Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
  • G01N33/56983—Viruses
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/005—Assays involving biological materials from specific organisms or of a specific nature from viruses
  • G01N2333/08—RNA viruses
  • G01N2333/11—Orthomyxoviridae, e.g. influenza virus
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2500/00—Screening for compounds of potential therapeutic value
  • G01N2500/02—Screening involving studying the effect of compounds C on the interaction between interacting molecules A and B (e.g. A = enzyme and B = substrate for A, or A = receptor and B = ligand for the receptor)
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
  • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

• Influenza is caused by an RNA virus of the orthomyxoviridae family. There are three types of these viruses and they cause three different types of influenza: type A, B and C.
• Influenza virus type A viruses infect mammals (humans, pigs, ferrets, horses) and birds. This is very important to civilization, as this is the type of virus that has caused worldwide pandemics.
• Influenza virus type B also known simply as influenza B
• Influenza type C viruses also infect only humans. They infect most people when they are young and rarely causes serious illness.
• RT-PCR Reverse-transcriptase PCR-based diagnostics
• RT PCR is not easily adapted to high throughput screening of subjects in an epidemic setting or to field uses in an agricultural or point-of-care setting.
• the complexity, diversity and rapid emergence of new influenza strains has made diagnosis of high risk strains difficult, and therefore rapid response is at present nearly impossible.
• epidemiologists diversity resulting from high mutation rates and genetic reassortment make it difficult to anticipate where new strains may originate and respond with the timely introduction of new diagnostic primers for PCR.
• the diversity of influenza dictates the necessity of multiplex PCR approaches.
• PCT/US06/41748 filed October 21, 2006, USSN 11/481,411, 60/792,274, filed 04/14/06, 60/765,292, filed 2/02/06, 60/726,377, filed 10/13/05; and 60/696,221, filed 7/01/05 are directed to related subject matter and are incorporated by reference in their entirety for all purposes.
• the invention provides method of detecting influenza A.
• the methods involve contacting a sample from a subject with a PDZ domain that specifically binds to a PL of an NSl protein of a pathogenic strain of influenza A; detecting presence or absence of specific binding of the PDZ domain to the NSl protein of pathogenic influenza A in the sample to determine presence or absence of the pathogenic influenza A in the sample; contacting the patient sample with a PDZ domain that specifically binds to a PL of an NSl protein of a seasonal subtype influenza A; and detecting presence or absence of specific binding of the PDZ domain to the NSl protein of the seasonal subtype influenza A to determine presence or absence of the seasonal subtype influenza A in the sample.
• the PDZ domain that specifically binds to the PL of an NSl protein of pathogenic influenza A is a PSD95 domain.
• the PDZ domain that specifically binds to the PL of an NSl protein of a seasonal subtype influenza A is an INADL domain 8.
• the sample is an orally obtained sample.
• the subject is a human showing symptoms of influenza.
• the specific binding of the PSD95 PDZ domain to the NSl protein is detected by a sandwich assay in which the sample is contacted with an antibody that binds to the NSl protein, and a complex of the PSD95 PDZ domain and the antibody both specifically bound to the NSl protein is detected.
• the specific binding of the INADL PDZ domain to the NSl protein is detected by a sandwich assay in which a complex of the INADL PDZ domain and the antibody both specifically bound to the NSl protein is detected.
• the at least one PDZ domain of PSD95 comprises a PDZ domain 2 of PSD95.
• the at least one PDZ domain comprises at least three copies of PSD95 domain 2.
• the at least one PDZ domain comprises domains 1, 2 and 3 of PSD95.
• the at least one PDZ domain of INADL comprises domain 8 of INADL.
• the at least one PDZ domain of INADL comprises three copies of domain 8 of INADL.
• the invention further provides methods of detecting influenza A.
• the methods involve contacting a sample from a subject with first and second pan specific antibodies that bind to different epitopes of an NSl protein of influenza A; detecting presence or absence of a complex between the first and second antibodies and the NSl protein to indicate presence or absence of influenza A.
• the first and second antibodies each bind to an epitope within residues 8-21, 9-20, 29-38 or 45-49 of Fig. IA.
• the first and second antibodies compete with different antibodies selected from the group consisting of F64 3H3, F68 8E.6, F64 6G12, F68 10A5, F80 7E8, F80 8F6, F80 9Bl, F81 1C12, F81 1F3, F81 4D5, and F64 IAlO.
• the invention further provides a method of detecting influenza A.
• the method involves contacting a sample from a subject with at least one PDZ domain and at least one pan-specific antibody that binds to the NS 1 protein of influenza A ; detecting presence or absence of the NSl protein of influenza A in the sample from presence of absence of a complex of the at least one PDZ domain and pan-specific antibody specifically bound to the NSl protein.
• the pan-specific antibody is a capture antibody immobilized to a solid phase.
• the pan-specific antibody is a detection antibody.
• the pan-specific antibody specifically binds to an epitope of the NSl protein with residues 9-20, 29-38 or 45-49 of Fig. IA.
• the pan specific antibody is a monoclonal.
• the pan specific antibody is a mixture of two monoclonals.
• the pan specific antibody is a monoclonal antibody that competes with an antibody selected from the group consisting of F64 3H3, F68 8E6, F64 6G12, F68 10A5, F80 7E8, F80 8F6, F80 9Bl, F81 1C12, F81 1F3, F81 4D5, and F64 IAlO for specific binding to an NSl protein.
• the patient sample is contacted with at least two PDZ domains attached to different regions of a support.
• the at least two PDZ domains are a PSD95 domain and an INADL domain.
