from B-cells. Preferably, said B- cells are obtained from patients which have successfully survived an infection by SARS-CoV- 2 or subjects that have been successfully vaccinated. More specifically, generating the polynucleotide sequence may comprise the following steps: (a) Single cell sorting was performed on bait+ memory B cells; (b) Ig gene amplification and sequencing (Murugan et al., 2015 Eur J Immunol. 45(9):2698-700); (c) Obtaining Ig gene features of the antibody sequences (Imkeller et al., 2016 BMC Bioinformatics 17, 67); (d) Analyzing Ig gene features and cloning antibodies exhibiting the following features: all isotypes with preference for IgG, germline and somatic hyper-mutations, diverse Ig segments in heavy and light chain, from all time points of B-cell sample collection; (e) Cloning and expression of the antibodies (Tiller et al., 2008, J Immunol Methods. 329(1-2): 112-124). Functional assessment of antibodies may be carried out as described in the accompanying Examples, below. It will be understood that the polynucleotide of the invention may also be obtained by using other techniques known in the art.
Introducing the polynucleotoide or vector generated as described before into a host cell for expression can be done by all techniques available in the art, including salt-based transfection, lipofection, electroporation, injection, viral transfection techniques and the like. The polynucleotide or vector may be stably integrated into the genome of the host cell or may be transiently present.
Obtaining the antibody from the host cell can be achieved by purifying or partially purifying the antibody from the host cells or host cell culture. For protein purification, various techniques may be used including precipitation, filtration, ultra-filtration, extraction, chromatography techniques such as ion-exchange-, affinity- and/or size exclusion chromatography, HPLC or electrophoresis. The skilled person is well aware of how an antibody may be purified in order to provide it in isolated form. Preferred techniques are those described in the accompanying Examples below.
Yet, the invention relates to the use of the host cell of the invention for producing the antibody of the invention.
The host cell of the present invention may, typically, be cultured under suitable conditions and for time sufficient for expression of the polynucleotide or vector of the invention such that the antibody will be produced. The antibody may be obtained from a host cell culture as described elsewhere herein.
The present invention relates to an antibody, a polynucleotide or a vector as defined herein above in accordance with the invention for use in treating and/or preventing a disease or condition. Preferably, the disease or condition referred to herein is associated with SARS-CoV- 2 infection in a subject.
The antibody, polynucleotide or vector according to the present invention may be formulated as a medicament for use in in treating and/or preventing a disease or condition. Such a medicament is, preferably, for topical or systemic administration. Conventionally a medicament will be administered intra-muscularly or subcutaneously. However, depending on the nature and the desired therapeutic effect and the mode of action, the medicament may be administered by other routes as well. In particular, in accordance with the present invention, aerosol formulations or sprays applying medicament in the respiratory systems such as the nasal tract or the lung are also conceivable. The medicament is, preferably, administered in conventional dosage forms prepared by combining the ingredients with standard pharmaceutical carriers according to conventional procedures. These procedures may involve mixing or dissolving the ingredients as appropriate to the desired preparation. Preferably, a solution is envisaged for the medicament. It will be appreciated that the form and character of the pharmaceutical acceptable carrier is dictated by the amount of active ingredient with which it is to be combined, the route of administration and other well-known variables. A carrier must be acceptable in the sense of being compatible with the other ingredients of the formulation and being not deleterious to the recipient thereof. The pharmaceutical carrier employed may include a solid, a gel, or a liquid. Examples for solid carriers are lactose, terra alba, sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, stearic acid and the like. Exemplary of liquid carriers are phosphate buffered saline solution, syrup, oil, water, emulsions, various types of wetting agents, are distilled water, physiological saline, Ringer's solutions, dextrose solution, and Hank's solution, and the like. Similarly, the carrier may include time delay material well known to the art, such as glyceryl mono-stearate or glyceryl distearate alone or with a wax. For polynucleotides or vectors, liposomal carriers or genetically engineered viruses may be considered as well. In particular, if a long-term application of the antibody is envisaged, a genetically engineered virus may be administered that produces the antibody of the invention over a long period within an organism to be treated. Said suitable carriers comprise those mentioned above and others well known in the art, see, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pennsylvania. In addition, the medicament may also include other carriers, adjuvants, or non-toxic, non-therapeutic, non-immunogenic stabilizers and the like. It is to be understood that the formulation of a medicament takes place under GMP standardized conditions or the like in order to ensure quality, pharmaceutical security, and effectiveness of the medicament.
A therapeutically effective dosage of the antibody or polynucleotide of the invention refers to an amount to be used in medicament. A therapeutically effective dosage is an amount of the antibody or polynucleotide that prevents, ameliorates or treats the symptoms accompanying a disease or condition referred to in this specification. Therapeutic efficacy and toxicity of the compound can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio between therapeutic and toxic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50. The dosage regimen will be determined by the attending physician and other clinical factors. As is well known in the medical arts, dosages for any one patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. Progress can be monitored by periodic assessment. The medicament referred to herein is administered at least once in order to treat or ameliorate or prevent a disease or condition recited in this specification. However, the said medicament may be administered more than one time.
The term "treating" as used herein refers to any improvement, cure or amelioration of the disease or condition as referred to herein. It will be understood that treatment may not occur in 100% of the subjects to which the antibody has been administered. The term, however, requires that the treatment occurs in a statistically significant portion of subjects (e.g. a cohort in a cohort study). Whether a portion is statistically significant can be determined without further ado by a person skilled in the art using various well-known statistic evaluation tools, e.g., determination of confidence intervals, p-value determination, Student's t-test, Mann-Whitney-U test etc. Details are found in Dowdy and Wearden, Statistics for Research, John Wiley & Sons, New York 1983. Preferred confidence intervals are at least 90%, at least 95%, at least 97%, at least 98% or at least 99 %. The p-values are, preferably, 0.05, 0.01, 0.005, 0.001, or 0.0001.
