# Patent

## Title
Immunoassay for SARS-CoV-2 neutralizing antibodies and materials therefor

## Abstract

The present invention relates to the development of novel immunoassays for the detection of neutralizing antibodies and/or high avidity neutralizing antibodies to SARS-CoV-2 spike protein variants or fragments thereof and, optionally, one or more cytokine in patient samples. Novel multiplex and singleplex immunoassays for the detection of neutralizing antibodies and/or high avidity neutralizing antibodies to SARS-CoV-2 spike protein variants or fragments thereof and, optionally, one or more cytokine in patient samples are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application Ser. No. 63/053,888, filed Jul. 20, 2020, Ser. No. 63/088,195, filed Oct. 6, 2020 and Ser. No. 63/114,685, filed Nov. 17, 2020, the disclosures of which are hereby incorporated by reference in their entirety, including all figures, tables and amino acid or nucleic acid sequences.


The Sequence Listing for this application is labeled “Seq-List.txt” which was created on Jul. 15, 2021 and is 41 KB. The entire content of the sequence listing is incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
SARS-CoV-2, a coronavirus, is the causative viral agent of the disease COVID-19 which is a highly infectious human respiratory infection that threatens global public health. As of July 2020 this virus was known to have infected at least 10.2 million people worldwide with at least 502,000 known deaths.
Coronavirus (CoV) is an enveloped virus that contains a single-stranded positive-sense RNA. SARS-CoV-2, formerly known as 2019-nCoV, is a newly emerging coronavirus that mainly affects the respiratory tract that can lead to Severe Acute Respiratory Syndrome (SARS). The underlying disease caused by this virus is named COVID-19. Coronaviruses have been responsible for several outbreaks in the world during the two last decades. In 2003 and 2014, coronaviruses caused outbreaks mainly in Asia (SARS-CoV) and in the Middle East (MERS-CoV), respectively. Before the emergence of the new SARS-CoV-2, six coronaviruses were known to affect humans (SARS-CoV, MERS-CoV and four other coronaviruses that cause mild upper and lower respiratory syndromes).
SARS-CoV-2 was first identified in December 2019, in Wuhan City, Hubei Province, China, after several patients developed severe pneumonia similar to that caused by SARS-CoV. The virus has since rapidly spread around the globe and in March 2020, WHO officially announced COVID-19 as a pandemic. Person to-person transmission of the virus resulted in quick spreading of COVID-19 and the high number of patients requiring intensive care resulted in the establishment of containment measures. Individuals infected with COVID-19 exhibit disease symptoms about 2 to 14 days after infection.
The virus has been detected in respiratory secretions, which are considered as the primary means of transmission. Once viral particles enter the respiratory tract, the virus attaches to pulmonary cells via the ACE-2 receptors and are then endocytosed. SARS-CoV-2 can also be transmitted via the fecal route.
Patients positive for SARS-CoV-2 and that are symptomatic are diagnosed with COVID-19. Symptoms can vary drastically and notably include fever, dry cough, anosmia, sputum production, headaches, dyspnea, fatigue, nausea, and diarrhea. While some cases can be asymptomatic, others can lead to acute respiratory distress syndrome (ARDS) that is associated with a “cytokine storm” and even death.
Serological testing plays a critical role in understanding and combating the viral outbreaks. Serological testing can provide robust epidemiological data that are invaluable in determining the rates of infection and thus true mortality metrics. In addition, it can aid in determining individuals that mount a robust immune response who then can be donors for therapeutics agents, such as immune (convalescent) plasma. Serological testing can also help determine the immune response of asymptomatic individuals and/or vaccinated individuals.
The SARS-CoV-2 genome codes for four main structural proteins: spike (S), envelope (E), nucleoprotein (N) and membrane (M) proteins. The spike glycoproteins were found to bind to the ACE-2 receptors for entry into the cell. Studies indicate that IgG antibodies are primarily to the S and N proteins. The spike protein has two primary subunits: subunit 1 (S1) which includes the Receptor Binding Domain (RBD) that attaches the virus to the cell membrane, binding to the human ACE2 receptor. Subunit 2 (S2) mediates the fusion of the virus and cellular membranes.
A neutralizing antibody from infected or vaccinated individuals can block the binding between ACE2 receptor and spike proteins. However, it has been revealed that the viral spike proteins tend to mutate during its spread in the population which results in escape from neutralizing antibodies raised against the wild type spike protein, such as those that may be found in a vaccine. This invention identifies neutralizing antibody for multiple spike proteins capable of interacting with the ACE2 receptor.
BRIEF SUMMARY OF THE INVENTION
The present invention relates to the development of novel immunoassays for the detection of individuals infected by SARS-CoV-2 by detecting SARS-CoV-2 expressing spike protein variants and/or antibodies that neutralize SARS-CoV-2 spike protein variants. The immunoassays can be performed via a standard immunoassay format or on an automated platform. In various embodiments, the immunoassays use one or more SARS-CoV-2 spike protein variants or fragments thereof. The SARS-CoV-2 spike protein variants or fragments thereof can be immobilized on a substrate and used for the detection of neutralizing antibodies in biological samples obtained from subjects (also referred to as “patient samples”), optionally in combination with one or more cytokine in the biological sample. Other aspects of the invention provide antigen/substrate combinations for use in the immunoassays described herein.
The present invention also relates to the development of a novel singleplex and/or multiplex immunoassay for the detection of neutralizing and/or protective antibodies. A multiplex immunoassay can further detect high avidity neutralizing and/or protective antibodies, for SARS-CoV-2 spike protein variants or fragments thereof and, optionally, one or more cytokine selected from IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), and monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α in patient samples suspected of infection by the virus. The disclosed singleplex and/or multiplex immunoassays are designed to identify those subjects (patient samples) that contain antibodies capable of neutralizing and/or blocking the binding of the ACE2 receptor to a particular SARS-CoV-2 spike protein variants or fragment thereof and, optionally, levels of one or more cytokine in a patient infected by SARS-CoV, treated with an antibody that neutralizes SARS-CoV-2 spike protein variants or fragments thereof, or a subject immunized with a vaccine comprising a SARS-CoV2 spike protein, including the SARS-CoV-2 spike protein variants or fragments thereof disclosed herein, or a fragment thereof. The immunoassays disclosed herein can be used to evaluate the effectiveness of a vaccine against SARS-CoV-2 spike protein and variants thereof with respect to the generation of neutralizing antibodies and/or evaluate the presence of neutralizing antibodies in convalescent plasma or an antibody cocktail that is to be administered to a subject or at various time points after administration of convalescent plasma or an antibody cocktail comprising spike protein neutralizing antibodies to a subject.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 illustrates one aspect of the invention in which neutralizing antibodies to SARS-CoV-2 spike protein variants or fragments thereof are identified.
FIG. 2 illustrates one aspect of the invention in which neutralizing antibodies to SARS-CoV-2 spike protein variants or fragments thereof block the binding of hACE2 to SARS-CoV-2 spike protein variants or fragments thereof. The assay uses biotinylated hACE2 and streptavidin-phycoerythrin to permit detection of the neutralizing antibodies.
FIG. 3 illustrates one aspect of the invention in which high avidity neutralizing antibodies to SARS-CoV spike protein domains, variants, or fragments thereof are identified; the addition of 1 M NaCl destabilizes low avidity antibody binding.
FIG. 4 illustrates a neutralizing antibody inhibition curve of the RBD-biotinylated ACE2 interaction with sera from two COVID 19 patients. % inhibition=1−(relative fluorescent intensity (RFI) of each diluted samples/Matrix RFI).
FIGS. 5A and 5B demonstrate the correlation between anti-RBD binding IgG antibody and neutralizing antibody.
FIGS. 6-9 illustrate neutralizing antibodies present in samples for various mutants under low salt conditions (LS=0.15 M NaCl, FIGS. 6 and 7) and high salt conditions (HS=1 M NaCl, FIGS. 8 and 9) for samples obtained before March 2020 and after June 2020.
FIGS. 10-11 illustrate antibody mediated inhibition after normalization to 100% of the wild type. RBD mutants demonstrated differential nAb response for samples collected before and after June 2020.