• the invention further provides a method of detecting influenza B.
• the method involves contacting a sample with first and second pan specific antibodies that bind to different epitopes of an NSl protein of influenza B; detecting presence or absence of a complex between the first and second antibodies and the NSl protein to indicate presence or absence of influenza B.
• the first and second antibodies each bind to an epitope within residues 10-28, 40-45, 50-57, 67-74, 84-100, 154-159, 169-173, 185-191, 212-224, 226-240 of Fig. 2.
• the first and second antibodies compete with different antibodies selected from the group consisting of F89 1F4, F94 3Al, and F89-1F8.
• the invention further provides methods of detecting influenza.
• the methods comprise contacting a sample from a subject with first and second pan-specific antibodies binding to different epitopes of an influenza B NSl protein and first and second pan-specific antibodies binding to different epitopes of an influenza A NSI protein; determining presence or absence of a complex formed between the influenza B NSl protein and the first and specific pan-specific antibodies binding to it to indicate presence or absence of influenza B in the sample and determining presence or absence of a complex formed between the influenza A NSl protein and the first and second pan-specific antibodies binding to it to indicate presence or absence of influenza A in the sample.
• the methods further comprise contacting the patient sample with a PDZ domain specific for a PL of an NSl protein from a pathogenic strain of influenza A; and detecting presence or absence of specific binding of the PDZ domain to the NSl protein of the pathogenic strain of influenza A to indicate presence or absence of the pathogenic strain of influenza A.
• the first and second pan- specific antibodies for influenza A are capture and detection antibodies respectively, and the presence of specific binding of the PDZ domain to the NSl protein is detected by detecting a complex formed between the PDZ domain, the NS 1 protein and the detection antibody.
• the methods further comprise contacting the patient sample with a PDZ domain specific for a PL of an NSl protein of a seasonal subtype of influenza A; and detecting presence or absence of specific binding of the PDZ domain to the NSl protein of the seasonal subtype of influenza A to indicate presence or absence of the seasonal subtype of influenza A.
• Fig. IA shows the invariant amino acid residues between NSl proteins from three subtypes of influenza A 5 HlNl, H3N2 and H5N1. As described below, segments of NSl protein including clusters of invariant amino acid residues are useful for inducing pan-specific antibodies.
• Fig. IB shows amino acid residues found in the NSl protein of H5N1 but not found in H3N2 or HlNl. Clusters of these residues particularly the clusters at positions 21-28 and at the C-terminus are useful for preparing an antibody that binds to H5N1 without binding to the other two subtypes.
• Fig. 2 shows a consensus sequence of residues of the NSl protein from different strains of influenza A.
• Fig. 3 shows a consensus sequence of residues of the NSl protein form different strains of influenza B. Underlined residues are invariable between different strains.
• Fig. 4 shows the results of testing nasal secretions from six human Flu A positive samples.
• Fig. 5 shows NSl expression in MDCK cells infected with A/PR/8/34.
• Fig. 6 shows that PDZ interacts with NSl in cells.
• Fig. 7 shows that INADL d8 interacts with H3N2 NSl in cells.
• FIG. 8 shows a lateral flow format for an NSl diagnostic using a PDZ capture agent and monoclonal antibody detect agent AU-4B2.
• FIG. 9 shows a lateral flow format using a monoclonal antibody capture agent and a monoclonal antibody detect agent AU-4B2.
• FIGs. 10A-F exemplary lateral flow Influenza test formats.
• Fig. 11 Detection of recombinant NSl from two strains of influenza B in a lateral flow assay using various combinations of capture and detection antibody.
• Fig. 12 Detection of NSl from influenza B in clinical samples.
• Fig. 13 Chart showing suitable combinations of capture and detection antibody for detection of NSl from influenza B.
• Figs. 14 A, B and C Binding of a peptide comprising either 1 copy or 3 copies of PSD95 domain 2 to NSl protein.
• Fig 14A Sequence of a GST fusion peptide comprising 3 copies of PSD95 domain 2 (SEQ ID NO: 11).
• GST-derived sequence including GST peptide sequence and cloning linker sequence, is italicized (amino acids 1-242 and 243-244 respectively).
• Native PSD95 domain 2 sequence is in bold (corresponding to amino acids 197 to 288 of NCBI Ace. No.
• Fig 14B Lateral flow assay detecting binding of 0, 25, 100 or 500 pg of peptide to NSl of a peptide comprising a single copy of PSD95 domain 2 and a peptide comprising three copies of PSD95 domain 2.
• Fig. 14C Lateral flow assay detecting binding of 0, 25, 100 or 500 picograms of peptide comprising PSD95 PDZ domain (1, 2, 3) to NSl compared with binding of a peptide comprising a single copy of PSD95 domain 2.
• Avian influenza A means an influenza A subtype that infects an avian subject and is transmissible between avian subjects.
• Representative examples of avian influenza hemmagglutinin subtypes include H5, H6, H7, H9 and HlO and representative strains include H5N1, H6N2, H7N3, H7N7, H9N2, H10N4 and H10N5. Some strains of Avian influenza can also infect humans.
• the avian subject to be tested or treated is selected from the group consisting of chickens, turkeys, ducks, geese, quail, ostrich, emus and exotic birds such as parrots, cockatoos and cockatiels. More preferably, the avian subject to be tested is a chicken, turkey, goose or quail.