The term “preventing” as used herein refers to significantly reducing the likelihood with which the disease or condition develops in a subject within a defined window (prevention window) starting from the administration of the antibody onwards. Typically, the prevention window is within 1 to 5 days, within 1 to 3 weeks, within 1 to 3 months or within 3 to 6 months or 3 to 12 months. However, it will be understood that the preventive window may, dependent on the kind of medicament, also be several years up to the entire life time. The prevention window depends on the amount of antibody, polynucleotide or vector which is administered and the applied dosage regimen. Typically, suitable prevention windows can be determined by the clinician based on the amount of antibody or polynucleotide to be administered and the dosage regimen to be applied without further ado. It will be understood that prevention may not occur in 100% of the subjects to which the antibody has been administered. The term, however, requires that the prevention occurs in a statistically significant portion of subjects (e.g. a cohort in a cohort study). Whether a portion is statistically significant can be determined without further ado by a person skilled in the art using various well-known statistic evaluation tools, e.g., determination of confidence intervals, p-value determination, Student's t-test, Mann-Whitney-U test etc. Details are described elsewhere herein.
The term “disease or condition referred to herein is associated with SARS-CoV-2 infection in a subject” refers to any disease or condition resulting directly or indirectly from an infection by SARS-CoV-2. Preferably, the disease referred to herein is Covid 19. Moreover, the term also encompasses any symptom associated with SARS-CoV-2 infection. Typically, such symptoms may be fever, cough, headache, fatigue, breathing difficulties, loss of smell, and loss of taste, respiratory failure, or multi-organ dysfunction.
The present invention also relates to a composition comprising (i) an antibody as defined herein above and can block at least one of the antibodies belonging to Classi, Class2 and Class3 and hACE2 from binding to WT SARS-CoV-2 RBD and (ii) an antibody as defined herein above and can block at least one of the antibodies belonging to Classi, Class2 and Class3 but not hACE2 from binding to the RBD of WT SARS-CoV-2 RBD for use in treating and/or preventing a disease or condition. The present invention also relates to an antibody as defined herein above in accordance with the present invention for use in diagnosing SARS-CoV-2 infection.
The term “diagnosing” as used herein means assessing whether a subject has been infected by SARS-CoV-2, or not. Alternatively, the term also encompasses determining the virus load of an infected subject, i.e. the amount of virus present in said subject or a sample thereof. As will be understood by those skilled in the art, such an assessment is usually not intended to be correct for 100% of the subjects to be diagnosed. The term, however, requires that the assessment is correct for a statistically significant portion of the subjects (e.g. a cohort in a cohort study). Whether a portion is statistically significant can be determined without further ado by the person skilled in the art using various well known statistic evaluation tools, e.g., determination of confidence intervals, p-value determination, Student's t-test, Mann- Whitney test etc..
The present invention also relates to the use of the antibody of the invention for determining the presence of SARS-CoV-2 in a non-diagnostic sample.
The term “non-diagnostic sample” as used herein refers to any sample from the environment that is not used for the diagnosis of a SARS-CoV-2 infection. Such samples may be samples of gaseous samples such as air or liquid samples. For example, gaseous samples may be investigated for the presence or absence of SARS-CoV-2 when monitoring and evaluating the indoor quality of air, the efficacy of air filtration systems, the quality of gaseous products and the like. Liquid samples may be investigated for the presence or absence of SARS-CoV-2 in order to monitor the distribution of the virus, e.g., by assessing its presence or absence in waste waters, the quality of liquids, the quality of water in the environment or drinking water and the like.
The present invention also relates to a method for diagnosing SARS-CoV-2 infection in a subject suspected to be infected by said SARS-CoV-2 comprising the steps of a) contacting the antibody of the invention with a sample of said subject; and b) determining binding of SARS-CoV-2 to said antibody, whereby the SARS- CoV-2 infection is to be diagnosed.
The term “subject” as used herein relates to animals, preferably mammals, and, more preferably, humans. The subject according to the present invention shall be a subject suffering from or suspected to suffer from SARS-CoV-2 infection. Typically, such a subject shows already symptoms associated with SARS-CoV-2 infection or has been in contact with one or more other subjects known to suffer from SARS-CoV-2 infection and, thus, is at risk of being infected as well.
The term “sample” refers to a sample of a body fluid, to a sample of separated cells or to a sample from a tissue or an organ. Samples of body fluids can be obtained by well-known techniques and include, preferably, samples of blood, plasma, serum, urine, saliva or exhausted air more preferably, samples of blood, plasma or serum. Tissue or organ samples may be obtained from any potentially infected tissue or organ by, e.g., biopsy or surface scratching.
The term “contacting” as referred to herein means that the sample of the subject is brought into physical proximity to the antibody of the invention such that SARS-CoV-2 viruses comprised in the sample may be bound by said antibody. Contacting is typically carried out under conditions and for a time sufficient to allow for specific binding of the antibody to a SARS- CoV-2 virus. The skilled person is well aware of how to choose suitable conditions and how long those conditions shall be applied. Preferred conditions are also described in the accompanying Examples, below.
Upon binding of the antibody to the virus, said binding shall be determined. For determining binding of SARS-CoV-2 to said antibody, various well-known techniques may be used. For example, the formation of a complex between the antibody of the invention and the virus may be determined by a secondary antibody capable of generating a detectable signal upon binding. Alternatively, the virus upon binding to the antibody may release a component from said antibody which upon release generated a detectable signal. The aforementioned principles may be realized by assays that are carried out in solution using beads comprising the antibody or the invention or can be carried out on test stripes that comprise the antibody of the invention in immobilized form. Moreover, the formation of the complex between the antibody and the virus may be determined by measuring differences in physical or chemical properties of the antibody with and without virus bound thereto. Various formats for electrochemical assays are known to the person skilled in the art.
The aforementioned method may be used qualitatively, i.e. an infection will be diagnosed, or quantitatively, i.e. the virus load during an infection will be diagnosed. For the latter case, it will be understood that the determined amount of viruses may be compared to a reference in order to determine the virus load. The present invention also relates to a method for determining SARS-CoV-2 in a nondiagnostic sample comprising the steps of: a) contacting the antibody of the invention with said sample; and b) determining binding of SARS-CoV-2 to said antibody, whereby the presence of SARS-CoV-2 is to be determined.