DETAILED DESCRIPTION OF THE INVENTION
As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Furthermore, to the extent that the terms “including”, “includes”, “having”, “has”, “with”, or variants thereof are used in either the detailed description and/or the claims, such terms are intended to be inclusive in a manner similar to the term “comprising”. The transitional terms/phrases (and any grammatical variations thereof) “comprising”, “comprises”, “comprise”, “consisting essentially of”, “consists essentially of”, “consisting” and “consists” can be used interchangeably.
The term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the art. Alternatively, “about” can mean a range of up to 0-20%, 0 to 10%, 0 to 5%, or up to 1% of a given value.
In the present disclosure, ranges are stated in shorthand, so as to avoid having to set out at length and describe each and every value within the range. Any appropriate value within the range can be selected, where appropriate, as the upper value, lower value, or the terminus of the range. For example, a range of 0.1-1.0 represents the terminal values of 0.1 and 1.0, as well as the intermediate values of 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, and all intermediate ranges encompassed within 0.1-1.0, such as 0.2-0.5, 0.2-0.8, 0.7-1.0, etc. Values having at least two significant digits within a range are envisioned, for example, a range of 5-10 indicates all the values between 5.0 and 10.0 as well as between 5.00 and 10.00 including the terminal values.
The present disclosure may refer to items, such as labels, solid supports, beads, analytes, etc. according to number or letter (e.g., Detectable label 1, bead (ii), etc.). Where this nomenclature is used, these numbers and letters are meant to distinguish the item from other items of the same type (e.g., bead (i) vs. bead (ii)), and are not meant to associate a specific property with the number or letter. Any methods, devices and materials similar or equivalent to those described herein can be used in the practice of this invention. The following definitions are provided to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the present disclosure.
Multiplex assays are analyses that simultaneously measure the levels of more than one analyte in a single sample. Multiplex assay methods and reagents are described, e.g., in U.S. Pat. No. 6,872,578 and WO2008148883 (each of which is hereby incorporated by reference in its entirety). In the context of this application, the analytes to be measured are neutralizing and/or protective antibodies specific to the SARS-CoV-2 spike protein variants, or fragments thereof affixed to the solid substrates disclosed herein.
Singleplex assays are analyses that measure the level of one analyte in a single sample. In the context of this application, the analyte to be measured is a neutralizing and/or protective antibody specific to the SARS-CoV-2 spike protein or a fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof affixed to the solid substrates disclosed herein.
The term “solid support” or “substrate” (and grammatical equivalents of these terms) are used to denote a solid inert surface or body to which an agent, such as an antibody or a peptide or protein can be immobilized. These terms (“solid support” or “substrate” (and grammatical equivalents of these terms)) may be used interchangeably. Non-limiting examples of a solid support or substrate include plastic, polystyrenes, nitrocellulose, membranes, chips, and particles. If solid supports other than particles are used, for instance, glass, polymeric or silica chips (such as microchips), plates, slides, etc., the peptides and/or proteins (target analytes) disclosed herein can be immobilized on the surface of the support at specific locations (e.g., in specific wells of a plate (e.g., microtiter plate) or at specific locations on a chip, microchip, plate or slide). Thus, it is possible to differentiate neutralizing antibodies specific for spike protein variants within a sample by the location at which specific binding between antibodies in a sample and the spike protein variants, or fragments thereof occurs on the surface of the support.
Alternatively, lateral flow immunoassays can be performed in a manner analogous to those disclosed in U.S. Pat. Nos. 5,851,776 and 6,777,190 (each of which is hereby incorporated by reference in their entireties and which relate to lateral flow chromatographic assays on a membrane or other porous or non-porous materials). The specific binding of antibodies to the spike protein variants or fragments thereof that are immobilized at discrete locations on the membrane or other porous or non-porous material is then detected using conventional methods. The term “particle” is used herein to refer to a solid or semisolid body, often with linear dimensions on the micron scale (i.e., less than about 100 microns), of any shape or surface texture. Except as noted, the term is used interchangeably with “particle,” which refers to a micron scale particle, and “bead,” which refers to particles that are spherical or near-spherical in shape, often polymeric in composition. Where used in this application, the terms “particle” and “bead” (and grammatical equivalents of these terms) can be interchanged without altering the context of the passages within this application).
The term “immobilized” as used herein denotes a molecular-based coupling that is not significantly de-coupled under the conditions imposed during the steps of the assays described herein. Such immobilization can be achieved through a covalent bond, a non-covalent bond, an ionic bond, an affinity interaction (e.g., avidin-biotin or polyhistidine-Ni++), or any other chemical bond.
Immobilization of the spike protein variants or fragments thereof disclosed in this application can be performed by covalent or non-covalent immobilization on a substrate. For example, non-covalent immobilization can be non-specific (e.g., non-specific binding of a combination of one or more spike protein variants or fragments thereof to a polystyrene surface). Specific or semi-specific binding to a substrate can be achieved by the spike protein variants or fragments thereof having a moiety that enables covalent or non-covalent binding of the peptide and/or protein to the substrate that is coated with a ligand that binds to the moiety. For example, the moiety can be a biotin or biotinyl group or an analogue thereof bound to an amino acid group of the spike protein variants or fragment thereof, such as 6-aminohexanoic acid, and the ligand (biotin binding ligand) is avidin, streptavidin or an analogue thereof. Alternatively, the moiety can be a His-His-His-His-His-His peptide and the substrate can be derivatized with a Nitrilotriacetic Acid derivative (NTA) charged with Ni++ ions.
Various substrates suitable for use in the disclosed methods include, and are not limited to, magnetic beads, polystyrene beads, latex beads, beads comprising co-polymers, such as styrene-divinyl benzene; hydroxylated styrene-divinyl benzene; polystyrene; carboxylated polystyrene; carbon black; non-activated, polystyrene or polyvinyl chloride activated glass; or epoxy-activated porous magnetic glass. In other embodiments, the substrate can be the floor or wall of a microtiter well; a filter surface or membrane (e.g., a nitrocellulose membrane or a PVDF (polyvinylidene fluoride) membrane, such as an Immobilon membrane); a hollow fiber; a beaded chromatographic medium (e.g., an agarose or polyacrylamide gel); a magnetic bead; a fibrous cellulose matrix; an HPLC matrix; an FPLC matrix; or any other suitable carrier, support or surface. In one embodiment of the invention, the disclosed SARS-CoV-2 spike protein variants or fragments thereof are immobilized onto polystyrene beads (microspheres), wherein each protein is immobilized onto a bead with a unique detectable physical parameter, and are analyzed by a platform capable of distinguishing the detectable physical parameter. Such beads can, optionally, also contain a magnetic core. Such assays may be referred to as “multiplex immunoassays” and are discussed in detail below.
Devices for performing specific binding assays, especially immunoassays, are known and can be readily adapted for use in the present methods. Solid phase assays, in general, are easier to perform than heterogeneous assay methods which require a separation step, such as precipitation, centrifugation, filtration, chromatography, or magnetism, because separation of reagents is faster and simpler. Solid-phase assay devices include microtiter plates, flow-through assay devices, chips, microchips, lateral flow substrates dipsticks and immunocapillary or immunochromatographic immunoassay devices.
The terms “receptacle,” “vessel,” “tube,” “well,” etc. refer to a container that can hold reagents or an assay. If the receptacle is in a kit and holds reagents, it will typically be closed or sealed. If the receptacle is being used for an assay, it will typically be open or accessible during steps of the assay.
The terms “patient sample” or “biological sample” encompasses a variety of sample types obtained from an organism, such as a human. The term encompasses bodily fluids, such as blood, blood components, saliva, nasal mucous, serum, plasma, cerebro-spinal fluid (CSF), urine and other liquid samples of biological origin, solid tissue biopsy, tissue cultures, or supernatant taken from cultured patient cells. In the context of the present disclosure, the biological sample is typically a bodily fluid with detectable amounts of antibodies, e.g., blood or a blood component (e.g., plasma or serum) or a nasal secretion (mucous). The biological sample can be processed prior to assay, e.g., to remove cells or cellular debris. The term encompasses samples that have been manipulated after their procurement, such as by treatment with reagents, solubilization, sedimentation, or enrichment for certain components.
The term “antibody” as used herein refers to a polypeptide encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, which specifically bind and recognize an analyte (antigen). The recognized immunoglobulin light chains are classified as either kappa or lambda. Immunoglobulin heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. An example of a structural unit of immunoglobulin G (IgG antibody) is a tetramer. Each such tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms “variable light chain” (VL) and “variable heavy chain” (VH) refer to these light and heavy chains, respectively.
Antibodies exist as intact immunoglobulins or as well-characterized fragments produced by digestion of intact immunoglobulins with various peptidases. Thus, for example, pepsin digests an antibody near the disulfide linkages in the hinge region to produce F(ab′)2, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab′)2 dimer can be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab′)2 dimer into two Fab′ monomers. The Fab′ monomer is essentially an Fab with part of the hinge region (see, Paul (Ed.), Fundamental Immunology, Third Edition, Raven Press, N.Y. (1993)). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term “antibody,” as used herein, also includes antibody fragments either produced by the modification of whole antibodies.
Antibodies are commonly referred to according their targets. While the nomenclature varies, one of skill in the art will be familiar and understand that several names can be applied to the same antibody. For example, an antibody specific for IgM can be called “anti-IgM,” “IgM antibody,” “anti-IgM antibody,” etc.
The terms “specific for,” “specific to”, “specifically binds,” and grammatically equivalent terms refer to a molecule (e.g., antibody or antibody fragment) that binds to its target with at least 2-fold greater affinity than non-target compounds, e.g., at least any of 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 25-fold, 50-fold, or 100-fold greater affinity. For example, antibodies that specifically binds a given antibody target will typically bind the antibody target with at least a 2-fold greater affinity than a non-antibody target. Specificity can be determined using standard methods, e.g., solid-phase ELISA immunoassays (see, e.g., Harlow & Lane, Using Antibodies, A Laboratory Manual (1998) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity).
The term “binds” with respect to an antibody target (e.g., antigen, analyte), typically indicates that an antibody binds a majority of the antibody targets in a pure population (assuming appropriate molar ratios). For example, an antibody that binds a given antibody target typically binds to at least %3 of the antibody targets in a solution (e.g., at least any of 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100%). One of skill will recognize that some variability will arise depending on the method and/or threshold of determining binding.
The terms “label,” “detectable label,” “detectable moiety,” and like terms refer to a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include fluorescent dyes (fluorophores), luminescent agents, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, enzymes acting on a substrate (e.g., horseradish peroxidase), digoxigenin, 32P and other isotopes, haptens, and proteins which can be made detectable, e.g., by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide. The term includes combinations of single labeling agents, e.g., a combination of fluorophores that provides a unique detectable signature, e.g., at a particular wavelength or combination of wavelengths. Any method known in the art for conjugating label to a desired agent may be employed, e.g., using methods described in Hermanson, Bioconjugate Techniques 1996, Academic Press, Inc., San Diego.
The term “positive,” when referring to a result or signal, indicates the presence of an analyte or item that is being detected in a sample. The term “negative,” when referring to a result or signal, indicates the absence of an analyte or item that is being detected in a sample. Positive and negative are typically determined by comparison to at least one control, e.g., a threshold level that is required for a sample to be determined positive, or a negative control (e.g., a known blank). A “control” sample or value refers to a sample that serves as a reference, usually a known reference, for comparison to a test sample. For example, a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g., in the absence of the test compound (negative control), or in the presence of a known compound (positive control). A control can also represent an average value gathered from a number of tests or results. For the assays used in the subject invention, control beads can be included, for example, a serum verification bead (SVB) and/or an internal standard bead (ISB) can be used. One of skill in the art will recognize that controls can be designed for assessment of any number of parameters, and will understand which controls are valuable in a given situation and be able to analyze data based on comparisons to control values. Controls are also valuable for determining the significance of data. For example, if values for a given parameter are variable in controls, variation in test samples will not be considered as significant.
A “calibration control” is similar to a positive control, in that it includes a known amount of a known analyte. In the case of a multiplex assay, the calibration control can be designed to include known amounts of multiple known analytes. The amount of analyte(s) in the calibration control can be set at a minimum cut-off amount, e.g., so that a higher amount will be considered “positive” for the analyte(s), while a lower amount will be considered “negative” for the analyte(s). In some cases, multilevel calibration controls can be used, so that a range of analyte amounts can be more accurately determined. For example, an assay can include calibration controls at known low and high amounts, or known minimal, intermediate, and maximal amounts.
The term “diagnosis” refers to a relative probability that a subject has an infection, disorder or disease. Similarly, the term “prognosis” refers to a relative probability that a certain future outcome may occur in the subject. For example, in the context of the present disclosure, prognosis can refer to the likelihood that an individual has been infected by SARS-CoV-2 and has, or will develop, disease. The terms are not intended to be absolute, as will be appreciated by any one of skill in the field of medical diagnostics.
“Subject,” “patient,” “individual” and grammatical equivalents thereof are used interchangeably and refer to, except where indicated, mammals, such as humans and non-human primates, as well as rabbits, felines, canines, rats, mice, squirrels, goats, pigs, deer, and other mammalian species. The term does not necessarily indicate that the subject has been diagnosed with a particular disease, but typically refers to an individual under medical or veterinary supervision. A patient can be an individual that is seeking treatment, monitoring, adjustment or modification of an existing therapeutic regimen, etc. In the context of this application, the “subject,” “patient,” or “individual” has: a) been exposed to or infected with SARS-CoV-2; b) immunized with a vaccine comprising the SARS-CoV-2 spike protein (or fragments thereof) or a vaccine comprising spike protein variants or fragments thereof; or c) been treated with a neutralizing antibody for the SARS-CoV-2 spike protein (or fragments thereof) or with neutralizing antibody specific for SARS-CoV-2 spike protein variants or fragments thereof (e.g., convalescent plasma or other neutralizing antibody, such as a composition comprising one or more antibodies that neutralize the SARS-CoV-2 spike protein or variants thereof (an antibody cocktail). The immunoassays disclosed herein are capable of detecting the binding of neutralizing antibodies for specific for SARS-CoV-2 spike protein variants or fragments thereof in biological samples from any of these types of subjects.
As used herein, a “chaotropic agent” or “chaotrop” refers to a chemical compound that destabilizes the three-dimensional structure of proteins. In certain embodiments, a chaotropic agent may refer to an ionic chaotrop (e.g., a chaotropic ion or a chaotropic salt) or, alternatively, to a nonionic chaotrop. Non-limiting examples of chaotropic salts include: guanidinium salts, e.g., guanidinium chloride, guanidinium nitrate, guanidinium thiocyanate; thiocyanate salts, e.g., ammonium thiocyanate, potassium thiocyanate, sodium thiocyanate, lithium thiocyanate, calcium thiocyanate, guanidinium thiocyanate; perchlorate salts, e.g., ammonium perchlorate, sodium perchlorate, lithium perchlorate, magnesium perchlorate, calcium perchlorate; iodate salts, e.g., ammonium iodate, potassium iodate, sodium iodate, lithium iodate, magnesium iodate, calcium iodate; chlorate salts, e.g., sodium chlorate, lithium chlorate, magnesium chlorate, calcium chlorate; chloride salts, e.g., sodium chloride, potassium chloride, calcium, chloride, and ammonium chloride. Nonionic chaotropes include, without limitation, urea and thiourea.
As used herein, “avidity” is a measure of the total binding strength of an antigen comprising various antigenic determinants and antibodies, i.e., the stability of the complex formed between the antigen and the antibody. Avidity refers to the total binding force between antigens and antibodies; therefore, the phrases “high avidity antibody” or “low avidity antibody” reflect the relative binding force of an antibody to an antigen. As used herein, a high avidity antibody can maintain a bond to an antigen when exposed to a chaotropic agent; while, a low avidity antibody may not be able to maintain a bond to an antigen when exposed to same chaotropic agent at the same concentration.
The term “ACE2 receptor(s)” (ACE2R) includes truncated and/or modified ACE2 receptors that can have one, two, three, four, five, ten, 50, 100, 250, 500 or more amino acids removed, added, and/or substituted. A modified ACE2 receptor includes an ACE2 receptor fusion protein in which the ACE2 receptor, or a fragment or variant thereof is fused to an immunoglobulin Fc domain. For example, the Fc domain can be fused to the C-terminus of the ACE2 receptor, or a fragment or variant of the ACE2 receptor to form an ACE2R-Fc fusion protein. The fragment or variant of the ACE2 receptor can comprise a minimal domain from ACE2R that is sufficient to bind to the RBD, for example amino acids Ser19-Asp615 of ACE2R or amino acids 12-327 of the ACE2R. In various embodiments, human ACE2R (SEQ ID NO: 4) can be used. A “labeled ACE2 receptor” includes an ACE2 receptor that is detectably labeled (for example, with PE) or is a biotinylated, avidinated, or streptavidinated ACE2 receptor (including truncated and/or modified ACE2 receptors or ACE2 fusion proteins). In various embodiments, ACE2R-Fc fusion proteins can be biotinylated, avidinated, or streptavidinated on the Fc portion of the fusion protein.
The terms “structural protein” “peptide”, “antigen”, “analyte”, and “fragment” (and grammatical equivalents thereof) can be used interchangeably and refer to the disclosed SARS-CoV-2 spike protein variants or fragments thereof that are disclosed herein and/or the unmutated SARS-CoV-2 spike protein or fragments thereof (SEQ ID NO: 3). As discussed herein, fragments of the disclosed SARS-CoV-2 spike protein, SARS-CoV-2 spike protein variants are between 5 and (n−1) consecutive amino acids of a given SARS-CoV-2 spike protein (SEQ ID NO: 1 or SEQ ID NO: 2 or SEQ ID NO: 3). In each instance, a fragment of the spike protein variant will include, within its span of consecutive amino acids, the amino acid mutation associated with the mutant spike protein (which are identified in Table 1 and Table 2). The numbering of the amino acid mutation is in relation to the amino acid numbering in SEQ ID NOs: 1 or 2.







TABLE 1







Spike protein variants











Amino acid 




Protein
mutation
aa range
AA substitution





S1
367
319-541
Any amino acid, preferably F, L,





A, V, I, M, Y or W


S1
342
319-541
Any amino acid, preferably L, A,





V, I, M. F, Y or W


S1
435
319-541
Any amino acid, preferably S, T,





N or Q


S1
458
319-541
Any amino acid, preferably R, H





or K


S1
483
319-541
Any amino acid, preferably A, L,





V, I, M, F, Y or W


S1
354
319-541
Any amino acid, preferably D or E


S1/S2
683, 685, 986, 
  1-1213
Any amino acid, preferably L, A,



and/or 987

V, I, M, F, Y, G, P or W
















TABLE 2







Preferred Spike protein variants












Protein
Mutant Type
AA Range
ACE2 Binding







S1
V367F
aa 319-541
+



S1
F342L
aa 319-541
+



S1
A435S
aa 319-541
+



S1
K458R
aa 319-541
+



S1
V483A
aa 319-541
+



S1
N354D
aa 319-541
+



S1/S2
R683A, R685A, 
aa 1-1213 
+




K986P, V987P










With respect to the amino acid mutations at positions 683, 685, 986, and 987, any combination of 2, 3 or 4 amino acid mutations can exist in the spike protein variant or a fragment thereof. In certain embodiments, three or all four amino acid mutations exist within the spike protein variant or fragment thereof. Thus, fragments of the spike protein variants that can be immobilized on a solid support are fragments of S1 and can be between 5 and 685 consecutive amino acids in length, provided that the fragment includes one or more of the amino acid substitutions identified in Table 1 or 2 (for example, amino acids 13-685 or amino acids 319-541 of SEQ ID NO: 1 or 2). Preferred embodiments provide for spike protein variants, or fragments thereof, that contain a single amino acid substitution as identified in Tables 1 and 2. The length or a fragment can include or exclude signal peptides that are processed (for example amino acids 1-12 of SEQ ID NO: 1 or SEQ ID NO: 2). In some embodiments, the amino acid at position 354 of SEQ ID NO. 2 is Asx (aspartic acid or asparagine). Spike protein variants of SEQ ID NO: 2, thus, can contain either aspartic acid or asparagine at position 354 and one or more other mutations identified in Tables 1 and 2 (i.e., at positions 342, 367, 435, 458, 483, 683, 685, 986, and/or 987). Thus, in the case of the spike protein variants, the length can include or exclude the signal peptide of the protein. In some embodiments, an “analyte” may be a neutralizing antibody specific for a SARS-CoV-2 spike protein variant or fragment thereof. In such embodiments, the use of the term in the context of detecting the antibody as the analyte will be clear. In yet other embodiments, one or more of the following chemokines and cytokines are included as an “analyte” or “analytes” that are to be detected and/or quantified: IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), and monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α. While IL-1beta, IFN-γ, IFN-γ-induced protein 10 (IP-10), and monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α are either classified as cytokines or chemokines (in the case of IP-10), this collection of cytokines and chemokines (IL-1beta, IFN-γ, IFN-γ-induced protein 10 (IP-10), and monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α) can be referred to herein as “cytokines” “cytokine”, or “one or more cytokine”. As discussed above, the use of the term in the context of detecting or immobilizing these chemokines and/or cytokines (“cytokines”, “cytokine”, or “one or more cytokine”) will be clear.