• Pathogenic strain of influenza A when used in the context of distinguishing between different strains of influenza virus means a "notifiable avian influenza" (NAI) virus according to the guidelines set forth by the OIE World Organization for Animal Health, World Health Organization or their designated representatives e.g., as set forth in the OIE “Manual of Diagnostic Tests and Vaccines for Terrestrial Animals, 5th edition, 2004 (www.oie.int).
• NAI notifiable avian influenza
• the subject pathogenic strain has "high pathogenicity" in a representative test for virulence or an H5 or H7 virus with an influenza A hemmagglutinin (HA) precursor protein HAO cleavage site amino acid sequence that is similar to any of those that have been observed in virulent viruses, i.e., as defined by the OIE or a representative similar national or international organization or trade association.
• HA hemmagglutinin
• HAO cleavage site amino acid sequences in virulent H5 and H7 strains of influenza A comprise multiple basic amino acids (arginine or lysine) at the cleavage site of the viral precursor hemagglutinin protein, e.g., where low virulence strains of H7 viruses have PEIPKGR*GLF (SEQ ID NO:20) or PENPKGR*GLF (SEQ ID NO:21) highly pathogenic strains have -PEIPKKKKR*GLF (SEQ ID NO:22), PETPKRKRKR*GLSF (SEQ ID NO:23), PEIPKKREKR*GLF (SEQ ID NO:24) or PETPKRRRR*GLF (SEQ ID NO:25).
• PEIPKKKKR*GLF SEQ ID NO:20
• PENPKGR*GLF SEQ ID NO:21
• highly pathogenic strains have -PEIPKKKKR*GLF (SEQ ID NO:22), PETPKRKRKR*GLSF (S
• Current representative tests for virulence include inoculation of 4-8 week old chickens with infectious virus wherein strains are considered to be highly pathogenic if they cause more than 75% mortality within 10 days; and/or, any virus that has an intravenous pathogenicity index (IVPI) greater than 1.2, wherein intravenously inoculated birds are examined at 24- hour intervals over a 10-day period; scored for "0", normal; "1" sick; “2” severely sick”; “3” dead; and, the mean score calculated as the IVPI.
• IVPI intravenous pathogenicity index
• HPNIA highly pathogenic NAI virus
• Current representative examples of NAI include the H5 and H7 strains of influenza A.
• Current representative examples of HPNIA include H5N1.
• Less Pathogenic strain of influenza A means an avian influenza A that is notifiable, i.e., an NAI isolate (supra), but which is not pathogenic for chickens and does not have an HAO cleavage site amino acid sequence similar to any of those that have been observed in virulent viruses, i.e., a strain referred to by the OIE as a "low pathogenicity avian influenza (LPAI). Can we have an example of a less pathogenic strain.
• LPAI low pathogenicity avian influenza
• strains of influenza A that are not classified as highly pathogenic or less pathogenic are referred to as seasonal flu. Most strains of influenza A HlNl are seasonal flu. However, one strain responsible for the 1918 Spanish flu is highly pathogenic.
• PDZ domain means an amino acid sequence homologous over about 90 contiguous amino acids; preferably about 80-90; more preferably, about 70-80, more preferably about 50-70 amino acids with the brain synaptic protein PSD95, the Drosophila septate junction protein Discs-Large (DLG) and/or the epithelial tight junction protein ZOl (ZOl).
• DHRs Discs-Large homology repeats
• GLGF epithelial tight junction protein ZOl
• PDZ domains are found in diverse membrane- associated proteins including members of the MAGUK family of guanylate kinase homologs, several protein phosphatases and kinases, neuronal nitric oxide synthase, tumor suppressor proteins, and several dystrophin-associated proteins, collectively known as syntrophins.
• the instant PDZ domains encompass both natural and non-natural amino acid sequences.
• Representative examples of PDZ domains include polymorphic variants of PDZ proteins, as well as, chimeric PDZ domains containing portions of two different PDZ proteins and the like.
• the instant PDZ domains contain amino acid sequences which are substantially identical to those disclosed in US Patent Application No.
• Non-natural PDZ domains include those in which the corresponding genetic code for the amino acid sequence has been mutated, e.g., to produce amino acid changes that alter (strengthen or weaken) either binding or specificity of binding to PL.
• a PDZ domain or a variant thereof has at least 50, 60, 70, 80 or 90% sequence identity with a PDZ domain from at least one of brain synaptic protein PSD95, the Drosophila septate junction protein Discs-Large (DLG) and/or the epithelial tight junction protein ZOl (ZOl), and animal homologs.
• a variant of a natural PDZ domain has at least 90% sequence identity with the natural PDZ domain. Sequence identities of PDZ domains are determined over at least 70 amino acids within the PDZ domain, preferably 80 amino acids, and more preferably80-90 or 80-100 amino acids.
• Amino acids of analogs are assigned the same numbers as corresponding amino acids in the natural human sequence when the analog and human sequence are maximally aligned. Analogs typically differ from naturally occurring peptides at one, two or a few positions, often by virtue of conservative substitutions.
• allelic variant is used to refer to variations between genes of different individuals in the same species and corresponding variations in proteins encoded by the genes.
• An exemplary PDZ domain for PSD95 d2 is provided as SEQ ID NO:1.
• PDZ protein used interchangeably with “PDZ-domain containing polypeptides” and “PDZ polypeptides”, means a naturally occurring or non-naturally occurring protein having a PDZ domain (supra).
• Representative examples of PDZ proteins have been disclosed previously (supra) and include CASK, MPPl, DLGl, DLG2, PSD95, NeDLG, TIP-33, TIP- 43, LDP, LIM, LIMKl, LIMK2, MPP2, AF6, GORASPl, INADL, KIAA0316, KIAA1284, MAGIl, MAST2, MINTl, NSP, NOSl, PAR3, PAR3L, PAR6 beta, PICKl, Shank 1, Shank 2, Shank 3, SITAC-18, TIPl, and ZO-I .