The term “determining” as used herein refers to determining the presence, absence or amount of SARS-CoV-2 in the non-diagnostic sample. Thus, the term typically encompasses qualitative determination as well as quantitative determination. The skilled artisan is well aware of how quantification of SARS-CoV-2 can be made in the context of a quantitative determination and how suitable calibration measures can be provided.
Yet, the invention relates to a kit for diagnosing SARS-CoV-2 infection in a subject comprising the antibody of the invention and detection reagents for determining binding of SARS-CoV-2 to said antibody.
The term “kit” as used herein refers to a collection of components as referred to before required for diagnosing SARS-CoV-2 infection in a subject. Typically, the components of the kit are provided in separate containers or within a single container. The kit shall in addition to the antibody of the invention also comprise detection reagents for binding of SARS-CoV-2 to said antibody. These reagents may include components that may generate a detectable signal upon binding of the antibody of the invention to the SARS-CoV-2. Moreover, such reagents may encompass any washing or buffer solutions required for determining binding. The container also typically comprises instructions for diagnosing SARS-CoV-2 infection in a subject. These instructions may be in the form of a manual or may be provided by a computer program code.
Finally, the invention relates to a kit for determining SARS-CoV-2 in a non-diagnostic sample comprising the antibody of the invention and detection reagents for determining binding of SARS-CoV-2 to said antibody.
The following are particular preferred embodiments of the present invention.
Embodiment 1 : An antibody which specifically binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10'9 M. Embodiment 2: The antibody of embodiment 1, wherein said antibody neutralizes SARS-CoV-
2 in vitro with IC50 of at most 1.0 pg/ml, at most 0.1 pg/ml or at most 0.01 pg/ml.
Embodiment 3: The antibody of embodiment 1 to 2, wherein said SARS-CoV-2 is selected from the group consisting of wildtype (WT) SARS-CoV-2, SARS-CoV-2 alpha variant (B.1.1.7), SARA-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2), and SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants.
Embodiment 4: The antibody of any one of embodiments 1 to 3, wherein the said antibody can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2.
Embodiment 5: The antibody of any one of embodiments 1 to 4, wherein said antibody comprises at least one heavy chain CDR said heavy chain CDR being
(I) a heavy chain CDR1 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 1, 16 to 23 and 24 to 30;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 16 to 23 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1, 24 to 30 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(II) a heavy chain CDR2 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 2, 3, 31 to 38 and 39 to 47;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 2 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 3 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 31 to 38 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 39 to 47 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; or
(III) a heavy chain CDR3 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 4, 5, 48 to 55 and 56 to 65;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 4 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 5 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 48 to 55 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 56 to 65 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant. Embodiment 6: The antibody of any one of embodiments 1 to 5, wherein said antibody comprises at least one light chain CDR, said light chain CDR being
(I) a light chain CDR1 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 6, 7, 66 to 71 and 72 to 80;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 6 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 RBD and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 7 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 RBD and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 66 to 71 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 69, 72 to 80 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(II) a light chain CDR2 having an amino acid sequence selected from the group consisting of: (a) an amino acid sequence as shown in any one of SEQ ID NOs: 8, 9, 81 to 83 and 84 to 88;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 8 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 9 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 9, 81 to 83 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 82, 84 to 88 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; or
(III) a light chain CDR3 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 10, 11, 89 to 96 and 97 to 105;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 10 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 11 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 89 to 96 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 97 to 105 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
Embodiment 7: The antibody of any one of embodiments 1 to 6, wherein said antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 12, 13, 106 to 123;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 12 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 13 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 106 to 113 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 114 to 123 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
Embodiment 8: The antibody of any one of embodiments 1 to 7, wherein said antibody comprises a light chain having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 14, 15, 124 to 141;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
14 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
15 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 124 to 131 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 132 to 141 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant.
Embodiment 9: A polynucleotide encoding the antibody of any one of embodiments 1 to 8.
Embodiment 10: The polynucleotide of embodiment 9, wherein said polynucleotide is RNA or DNA.
Embodiment 11 : A vector or expression construct comprising the polynucleotide of embodiment 9 or 10.
Embodiment 12: A host cell comprising the polynucleotide of embodiment 9 or 10 or the vector or expression construct of embodiment 11.
Embodiment 13: The host cell of claim 12, wherein said host cell is a bacterial cell, a fungal cell, an animal cell or a plant cell.
Embodiment 14: A non-human transgenic organism comprising the polynucleotide of embodiment 9 or 10 or the vector or expression construct of embodiment 11.
Embodiment 15: The non-human transgenic organism of embodiment 14, wherein said organism is an animal or a plant.
Embodiment 16: A method for producing the antibody of any one of embodiments 1 to 8 comprising (i) expressing the polynucleotide of embodiment 9 or 10 or the vector of embodiment 11 in a host cell and (ii) obtaining the said antibody from said host cell.
Embodiment 17: Use of the host cell of embodiment 12 or 13 for producing the antibody of any one of embodiments 1 to 8. Embodiment 18: An antibody as defined in any one of embodiments 1 to 8, a polynucleotide as defined in embodiment 9 or 10 or a vector as defined in embodiment 11 for use in treating and/or preventing a disease or condition.
Embodiment 19: The antibody, polynucleotide or vector of embodiment 18, wherein said disease or condition is associated with SARS-CoV-2 infection in a subject.
Embodiment 20: A composition comprising (i) an antibody as defined in any one of embodiments 1 to 8 and can block at least one antibody belonging to Classi, Class2 or Class3 and hACE2 from binding to WT SARS-CoV-2 RBD and (ii) an antibody as defined in any one of embodiments 1 to 8 and can block at least one antibody belonging to Classi, Class2 or Class3 but not hACE2 from binding to the RBD of WT SARS-CoV-2 RBD for use in treating and/or preventing a disease or condition.
Embodiment 21 : The antibody, polynucleotide or vector of embodiment 20, wherein said disease or condition is associated with SARS-CoV-2 infection in a subject.
Embodiment 22: An antibody as defined in any one of embodiments 1 to 8 for use in diagnosing SARS-CoV-2 infection.