As discussed above, the present invention relates to the development of a novel multiplex immunoassay for the detection of neutralizing antibodies for SARS-CoV-2 spike protein variants or fragments thereof and, optionally, one or more cytokine selected from IL-1beta, IFN-γ, IFN-γ-induced protein 10 (IP-10), and monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α in patient samples suspected of infection by the virus. The disclosed immunoassays are designed to identify those subjects (patient samples) that contain antibodies capable of blocking the binding of the ACE2 receptor to a particular SARS-CoV-2 spike protein variants or fragment thereof and, optionally, levels of one or more cytokine in a patient or a subject immunized with a vaccine comprising SARS-CoV2 spike protein, or a fragment thereof. The immunoassay can be performed via a standard immunoassay using ELISA, lateral flow, magnetic assays with manual or using automated platforms. Particularly, the disclosed immunoassay uses one or more SARS-CoV-2 spike protein variant or fragment thereof that contains an amino acid substitution and any combination of the disclosed SARS-CoV-2 spike protein variants (e.g., any combination of two, three, four, five, six, seven, eight, or nine SARS-CoV-2 spike protein variants) and, optionally, one or more cytokine selected from IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α (e.g., any combination of one, two, three, four, five, six, seven, eight, nine, ten, or eleven of these analytes).
Another embodiment provides an immunoassay in which a single SARS-CoV-2 spike protein variant or fragment thereof is immobilized on a substrate. Thus, the disclosed immunoassay comprises contacting a substrate to which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized under conditions effective to bind antibodies found in a biological sample to the immobilized SARS-CoV-2 spike protein variant or fragment thereof. Antibodies bound to the SARS-CoV-2 spike protein variant or fragment thereof that is attached to a substrate can then be detected by a species specific anti-IgM, anti-IgG, anti-IgA, anti-IgD, anti-IgE, anti-kappa, or anti-lambda antibody that is labeled (e.g., anti-human, anti-rabbit, anti-canine, anti-rat, anti-mouse, anti-squirrel, anti-goat, anti-pig or anti-deer antibody). For example, anti-IgG-PE and/or anti-IgM-PE reporters can be used to detect and/or quantify the SARS-CoV-2 spike protein variant specific antibodies in biological samples obtained from individuals suspected of infection by the virus or immunized with a vaccine comprising the SARS-CoV2 spike protein. Alternatively, it is possible to utilize species specific light chain specific antibodies (species specific kappa or lambda specific antibodies) as a detection reagent to identify samples containing antibodies that bind to a given SARS-CoV-2 spike protein variant or fragment thereof. In certain preferred embodiments, the species specific antibodies are anti-human antibodies.
Other embodiments provide for the use of labeled ACE2 receptor, including truncated and/or modified ACE2 receptors and/or ACE2R-fusion proteins (e.g., ACE2R-Fc fusion proteins) that are labeled, to detect substrates to which SARS-CoV-2 spike protein variants or fragments thereof are immobilized and to which a neutralizing antibody has not bound. The truncated and/or modified ACE2 receptor can have one, two, three, four, five, ten, 50, 100, 250, 500 or more amino acids removed, added, and/or substituted. Alternatively, the ACE2 receptor can be fused to an immunoglobulin Fc domain. For example, the Fc domain can be fused to the C-terminus of ACE2R, or a fragment or variant of the ACE2 receptor protein. The fragment or variant of the ACE2 receptor can comprise a minimal domain from ACE2R that is sufficient to bind to the RBD. Additionally, the ACE2 receptor, truncated or modified ACE2 receptor or an ACE2R fusion protein (e.g., ACE2R-Fc) can be biotinylated or avidinated. In preferred embodiments, the Fc domain of an ACE2R-Fc fusion protein can be biotinylated or avidinated. In such embodiments, it is possible to identify the binding of neutralizing antibody to a given SARS-CoV-2 spike protein variant or fragment thereof by the lack of labeled ACE2 receptor binding to a substrate to which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized. In other words, a labeled ACE2 receptor will only bind to those substrates to which no neutralizing antibodies are specifically bound by a SARS-CoV-2 spike protein variant or fragment thereof that is immobilized on a substrate.
The SARS-CoV-2 spike protein variant or fragment thereof disclosed herein can be immobilized on a solid support via covalent or non-covalent bonding. In embodiments where a SARS-CoV-2 spike protein variant or fragment thereof or cytokine is covalently immobilized on the substrate, carboxylated substrates, such as particles, plastics, polystyrenes or beads, are activated and esterified before adding the SARS-CoV-2 spike protein variant or fragment thereof or cytokine. Carboxyl activation is achieved using a water soluble carbodiimide, such as 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide (CMC). Esterification is achieved using NHS, NHSS or HOBt or other suitable reagents. After carboxyl activation and esterification, the SARS-CoV-2 spike protein variant or fragment thereof or cytokine are added to the activated surface in buffers with pH between 6-10 (an example of which is sodium acetate buffer pH 5.1, phosphate buffer pH 7.0 with or without detergent (e.g., CHAPS)). After the coupling, the substrate (e.g., beads) is blocked in buffers containing protein blockers, such as BSA, mouse IgG, bovine gamma globulin (BGG) or animal serum (goat, horse, murine). The protein blocker(s) can be present in an amount ranging from 0.1-10 weight/volume percent. The blocked antigen coupled substrates can then be washed with an appropriate buffer and used in a desired immunoassay format.
As discussed above, the disclosed invention is directed to an immunoassay which includes taking a sample of body fluid or tissue (e.g., a biological sample or a patient sample) likely to contain antibodies; contacting (reacting) the biological sample with a SARS-CoV-2 spike protein variant or fragment thereof (and/or one or more cytokine) under conditions effective for the formation of a specific protein-antibody complex (sometimes referred to as specific binding of the protein and the antibody or “an immunocomplex” of a given protein and antibodies that specifically bind the protein or fragment thereof); and assaying the contacted (reacted) sample for the presence of an antibody-analyte immunocomplex. The biological sample can be obtained from a SARS-CoV2 infected individual, an individual treated with neutralizing antibodies specific for SARS-CoV-2 spike protein variants or fragments, or an individual vaccinated with a vaccine comprising SARS-CoV2 spike protein.
In various embodiments, the disclosed method relates to a method that comprises taking a sample of body fluid or tissue (a biological sample or a patient sample) likely to contain antibodies specific for a SARS-CoV-2 spike protein variant or fragment thereof and detecting and/or quantifying the presence of the antibodies and/or one or more cytokine within the biological sample. Generally, IgM, IgA, and/or IgG antibodies are detected (although antibodies of other isotypes may also be detected). Alternatively, antibodies specific for kappa or lambda light chains can be used to detect antibodies specifically bound to the SARS-CoV-2 spike protein variant or fragment thereof or cytokine that is immobilized on a substrate. In various embodiments, the biological sample is a serum or plasma sample derived from a venous blood sample. Other body fluids, such as saliva, gastric secretions, nasal secretions, mucus, etc., that are known to contain antibodies may also be referred to as a biological sample and used in the disclosed immunoassays. As discussed above, the biological sample can be obtained from a SARS-CoV2 infected individual, an individual treated with neutralizing antibodies specific for SARS-CoV-2 spike protein variants or fragments or an individual vaccinated with a vaccine comprising SARS-CoV2 spike protein, such as a spike protein variant or fragment thereof as disclosed herein.
The presently described multiplex assays involve use of a solid support, typically particles or beads. For detection by flow cytometry, particles or beads that emit high levels of autofluorescence should be avoided since this will increase background signal and potentially render them unsuitable. Particles or beads created by standard emulsion polymerization from a variety of starting monomers generally exhibit low autofluorescence, while those that have been modified to increase porosity (“macroporous” particles) exhibit high autofluorescence. Autofluorescence in such particles or beads further increases with increasing size and increasing percentage of divinylbenzene monomer. Within these limitations, the size range of the particles or beads can vary and particular size ranges are not critical. In most cases, the aggregated size range of the particles or beads lies within the range of from about 0.3 micrometer to about 100 micrometers in particle or bead diameter, e.g., within the range of from about 0.5 micrometer to about 40 micrometers.
Magnetic particles or beads are commonly used in the art, and can make separation and wash steps more convenient for the presently described assays. “Magnetic particles,” “magnetically responsive material,” “magnetic beads,” and like terms denote a material that responds to a magnetic field. Magnetically responsive materials include paramagnetic materials (e.g., iron, nickel, and cobalt, as well as metal oxides, such as Fe3O4, BaFe12O19, CoO, NiO, Mn2O3, Cr2O3, and CoMnP), ferromagnetic materials, ferrimagnetic materials, and metamagnetic materials. Rather than constituting the entire particle or bead, the magnetically responsive material typically constitutes one component of the microparticle or bead, while the remainder consists of a polymeric material which can be chemically derivatized to permit attachment of an assay reagent (e.g., antigen/analyte or antibody). Methods of, and instrumentation for, applying and removing a magnetic field as part of an assay are known to those skilled in the art and reported in the literature. Examples of literature reports are Forrest et al., U.S. Pat. No. 4,141,687; Ithakissios, U.S. Pat. No. 4,115,534; Vlieger et al., Analytical Biochemistry 205:1-7 (1992); Dudley, Journal of Clinical Immunoassay 14:77-82 (1991); and Smart, Journal of Clinical Immunoassay 15:246-251 (1992).
The polymeric matrix that forms the microparticle or bead can be any material that is compatible with the presently described multiplex assay. The matrix should be inert to the components of the biological sample and to the assay reagents, have minimal autofluorescence, be solid and insoluble in the sample and in any other reagents or washes used in the assay, and capable of affixing an assay reagent to the microparticle. Examples of suitable polymers are polyesters, polyethers, polyolefins, polyalkylene oxides, polyamides, polyurethanes, polysaccharides, celluloses, and polyisoprenes. Crosslinking is useful in many polymers for imparting structural integrity and rigidity to the microparticle.
Functional groups for attachment of the assay reagent (e.g., antigen/analyte or antibody) can be incorporated into the polymer structure by conventional means. Examples of suitable functional groups are amine groups, ammonium groups, hydroxyl groups, carboxylic acid groups, and isocyanate groups. The assay reagent is typically covalently bound to the solid phase surface, either directly or indirectly, e.g., with a linking group. Linking groups can be used as a means of increasing the density of reactive groups on the solid phase surface and decreasing steric hindrance to increase the range and sensitivity of the assay, or as a means of adding specific types of reactive groups to the solid phase surface to broaden the range of types of assay reagents that can be affixed to the solid phase. Examples of suitable useful linking groups are polylysine, polyglycine, polyaspartic acid, polyglutamic acid and polyarginine.
Particles or beads of different types in a multiplex assay can be distinguished from one another, e.g., by size, weight, light scatter or absorbance, reflectance, shape, or label, e.g., fluorescent (dye) label. Where particle or bead size is used as a differentiation factor (distinguishing characteristic), the widths of the size subranges and the spacing between mean diameters of adjacent subranges are selected to permit differentiation of different types of particles or beads by flow cytometry, as will be apparent to those skilled in the use of and instrumentation for flow cytometry. Typically, a subrange for a given mean diameter is about ±5% CV or less of the mean diameter, where CV is the coefficient of variation and is defined as the standard deviation of the particle or bead diameter divided by the mean particle diameter times 100 percent. The mean diameters of subranges for different types of particles are generally spaced apart by at least about 6% of the mean diameter of one of the subranges, e.g., at least about 8% or 10% of the mean diameter of one of the subranges.
Light scatter can also be used to distinguish different types of particles or beads. Side angle light scatter varies with particle or beads size, granularity, absorbance and surface roughness, while forward angle light scatter is mainly affected by size and refractive index. Varying any of these qualities can result in light scatter differences that can serve as a means of distinguishing the various groups of particles or beads.
Still another example of a differentiation parameter is absorbance. When light is applied to particles or beads, the absorbance of the light by the particles or beads is indicated mostly by a change in the strength of the laterally (side-angle) scattered light while the strength of the forward-scattered light is relatively unaffected. Consequently, the difference in absorbance between various colored dyes associated with the particles or beads is determined by observing differences in the strength of the laterally scattered light.
Other physical parameters that can be used as differentiation parameters to distinguish the particles or beads of one group from those of another include excitable fluorescent dyes or colored dyes that impart different emission spectra and/or scattering characteristics to the particles or beads. Alternatively, different concentrations of one or more fluorescent dyes can be used for distinguishing or differentiating particles or beads.
When the distinguishable characteristic is a fluorescent dye or color, it can be coated on the surface of the particle or bead, embedded in the particle or bead, or bound to the molecules of the particle or bead material. Thus, fluorescent particles or beads can be manufactured by combining the polymer material with the fluorescent dye, or by impregnating the particle or bead with the dye. Particles or beads with dyes already incorporated and thereby suitable for use in the present invention are commercially available, from suppliers, such as Spherotech, Inc. (Libertyville, Ill., USA) and Molecular Probes, Inc. (Eugene, Oreg., USA).
Labels can be any substance or component that directly or indirectly emits or generates a detectable signal. In some embodiments, the labels are fluorophores, many of which are reported in the literature and thus known to those skilled in the art, and many of which are readily commercially available. Literature sources for fluorophores include Cardullo et al., Proc. Natl. Acad. Sci. USA 85: 8790-8794 (1988); Dexter, J. of Chemical Physics 21: 836-850 (1953); Hochstrasser et al., Biophysical Chemistry 45: 133-141 (1992); Selvin, Methods in Enzymology 246: 300-334 (1995); Steinberg, Ann. Rev. Biochem., 40: 83-114 (1971); Stryer, Ann. Rev. Biochem. 47: 819-846 (1978); Wang et al., Tetrahedron Letters 31: 6493-6496 (1990); and Wang et al., Anal. Chem. 67: 1197-1203 (1995). The following are non-limiting examples of fluorophores that can be used as labels:
4-acetamido-4′-isothiocyanatostilbene-2,2′disulfonic acid; acridine; acridine isothiocyanate; 5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS); 4-amino-N-[3-vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate; N-(4-anilino-1-naphthyl)maleimide; anthranilamide; BODIPY; Brilliant Yellow; coumarin; 7-amino-4-methylcoumarin (AMC, Coumarin 120); 7-amino-4-trifluoromethylcoumarin (Coumaran 151); cyanine dyes; cyanosine; 4′,6-diaminidino-2-phenylindole (DAPI); 5′,5′′-dibromopyrogallol-sulfonaphthalein (Bromopyrogallol Red); 7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin; diethylenetriamine pentaacetate; 4,4′-diisothiocyanatodihydro-stilbene-2,2′-disulfonic acid; 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid; 5-[dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansylchloride); 4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL); 4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC); eosin; eosin isothiocyanate; erythrosin B; erythrosin isothiocyanate; ethidium; 5-carboxyfluorescein (FAM); 5-(4,6-dichlorotriazin-2-yl)aminofluorescein (DTAF); 2′,7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE); fluorescein; fluorescein isothiocyanate; fluorescamine; IR144; IR1446; Malachite Green isothiocyanate; 4-methylumbelliferone; ortho cresolphthalein; nitrotyrosine; pararosaniline; Phenol Red; phycoerythrin ((PE) including but not limited to B and R types); o-phthaldialdehyde; pyrene; pyrene butyrate; succinimidyl 1-pyrene butyrate; quantum dots; Reactive Red 4 (CibacronTM Brilliant Red 3B-A); 6-carboxy-X-rhodamine (ROX); 6-carboxyrhodamine (R6G); lissamine rhodamine B sulfonyl chloride rhodamine; rhodamine B; rhodamine 123; rhodamine X isothiocyanate; sulforhodamine B; sulforhodamine 101; sulfonyl chloride derivative of sulforhodamine 101 (Texas Red); N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA); tetramethyl rhodamine; tetramethyl rhodamine isothiocyanate (TRITC); riboflavin; rosolic acid; and lanthanide chelate derivatives.
Particular fluorophores for use in the disclosed immunoassays include fluorescein, fluorescein isothiocyanate, phycoerythrin (PE), rhodamine B, and Texas Red (sulfonyl chloride derivative of sulforhodamine 101). Any of the fluorophores in the list preceding this paragraph can be used in the presently described assays, either to label the particle or bead, or to label a binding agent (e.g., an antibody or streptavidin). Fluorochromes can be attached by conventional covalent bonding, using appropriate functional groups on the fluorophores and on the particle or bead or binding agent (e.g., an antibody or streptavidin). The recognition of such groups and the reactions to form the linkages will be readily apparent to those skilled in the art. Other labels that can be used in place of the fluorophores are radioactive labels and enzyme labels. These are likewise known in the art. Flow cytometry methods and instrumentation are known in the art. Descriptions of instrumentation and methods can be found, e.g., in Introduction to Flow Cytometry: A Learning Guide (2000) Becton, Dickinson, and Company; McHugh, “Flow Microsphere Immunoassay for the Quantitative and Simultaneous Detection of Multiple Soluble Analytes,” Methods in Cell Biology 42, Part B (Academic Press, 1994).
The disclosed invention also pertains to kits and compositions for the detection of neutralizing antibodies, protective antibodies, high avidity neutralizing antibodies, and/or high avidity protective antibodies specific for SARS-CoV-2 spike protein variants or fragments thereof in a subject. The singleplex and/or multiplex assay disclosed herein provides for the detection and/or quantification of neutralizing antibodies (e.g., immunoglobulin G (IgG) antibodies, IgA, and/or IgM antibodies) specific for SARS-CoV-2 spike protein variants or fragments thereof. The multiplex assay disclosed herein also provides for the detection and/or quantification of high avidity neutralizing antibodies specific for the SARS-CoV-2 spike protein, SARS-CoV-2 spike protein variants or fragments thereof. In certain embodiments, the kits and compositions for the detection of neutralizing antibodies can contain chaotropic agents. The chaotropic agents can be ionic, such as, for example, sodium chloride and sodium thiocyanate, or non-ionic, such as, for example, urea.