• the instant non-natural PDZ domain polypeptides useful in screening assays may contain e.g. a PDZ domain that is smaller than a natural PDZ domain.
• a non-natural PDZ domain may optionally contain a "GLGF" motif, i.e., a motif having the GLGF amino acid sequence (SEQ ID NO:26), which typically resides proximal, e.g. usually within about 10-20 amino acids N-terminal, to an PDZ domain.
• GLGF motif SEQ ID NO:26
• the latter GLGF motif (SEQ ID NO:26), and the 3 amino acids immediately N-terminal to the GLGF motif (SEQ ID NO:26) are often required for PDZ binding activity.
• non- natural PDZ domains may be constructed that lack the ⁇ -sheet at the C-terminus of a PDZ domain, i.e., this region may often be deleted from the natural PDZ domain without affecting the binding of a PL.
• Some exemplary PDZ proteins are provided and the GI or accession numbers are provided in parenthesis: PSMD9 (9184389), af6 (430993), AIPC (12751451), ALP (2773059), APXL-I (13651263), MAGI2 (2947231), CARDIl (1282772), CARDI4 (13129123), CASK (3087815), CNKl (3930780), CBP (3192908), Densin 180 (16755892), DLGl (475816), DLG2 (12736552), DLG5 (3650451), DLG6 splice var 1 (14647140), DLG6 splice var 2 (AB053303), DVLl (2291005), DVL2 (2291007), DVL3 (6806886), ELFIN 1 (2957144), ENIGMA (561636), ERBIN (8923908), EZRIN binding protein 50 (3220018), FLJOOOI l (10440342), FL
• PDZ ligand means a naturally occurring protein that has an amino acid sequence which binds to and forms a molecular interaction complex with a PDZ- domain.
• Representative examples of PL have been provided previously in prior US and International patent applications (supra). Additional examples of influenza A PL are provided in the Examples section, below.
• Specific binding between a binding agent, e.g., an antibody or a PDZ domain and an NSl protein refers to the ability of a capture- or detection-agent to preferentially bind to a particular viral analyte that is present in a mixture of different viral analytes.
• a binding agent e.g., an antibody or a PDZ domain
• NSl protein refers to the ability of a capture- or detection-agent to preferentially bind to a particular viral analyte that is present in a mixture of different viral analytes.
• some antibodies described in the application specifically bind to NSl from influenza B without specifically binding to NS 1 from influenza A, and vice versa.
• Specific binding also means a dissociation constant (KD) that is less than about 10 "6 M; preferably, less than about 10-7M; and, most preferably, less than about 10 "8 M, In some methods, specific binding interaction is capable of discriminating between proteins having or lacking a PL with a discriminatory capacity greater than about 10- to about 100-fold; and, preferably greater than about 1000- to about 10,000-fold.
• KD dissociation constant
• Capture agent/analyte complex is a complex that results from the specific binding of a capture agent, with an analyte, e.g. an influenza viral NSl protein.
• a capture agent and an analyte specifically bind, i.e., the one to the other, under conditions suitable for specific binding, wherein such physicochemical conditions are conveniently expressed e.g. in terms of salt concentration, pH, detergent concentration, protein concentration, temperature and time.
• the subject conditions are suitable to allow binding to occur e.g. in a solution; or alternatively, where one of the binding members is immobilized on a solid phase.
• Suitable conditions preferably result in binding interactions having dissociation constants (KD) that are less than about 10 "6 M; preferably, less than about 10 "7 M; and, most preferably less than about 10 "8 M.
• KD dissociation constants
• Solid phase means a surface to which one or more reactants may be attached electrostatically, hydrophobically, or covalently.
• Representative solid phases include e.g.: nylon 6; nylon 66; polystyrene; latex beads; magnetic beads; glass beads; polyethylene; polypropylene; polybutylene; butadiene-styrene copolymers; silastic rubber; polyesters; polyamides; cellulose and derivatives; acrylates; methacrylates; polyvinyl; vinyl chloride; polyvinyl chloride; polyvinyl fluoride; copolymers of polystyrene; silica gel; silica wafers glass; agarose; dextrans; liposomes; insoluble protein metals; and, nitrocellulose.
• Solid phases include those formed as beads, tubes, strips, disks, filter papers, plates and the like. Filters may serve to capture analyte e.g. as a filtrate, or act by entrapment, or act by covalently binding.
• a solid phase capture reagent for distribution to a user may consist of a solid phase coated with a "capture reagent", and packaged (e.g., under a nitrogen atmosphere) to preserve and/or maximize binding of the capture reagent to an influenza NS 1 analyte in a biological sample.
• Bio samples include tissue fluids, tissue sections, biological materials carried in the air or in water and collected there from e.g. by filtration, centrifugation and the like, e.g., for assessing bioterror threats and the like.
• Alternative biological samples can be taken from fetus or egg, egg yolk, and amniotic fluids.
• Representative biological fluids include urine, blood, plasma, serum, cerebrospinal fluid, semen, lung lavage fluid, feces, sputum, mucus, water carrying biological materials and the like.
• biological samples include nasopharyngeal or oropharyngeal swabs, nasal lavage fluid, tissue from trachea, lungs, air sacs, intestine, spleen, kidney, brain, liver and heart, sputum, mucus, water carrying biological materials, cloacal swabs, sputum, nasal and oral mucus, and the like.