Embodiment 23: Use of an antibody as defined in any one of embodiments 1 to 8 for determining SARS-CoV-2 in a non-diagnostic sample.
Embodiment 24: A method for diagnosing SARS-CoV-2 infection in a subject suspected to be infected by said SARS-CoV-2 comprising the steps of: a) contacting the antibody of any one of embodiments 1 to 8 with a sample of said subject; and b) determining binding of SARS-CoV-2 to said antibody, whereby the S ARS-CoV- 2 infection is to be diagnosed.
Embodiment 25: A method for determining SARS-CoV-2 in a non-diagnostic sample comprising the steps of: a) contacting the antibody of any one of embodiments 1 to 8 with said sample; and b) determining binding of SARS-CoV-2 to said antibody, whereby the SARS- CoV-2 is to be determined. Embodiment 26: A kit for diagnosing SARS-CoV-2 infection in a subject comprising the antibody of any one of embodiments 1 to 8 and detection reagents for determining binding of SARS-CoV-2 to said antibody.
Embodiment 27: A kit for determining SARS-CoV-2 in a non-diagnostic sample comprising the antibody of any one of embodiments 1 to 8 and detection reagents for determining binding of SARS-CoV-2 to said antibody.
All references cited throughout this specification are herewith incorporated by reference in their entirety as well as with respect to the specifically mentioned disclosure content.
FIGURES
Figure 1: Antibody binding to spike protein and RBD detected in ELISA. Binding of reactive antibodies to spike and RBD is comparable to positive controls. Area under the binding curve (AUC) was calculated for each antibody. Out of 263 mAbs, 113 showed binding to spike protein and/or RBD based on our cut-off AUC. A) Spike, B) RBD, C) AUC Spike, D) AUC RBD.
Figure 2: Majority of spike binding antibodies (58%) target RBD while a considerable proportion (29%) of antibodies target epitopes in Spike other than RBD.13% of antibodies with weak binding to RBD may recognize hidden (inaccessible) epitopes of the trimeric spike protein.
Figure 3: Antibodies with high affinity to RBD can be identified. RBD reactive antibodies show a range of affinities (10‘5 M to IO'10 M). Affinity measurement using the same method allowed for a direct comparison to the published antibodies including antibodies in clinical use. Antibodies with comparable affinity (10‘7 - 10'9 M) to or even higher affinity (< 10'9 M) than the published antibodies were identified.
Figure 4: RBD binding antibodies show efficient in vitro SARS-CoV-2 neutralization. mAbs that bind to the epitopes in spike protein other than RBD do not show virus neutralization. The majority of RBD-binding antibodies show, however, no neutralizing capacity. 19% of RBD- binding antibodies show various degree of virus neutralization (IC50 < 1.0 ug/ml). Figure 5: High antibody affinity critical but not sufficient for virus neutralization. Virusneutralizing antibodies show affinities of 10'7 M or lower (IC50 < 1.0 ug/ml). 27% and 23% of antibodies with affinity less 10'7 M and 10'9 M, respectively, show virus neutralization. The majority of high affinity anti-RBD antibodies do not neutralize virus and therefore target nonneutralizing epitopes. The potency of the antibodies depends on their affinity (the higher the better) and epitope specificity. The data demonstrate that high affinity alone is not enough.
Figure 6: Antibodies with distinct binding profiles were identified. Antibodies found in the present studies (mAbl) are compared to known antibodies (mAb2).
Figure 7: Distribution of the antibodies found in the present studies to different classes. High affine antibodies are often enriched in Classl/2, S309 or none (not yet defined). High affinity is often associated with low kinetic off rate - sign of efficient selection in the germinal center driven B cell response. Rare class antibody with high affinity such as Class2/3 has high kinetic on rate and good off rate.
Figure 8: Antibodies with distinct binding profile differ in blocking hACE2 binding to RBD. Majority of Classl/2, 1/2/3, 1/3, 1/3/4, 1/4 antibodies block hACE2 binding to WT RBD, suggesting their epitope overlaps with the hACE2 interaction site in RBD. Antibodies belonging to Classi, 4, S309 and none class do not block hACE2 binding to WT RBD, suggesting they do not bind to receptor binding motif (RBM) in RBD.
Figure 9: Virus neutralization limited to antibodies with a few distinct binding profiles. High affine antibodies in Classl/2, Classl/2/3 and Class2/3 show efficient virus neutralization - protective epitopes. High affinity in antibodies with other binding profiles such as S309 and none classes does not result in virus neutralization - non-protective epitopes
Figure 10: Neutralizing antibodies may or may not block hACE2 binding to RBD. Using SPR, hACE2 interaction with RBD upon binding to mAbl was measured. All Classl/2 mAbs block hACE2 interaction with RBD, while Class2/3 mAb does not. This suggests Classl/2 and Class2/3 antibodies neutralize virus by binding to different epitopes.
Figure 11: Some of Classl/2 and Class2/3 antibodies have non-overlapping epitopes in RBD. Three Classl/2 antibodies and one Class2/3 antibody were tested against each other to block binding to RBD. Two of three Classl/2 antibodies did not block Class2/3 antibody from binding to RBD. Classl/2/3 mAb (2939) blocks Class2/3 (3279) but not Classl/2 (1255) mAbs from binding to RBD. Figure 12: Antibodies with non-overlapping epitopes show synergy in virus neutralization. High affinity binding to non-overlapping epitopes by mAbs 3279 and 1255 translates into more efficient virus neutralization when used in cocktail compared to on their own. Starting concentration was 10 pg/ml for all mABs.
Figure 13: High affine antibodies show broad VoC virus neutralization. High affine antibodies belonging to Classl/2 and Class2/3 show high neutralization capacity against three Variants of Concern (VoCs) tested. High affine antibodies with S309 profile show specific neutralization against alpha variant but not against WT or other variants.
Figure 14: General trend in loss of antibody affinity to Omicron variant RBD. Only three control mAbs (S309, REGN10933 and CR3022) have measurable binding to Omicron RBD, while the rest lost binding completely. mAbs from this study show increased, similar, decreased or complete loss in affinity to Omicron RBD compared to WT RBD.