Neutralizing antibodies can be antibodies generated within an infected or vaccinated subject, for example, a human. Alternatively, neutralizing and/or protective antibodies can be administered as therapeutic agents and the disclosed assays can detect the presence of such antibodies in samples obtained from a treated subject. For example, human neutralizing monoclonal antibodies B38 and H4 (disclosed in Wu et al., Science, 2020, 368(5496):1274-1278, which is hereby incorporated by reference in its entirety) or the 47D11 human monoclonal antibody disclosed in Wang et al. (Nature Communications, doi.org/10.1038/s41467-020-16452-w, published 14 May 2020, “A human monoclonal antibody blocking SARS-CoV-2 infection”) which is hereby incorporated by reference in its entirety) are therapeutic antibodies that can be administered to a SARS-CoV2 infected subject and the binding of these neutralizing and/or protective antibodies to a SARS-CoV-2 spike protein variant or fragment thereof can be detected using the disclosed multiplex immunoassays. Alternatively, neutralizing antibodies that can be detected in the disclosed multiplex immunoassays include chimeric, humanized or other forms of recombinant antibodies, such as a CDR-grafted antibody, a nanobody, or an antigen-binding portion of any thereof. Other neutralizing and/or protective antibodies include recombinant antibody formats, such as Fv, single domain antibodies (e.g., VH or VL or VHH), scFv, bi, tri or tetra-valent antibodies, Bis-scFv, diabodies, triabodies, tetrabodies and fragments thereof that neutralize SARS-CoV-2 spike protein variants or fragments thereof. Such antibodies can be generated according to methods well-known in the art. Additionally, as would be clear to those skilled in the art, at least one of the antigen binding portions of a bi-valent antibody, tri-valent antibody, tetra-valent antibody, bis-scFv, diabody, triabody, tetrabody or a fragment thereof that specifically binds to and neutralizes a SARS-CoV-2 spike protein variant or fragment thereof.
In certain embodiments, high avidity neutralizing and/or protective antibodies can be distinguished from low avidity neutralizing and/or protective antibodies using chaotropic agents. The chaotropic agents can be added to the immunoassay reactions to destabilize weaker bonds between antibodies and antigens, leaving only high avidity antigen-antibody complexes. After the chaotropic agents are added, low avidity antigen-antibody complexes are destabilized; therefore, the remaining bonded antigen-antibody complexes demonstrate the existence of a high avidity neutralizing antibodies. In certain embodiments, the designation of high or low avidity is a relative designation and not indicative of a specific binding strength. The avidity designation can be relative to other antibodies in the multiplex assay or to antibodies in separate assays. The designation can be determined by adding one or more chaotropic agents to an assay and determining which antibodies remain bound to an antigen. The chaotropic agents can vary in concentration in order to distinguish relative antibody avidity.
The multiplex assay disclosed herein can detect and/or quantify the amount of specific neutralizing antibodies bound to substrates onto which SARS-CoV-2 spike protein variants or fragments thereof are immobilized and, optionally, detect and/or quantify one or more cytokine selected from IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α (e.g., any combination of one, two, three, four, five, six, seven, eight, nine, ten, or eleven of these analytes) present in a biological sample. In another embodiment, this application provides a multiplex assay that can detect and/or quantify the amount of specific, neutralizing, high avidity antibodies bound to substrates onto which a SARS-CoV-2 spike protein or fragment thereof and/or a SARS-CoV-2 spike protein variant or fragment thereof are immobilized.
Various of the presently described assays offer detection in at least two dimensions, e.g., the identity of the immobilizing bead (e.g., beads bearing a single SARS-CoV-2 spike protein variant or fragment thereof and the presence and/or amount of antibody and/or high avidity neutralizing antibody bound to a SARS-CoV-2 spike protein or fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof immobilized on the beads and, optionally, the presence and/or amount of one or more cytokine selected from IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α (e.g., any combination of one, two, three, four, five, six, seven, eight, nine, ten, or eleven of these analytes). This multidimensional aspect allows for a multiplex format, so that more than one analyte can be detected in a single assay.
Thus, one aspect of the invention provides for combinations of substrate populations. These substrate combinations are made up of two or more (e.g., two, three, four, five, six, seven or more) distinct and unique detectable physical parameters (e.g., dye signatures), each distinct and unique detectable physical parameter being associated with a single substrate population.
In some embodiments, the presence and/or amount of neutralizing antibody, protective antibody, high avidity protective antibody, and/or high avidity neutralizing antibody specific to a SARS-CoV-2 spike protein or fragment thereof and/or a SARS-CoV-2 spike protein variant or fragment thereof and, optionally, the presence and/or amount of one or more cytokine are measured in the same single receptacle or vessel (tube, well, cuvette, etc.) in the presence of beads. As discussed above, each bead population carries a specific detectable physical parameter (e.g., dye signature) and a SARS-CoV-2 spike protein variant or fragment thereof or, in some embodiments, a SARS-CoV-2 spike protein or fragment thereof. Thus, the beads can carry a single SARS-CoV-2 spike protein variant or fragment thereof. Bead populations that carry a specific detectable physical parameter (e.g., dye signature) can also be used to detect the presence of a cytokine.
For detecting cytokines present in a sample, cytokine specific antibodies can be immobilized on a solid support (e.g., microparticles, beads, or surface, such as a chip, microtiter plate, membrane, or glass). In some immobilization protocols, carboxylated beads can be activated and esterified before adding antibodies and/or a SARS-CoV-2 spike protein variant or fragment thereof. Carboxyl activation can be achieved using a water soluble carbodiimide, such as 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide (CMC). Esterification can be achieved using NHS, NHSS or HOBt. After the carboxyl activation and esterification, the antibodies and SARS-CoV-2 spike protein variant or fragment thereof can added to the activated surface in buffers with pH between 6-10. For example sodium acetate buffer pH 5.1, phosphate buffer pH 7.0 with or without detergent (e.g., CHAPS, ionic and zwitterionic detergents). After coupling/immobilization, the solid support can be blocked in buffers containing protein blocker (such as BSA, mouse IgG, bovine gamma globulin (BGG), animal serum (goat, horse, murine)). The protein blocker(s) can be present in amounts ranging from 0.1-10 weight/volume percent.
A first aspect and second aspect of the invention provides a pair of immunoassays. These immunoassay formats provide for the detection of neutralizing antibodies specific for a SARS-CoV-2 spike protein variant or fragment thereof and, optionally, the presence and/or amounts of one or more cytokine. In these immunoassays, a solid support (for example, fluorescently labeled beads (also referred to as dyed beads) that can be distinguished from one another via a different fluorescent dye/signature) is coated with a SARS-CoV-2 spike protein variant or fragment thereof. Another dyed bead (which is differentially labeled) can be coated with one or more antibody specific for a cytokine where cytokines are being detected. The coated solid support(s) are then combined with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 virus, along with a sample diluent and incubated to facilitate the binding neutralizing antibodies capable of specifically binding to a SARS-CoV-2 spike protein variant or fragment thereof on the coated solid supports. Labeled ACE2 receptor, including truncated, modified ACE2 receptors or ACE2 fusion proteins (e.g., ACE2R-Fc), can, optionally, be incubated along with the sample. In another optional embodiment, the coated solid support(s) is washed to remove unbound sample and labeled ACE2 receptor is then added to the coated solid support(s). Other embodiments omit that addition of labeled ACE2 receptor to the coated solid substrate(s). After incubation, unbound sample can be washed away and labeled anti-Ig (anti-IgG, IgM, IgA, anti-kappa, or anti-lambda) antibodies can be added to allow for detection of neutralizing antibodies from the sample bound to SARS-CoV-2 spike protein variants or fragments thereof immobilized on the solid support. Where one or more cytokine is being detected or quantified in combination with of antibodies that neutralize SARS-CoV-2 spike protein variants or fragments thereof, labeled antibodies specific to the selected cytokine(s) can be used to detect the presence or quantify the cytokine(s). The reaction can be incubated and washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex platforms, such as LX-200, Magpix, Flexmap 360, etc. The identity of each assay is determined by the fluorescence signature of the dyed beads, and the amount of a neutralizing antibody captured by the antigen or cytokine is determined by the fluorescence intensity of the attached labeled anti-Ig. The sample fluorescence intensity is compared to a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. Results for each coated protein may be reported individually, as a group or some type of predefined algorithm or any combination thereof. As discussed above, the biological sample can be obtained from a SARS-CoV2 infected individual, an individual treated with neutralizing antibodies specific for SARS-CoV-2 spike protein variants or fragments or an individual vaccinated with a vaccine comprising SARS-CoV2 spike protein, such as the spike protein variants or fragments thereof that are disclosed herein.
In a second aspect of the invention, ACE2 receptor (preferably human ACE2 receptor and/or including truncated, modified ACE2 receptors, or ACE2 fusion proteins) can be used to identify substrates on which SARS-CoV-2 spike protein variants or fragments thereof are immobilized and to which no neutralizing antibodies are bound. This multiplex assay is illustrated in FIG. 1. In this aspect of the invention, the ACE2 receptor can be labeled or unlabeled. Thus, one embodiment provides a population of beads comprising one or more subpopulations of beads onto which SARS-CoV-2 spike protein variants or fragments thereof are immobilized. This population of beads is mixed (contacted) with mixture of ACE2 receptor and a sample or the population of beads is first contacted with a sample, the population of beads is washed and ACE2 receptor is then added to the washed population of beads. After incubation of the washed population of beads with the ACE2 receptor, the population of beads is washed and then contacted with biotinylated antibodies specific for ACE2 receptor. The population of beads is washed to remove unbound biotinylated antibody and streptavidin-PE is added to the population of beads. The population of beads can be washed and then compared to control samples. A negative signal (the absence of a signal or a reduced signal for a SARS-CoV2 spike protein, a given SARS-CoV-2 spike protein variant or fragment thereof) indicates the existence of the neutralizing antibodies in the sample. The biological sample can be obtained from a SARS-CoV2 infected individual, an individual treated with neutralizing antibodies specific for SARS-CoV-2 spike protein variants or fragments or an individual vaccinated with a vaccine comprising SARS-CoV2 spike protein, such as the spike protein variants or fragments thereof that are disclosed herein.
A second embodiment utilizes labeled ACE2 receptor, including truncated and/or modified ACE2 receptors, or ACE2 fusion proteins, for the detection SARS-CoV-2 spike protein variants or fragments thereof to which no neutralizing antibody is bound. In this embodiment, a population of beads comprising one or more subpopulations of beads onto which SARS-CoV-2 spike protein variants or fragments thereof are immobilized is provided. This population of beads is mixed (contacted) with mixture of labeled ACE2 receptor and a sample or the population of beads is first contacted with a sample, the population of beads is washed and labeled ACE2 receptor is then added to the washed population of beads. The population of beads is washed to remove unbound labeled-ACE2 receptor and serum proteins (e.g., antibodies) and then compared to control samples. A negative signal (the absence of a signal or a reduced signal for a SARS-CoV-2 spike protein, a given SARS-CoV-2 spike protein variant or fragment thereof) indicates the existence of the neutralizing antibodies in the sample. The biological sample can be obtained from a SARS-CoV2 infected individual, an individual treated with neutralizing antibodies specific for SARS-CoV-2 spike protein variants or fragments or an individual vaccinated with a vaccine comprising SARS-CoV2 spike protein, such as the spike protein variants or fragments thereof that are disclosed herein.
A third aspect of the invention provides immunoassays for the detection of high avidity antibodies. In these immunoassays, a solid support (for example, fluorescently labeled beads (also referred to as dyed beads) that can be distinguished from one another via a different fluorescent dye/signature) is coated with a SARS-CoV-2 spike protein or a fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof. The coated solid support(s) are then combined with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 virus, along with a sample diluent and incubated to facilitate the binding of neutralizing antibodies capable of specifically binding to a SARS-CoV-2 spike protein or a fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof on the coated solid supports. The biological sample is then removed from the solid support and, optionally washed to remove unbound proteins and antibodies. One or more chaotropic agent (e.g., 1 M NaCL) is then added to the solid support to displace low avidity antibody. After an incubation period, the chaotropic agent(s) and unbound low avidity antibodies are removed (e.g., by centrifugation and aspiration) from the coated solid supports and the coated solid supports can be washed. The coated solid support(s) is washed and labeled or biotinylated ACE2 receptor is then added to the coated solid support(s) and a signal is detected. The presence of high avidity antibodies is determined by a reduced signal or the lack of signal from the labeled ACE2 receptor (relative to a control). The one or more chaotropic agents can be used at a concentration of about 0.1M to about 8M, when added to the coated solid supports to which antibodies are bound. Non-limiting examples of the chaotropic agents are sodium chloride, urea, guanidine hydrochloride, guanidine thiocyanate and/or or sodium thiocyanate. The effective concentrations of urea and/or sodium thiocyanate can be between 0.1M and 8M. The effective concentration of guanidine thiocyanate can be between 0.1M and 6M. The effective concentrations of sodium chloride can be between 0.1M and 5M. Then, labeled streptavidin-PE (Phycoerythrin) can be added to allow for detection.
The relative “high” or “low” avidities can be determined by comparing the signals between two or more antibody subpopulations. The signals of the two or more antibody subpopulations can be measured throughout the assay, i.e. before and after the addition of the chaotropic agent. Alternatively, the signals of the two or more antibody subpopulations can be measured at the conclusion of the assay.
Other embodiments omit the addition of labeled ACE2 receptor to the coated solid substrate(s) and utilize labeled anti-Ig antibodies for the detection of high avidity antibodies. In this embodiment, after incubation with one or more chaotropic agent, low avidity antibodies and chaotropic agent are removed and/or washed away and labeled anti-Ig (anti-IgG, IgM, IgA, anti-kappa, or anti-lambda) antibodies can be added to allow for detection of high avidity binding antibodies from the sample that are bound to a SARS-CoV-2 spike protein or fragments thereof or SARS-CoV-2 spike protein variants or fragments thereof immobilized on the solid support. The presence of a signal indicates the presence of high avidity antibodies within the sample, which can be quantified by comparison to control samples. The one or more chaotropic agents can be used at a concentration of about 0.1M to about 10M, when added to the coated solid supports to which antibodies are bound. Non-limiting examples of the chaotropic agents are sodium chloride, urea, guanidine hydrochloride, guanidine thiocyanate, and/or or sodium thiocyanate.
A fourth aspect of the invention provides singleplex immunoassays for the detection neutralizing antibodies. In these immunoassays, a solid support (for example, fluorescently labeled beads (also referred to as dyed beads) is coated with a SARS-CoV-2 spike protein or a fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof. The coated solid support is then combined with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 virus, along with a sample diluent and incubated to facilitate the binding of neutralizing antibodies capable of specifically binding to a SARS-CoV-2 spike protein or a fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof on the coated solid supports. The biological sample is then removed from the solid support and, optionally washed to remove unbound proteins and antibodies. The coated solid support is washed and labeled or biotinylated ACE2 receptor is then added to the coated solid support and a signal is detected. The presence of neutralizing antibodies is determined by a reduced signal or the lack of signal from the labeled ACE2 receptor (relative to a control).
Detection of labeled ACE2 receptor or labeled anti-Ig can be performed using a Bio-Plex 2200, Bio-Plex 200 or Luminex platforms, such as LX-200, Magpix, Flexmap 360, etc. The identity of each assay is determined by the fluorescence signature of the dyed beads, and the amount of high avidity neutralizing antibody captured by the SARS-CoV-2 spike protein or fragment thereof or a SARS-CoV-2 spike protein variant or fragment thereof is determined by the fluorescence intensity of the attached labeled anti-Ig or the labeled ACE2 receptor. The sample fluorescence intensity is compared to a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. Alternatively, the neutralizing concentration of the antibody—the concentration at which 50% of the antigens are neutralized—can be determined using serial dilutions. Results for each coated protein may be reported individually, as a group or some type of predefined algorithm or any combination thereof. As discussed above, the biological sample can be obtained from a SARS-CoV2 infected individual, an individual treated with neutralizing and/or protective antibodies specific for SARS-CoV-2 spike protein variants or fragments or an individual vaccinated with a vaccine comprising SARS-CoV2 spike protein, such as the spike protein variants or fragments thereof that are disclosed herein. As discussed above, each of the disclosed immunoassays can utilizes SARS-CoV-2 spike protein variants or fragments thereof as an analyte. In the context of the invention, a fragment of any particular SARS-CoV-2 spike protein variant can comprise about 5 to about 50, about 10 to about 40, about 15 to about 30, about 20, about 10 or about 5 amino acids, provided that the span of amino acids includes one or more amino acid mutation identified in Table 1. As discussed above, fragments of a SARS-CoV-2 spike protein variant can range in length from 5 amino acids to (n−1) consecutive amino acids of the protein, where n is the total length of the SARS-CoV-2 spike protein, the S1 fragment of the spike protein or the S2 fragment of the spike protein. Thus, for the spike protein, the fragment length is between 5 and 1272 consecutive amino acids in length. In one embodiment, a fragment of the spike protein spans amino acids 13-1213 of the spike protein sequence. In another embodiment, the fragment is the RBD of the S1 protein or a fragment of the RBD. For the S1 protein (amino acids 13-685 of the disclosed spike protein length), a fragment is between 5 and 672 consecutive amino acids of the S1 sequence. For the S2 protein (amino acids 686-1273 of the disclosed spike protein), the fragment length is between 5 and 588 consecutive amino acids in length.