• Representative biological samples also include foodstuffs, e.g., samples of meats, processed foods, poultry, swine and the like.
• Biological samples also include contaminated solutions (e.g., food processing solutions and the like), swab samples from out-patient sites, hospitals, clinics, food preparation facilities (e.g., restaurants, slaughter houses, cold storage facilities, supermarket packaging and the like).
• Biological samples may also include in situ tissues and bodily fluids (i.e., samples not collected for testing), e.g., the instant methods may be useful in detecting the presence or severity or viral infection in the eye e.g., using eye drops, test strips applied directly to the conjunctiva; or, the presence or extent of lung infection by e.g. placing an indicator capsule in the mouth or nasopharynx of the test subject.
• a swab or test strip can be placed in the mouth.
• the biological sample may be derived from any tissue, organ or group of cells of the subject.
• a scrape, biopsy, or lavage is obtained from a subject.
• Biological samples may include bodily fluids such as blood, urine, sputum, and oral fluid; and samples such as nasal washes, swabs or aspirates, tracheal aspirates, chancre swabs, and stool samples.
• nasopharyngeal specimens such as nasal swabs, washes or aspirates, or tracheal aspirates in the case of high risk influenza A viruses involved in respiratory disease, oral swabs and the like.
• the biological sample may be suspended in an isotonic solution containing antibiotics such as penicillin, streptomycin, gentamycin, and mycostatin.
• substantially identical means that two peptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights, share at least 65 percent sequence identity, preferably at least 80 or 90 percent sequence identity, more preferably at least 95 percent sequence identity or more (e.g., 99 percent sequence identity or higher). Preferably, residue positions which are not identical differ by conservative amino acid substitutions.
• Isolated or purified generally refers to isolation of a substance (compound, polynucleotide, protein, polypeptide, polypeptide composition) such that the substance comprises a significant percent (e.g., greater than 2%, greater than 5%, greater than 10%, greater than 20%, greater than 50%, or more, usually up to about 90%- 100%) of the sample in which it resides.
• a substantially purified component comprises at least 50%, 80%-85%, or 90-95% of the sample.
• Techniques for purifying polynucleotides and polypeptides of interest are well-known in the art and include, for example, ion-exchange chromatography, affinity chromatography and sedimentation according to density. Generally, a substance is purified when it exists in a sample in an amount, relative to other components of the sample that is not found naturally.
• Subject is used herein to refer to a man and domesticated animals, e.g. mammals, fishes, birds, reptiles, amphibians and the like.
• SGC Signal generating compound
• PL PL
• PDZ a chemical linking method as disclosed further below and is capable of reacting to form a chemical or physical entity (i.e., a reaction product) detectable in an assay according to the instant disclosure.
• reaction products include precipitates, fluorescent signals, compounds having a color, and the like.
• Representative SGC include e.g., bioluminescent compounds (e.g., luciferase), fluorophores (e.g., below), bioluminescent and chemiluminescent compounds, radioisotopes (e.g., 131 I, 125 I, 14 C, 3 H, 35 S, 32 P and the like), enzymes (e.g., below), binding proteins (e.g., biotin, avidin, streptavidin and the like), magnetic particles, chemically reactive compounds (e.g., colored stains), labeled oligonucleotides; molecular probes (e.g., CY3, Research Organics, Inc.), and the like.
• bioluminescent compounds e.g., luciferase
• fluorophores e.g., below
• bioluminescent and chemiluminescent compounds e.g., radioisotopes (e.g., 131 I, 125 I, 14 C, 3 H, 35
• fluorophores include fluorescein isothiocyanate, succinyl fluorescein, rhodamine B, lissamine, 9,10-diphenlyanthracene, perylene, rubrene, pyrene and fluorescent derivatives thereof such as isocyanate, isothiocyanate, acid chloride or sulfonyl chloride, umbelliferone, rare earth chelates of lanthanides such as Europium (Eu) and the like.
• Representative SGCs useful in a signal generating conjugate include the enzymes in: IUB Class 1, especially 1.1.1 and 1.6 (e.g., alcohol dehydrogenase, glycerol dehydrogenase, lactate dehydrogenase, malate dehydrogenase, glucose-6-phosphate dehydrogenase, glyceraldehyde-3 -phosphate dehydrogenase and the like); IUB Class 1.11.1 (e.g., catalase, peroxidase, amino acid oxidase, galactose oxidase, glucose oxidase, ascorbate oxidase, diaphorase, urease and the like); IUB Class 2, especially 2.7 and 2.7.1 (e.g., hexokinase and the like); IUB Class 3, especially 3.2.1 and 3.1.3 (e.g., alpha amylase, cellulase, ⁇ -galacturonidase, amyloglucosidase,
• Fluorescent proteins include, but are not limited to the following: namely, (i) green fluorescent protein (GFP), i.e., including, but not limited to, a "humanized” versions of GFP wherein codons of the naturally-occurring nucleotide sequence are exchanged to more closely match human codon bias; (ii) GFP derived from Aequoria victoria and derivatives thereof, e.g., a "humanized” derivative such as Enhanced GFP, which are available commercially, e.g., from Clontech, Inc.; (iii) GFP from other species such as Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al.
• GFP green fluorescent protein
• the subject signal generating compounds may be coupled to a PL or PDZ domain polypeptide. Attaching certain SGC to proteins can be accomplished through metal chelating groups such as EDTA. The subject SGC share the common property of allowing detection and/or quantification of an influenza PL analyte in a test sample.