Figure 15: Non-neutralizing antibody classes retain high affinity to Omicron RBD. High affinity in antibodies with binding profiles such as S309 does not result in WT virus neutralization. Majority of the mAbs belonging to the non-neutralizing antibody classes bind to Omicron RBD with similar or higher affinity in comparison to WT RBD.
Figure 16: Neutralizing antibody classes bind to Omicron RBD with reduced affinity. High affine antibodies in Classl/2, Classl/2/3 and Class2/3 show efficient WT virus neutralization. Majority of the mAbs belonging to the three classes bind to Omicron RBD with reduced affinity in comparison to WT RBD. mAbs 1255 in Classl/2 and 2939 in Classl/2/3 retain higher binding to Omicron RBD compared to other antibodies of the respective classes.
Figure 17: Two high affine mAbs bind to Omicron RBD without blocking each other. High affine antibodies (1255 and 2939) can both bind to WT and Omicron RBD without blocking each other - suggesting they bind non-overlapping epitopes.
Figure 18: Two high affine mAbs differ in blocking hACE2 binding to Omicron RBD. 1255 blocks whereas 2939 does not block hACE2 interaction with both WT and Omicron RBD, indicating the difference in their binding site overlap with hACE2 interaction site.
Figure 19: mAbs from this study compared to currently used antibodies in clinics. Figure 20: 2939 and 1255 show high Omicron variant neutralization capacity. mAh 2939 show better Omicron neutralization than therapeutically used mAh S309 - VIR Biotechnology (Sotrovimab). Given antibodies were mixed with defined amounts of SARS-CoV-2 virus particles and after 30 minutes, the mixture was added to VeroE6 cells. After 24 hours, SARS- CoV-2 replication in the inoculated cells was measured by fixing the cells and immunostaining of the viral nucleocapsid protein. By testing 10 serial dilutions of the antibody solution, dosedependent neutralization capacity, expressed as IC50 value, was calculated by non-linear regression sigmoidal dose response analysis using the GraphPad Prism 7 software package.
Figure 21: Virus neutralizing capacity may differ between variants. mAbs that do not neutralize WT virus show weak neutralizing capacity of the Omicron variant. Inhibition values of these mAbs (IC50 values) are still lower than those of antibodies 1255 and 2939.
Figure 22: Virus neutralization using mAb S309; upper curve omicron, middle curve delta, lower curve WT (strain H2P4, Steuten 2021).
EXAMPLES
The invention will be illustrated by the following Examples. The Examples shall not be construed as limiting the scope of the invention.
Example 1: Isolation of anti-RBD antibodies
Plasmids encoding His-tagged versions of full length spike protein and RBD were kindly provided by Florian Krammer (Amanat et al., 2020 Nat Med 26, 1033-1036). Spike and RBD proteins were recombinantly expressed in HEK293F cells (Thermo Fischer Scientific) and purified using affinity column chromatography. Using commercially available kits, RBD was biotinylated and spike was labelled with A647 and both proteins were used as baits to detect antigen reactive memory B cells in FACS. PBMCs from hospitalized patients and convalescent donors were incubated with 0.125 ug/ml of biotinylated RBD and 0.5 ug/ml of spike_A647 along with the following mouse anti-human antibodies at the noted dilutions: CD19-Brilliant Violet 786 (BV786) (SJ25C1) at 1: 10, CD27-phycoerythrin (M-T271) at 1:5, IgG- BV510(G18-145) at 1 :20, CD138-BV421 (MI15) at 1 :20, IgD-allophycocyanin (APC)-H7 (IA6-2) at 1 :20 and CD38-BV605 (HB7) at 1 :20. Upon 30 min incubation on ice, the cells were washed and stained with Streptavidin- fluorescein isothiocyanate (FITC) at 1 : 1000 and 7- Aminoactinomycin D (7AAD) (Invitrogen) at 1 :400. Memory B cells (7AAD-CD19+CD27+ B cells) positive for binding to at least one of the baits were single cell sorted using FACSAria III (BD Biosciences) with FACSDiva software enabled for index sorting option.
Ig genes from single B cells were amplified as matrix PCR approach as previously described (Murugan et al., 2015 Eur J Immunol. 45(9):2698-700). In brief, reverse transcription was performed using random hexamers and the resulting complementary DNA was used as template to amplify IGH, IGK and IGL genes with barcoded primer matrix in the second PCR. Pooled and purified amplicons were ligated with adaptors and sequenced using Illumina MiSeq 2x300 bp paired end sequencing. The sequence reads were further analyzed using sciReptor to obtain and integrate Ig gene information of heavy and light genes with flow cytometry index data (Imkeller et al., 2016 BMC Bioinformatics 17, 67). Single cells with paired and functional Ig genes on both loci were used for analysis.
Antibodies of different isotypes with preference for IgG, encoded by germline and somatically mutated Ig genes were selected for cloning and recombinant expression as described previously (Tiller et al., 2008, J Immunol Methods. 329(1-2): 112-124). In brief, Ig gene specific primers tagged with restriction enzyme binding sites were used to amplify heavy and light chain genes and clone them into the corresponding expression vectors (IgG, Igk and IgA). Vectors containing successfully cloned heavy and light genes were cotransfected into HEK293F cells (Thermo Fischer Scientific) and recombinant monoclonal antibodies were expressed.