SARS-CoV-2 Spike Protein (1273 AA MW 141178)



SARS-CoV-2 S1 Protein (AA 13-685)


SARS-CoV-2 S2 Protein (AA 686-4273)


SEQ ID NO: 1



MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNV



 


TWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNAT


 


NVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF


 


KNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY


 


LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEK


 


GIYQTSNFRVQPTESIVRFPNITNLCPFGEVXMATRFASVYAWXRKRISNCVADYSXLYNSA


 


SFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVI


 


XWNSNNLDSKVGGNYNYLYRLFRXSNLKPFERDISTEIYQAGSTPCNGXEGFNCYFPLQSYG


 


FQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK


 


FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV


 


PVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPR


 


XAXSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEXLPVSMTKTSVDCTMYICG


 


DSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQIL


 


PDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDE


 


MIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSA


 


IGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDXXEAEVQ


 


IDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQ


 


SAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT


 


TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVN


 


IQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSC


 


CSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT


 


>QJF75467.1 surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]


SARS-CoV-2 Spike Protein (1273 AA MW 141178)


SARS-CoV-2 S1 Protein (AA 13-685)


SARS-CoV-2 S2 Protein (AA 6861273)


SEQ ID NO: 2



MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNV



 


TWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNAT


 


NVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF


 


KNLRSFVFKNIDGYFKIYSKHTPINLVRQLPQGFSALEPLVDLPIGINITRFQTLLALHRSY


 


LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEK


 


GIYQTSNFRVQPTESIVRFPNITNLCPFGEVXNATRFASVYAWXRKRISNCVADYSXLYNSA


 


SFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLFDDFTGCVI


 


XWNSNNLDSKVGGNYNYLYRLFRXSNLKPFERDISTEIYQAGSTPCNGXEGFNCYFPLQSYG


 


FQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK


 


FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV


 


PVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPR


 


XAXSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICG


 


DSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQIL


 


PDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDE


 


MIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSA


 


IGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDXXEAEVQ


 


IDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQ


 


SAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT


 


TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVN


 


IQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSC


 


CSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT


 


YP_909724390.1 surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]


SARS-CoV-2 Spike Protein (1273 AA MW 141178)


SARS-CoV-2 S1 Protein (AA 13-685)


SARS-CoV-2 S2 Protein (AA 686-1273)


SEQ ID NO: 3



MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNV



 


TWFHAIHVSGTNGTKRFDNPVLPFMDGVYFASTEKSMIIRGWIFGTTLDSKTQSLLIVNNAT


 


NVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF


 


KNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY


 


LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEK


 


GIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSA


 


SFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVI


 


AWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYG


 


FQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK


 


FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEV


 


PVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPR


 


RAR/SVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDGTMYIC


 


GDSTSCSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQI


 


LPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTD


 


EMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNS


 


AIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEV


 


QIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFP


 


QSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQII


 


TTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVV


 


NIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTS


 


CCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT


 


ACE2 [Homo sapiens]


GenBank: BAB40370.1


>BAB40370.1 ACE2 [Homo sapiens]


SEQ ID NO: 4



MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNM



 


NNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMS


 


TIYSTGKVCNPDNPQECLLLEPGLNEIMANSIDYNERLWAWESWRSEVGKQLRPLYEEYVVL


 


KNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKL


 


MNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKE


 


AEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTA


 


HHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNET


 


EINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDET


 


YCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML


 


RLGKSEPWTIALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKV


 


RISLKSALGDRAYEWMDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFN


 


FFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVSIWLI


 


VFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENPYASIDISKGENNPGFQNTDDVQTSF