• the subject SGC are detectable using a visual method; preferably, an a method amenable to automation such as a spectrophotometric method, a fluorescence method, a chemiluminescent method, a electrical nanometric method involving e.g., a change in conductance, impedance, resistance and the like and a magnetic field method.
• a visual method preferably, an a method amenable to automation such as a spectrophotometric method, a fluorescence method, a chemiluminescent method, a electrical nanometric method involving e.g., a change in conductance, impedance, resistance and the like and a magnetic field method.
• the epitope of a mAb is the region of its antigen to which the mAb binds.
• Two antibodies bind to the same or overlapping epitope if one competitively inhibits (blocks) binding of a prototypical antibody defining the competition group to the antigen (an NSl protein of influenza A or influenza B, in the assays below). That is, a 3-fold of 5-fold excess of one antibody inhibits binding of the other by at least 50% but preferably 75%, 90% or even 99% as measured in a competitive binding assay compared to a control lacking the competing antibody (see, e.g., Junghans et al., Cancer Res. 50:1495, 1990, which is incorporated herein by reference).
• two antibodies have the same epitope if all amino acid mutations in the antigen that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
• Two antibodies have overlapping epitopes if some amino acid mutations that reduce or eliminate binding of one antibody reduce or eliminate binding of the other.
• Detecting "presence" or "absence” of an analyte includes quantitative assays in which only presence or absence of analyte is detected and quantitative assays in which presence of analyte is detected as well as an amount of analyte present.
• NSl protein of influenza protein is an abundant protein in subjects infected with influenza A and B and thus useful for detection of these viruses.
• the '411 application also shows that the NSl proteins of influenza A (although not influenza B) contain PL regions. These PL regions can be readily detected using PDZ domains and thus provide a basis for detecting influenza A and distinguishing it from other types of influenza.
• PL's from pathogenic subtypes of influenza A differ from those in seasonal subtypes of influenza. Differential detection of PL's using different PDZ domains thus provides a basis to distinguish between pathogenic and seasonal subtypes of influenza A.
• pan-specific antibodies i.e., that react with all or at least multiple strains within an influenza type.
• influenza viruses belong to the Orthomyxoviridae family, and are classified into types A, B, and C based upon antigenic differences in their nucleoprotein (NP) and matrix protein (Ml). Further subtyping into strains is commonly based upon assessing the type of antigen present in two virion glycoproteins, namely, hemagglutinin (HA; H) and neuraminidase (NA; N). HA and NP are virulence factors mediating attachment of the virion to the surface of host cells. Thus, H5N1, HlNl and H3N2 are examples of subtypes of influenza A. Within each subtype there are hundreds of strains.
• non-structural proteins 1 and 2 The non-structural viral protein NSl has multiple functions including the regulation of splicing and nuclear export of cellular mRNAs and stimulation of translation, as well as the counteracting of host interferon ability.
• the NS 1 protein has been identified and sequenced in influenza viruses and exemplary sequences can be found in the NCBI database.
• the NSl proteins from influenza A, B and C do not in general show antigenic cross reactivity. Within a type (e.g., influenza A), there is considerable variation in sequence between subtypes, but some antigenic crossreactivity depending on which antibody is used.
• the GenBank accession numbers of some exemplary NSl sequences from influenza type A, subtypes HlNl, H3N2 and H5N1 respectively, are CY003340, CY003324, DQ266101.
• the GenBank accession numbers of some exemplary NSl sequences from influenza type B are AAA43690 and BAD29872.
• the NSl protein in other strains of influenza either influenza type A, type B or type C means a protein having the greatest sequence similarity to one of the proteins identified as an NSl protein in known influenza strains of the same subtype, using as sequence for example, one of the GenBank accession numbers given above.
• Table 1 lists the PL regions of influenza A subtypes H5N1, HlNl and H3N2.
• H5N1 is the most clinically relevant subtype of pathogenic strains.
• HlNl and H3N2 are the most clinically relevant subtypes of seasonal influenza A.
• the table also indicates whether various PDZ domains bind to the indicated PL.
• the table can be used to select PDZ domains for differential detection of pathogenic and seasonal subtypes of influenza A. For example, a PSD95 domain is useful for detecting pathogenic subtypes of influenza A, and INADL domain 8 is useful for detecting seasonal subtypes of influenza A.
• the PSD95 domain can be any of PDZ domains 1, 2, and 3 of PSD95, or combinations thereof.
• a preferred detection reagent is a protein formed from three copies of domain 2 of PSD95 in a PSD95. That is, three tandem copies interspersed by segments of PSD95 flanking its PDZ domains, hi such a protein two of the copies of domain 2 of PSD95 effectively replace natural domains 1 and 3 of PSD95.
• Another preferred detection reagent is a protein containing PDZ domains 1, 2 and 3 of PSD95.
• Assay conditions such as buffer and temperature can be used to modulate binding to favor detection of a particular strain or differentiation among the different strains.
• the symbols used in the table mean as follows: ++ relatively strong binding, + detectable but relatively weak binding, +/- detectable but relatively weak binding or undetectable binding, - undetectable binding.
• Detectable binding means that the signal from binding is greater in a sample containing NSl of the indicated subtype relative to a control lacking the NSl of the indicated subtype to a significant extent taking into account random variation due to experimental error.
• Undetectable binding means that the signal from binding to a sample containing NSl of the indicated subtype is within the margin of error from the signal in a control lacking NSl of the indicated subtype.
• a preferred format for subtyping influenza A uses a PDZ from PDS95 as shown in the table in combination with an INDAL PDZ domain 8.