Example 2: Characterization of anti-RBD antibodies
Antibody binding to spike protein and recombinant RBD fragments was investigated by ELISA. High binding 384-well plates were coated with 2 ng/ pl spike protein or 4 ng/ pl RBD in PBS. 25 pl/ well of the respective solution was added and incubated over night at 4 °C. The next day, ELISA plates were washed thrice with 0.05 % Tween in PBS (PBS-T) using the Tecan plate washer and blocked with 1 % BSA in PBS for 1 h at RT. Four dilutions of each antibody supernatant in PBS were prepared in a 1 :4 serial dilution with an initial concentration of 4 pg/ ml. PBS and the monoclonal antibody mGO53 were used as negative control while the monoclonal antibodies CR3022 and S309 were used as positive controls. After blocking, ELISA plates were washed three times with PBS-T and samples were loaded onto the plates. 15 pl/ well of diluted antibodies was added to the plates and incubated for 2 h at RT. ELISA plates were washed thrice with PBS-T. HRP-conjugated anti-human IgG-Fcy (Jackson ImmunoResearch) was diluted 1 : 1000 in blocking buffer, loaded onto the ELISA plate (15 pl/ well) and incubated for 1 h at RT. After washing the plate three times with PBS-T, ELIS As were developed using 20 pl/ well of 1 : 1000 dilution H2O2 in ABTS solution. Absorbance was measured at 405 nm every 2 min in a total of 20 min using Tecan MIOOOPro plate reader. Reactivity of the antibodies was assessed by calculating the area under the curve (AUC) of the absorbance measured of the four dilutions using GraphPad Prism 8.
It was found that binding of reactive antibodies to spike and RBD is comparable to positive controls. The area under the binding curve (AUC) was calculated for each investigated antibody. Out of 263 mAbs, 113 showed binding to spike protein and/or RBD based on our cutoff (AUC>3); see Fig. 1 and 2.
Moreover, affinity to RBD was further investigated by Surface Plasmon Resonance (SPR) measurements. Briefly, SPR based assay was performed to determine affinity of RBD-binding antibodies using Biacore T200 system and Biacore sensor chip CM5. Two flow cells were immobilized with anti-human Fab antibodies using human Fab capture kit by following manufacturer’s instructions. Antibody samples (40 pg/ ml) as well as the negative control mGO53 (40 pg/ ml) were captured in the sample and reference flow cells, respectively. Stabilization of both flow cells was performed by SPR running buffer at 10 pl/ min flow rate for 10 min. A serial dilution of RBD was performed in SPR running buffer and the following concentrations were injected into both the flow cells: 0 nM, 12.4 nM, 37.0 nM, 111.1 nM, 333.3 nM and 1000 nM using a flow rate of 30 pl/ min. Dissociation and association took place at 25 °C for 60 s and 180 s, respectively. Between the injections of different sample antibodies, flow cells were regenerated using 10 mM glycine in HC1. Data was analyzed using a 1 : 1 binding model or steady-state kinetic analysis using Biacore T200 software V2.0.
Results are shown in Fig. 3. RBD reactive antibodies showed broad range of affinity to RBD (10‘5 M to IO'10 M). Affinity measurement using the same method allowed for a direct comparison to the published antibodies including antibodies in clinical use. Antibodies with comparable affinity (10‘7 - 10'9 M) to or even higher affinity (< 10'9 M) than the published antibodies were identified.
Example 3: Virus neutralization by antibodies
Neutralization titers were determined in titration experiments using VeroE6 cells. Virus stocks were produced by isolation and amplification of the SARS-CoV-2 WT (isolate H2P4, Steuten 2021), the B.l.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta) and the B.1.1.529.1 (omicron) variant from nasopharyngeal and oropharyngeal swabs of PCR-confirmed SARS-CoV-2 positive patients (Benning et al., 2021 Clin J Am Soc Nephro 17 (1) 98-106; Mallm et al., 2021, medRxiv). SARS-CoV-2 WT, B. l.1.7 (alpha), B.1.351 (beta) and B.1.617.2 (delta) variant were amplified in VeroE6 cells and virus titers of stocks were determined by plaque assay and Tissue Culture Infectious Dose (TCID) 50 assay in VeroE6 cells. To avoid rapid cell culture adaptation, stocks of the B.1.1.5291 (omicron) variant were produced in Calu-3 cells and titers were determined in VeroE6 cells using TCID 50 assay. For neutralization assays, monoclonal antibodies were diluted 1 :3 for 10 steps with a test range from 0.5 ng/ml to 10 pg/ml and were incubated with 6xl04 TCID 50 of SARS-CoV-2 WT, B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta) and the B.1.1.529.1 (omicron) variant. After 1 h at 37 °C, the mixture was added to VeroE6 cells and cells were fixed in the plates with 5% formaldehyde 24 h later. Virus replication was determined by immunostaining for the viral nucleocapsid protein using an incell ELISA. S309 and mGO53 were used as positive and negative controls, respectively. Data were normalized to a mock-infected (0%) and a no-serum control (100%). The inhibitory concentration 50 (IC50) is defined by non-linear regression sigmoidal dose response analysis using the GraphPad Prism 7 software package
Virus neutralization was observed only among the antibodies that bound to the RBD, but not to the other epitopes in spike. Antibodies with better neutralizing capacity compared to the published antibodies were identified. Indeed, the virus neutralizing capacity was observed only among antibodies with high affinity. (RBD Kd < 10-7 M). Nevertheless, only 27% and 23% of antibodies with RBD Kd < 10-7M and RBD Kd < 10-9M, respectively, neutralized the virus. This suggests the potency of antibodies depends on both epitope specificity and high affinity. Refer to Fig. 4 and 5.
Example 4: Antibody binding region in RBD elucidated by a blocking assay using published antibodies with known epitopes and hACE2
Based on the epitopes recognized in RBD, antibodies are grouped into different classes. Antibodies of the same class do not necessarily target the same epitope or bind in the same mode. The class categories are not absolute, i.e. antibodies can belong to more than one class depending on the exact target epitope. In order to identify the potential epitope and class of the antibodies from this study, an assay was developed to measure their capacity in blocking previously reported antibodies with known epitopes/classes from binding to RBD.
Blocking assay was performed using Biacore T200 system and Biacore sensor chip CM5. A flow cell was immobilized with anti-human IgG antibodies using human antibody capture kit by following manufacturer’s instructions. Sample antibody (mAbl) was captured in the flow cell at 20 pg/ml, followed by the capture mGO53 at 100 pg/ml. Stabilization of the flow cell was performed by SPR running buffer at 10 pl/ min flow rate for 5 min. To measure binding, injection ofRBD at 1 pM was immediately followed by an injection of 20 pg/ml mAb2 using dual injection option. Binding values were calculated by measuring the difference in response units before and after the injection of mAb2 and subtracting the background binding as measured by performing the same steps while injecting the running buffer instead ofRBD. Between the injections of different sample antibodies, flow cell was regenerated using 3 M MgC12. Data was analyzed using using Biacore T200 software V2.0.