Various non-limiting embodiments include:
1. A substrate comprising a population of particles or beads comprising two or more separate subpopulations of particles or beads, each subpopulation of particles or beads being distinguishable by a specific detectable parameter and each subpopulation of beads comprising a distinct SARS-CoV-2 spike protein variant or fragment thereof immobilized thereon and, optionally, a further subpopulation of beads comprising a SARS-CoV-2 spike protein or fragment thereof immobilized thereon.
2. The substrate according to embodiment 1, wherein said substrate is glass, plastic, polystyrene or nitrocellulose.
3. The substrate according to embodiment 1 or 2, wherein said substrate is a particle.
4. The substrate according to embodiment 1 or 2, wherein said substrate is a bead.
5. The substrate according to embodiment 4, wherein said population comprises two or more separate subpopulations of particles or beads selected from:
a) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation V367X immobilized on a first particle or bead having a first specific detectable physical parameter, where X is any amino acid or X is F;
b) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation F342X immobilized on a second particle or bead having a second specific detectable physical parameter, where X is any amino acid or X is L;
c) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation A435X immobilized on a third particle or bead having a third specific detectable physical parameter, where X is any amino acid or X is S;
d) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation K458X immobilized on a fourth particle or bead having a fourth specific detectable physical parameter, where X is any amino acid or X is R;
e) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation V483X immobilized on a fifth particle or bead having a fifth specific detectable physical parameter, where X is any amino acid or X is A;
f) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation V483X immobilized on a sixth particle or bead having a sixth specific detectable physical parameter, where X is any amino acid or X is A;
g) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation N354X immobilized on a seventh particle or bead having a seventh specific detectable physical parameter, where X is any amino acid or X is D;
h) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutations R683X1 and/or R685X2 immobilized on an eighth particle or bead having an eighth specific detectable physical parameter, where X1 and X2 are any amino acid or X1 and X2 are A;
i) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutations K986X3 and/or V987X4 immobilized on a ninth particle or bead having a ninth specific detectable physical parameter, where X3 and X4 are any amino acid or X3 and X4 are P;
j) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutations R683X1, R685X2, K986X3, and V987X4 immobilized on a tenth particle or bead having a tenth specific detectable physical parameter, where X1 is any amino acid or X1 is A; X2 is any amino acid or X2 is A; X3 is any amino acid or X3 is P; and X4 is any amino acid or X4 is P; and
k) a SARS-CoV-2 spike protein or fragment thereof immobilized on an eleventh particle or bead having an eleventh specific detectable physical parameter.
6. The substrate according to embodiment 5, wherein said population of particles or beads comprises two, three, four, five, six, seven, eight, nine, ten or more subpopulations of particles or beads, each subpopulation having a specific detectable physical parameter.
7. The substrate according to any one of embodiments 4-6, wherein the specific detectable physical parameter is a fluorescent dye (fluorophore), luminescent agent, electron-dense reagent, radioisotope or particle size.
8. The substrate according to embodiment 7, wherein the specific detectable parameter is a fluorophore.
9. A method for detecting neutralizing and/or protective antibodies in a mammal comprising obtaining a biological sample from the mammal, contacting said biological sample with a substrate comprising a substrate according to any one of embodiments 1-8 and detecting the presence or absence of neutralizing antibodies bound to SARS-CoV-2 spike protein variants or fragments thereof on the surface of said substrate.
10. The method according to embodiment 9, wherein the mammal is a human, non-human primate, canine, or feline.
11. The method according to any one of embodiments 9-10, wherein the presence or absence of neutralizing antibodies comprises contacting the substrate with human ACE2 receptor and detecting the presence or absence of ACE2 receptor binding to substrate subpopulations onto which SARS-CoV-2 spike protein variants or fragments thereof have been immobilized, the detection of ACE2 receptor binding to a substrate subpopulation indicated a lack of neutralizing antibody specific for a specific a SARS-CoV-2 spike protein variant or fragment thereof.
12. The method according to embodiment 11, wherein ACE2 receptor binding to a substrate subpopulation is detected using an antibody specific for ACE2 receptor that is detectably labeled.
13. The method according to embodiment 11, wherein ACE2 receptor binding to a substrate subpopulation is detected using ACE2 receptor that is detectably labeled.
14. The method according to embodiment 13, wherein the ACE2 receptor is labeled with phycoerythrin (PE) or is biotinylated and detected using streptavidin-PE.
15. The method according to embodiment 9 or 10, wherein neutralizing antibody bound to a substrate comprising a given a SARS-CoV-2 spike protein variant or fragment thereof is detected using a species specific anti-immunoglobulin (Ig) antibody.
16. The method according to embodiment 15, wherein the anti-Ig antibody is biotinylated and binding to neutralizing antibody is detected with a labeled avidin or streptavidin.
17. The method according to embodiment 15, wherein the anti-Ig antibody is labeled.
18. The method according to embodiment 16 or embodiment 17, wherein the label is a fluorophore.
19. The method according to embodiment 18, wherein the fluorophore is PE.
20. The method according to any one of embodiments 9-19, said method further comprising detecting the presence, absence or amounts of cytokines selected from IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α in said biological sample.
21. The method according to embodiment 20, wherein the detection of said one or more cytokine comprises contacting one or more subpopulations of beads onto which cytokines are immobilized by an antibody specific for each selected cytokine and detecting bound cytokine with antibodies specific for the cytokine and determining the fluorescence intensity for each subpopulation of beads to which cytokines are bound.
22. The method according to embodiment 21, the sample fluorescence intensity is compared to a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result.
23. The method according to any one of embodiments 20-22, wherein said detection comprises contacting the substrate contacted with said biological sample with anti-immunoglobulin (anti-Ig) antibodies and, optionally, cytokine specific antibodies that are detectably labeled with a fluorescent dye (fluorophore), luminescent agent, electron-dense reagent, or radioisotope.
24. The method according to embodiment 23, wherein said anti-Ig antibodies are detectably labeled with a fluorophore and said anti-cytokine antibodies are labeled with a fluorophore, and when assayed, and the sample fluorescence intensity is compared to a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result.
25. The method according to any one of embodiments 20-22, wherein said detection comprises contacting the substrate contacted with said biological sample with anti-Ig antibodies and cytokine specific antibodies, when assayed, that are biotinylated and contacting said biotinylated antibodies with a biotin-binding ligand that is detectably labeled and determining the fluorescence intensity for each subpopulation of beads.
26. The method according to embodiment 25, the sample fluorescence intensity is compared to a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result of total Ig bound to said substrate.
27. The method according to any one of embodiments 20-26, wherein said one or more cytokine is IL-6 and/or IL-2R.
28. The method according to any one of embodiments 20-27, wherein said one or more cytokine is selected from IL-6, IL-2R, granulocyte colony-stimulating factor, IP-10, MCP-1, macrophage inflammatory protein-1A, TNF-α, and combinations thereof.
29. The method according to any one of embodiments 9-28, wherein the neutralizing antibody is a polyclonal antibody or a monoclonal antibody.
30. The method according to embodiment 29, wherein the polyclonal or monoclonal antibody is a human polyclonal or a human monoclonal antibody.
31. The method according to embodiment 29, wherein the neutralizing antibody is a recombinant antibody selected from a humanized antibody, a chimeric antibody, a CDR-grafted antibody, a nanobody, a Fv, a single domain antibody, such as a VH, a VL or VHH, a scFv, a bi-valent antibody, a tri-valent antibody, a tetra-valent antibodies, bis-scFv, diabodies, triabodies, tetrabodies and fragments thereof, provided that at least one of the antigen binding portions of said bi-valent antibody, tri-valent antibody, tetra-valent antibody, bis-scFv, diabodies, triabodies, tetrabodies or fragments thereof neutralizes a SARS-CoV-2 spike protein variant or fragment thereof.
32. A method for detecting high avidity neutralizing antibodies in a mammal comprising obtaining a biological sample from the mammal, contacting said biological sample with a substrate comprising a substrate according to any one of embodiments 1-8 and detecting the presence or absence of high avidity neutralizing antibodies bound to SARS-CoV-2 spike protein variants or fragments thereof on the surface of said substrate.
33. The method according to embodiment 32, wherein the mammal is a human, non-human primate, canine, or feline.
34. The method according to any one of embodiment 32-33, wherein the method comprises:
a) contacting the substrate with the biological sample;
b) optionally removing the biological sample from the substrate and washing the substrate to remove unbound material and antibody;
c) contacting the substrate with one or more chaotropic agents;
d) removing the one or more chaotropic agents from the substrate;
e) optionally, washing the substrate; and
f) detecting the presence or absence of high avidity neutralizing antibody binding to substrate subpopulations onto which SARS-CoV-2 spike protein or fragments thereof and SARS-CoV-2 spike protein variants or fragments thereof have been immobilized.
35. The method according to embodiment 34, wherein the chaotropic agent is sodium chloride, sodium thiocyanate, and/or urea.
36. The method according to embodiments 32-35, wherein the method comprises detecting SARS-CoV-2 spike protein or fragments thereof and/or SARS-CoV-2 spike protein variants or fragments thereof present on the substrate with an ACE2 receptor.
37. The method according to embodiment 36, wherein ACE2 receptor binding to the substrate is detected using ACE2 receptor that is detectably labeled or with an antibody specific for the ACE2 receptor that is detectably labeled.
38. The method according to embodiment 37, wherein the ACE2 receptor is labeled with phycoerythrin (PE) or is biotinylated and detected using streptavidin-PE.
39. The method according to any one of embodiments 32-35, wherein high avidity neutralizing antibody bound to a substrate comprising a given a SARS-CoV-2 spike protein or fragment thereof and/or a SARS-CoV-2 spike protein variant or fragment thereof is detected using a species specific anti-immunoglobulin (Ig) antibody.
40. The method according to embodiment 39, wherein the anti-Ig antibody is biotinylated and binding to neutralizing antibody is detected with a labeled avidin or streptavidin.
41. The method according to embodiment 39, wherein the anti-Ig antibody is labeled.
42. The method according to embodiment 40 or embodiment 41, wherein the label is a fluorophore.
43. The method according to embodiment 42, wherein the fluorophore is PE.
44. A method for detecting a neutralizing antibody in a mammal comprising obtaining a biological sample from the mammal, contacting said biological sample with a substrate according to embodiment 1 and detecting the presence or absence of a neutralizing antibody bound to a SARS-CoV-2 spike protein variant or fragment thereof on the surface of said substrate, said biological sample being obtained from individuals suspected of infection by the virus, treated with SARS-CoV-2 neutralizing antibodies or convalescent plasma, or immunized with a vaccine comprising the SARS-CoV2 spike protein.
45. The method according to embodiment 44, wherein the mammal is a human, non-human primate, canine, or feline.
46. The method according to any one of embodiment 44-45, wherein the method comprises:
a) contacting the substrate with the biological sample;
b) optionally removing the biological sample from the substrate and washing the substrate to remove unbound material and antibody; and
c) detecting the presence or absence of a neutralizing antibody binding to a substrate population onto which a SARS-CoV-2 spike protein or fragment thereof or SARS-CoV-2 spike protein variant or fragment thereof has been immobilized.
47. The method according to embodiments 44-46, wherein the method comprises detecting a SARS-CoV-2 spike protein or fragment thereof or SARS-CoV-2 spike protein variant or fragment thereof present on the substrate with an ACE2 receptor.
48. The method according to embodiment 47, wherein ACE2 receptor binding to the substrate is detected using ACE2 receptor that is detectably labeled or with an antibody specific for the ACE2 receptor that is detectably labeled.
49. The method according to embodiment 48, wherein the ACE2 receptor is labeled with phycoerythrin (PE) or is biotinylated and detected using streptavidin-PE.
50. The method according to embodiment 49, wherein the ACE2 receptor is a biotinylated ACE2-Fc fusion and is detected using streptavidin-PE.
51. The method according to any preceding embodiment, wherein the ACE2 receptor is a truncated or modified ACE2 receptor or is an ACE2 receptor fusion protein.
52. The method according to embodiment 51, wherein the ACE2 receptor fusion protein comprises an immunoglobulin Fc domain fused to the carboxyl-terminus of the ACE2 receptor.
53. The method according to embodiment 52, wherein the fusion protein is biotinylated on the Fc domain.
EXAMPLES
Example 1—Measurement of Neutralizing Antibodies Specific for SARS-CoV-2 Spike Protein Variants or Fragments Thereof
A population of fluorescently labeled beads comprising a plurality of subpopulations of fluorescently labeled beads to which individual SARS-CoV-2 spike protein variants or fragments thereof are immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine comprising SARS-CoV2 spike protein along with a sample diluent. After incubation unbound sample was washed away and biotinylated human ACE2 receptor is added to the washed beads and incubated. Unbound biotinylated human ACE2 receptor is then washed away and labeled streptavidin-PE (Phycoerythrin) is added. The reaction is incubated and then washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. A lack of signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof are present in the sample. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are no neutralizing antibodies in the sample.
FIG. 4 shows percent inhibition of the RBD-biotinylated ACE2 interaction by sera from two COVID-19 patients. Samples were diluted serially in the base matrix and tested for the presence of neutralizing antibodies by the Bio-Plex 2200 assay. The neutralization potency was quantified by calculating the half maximal inhibitory concentration (IC50) of each sample. The percent inhibition is calculated using the following formula: 1−(RFI of each diluted samples/Matrix RFI). Sample 1 showed an IC50 at a 0.135 dilution, sample 2 demonstrated an IC50 at 0.110 dilution of the original sample. These results support the utility of the Bio-Plex 2200 assay in quantitating neutralizing antibodies.
Example 2—Multiplex Detection of Neutralizing Antibodies Specific for SARS-CoV-2 Spike Protein Variants or Fragments Thereof
A population of fluorescently labeled beads comprising a plurality of subpopulations of fluorescently labeled beads to which individual SARS-CoV-2 spike protein variants or fragments thereof are immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine comprising SARS-CoV2 spike protein along with a sample diluent. After incubation unbound sample was washed away and human ACE2 receptor is added to the washed beads and incubated. Unbound human ACE2 receptor is then washed away. Biotinylated antibody specific for human ACE2 receptor is added. The reaction is incubated and then washed and streptavidin-PE is added to the washed population of beads and incubated. After incubation, the population of beads is washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. A lack of signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof are present in the sample. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are no neutralizing antibodies in the sample.
Example 3—Multiplex Detection of Neutralizing Antibody for SARS-CoV-2 Spike Protein Variants or Fragments Thereof and IL-6
A population of fluorescently labeled beads comprising: 1) a subpopulation of fluorescently labeled beads to which antibodies specific to IL-6 have been immobilized; and 2) one or more subpopulations of fluorescently labeled beads to which SARS-CoV-2 spike protein variants or fragments thereof have been immobilized is combined with patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 virus or a biological sample from a subject vaccinated with a vaccine comprising spike protein. After incubation unbound sample is washed away. Biotinylated antibody specific for IL-6 and biotinylated human ACE2 receptor is added to the washed beads and allowed to incubate. The biotinylated antibody binds to IL-6 bound to the beads on which antibodies specific to IL-6 have been immobilized and biotinylated human ACE2 receptor binds to SARS-CoV-2 spike protein variant or fragment thereof immobilized on a relevant subpopulation of beads to which no neutralizing antibody is bound. Unbound biotinylated reagents are then washed away and labeled streptavidin-PE (phycoerythrin) is added to allow for detection of IL-6 in the sample and beads to which no neutralizing antibody was bound to a given SARS-CoV-2 spike protein variant or fragment thereof. The reaction is incubated and then washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The identity of bead subpopulation is determined by the fluorescence signature of the dyed beads, and the amount and/or presence of IL-6 is determined by the fluorescence intensity of the bound labeled Streptavidin. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. A lack of signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof are present in the sample. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are no neutralizing antibodies in the sample.
Example 4—Multiplex Detection of Neutralizing Antibodies Specific for SARS-CoV-2 Spike Protein Variants or Fragments Thereof and IL-6
A population of fluorescently labeled beads comprising: 1) one or more subpopulations of fluorescently labeled beads to which SARS-CoV-2 spike protein variants or fragments thereof have been immobilized; and 2) a subpopulation of fluorescently labeled beads to which monoclonal and/or polyclonal antibodies specific for IL-6 have been immobilized is combined with patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 virus or immunized with a SARS-CoV-2 vaccine comprising spike protein. After incubation unbound sample is washed away. Human ACE2 receptor is added to the washed beads and allowed to incubate. Unbound human ACE2 receptor is washed away and biotinylated antibody specific for human ACE 2 and biotinylated antibody specific for IL-6 is added to the washed beads and allowed to incubate. The biotinylated antibody binds to IL-6 bound to antibodies immobilized on its respective bead subpopulation and human ACE2 bound to one or more subpopulations of beads onto which a given spike protein variant or fragment thereof that has been immobilized and to which no neutralizing antibody may then be detected by the addition of streptavidin-labeled PE. Unbound biotinylated reagents are then washed away and labeled streptavidin-PE (Phycoerythrin) is added to allow for detection of IL-6 and bound neutralizing antibody specific for a spike protein variant or fragment thereof. The reaction is incubated and then washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The identity of bead subpopulation is determined by the fluorescence signature of the dyed beads, and the amount of IL-6 captured is determined by the fluorescence intensity of the bound labeled streptavidin. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. A lack of signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof are present in the sample. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are no neutralizing antibodies in the sample.
Example 5—Multiplex Detection of Neutralizing Antibodies Specific for SARS-CoV-2 Spike Protein Variants or Fragments Thereof
A population of fluorescently labeled beads comprising a plurality of subpopulations of fluorescently labeled beads to which individual SARS-CoV-2 spike protein variants or fragments thereof are immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine comprising SARS-CoV2 spike protein along with a sample diluent. After incubation unbound sample was washed away and biotinylated antibody specific for human immunoglobulin (anti-IgA, anti-IgM, anti-IgG, anti-kappa chain, and/or anti-lambda chain antibody) is added to the washed beads and incubated. Unbound biotinylated anti-human antibody is then washed away and labeled streptavidin-PE (Phycoerythrin) is added. The reaction is incubated and then washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result. A lack of signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that no neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof are present in the sample. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are neutralizing antibodies in the sample and the amount of neutralizing antibody can also be quantified. The sample fluorescence intensity can be compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result for the amount of neutralizing antibody present in the sample.
Example 6—Multiplex Detection of High Avidity Neutralizing Antibodies Specific for SARS-CoV-2 Spike Protein Variants or Fragments Thereof
A population of fluorescently labeled beads comprising a plurality of subpopulations of fluorescently labeled beads to which individual SARS-CoV-2 spike protein variants or fragments thereof are immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine. A SARS-CoV-2 neutralization assay combines an aliquot of patient sample, chaotropic agent sample diluent at various concentrations, and a biotinylated-human ACE2 protein. Following a short incubation, a bead mixture comprising coupled SARS-CoV-2 spike protein variants, RBD, and mutant variants or fragments thereof are added to the reaction vessel. After a period of incubation at about 37° C., the mixture is washed and the beads are suspended in streptavidin-PE conjugate reagent; the mixture is again incubated at 37° C. The excess unbound conjugate is removed in another wash cycle and the washed beads are resuspended in a wash buffer. The identity of the dyed beads is determined by the fluorescence of the dyes and the amount of biotinylated-human ACE2 captured by the SARS-CoV-2 spike protein variants, RBD and mutant variants or fragments thereof. The fluorescence of the attached phycoerythrin is determined using the Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform to detect binding of biotinylated ACE2 receptor. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate the relative fluorescence intensity (RFI) and, subsequently, a qualitative, semi-quantitative or quantitative result. A lack of signal or a reduced signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein (or fragment thereof) or a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates the presence of high avidity neutralizing antibodies and the amount of high avidity antibodies can also be quantitated. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are no neutralizing antibodies or there are low avidity neutralizing antibodies in the sample.
Table 3 shows percent inhibition in the presence and in the absence of a chaotropic agent (sodium chloride). While some COVID-19 samples show loss of neutralization effect in the presence of the chaotropic agent, other samples show no effect. Collectively, these results indicate the presence of high avidity antibodies that are not impacted by 1M sodium chloride. The determination of high avidity antibodies in a biological sample can provide additional diagnostic certainty in differentiating protective and/or sterilizing antibodies.