• detectable binding of the PSD95 domain without binding of the INDAL domain or significantly stronger (i.e., stronger beyond experimental error) binding of the PSD95 domain that that of the INADL domain is an indication that the influenza A subtype is H5N1 (pathogenic).
• detectable binding of the INADL domain to the sample without detectable binding of the PSD95 domain to the sample or significantly stronger binding of the INADL domain to the sample than of the PSD95 to the sample is an indication that the sample contains an influenza A subtype HlNl or H3N2 (both seasonal influenza).
• Detectable but weak binding of PSD95 domain 2 to the sample compared with undetectable binding distinguishes HlNl from H3N2 as indicated in the table.
• Detectable but relatively weak binding of PSD95 domains 1, 2 and 3 to a sample compared with binding of INADL to the sample is also an indication that the subtype is HlNl .
• the invention provides a collection of pan-specific antibodies for detection of influenza A.
• a pan specific antibody for influenza A specifically binds to the NSl protein from at least 2, 3 or 5 or all or substantially all known strains of influenza A.
• a pan specific antibody for influenza B specifically binds to the NSl protein from at least 2, 3, 5 or all or substantially all known strains of influenza B.
• Pan-specific antibodies can be defined by reference to either a numerically defined epitope or by a competition group defined by reference to an exemplary antibody.
• pan specific antibodies preferably specifically bind to an epitope within residues 8-21, 9-20, 29-38 or 45-49 of Fig. IA or Fig. 2.
• the X's in this sequence can be any amino acid but are preferably an amino acid occupying the corresponding position in an NS 1 protein from a strain of influenza, and more preferably the consensus amino acid occupying the corresponding position from at least two or preferably all known strains of influenza A.
• a consensus sequence of influenza A is provided in Fig. 2.
• Some pan specific antibodies specifically bind to an epitope within residues 9-11 or 13-16 of Fig. IA.
• Pan specific antibodies can also be defined by a competition group; the antibodies within a competition group compete with one another for specific binding to the same antigen (i.e., an SNl protein of influenza A or influenza B).
• Table 2 shows competition groups of panspecific antibodies binding to an NSl protein of influenza A.
• Each group is defined by a prototypical antibody (in column 2) with which other antibodies (column 3 ) in the group compete.
• Groups A, B and C are preferred. All of these antibodies bind to the NSl protein from at least strains H5N1, HlNl and H3N2. The antibodies in different groups do not compete with each other.
• Table 3 shows preferred antibodies for use in sandwich detection of the H5N1 pathogenic strain of influenza.
• a preferred capture agent is PSD95 domains 1, 2 and 3
• a preferred detection agent is an antibody preferably from Group A, or alternatively Group C or D.
• Table 4 shows competition groups for panspecific antibodies binding to the NSl protein of influenza B.
• Group C compete w/ each other Table 5 shows pairs of competing capture and detection antibodies. Detection antibodies are shown in the first row of the table and capture antibodies in the first column. Competition is shown with a C.
• Pan-specific antibodies for influenza type B can also be described by epitope specificity with reference to the consensus sequence of NSl proteins from influenza B strains shown in Fig. 2.
• Preferred antibodies specifically bind to an epitope occurring within residues 10-28, 40-45, 50-57, 67-74, 84-100, 154-159, 169-173, 185-191, 212-224, 226-240 of Fig. 2, and particularly underlined regions thereof, which indicate residues that are invariable between different strains of influenza type B.
• Residues included in one of the above regions that are not underlined i.e., vary between influenza type B strains
• the antibodies used can be nonhuman, humanized, chimeric, veneered, or human. Use of such antibodies is advantageous in avoiding false positives or negatives due to the presence of HAMA or heterophilic antibodies in the sample (US 6,680,209). Humanized, chimeric or veneered versions of the antibodies listed in the tables above are preferred. Such antibodies can also be used as pharmaceutical agents in treatment of influenza A or B.
• Antibodies can be made from antigen-containing fragments of the protein by standard procedures according to the type of antibody (see, e.g., Kohler, et al., Nature, 256:495, (1975); and Harlow & Lane, Antibodies, A Laboratory Manual (C.S.H.P., NY, 1988) Queen et al, Proc. Natl Acad. ScL USA 86:10029-10033 (1989) and WO 90/07861; Dower et al, WO 91/17271 and McCafferty et al, WO 92/01047 (each of which is incorporated by reference for all purposes).
• Immunization can be biased to generate panspecif ⁇ c antibodies by immunizing with multiple strains of influenza A or B, or by immunizing with one strain and boosting with another.
• a fragment from a highly conserved region of influenza A e.g., 8-21, 9-20, 29-38 or 45-49 or at least three contiguous amino acids of any of these of SEQ ID NO:l
• B NSl e.g., 10-28, 40-45, 50-57, 67-74, 84-100, 154-159, 169-173, 185- 191, 212-224, or 226-240 of SEQ ID NO:4 or subfragments of at least three contiguous amino acids thereof
• immunization with NSl of a single strain, or a fragment of NSl from a nonconserved region e.g., a PL region of influenza A
• antibody or "immunoglobulin” is used to include intact antibodies and binding fragments thereof. Typically, fragments compete with the intact antibody from which they were derived for specific binding to an antigen fragment including separate heavy chains, light chains Fab, Fab' F(ab')2, Fabc, and Fv. Fragments are produced by recombinant DNA techniques, or by enzymatic or chemical separation of intact immunoglobulins.
• antibody also includes one or more immunoglobulin chains that are chemically conjugated to, or expressed as, fusion proteins with other proteins.