Results for blocking capabilities viz-a-viz known SARS-CoV-2 antibodies are shown in Fig. 6 and 7. Antibodies belonging to Classl/2, Class4, S309 and none classes showed high affinity due to reduced kinetic off rate, suggesting they are selected efficiently in the germinal center driven B cell response.
Blocking of binding to hACE2 was also investigated. Blocking assay was performed using Biacore T200 system and Biacore sensor chip CM5. A flow cell was immobilized with antihuman IgG antibodies using human antibody capture kit by following manufacturer’s instructions. Sample antibody (mAbl) was captured in the flow cell at 20 pg/ml, followed by stabilization of the flow cell by SPR running buffer at 10 pl/ min flow rate for 5 min. To measure binding, injection ofRBD at 1 pM was immediately followed by an injection of 200 nM hACE2 using dual injection option. Binding values were calculated by measuring the difference in response units before and after the injection of hACE2 and subtracting the background binding as measured by performing the same steps while injecting the running buffer instead ofRBD. Between the injections of different sample antibodies, flow cell was regenerated using 3 M MgC12. Data was analyzed using using Biacore T200 software V2.0.
Results are shown in Fig. 8. The majority of Classl/2, 1/2/3, 1/3, 1/3/4, 1/4 antibodies block hACE2 binding to WT RBD, suggesting their epitope overlaps with the hACE2 interaction site in RBD. Antibodies belonging to Classi, 4, S309 and none class do not block hACE2 binding to WT RBD, suggesting they do not bind to receptor binding motif (RBM) in RBD. Fig. 9 shows that high affine antibodies in Classl/2, Classl/2/3 and Class2/3 show efficient virus neutralization (protective epitopes). However, high affinity in antibodies with other binding profiles such as S309 and none classes does not result in virus neutralization (non-protective epitopes). Using SPR, hACE2 interaction with RBD upon binding to mAbl was measured. All Classl/2 mAbs block hACE2 interaction with RBD, while Class2/3 mAb does not.
This suggests Classl/2 and Class2/3 antibodies neutralize virus by binding to different, nonoverlapping epitopes (Fig. 10). Three Classl/2 antibodies and one Class2/3 antibody were tested against each other to block binding to RBD. Two of three Classl/2 antibodies did not block Class2/3 antibody from binding to RBD. Classl/2/3 mAb (2939) blocks Class2/3 (3279) but not Classl/2 (1255) mAbs from binding to RBD (Fig. 11). Antibodies with non-overlapping epitopes show synergy in virus neutralization, e.g., high affinity binding to non-overlapping epitopes by mAbs 3279 and 1255 translates into more efficient virus neutralization when used in cocktail compared to on their own (Fig. 12). Moreover, high affine antibodies belonging to Classl/2 and Class2/3 show high neutralization capacity against three Variants of Concern (VoCs) tested. High affine antibodies with S309 profile show specific neutralization against alpha variant but not against WT or other variants (Fig. 13).
Example 5: Antibody binding and activity against the SARS-CoV-2 omicron variant
Among all VoCs, Omicron RBD has a particular high number of mutations (15 aa) compared to the WT RBD. Affinity for SARS-CoV-2 omicron variant was investigated next. SPR based assay was performed to determine affinity of RBD-binding antibodies using Biacore T200 system and Biacore sensor chip CM5. Two flow cells were immobilized with anti-human Fab antibodies using human Fab capture kit by following manufacturer’s instructions. Antibody samples (40 pg/ ml) as well as the negative control mGO53 (40 pg/ ml) were captured in the sample and reference flow cells, respectively. Stabilization of both flow cells was performed by SPR running buffer at 10 pl/ min flow rate for 10 min. A serial dilution of Omicron RBD was performed in SPR running buffer and the following concentrations were injected into both the flow cells: 0 nM, 12.4 nM, 37.0 nM, 111.1 nM, 333.3 nM and 1000 nM using a flow rate of 30 pl/ min. High affine antibodies were independently tested at 0 nM, 3 nM, 9.2 nM, 27.7 nM, 83.3 nM and 250 nM of Omicron RBD. Dissociation and association took place at 25 °C for 60 s and 180 s, respectively. Between the injections of different sample antibodies, flow cells were regenerated using 10 mM glycine in HC1. Data was analyzed using a 1 : 1 binding model or steady-state kinetic analysis using Biacore T200 software V2.0.
Only three control mAbs (S309, REGN10933 and CR3022) have measurable binding to Omicron RBD, while the rest lost binding completely. mAbs from this study show increased, similar, decreased or complete loss in affinity to Omicron RBD compared to WT RBD (Fig. 14). High affinity in antibodies with binding profiles such as S309 does not result in WT virus neutralization. However, the majority of the mAbs belonging to the non-neutralizing antibody classes bind to Omicron RBD with similar or higher affinity in comparison to WT RBD. High affine antibodies in Classl/2, Classl/2/3 and Class2/3 show efficient WT virus neutralization. The majority of the mAbs belonging to the three classes bind to Omicron RBD with reduced affinity in comparison to WT RBD (Fig. 15/16). mAbs 1255 in Classl/2 and 2939 in Classl/2/3 retain higher binding to Omicron RBD compared to other antibodies of the respective classes. High affine antibodies (1255 and 2939) can both bind to WT and Omicron RBD without blocking each other - suggesting they bind non-overlapping epitopes (Fig. 17). It was further found that 1255 blocks whereas 2939 does not block hACE2 interaction with both WT and Omicron RBD, indicating the difference in their binding site overlap with hACE2 interaction site (Fig. 18). Antibodies 2939 and 1255 show high Omicron variant neutralization capacity. Moreover, mAb 2939 show better Omicron neutralization than therapeutically used mAb S309 - VIR Biotechnology (Sotrovimab) (Fig. 19 and 20).