TABLE 3










BioPlex Neutralization Assay













BioPlex seology
RBD (% Inhibition)
S1 (% Inhibition)




IgG assay
(c/o: 20%)
(c/o: 14%)















Sample ID
RBD (Al)
S1 (Al)
High salt
Low Salt
High salt
Low Salt
Notes

















CV2QS103
95.0
64.3
 5%
55%
 6%
49%
Inhibition of Neutralization


CV2QS119
115.9
70.9
 0%
21%
 0%
17%
by high salt


CV2QS128
96.5
52.2
17%
25%
12%
21%
(Probably-Low avidity Ab)


CV2QS160
86.2
32.9
11%
28%
11%
17%



CV2QS186
95.5
65.1
13%
40%
17%
36%



CV2QS117
407.4
287.0
21%
72%
24%
69%
Neutralization reduced


CV2QS135
362.9
251.6
25%
43%
32%
44%
appreciably by high salt









(Probably-Low avidity Ab)









Note: High analyte specific IgG Ab


CV2QS101
277.9
222.6
73%
84%
71%
82%
No effect of high salt on


CV2QS126
322.3
209.8
62%
56%
57%
53%
neutralization


CV2QS142
267.7
259.9
56%
55%
55%
55%
(Probably-High avidity antibody)


CV2QS110
202.3
247.6
48%
40%
47%
42%



CV2QS151
85.3
45.8
 5%
 3%
 6%
 6%
No neutralizing Ab present


CV2QS152
101.6
67.7
 0%
11%
 0%
 7%
despite low to moderate


CV2QS149
77.3
39.7
 0%
 0%
 0%
 0%
levels of serology


CV2QS159
77.8
43.8
 0%
 0%
 0%
 0%
IgG antibodies


CV2QS165
39.9
18.6
 0%
 0%
 0%
 0%



CV2QS108
34.1
32.2
 0%
 0%
 0%
 0%



CV2QS124
21.7
10.6
 0%
 0%
 0%
 0%



CV2QS109
44.6
22.9
 0%
 0%
 0%
 0%



CV2QS133
54.0
31.0
 0%
 0%
 0%
 0%









Example 7—Multiplex Detection of High Avidity Neutralizing Antibodies Specific for SARS-CoV-2 Spike Protein Variants or Fragments Thereof
A population of fluorescently labeled beads comprising a plurality of subpopulations of fluorescently labeled beads to which individual SARS-CoV-2 spike protein variants or fragments thereof are immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine comprising SARS-CoV2 spike protein along with a sample diluent. Unbound sample is removed from the population of beads and the population of beads can be washed with a buffer. 1 M NaCl is then added to the beads and incubated with the population of beads. After a period of incubation, the 1 M NaCl and antibody (low avidity antibody) displaced during the incubation period are removed from the population of beads and the population of beads can be washed with a buffer. Biotinylated antibody specific for human immunoglobulin (anti-IgA, anti-IgM, anti-IgG, anti-kappa chain, and/or anti-lambda chain antibody) is added to the washed beads and incubated. Unbound biotinylated anti-human antibody is then washed away and labeled streptavidin-PE (Phycoerythrin) is added. The reaction is incubated and then washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate the relative fluorescence intensity (RFI) and, subsequently, a qualitative, semi-quantitative or quantitative result. A lack of signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein (or fragment thereof) or a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that low avidity neutralizing antibodies and/or no neutralizing antibodies to that SARS-CoV-2 spike protein variant or fragment thereof are present in the sample. The presence of a signal for a particular subpopulation of beads onto which a SARS-CoV-2 spike protein variant or fragment thereof has been immobilized indicates that there are high avidity neutralizing antibodies in the sample and the amount of the high avidity neutralizing antibody can also be quantified. For example, the sample fluorescence intensity can be compared to the fluorescence intensity of a set of standards or calibrators to generate a qualitative, semi-quantitative or quantitative result for the amount of high avidity neutralizing antibody present in the sample.
Example 8—Singleplex Detection of Neutralizing Antibodies Specific for a SARS-CoV-2 Spike Protein Variant or Fragment Thereof
A population of fluorescently labeled beads to which an individual SARS-CoV-2 spike protein, spike protein variant or fragment thereof is immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine comprising SARS-CoV2 spike protein along with a sample diluent. After incubation unbound sample is washed away and biotinylated human ACE2 receptor is added to the washed beads and incubated. The reaction is incubated and then washed and streptavidin-PE is added to the washed population of beads and incubated. After incubation, the population of beads is washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate the relative fluorescence intensity (RFI) and, subsequently, a qualitative, semi-quantitative or quantitative result. A lack of signal or a reduced signal (relative to a set of standards or calibrators) indicates that a neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof is present in the sample.
Example 9—Singleplex Detection of Neutralizing Antibodies Specific for a SARS-CoV-2 Spike Protein Variant or Fragment Thereof
A population of fluorescently labeled beads to which an individual SARS-CoV-2 spike protein, spike protein variant or fragment thereof is immobilized is contacted with a patient sample, e.g., a biological sample from an individual suspected of having been exposed to SARS-CoV-2 or a subject immunized with a vaccine comprising SARS-CoV2 spike protein along with a sample diluent. After incubation unbound sample is washed away. A biotinylated fusion protein comprising human ACE2 receptor fused to an immunoglobulin Fc domain (a hACE2R-Fc fusion protein biotinylated on the Fc domain) is added to the washed beads and incubated. The reaction is incubated and then washed and streptavidin-PE is added to the washed population of beads and incubated. After incubation, the population of beads is washed prior to detection using a Bio-Plex 2200, Bio-Plex 200 or Luminex LX-200 platform. The sample fluorescence intensity is compared to the fluorescence intensity of a set of standards or calibrators to generate the relative fluorescence intensity (RFI) and, subsequently, a qualitative, semi-quantitative or quantitative result. A lack of signal or a reduced signal (relative to a set of standards or calibrators) indicates that a neutralizing antibody to that SARS-CoV-2 spike protein variant or fragment thereof is present in the sample.
Example 10—SARS-CoV2 Neutralizing Antibody Assay—Specificity
A total of 583 samples comprising 483 hospital normal (sample from subjects undergoing routine checkups) and 100 samples from pregnant women were tested for anti SARS-COV2 neutralizing and IgG antibodies. All samples tested were acquired before November 2019. nAb (neutralizing antibody) assay testing was performed in the presence of high and low salt to detect high and low avidity antibodies, respectively. The percentages provided in Table 4 refer the percentage of samples that did not contain neutralizing antibodies or IgG specific for the SARS-Cov-2 antigens.














TABLE 4





Sample

RBD-

RBD-

RBD



population
N
HS
S1-HS
LS
S1-LS
IgG
S1 IgG







Hospital
483
 99.4%
 99.4%
99.6%
99.8%
 99.8%
100.0%


normals









Pregnant
100
100.0%
100.0%
98.0%
99.0%
100.0%
100.0%





HS: High salt (1M NaCl);


LS: Low Salt (0.15M NaCl)


nAb cutoff: 0.35 ug/mL;


Serology IgG assay cutoff: 10 U/mL






Example 11—SARS-CoV2 Neutralizing Antibody Assay—Cross Reactivity
Analytical specificity of a serology test is a measure of its ability to identify specific antibodies while excluding other non-specific antibodies. Cross-reactivity refers to the ability of a ligand to support binding of antibodies other than those intended to be measured and cause false positive test results. 283 samples collected from 32 diseased groups were tested for cross reactivity in the nAb and a serology IgG assay. The list shows cross reactivity for only two analytes; RBD and S1. nAb assay was performed in the presence of high (1 M NaCl) and low salt (0.15 M NaCl) to detect high and low avidity antibodies respectively.














TABLE 5





Cross reactants
N
RBD-HS
S1-HS
RBD-LS
S1-LS
RBD IgG
S1 IgG






















SARS IgG
5
0
0
1
0
0
0


MERS IgG Pos
5
0
0
0
0
0
0


Influenza A
14
0
1
1
1
0
0


Influenza B
9
0
0
0
0
0
0


Common Cold
9
0
0
0
0
0
0


Flu Vaccinated
7
0
0
0
0
0
0


2008 Flu Vaccine
36
0
0
0
0
0
0


BioAssay









validation panel









Haemophilus
5
0
0
0
0
0
0


influenza Ab









Parainfluenza virus
4
0
0
0
0
0
0


Ab Type I









Parainfluenza virus
2
0
0
0
0
0
0


Ab Type III









Metapneumovirus
5
0
0
0
0
0
0


(HMPV) IgG Pos









Rhinovirus IgG
5
0
0
0
0
0
0


Streptococcus
1
0
0
0
0
0
0


Pneumonia









Immunity Control









CMV IgG Pos
1
0
0
0
0
0
0


EBV VCA IgG Pos
23
0
0
0
0
0
0


Measles IgG Pos
13
0
0
0
0
0
0


MMRV IgG Pos
1
0
0
0
0
0
0


Mumps IgG Pos
14
0
0
1
1
0
0


Rubella IgG Pos
6
0
0
2
1
0
0


VZV IgG Pos
2
0
0
0
0
0
0


HCV Ab Pos
14
0
0
0
0
0
0


Hepatitis A IgG
20
1
1
0
0
0
0


Pos









Hepatitis B Pos Ab
21
0
0
0
0
0
0


Toxo IgG Pos
1
0
0
0
0
0
0


Syphilis IgG Pos
2
0
0
0
0
0
0


Elevated IgG
1
0
0
0
0
1
0


RF
47
0
0
1
1
0
0


ANA Positive
4
0
0
0
0
0
1


dsDNA Pos
2
1
1
0
0
1
0


Jo-1 Pos
1
0
0
0
0
0
0


RNP Pos
1
0
0
0
0
0
0


Sm Pos
2
0
0
0
0
0
0


Overall
283
2
3
6
4
2
1









Example 12—SARS-CoV2 Neutralizing Antibody Assay—Positivity Rate
578 unique samples from COVID patients were procured from commercial vendors. Of the 578 samples, 453 (78.4%) came with complete demographics and PCR test results. All samples were tested by the BioPlex 2200 serology IgG assay and neutralizing antibody (nAb) assay. While serology IgG data was collected for all four analytes (RBD, S1, S2 and N), the following table shows data for RBD and S1 analytes only. Testing for the presence of high and low avidity nAb was performed with RBD and S1 coupled beads only. High avidity antibodies were detected in the presence of 1M sodium chloride (HS) and 0.15 M NaCL (LS).







TABLE 6







Number of positive samples exhibiting IgG and neutralizing antibodies









Days post

# of Positive samples











symptom

CoV-2 nAb-HS
CoV-2 nAb-LS
BioPlex CoV-2 IgG














onset
N
RBD-HS
S1-HS
RBD-LS
S1-LS
RBD IgG
S1 IgG

















≤7
78
53
48
59
56
59
57


 8-14
67
53
49
54
50
55
53


15-30
124
97
85
110
102
112
109


31-60
226
190
169
203
198
212
209


>60
83
67
64
69
67
75
74
















TABLE 7







Percent positive samples exhibiting IgG and neutralizing antibodies











Days post

CoV-2 nAb-HS
CoV-2 nAb-LS
BioPlex CoV-2 IgG














symptom
N
RBD-HS
S1-HS
RBD-LS
S1-LS
RBD IgG
S1 IgG





≤7
 78
68%
62%
76%
72%
76%
73%


 8-14
 67
79%
73%
81%
75%
82%
79%


15-30
124
78%
69%
89%
82%
90%
88%


31-60
226
84%
75%
90%
88%
94%
92%


>60
 83
81%
77%
83%
81%
90%
89%









Example 13—SARS-CoV2 Neutralizing Antibody Assay—Concordance
For methodology comparison, the BioPlex 2200 neutralizing antibody assay was compared to a serologic IgG assay and the clinical status of the sample. Clinical status was established based on clinical findings coupled with the PCR test result. While negative agreements (% NA) are comparable between the nAb (neutralizing antibody), serology IgG and the clinical status irrespective of the avidity status, positive agreements (% PA) shows better correlation between the nAb, serology IgG and clinical status in the presence of low salt. Low salt (LS) refers to 0.15 M NaCl and high salt (HS) refers to 1 M NaCl). Negative agreement remained constant at low and high salt. However, positive agreement did not. This lends credence to the hypothesis that the antibody status does not predict the potency of neutralization.









TABLE 8









Neutralizing antibody












RBD-HS
RBD-LS


















Pos
Neg
PA (%)
NA (%)
Pos
Neg
PA (%)
NA (%)





Clinical
Pos
460
118
79.6
99.4
495
 83
85.6
98.8


Status
Neg
 5
861
(76.1-82.7)
(98.7-99.8)
 10
856
(82.5-88.3)
(97.9-99.4)


BioPlex
Pos
512
 76
87.1
98.6
556
 32
94.6
98.0


anti-RBD IgG
Neg
 13
939
(84.1-89.5)
(97.7-99.2)
 19
933
(92.4-96.1)
(96.9-98.7)















S1-1-HS
S1-LS


















Pos
Neg
PA (%)
NA (%)
Pos
Neg
PA (%)
NA (%)





Clinical
Pos
415
163
71.8
99.3
473
105
81.8
99.3


Status
Neg
 6
860
(68.0-75.3)
(98.5-99.7)
 6
860
(78.5-84.8)
(98.5-99.7)


BioPlex
Pos
467
104
81.8
99.1
556
 32
91.9
98.6


anti-S1 IgG
Neg
 9
960
(78.4-84.7)
(98.2-99.5)
 19
933
(89.4-93.9)
(97.6-99.1)









Example 14—SARS-CoV2 Neutralizing Antibody Assay—Correlation with the Serology Anti-RBD IgG Assay
675 COVID19 patient serum samples were tested on both SARS-CoV-2 serology IgG assay and neutralizing antibody assay. Among 675 patients, 453 were confirmed by PCR positive test results. The test results demonstrated the correlation between anti-RBD binding IgG antibody and neutralizing antibody. However, approximately 5% of the samples exhibit high serology IgG and low nAb response or vice versa as shown in FIGS. 5A and 5B.
Example 15—SARS-CoV2 Neutralizing Antibody Assay—Earlier Infected Patient Samples Lack Neutralizing Effects on Some of RBD Mutants
Twelve RBD mutants (F342L, N354D, V36F, E406Q, A435S, K458R, E471Q, S477N, V483A, P521R, P521S, and A522V) as well as wild type RBD, whole trimeric spike protein and the dominant pandemic mutant form D614G were tested in the neutralizing antibody assay. All RBD mutants demonstrate higher binding ability to ACE-2 receptor compared to wild type RBD, Trimeric spike protein and the D614G S1 mutant. The COVID19 patient serum samples demonstrated significantly lower inhibition on four RBD mutants—N354D, V367F, S477N and V483A, especially in earlier SARS-CoV2 infected patients (see Table 9 and FIGS. 6-11).























TABLE 9















Sino Bio
Sino Bio
Sino Bio
Sino Bio
Sino Bio
Sino Bio
Sino Bio
Sino Bio
Sino Bio




Icosagen
Icosagen
Sino Bio
Sino Bio
Sino Bio
Sino Bio
RBD
RBD
RBD
RBD
RBD
RBD
RBD
RBD
RBD



Recombinant
RBD
Trimeric Spike
S1 mutant
RBD mutant
RBD mutant
RBD mutant
mutant
mutant
mutant
mutant
mutant
mutant
mutant
mutant
mutant



protein vendor
WT sequence
Protein
D614G
F342L
N354D
V367F
E406Q
A435S
K458R
E471Q
S477N
V483A
P521R
P521S
A522V












Samples

LS























collected
Ave % inhibition
 52%
 49%
47%
31%
14%
13%
32%
23%
32%
39%
14%
17%
43%
39%
30%


before
RFI at 1 ug/mL of
10862
14268
15020
23526
26476
26833
23025
24298
23811
22841
24731
25144
22946
23065
23839


March
ACE-2

















(n = 30)
Normalized
100%
 94%
90%
59%
28%
25%
62%
45%
62%
75%
26%
32%
83%
75%
57%



% inhibition to WT


















RBD


























HS
























Ave % inhibition
 43%
 43%
41%
33%
12%
11%
32%
24%
32%
37%
13%
14%
40%
38%
28%



RFI at 1 ug/mL of
8648
13133
12517
21304
25954
26574
22642
23606
23210
20150
24541
24438
22109
22248
23670



ACE-2


















Normalized
100%
100%
95%
77%
27%
26%
75%
55%
75%
86%
29%
32%
92%
88%
64%



% inhibition to WT


















RBD














LS































RBD
RBD
RBD
RBD
RBD
RBD
RBD
RBD
RBD




RBD
Trimeric Spike
S1 mutant
RBD mutant
RBD mutant
RBD mutant
mutant
mutant
mutant
mutant
mutant
mutant
mutant
mutant
mutant




WT sequence
Protein
D614G
F342L
N354D
V367F
E406Q
A435S
K458R
E471Q
S477N
V483A
P521R
P521S
A522V





Samples
Ave % inhibition
 62%
 56%
53%
49%
27%
25%
50%
41%
50%
54%
30%
32%
58%
56%
49%


collected
RFI at 1 ug/mL of
10398
13143
14009
23324
24678
24927
22583
23888
23547
21939
24104
24222
21772
22730
23614


after
ACE-2

















June
Normalized
100%
 90%
85%
79%
43%
40%
80%
65%
80%
88%
48%
51%
94%
90%
79%


(n = 30)
% inhibition to WT


















RBD


























HS
























Ave % inhibition
 53%
 50%
45%
44%
24%
21%
45%
42%
50%
47%
29%
31%
52%
52%
47%



RFI at 1 ug/mL of
7956
11658
10858
18445
24401
24510
20096
23230
22633
17146
23893
23982
19464
19819
23273



ACE-2


















Normalized
100%
 94%
85%
83%
45%
40%
85%
79%
95%
89%
54%
58%
99%
97%
89%



% inhibition to WT


















RBD









FIGS. 6-9 illustrate neutralizing antibodies present in samples for various mutants under low salt conditions (LS=0.15 M NaCl, FIGS. 6 and 7) and high salt conditions (HS=1 M NaCl, FIGS. 8 and 9) for samples obtained before March 2020 and after June 2020. When antibody mediated inhibition was normalized to 100% of the wild type, RBD mutants demonstrated differential nAb response for samples collected before and after June 2020 (FIG. 10, low salt conditions and FIG. 11, high salt conditions). While high salt showed slightly elevated inhibition, the response pattern looked similar. Low salt conditions were 0.15 M NaCl and high salt conditions were 1 M NaCl.
REFERENCES


    1. Cheng Z J and Shan J. 2019 Novel coronavirus: where we are and what we know. Infection. 2020, April 48(2): 155-163. doi: 10.1007/s15010-020-01401-y.
    2. Cui J, Li F, and Shi Z L. Origin and evolution of pathogenic coronaviruses. Nature Reviews. 2020, Mar. 17: 181-192. doi: 10.1038/s41579-018-0118-9.
    3. He F, Deng Y, Li W. Coronavirus disease 2019: What we know? Journal of Medical Virology. 2020, Mar. 14. doi: 10.1002/jmv.25766.
    4. Guo L, Ren L, Yang S et al. Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19). Clinical Infectious Disease. 2020, Mar. 21, pii: ciaa310. doi: 10.1093/cid/ciaa310.
    5. Weiss S R and Navas-Martin S. Coronavirus Pathogenesis and the Emerging Pathogen Severe Acute Respiratory Syndrome Coronavirus. Microbiology and molecular biology reviews. 2005, December 69 (4): 635-664. doi:10.1128/MMBR.69.4.635-664.2005.
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    9. Fan Wu, Aojie Wang, Mei Liu, et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. 2020 Apr. 29 doi: doi.org/10.1101/2020.03.30.20047365.
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## Claims

1. A substrate comprising a population of particles or beads comprising two or more separate subpopulations of particles or beads, each subpopulation of particles or beads being distinguishable by a specific detectable parameter and each subpopulation of beads comprising a distinct SARS-CoV-2 spike protein variant or fragment thereof immobilized thereon and, optionally, a further subpopulation of beads comprising a SARS-CoV-2 spike protein or fragment thereof immobilized thereon.

2. The substrate according to claim 1, wherein said substrate is glass, plastic, polystyrene or nitrocellulose.

3. The substrate according to claim 1, wherein said population comprises two or more separate subpopulations of particles or beads selected from:
a) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation V367X immobilized on a first particle or bead having a first specific detectable physical parameter, where X is any amino acid or X is F;
b) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation F342X immobilized on a second particle or bead having a second specific detectable physical parameter, where X is any amino acid or X is L;
c) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation A435X immobilized on a third particle or bead having a third specific detectable physical parameter, where X is any amino acid or X is S;
d) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation K458X immobilized on a fourth particle or bead having a fourth specific detectable physical parameter, where X is any amino acid or X is R;
e) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation V483X immobilized on a fifth particle or bead having a fifth specific detectable physical parameter, where X is any amino acid or X is A;
f) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation V483X immobilized on a sixth particle or bead having a sixth specific detectable physical parameter, where X is any amino acid or X is A;
g) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutation N354X immobilized on a seventh particle or bead having a seventh specific detectable physical parameter, where X is any amino acid or X is D;
h) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutations R683X1 and/or R685X2 immobilized on an eighth particle or bead having an eighth specific detectable physical parameter, where X1 and X2 are any amino acid or X1 and X2 are A;
i) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutations K986X3 and/or V987X4 immobilized on a ninth particle or bead having a ninth specific detectable physical parameter, where X3 and X4 are any amino acid or X3 and X4 are P;
j) a SARS-CoV-2 spike protein variant or fragment thereof containing the mutations R683X1, R685X2, K986X3, and V987X4 immobilized on a tenth particle or bead having a tenth specific detectable physical parameter, where X1 is any amino acid or X1 is A; X2 is any amino acid or X2 is A; X3 is any amino acid or X3 is P; and X4 is any amino acid or X4 is P; and
k) a SARS-CoV-2 spike protein or fragment thereof immobilized on an eleventh particle or bead having an eleventh specific detectable physical parameter.

4. The substrate according to claim 3, wherein the specific detectable physical parameter is a fluorescent dye (fluorophore), luminescent agent, electron-dense reagent, radioisotope or particle size.

5. The substrate according to claim 4, wherein the specific detectable parameter is a fluorophore.

6. A method for detecting neutralizing and/or protective antibodies in a mammal comprising obtaining a biological sample from the mammal, contacting said biological sample with a substrate comprising a substrate according to claim 1 and detecting the presence or absence of neutralizing antibodies bound to SARS-CoV-2 spike protein variants or fragments thereof on the surface of said substrate.

7. The method according to claim 6, wherein the mammal is a human, non-human primate, canine, or feline.

8. The method according to claim 6, wherein the presence or absence of neutralizing antibodies comprises contacting the substrate with human ACE2 receptor and detecting the presence or absence of ACE2 receptor binding to substrate subpopulations onto which SARS-CoV-2 spike protein variants or fragments thereof have been immobilized, the detection of ACE2 receptor binding to a substrate subpopulation indicating a lack of neutralizing antibody specific for a specific a SARS-CoV-2 spike protein variant or fragment thereof.

9. The method according to claim 8, wherein ACE2 receptor binding to a substrate subpopulation is detected using an antibody specific for ACE2 receptor that is detectably labeled or an ACE2 receptor that is detectably labeled.

10. The method according to claim 6, wherein neutralizing antibody bound to a substrate comprising a given a SARS-CoV-2 spike protein variant or fragment thereof is detected using a species specific anti-immunoglobulin (Ig) antibody.

11. The method according to claim 6, said method further comprising detecting the presence, absence or amounts of cytokines selected from IL-1beta, IFN-γ, IFNγ-induced protein 10 (IP-10), monocyte chemoattractant protein 1 (MCP-1), IL-4, IL-10, IL-2R, IL-6, granulocyte colony-stimulating factor (G-CSF), macrophage inflammatory protein-1A, and TNF-α in said biological sample.

12. The method according to claim 11, wherein said one or more cytokine is selected from IL-6, IL-2R, granulocyte colony-stimulating factor, IP-10, MCP-1, macrophage inflammatory protein-1A, TNF-α, and combinations thereof.

13. A method for detecting high avidity neutralizing antibodies in a mammal comprising obtaining a biological sample from the mammal, contacting said biological sample with a substrate comprising a substrate according to claim 1 and detecting the presence or absence of high avidity neutralizing antibodies bound to SARS-CoV-2 spike protein variants or fragments thereof on the surface of said substrate.

14. The method according to claim 13, wherein the method comprises:
a) contacting the substrate with the biological sample;
b) optionally removing the biological sample from the substrate and washing the substrate to remove unbound material and antibody;
c) contacting the substrate with one or more chaotropic agents;
d) removing the one or more chaotropic agents from the substrate;
e) optionally, washing the substrate; and
f) detecting the presence or absence of high avidity neutralizing antibody binding to substrate subpopulations onto which SARS-CoV-2 spike protein or fragments thereof and SARS-CoV-2 spike protein variants or fragments thereof have been immobilized.

15. The method according to claim 14, wherein the chaotropic agent is sodium chloride, sodium thiocyanate, and/or urea.

16. The method according to claim 13, wherein the method comprises detecting SARS-CoV-2 spike protein or fragments thereof and/or SARS-CoV-2 spike protein variants or fragments thereof present on the substrate with an ACE2 receptor that is detectably labeled or with an antibody specific for the ACE2 receptor that is detectably labeled.

17. The method according to claim 13, wherein high avidity neutralizing antibody bound to a substrate comprising a given a SARS-CoV-2 spike protein or fragment thereof and/or a SARS-CoV-2 spike protein variant or fragment thereof is detected using a species specific anti-immunoglobulin (Ig) antibody, wherein the anti-Ig antibody is biotinylated and binding of said anti-IgG antibody to neutralizing antibody is detected with fluorophore labeled avidin or streptavidin or an anti-IgG antibody labeled with a fluorophore.

18. A method for detecting a neutralizing antibody in a mammal comprising obtaining a biological sample from the mammal, contacting said biological sample with a substrate according to claim 1 and detecting the presence or absence of a neutralizing antibody bound to a SARS-CoV-2 spike protein variant or fragment thereof on the surface of said substrate, said biological sample being obtained from individuals suspected of infection by the virus, treated with SARS-CoV-2 neutralizing antibodies or convalescent plasma, or immunized with a vaccine comprising the SARS-CoV2 spike protein.

19. The method according to claim 9, wherein the ACE2 receptor is a truncated or modified ACE2 receptor or is an ACE2 receptor fusion protein.

20. The method according to claim 19, wherein the ACE2 receptor fusion protein comprises an immunoglobulin Fc domain fused to the carboxyl-terminus of the ACE2 receptor.

21. The method according to claim 20, wherein the fusion protein is biotinylated on the Fc domain and is detected using streptavidin-PE.