In general, mAbs that do not neutralize WT virus show weak neutralizing capacity to Omicron variant virus. Inhibition values of these mAbs are still lower than 1255 and 2939 - suggesting the epitopes targeted by 1255 and 2939 are promising for protective vaccine responses (Fig. 21). Classl/2 (1255) and Class2/3 (3279) antibodies show broad neutralization and could be considered for therapeutic purposes or diagnostic purposes.
Example 6: Neutralization of SARS-CoV-2 variants
Capacity of antibodies to neutralize SARS-CoV-2 variant strains was tested by determining EC50 values for viral infection essentially as in Example 3 herein above. Results are summarized in Table 6 below.
Table 6: EC50 values (in pg/ml) of selected antibodies for SARS-CoV-2 variants; NC: not calculated.
Figure imgf000058_0001
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Claims

Claims An antibody which specifically binds to the receptor binding domain (RBD) of S ARS- CoV-2 spike protein with an equilibrium dissociation constant (Kd) of less than 10'9 M. The antibody of claim 1, wherein said antibody neutralizes SARS-CoV-2 in vitro with IC50 of at most 1.0 pg/ml, at most 0.1 pg/ml or at most 0.01 pg/ml. The antibody of claim 1 to 2, wherein said SARS-CoV-2 is selected from the group consisting of wildtype (WT) SARS-CoV-2, SARS-CoV-2 alpha variant (B.l.1.7), SARA-CoV-2 beta variant (B.1.1351) SARS-CoV-2 delta variant (B.1.617.2), and SARS-CoV-2 omicron variant (B.1.1.529) including its sub-variants. The antibody of any one of claims 1 to 3, wherein the said antibody can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2. The antibody of any one of claims 1 to 4, wherein said antibody comprises at least one heavy chain CDR said heavy chain CDR being
(I) a heavy chain CDR1 having an amino acid sequence selected from the group consisting of
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 1, 16 to 23 and 24 to 30;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant; (d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 16 to 23 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 1, 24 to 30 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(II) a heavy chain CDR2 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 2, 3, 31 to 38 and 39 to 47;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 2 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 3 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 31 to 38 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 39 to 47 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; or
(III) a heavy chain CDR3 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 4, 5, 48 to 55 and 56 to 65;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 4 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 5 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 48 to 55 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 56 to 65 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant. The antibody of any one of claims 1 to 5, wherein said antibody comprises at least one light chain CDR, said light chain CDR being
(I) a light chain CDR1 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 6, 7, 66 to 71 and 72 to 80;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 6 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 RBD and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 7 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 RBD and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 66 to 71 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 69, 72 to 80 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(II) a light chain CDR2 having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 8, 9, 81 to 83 and 84 to 88;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 8 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 9 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 9, 81 to 83 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 82, 84 to 88 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; or
(III) a light chain CDR3 having an amino acid sequence selected from the group consisting of: (a) an amino acid sequence as shown in any one of SEQ ID NOs: 10, 11, 89 to 96 and 97 to 105;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 10 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 11 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS- CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 89 to 96 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 97 to 105 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant. The antibody of any one of claims 1 to 6, wherein said antibody comprises a heavy chain having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 12, 13, 106 to 123;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO: 12 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
13 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 106 to 113 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 114 to 123 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant. The antibody of any one of claims 1 to 7, wherein said antibody comprises a light chain having an amino acid sequence selected from the group consisting of:
(a) an amino acid sequence as shown in any one of SEQ ID NOs: 14, 15 124 to 141;
(b) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
14 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant;
(c) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NO:
15 and wherein said antibody, preferably, can block at least one antibody belonging to Classi, Class2 or Class3 from binding to the RBD of WT-SARS- CoV-2 and/or wherein said antibody, preferably, blocks hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; (d) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 124 to 131 and wherein said antibody, preferably, can block at least one antibody belonging to Class3 from binding to the RBD of WT SARS-CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant; and
(e) an amino acid sequence which differs by at least one amino acid exchange, deletion and/or addition from the sequence as shown in any one of SEQ ID NOs: 132 to 141 and wherein said antibody, preferably, does not block any antibody belonging to any one of Classes 1 to 4 from binding to the RBD of WT SARS- CoV-2 and/or wherein said antibody, preferably, does not block hACE2 interaction with WT SARS-CoV-2 and SARS-CoV-2 omicron variant. A polynucleotide encoding the antibody of any one of claims 1 to 8. A vector or expression construct comprising the polynucleotide of claim 9. A host cell comprising the polynucleotide of claim 9 or the vector or expression construct of claim 10. A non-human transgenic organism comprising the polynucleotide of claim 9 or the vector or expression construct of claim 10. A method for producing the antibody of any one of claims 1 to 8 comprising (i) expressing the polynucleotide of claim 9 or the vector of claim 10 in a host cell and (ii) obtaining the said antibody from said host cell. An antibody as defined in any one of claims 1 to 8, a polynucleotide as defined in claim 9 or a vector as defined in claim 10 for use in treating and/or preventing a disease or condition, wherein said disease or condition is, preferably, associated with SARS-CoV- 2 infection in a subject. A composition comprising (i) an antibody as defined in any one of claims 1 to 8 and can block at least one antibody belonging to Classi, Class2 or Class3 and hACE2 from binding to WT SARS-CoV-2 RBD and (ii) an antibody as defined in any one of claims 1 to 8 and can block at least one antibody belonging to Classi, Class2 or Class3 but not hACE2 from binding to the RBD of WT SARS-CoV-2 RBD for use in treating and/or preventing a disease or condition, wherein said disease or condition is, preferably, associated with SARS-CoV-2 infection in a subject. An antibody as defined in any one of claims 1 to 8 for use in diagnosing SARS-CoV-2 infection. A method for diagnosing SARS-CoV-2 infection in a subject suspected to be infected by said SARS-CoV-2 comprising the steps of: a) contacting the antibody of any one of claims 1 to 8 with a sample of said subject; and b) determining binding of SARS-CoV-2 to said antibody, whereby the SARS- CoV-2 infection is to be diagnosed. A kit for diagnosing SARS-CoV-2 infection in a subject comprising the antibody of any one of claims 1 to 8 and detection reagents for determining binding of SARS-CoV-2 to said antibody.
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