• antibody also includes bispecific antibody.
• the antibodies described in the present application are mouse antibodies produced from hybridomas.
• any binding agent with specific affinity for NSl of influenza can be used as an antibody surrogate.
• Surrogates includes peptides from randomized phage display libraries screened against NSl from influenza A or B.
• Surrogates also include aptamers. Aptamers are RNA or DNA molecules selected in vitro from vast populations of random sequence that recognize specific ligands by forming binding pockets. Allosteric ribozymes are RNA enzymes whose activity is modulated by the binding of an effector molecule to an aptamer domain, which is located apart from the active site. These RNAs act as precision molecular switches that are controlled by the presence or absence of a specific effector.
• Aptamers can bind to nucleic acids, proteins, and even entire organisms. Aptamers are different from antibodies, yet they mimic properties of antibodies in a variety of diagnostic formats. Thus, aptamers can be used as a surrogate for panspecific antibodies.
• PDZ domains are preferred for detecting PL regions of NSl
• an antibody specifically binding to a PL region of a particular NSl protein of influenza A can be used as a surrogate for a PDZ domain specifically binding to that region.
• the invention provides methods of distinguishing between pathogenic and seasonal subtypes of influenza A as discussed above.
• a preferred format uses one or more PDZ domain as the capture reagent and one or more pan-specific antibodies as the detection reagent.
• use of domain 2 or domains 1, 2 and 3 of PSD95 and/or domain 8 of INADL are preferred as PDZ domain detection reagents.
• Preferred panspecific antibodies for use with a PDZ capture reagent are a pan specific antibody F68 8E6 (or an antibody that competes therewith) or F68 4B2 (or an antibody that competes therewith) as the detection antibody.
• the same or different panspecific antibody can be used with different PDZ domains in the same assay.
• the invention also provides methods of detecting influenza A in a manner that does not necessarily distinguish between subtypes of influenza A but can distinguish between influenza A and influenza B (or C). Such methods are performed using at least two pan specific antibodies to the NSl protein of influenza A binding to different epitopes.
• the two panspecific antibodies specifically bind to different epitopes defined numerically as described above or can be selected from different competition groups. Detection is preferably performed using a sandwich or lateral flow format as described in more detail below.
• One preferred combination of antibodies for detecting influenza A is F64 3H3 (or antibody that competes therewith) as the capture antibody, and F80 3D5 (or an antibody that competes therewith ) as the detection antibody.
• F68 4H9 or an antibody that competes therewith
• F68 8E6 or an antibody that competes therewith
• detection antibody Another preferred combination is F68 4H9 (or an antibody that competes therewith) as the capture antibody and F68 8E6 (or an antibody that competes therewith) as the detection antibody.
• Detecting of influenza A using two panspecific antibodies can be combined with differential detection of influenza A subtypes as described in (1) above. Such an assay indicates both whether influenza A is present, and if so, whether a pathogenic or seasonal subtype is present.
• the non-subtype-specific and subtype-specific assays can be performed separately or combined.
• One suitable format for combining the assays is to attach PDZ domain(s) for use in differential analysis to different regions of the same solid phase as an antibody capture reagent for use in non-subtype specific analysis.
• Binding of a PDZ domain to an NSl protein in the sample can be detected using a panspecific detection antibody.
• the panspecific detection antibody used to detect binding of the PDZ domain to the NSl protein can be the same or different as the panspecific antibody used for non-subtype specific analysis.
• a PSD95 domain, an INADL domain 8 and a panspecific capture antibody for influenza A are attached to different regions of a support, and a common panspecific detection antibody (binding to a different epitope than the panspecific capture antibody) is used to detect binding of each of the capture reagents to an influenza A NSl protein if present in the sample, as discussed above.
• Influenza B can be detected using first and second panspecific antibodies to the NSl protein of influenza B in analogous fashion to the assays described for detecting the NSl protein of influenza A, as described above. Such methods are performed using at least two pan specific antibodies to the NSl protein of influenza B binding to different epitopes. The two panspecific antibodies bind different epitopes defined numerically as described above or can be selected from different competition groups. Detection is preferably performed using a sandwich or lateral flow format as described in more detail below.
• a preferred combination of antibodies for detection of influenza B uses F89 6B5 (or an antibody that competes therewith) as the capture antibody and F94 3Al (or an antibody that competes therewith) or F94 1F9 (or an antibody that competes therewith) as the detection or detection antibody. Competition of antibodies is determined by binding to an NSl protein of influenza B.
• Each of the three assay types described above can effectively be combined to provide an assay capable of detecting influenza A (non-subtype specific), influenza B (non- subtype specific), influenza A (pathogenic subtype) and influenza A (seasonal subtype).
• the individual assays can be performed separately or together.
• One suitable format for combining the assays is to attach a panspecific capture antibody for the NS 1 protein of influenza A, a panspecific capture antibody for the NSl protein of influenza B, a PDZ domain for a PL of a pathogenic subtype of influenza A (e.g., a PSD95 domain as discussed above), and a PDZ domain for a PL of a seasonal subtype of influenza A (e.g., an INADL 8 domain) to a single support.
• the support is contacted with a sample from a subject and at least two panspecific detection antibodies.
• One detection antibody specifically binds to the NSl protein of influenza A at an epitope different from the capture antibody to the NSl protein of influenza A.
• the other detection antibody specifically binds to the NSl protein of influenza B at an epitope different from the capture antibody to the NSl protein of influenza B.
• the complexes that form indicate whether influenza A and/or B is present, and if influenza A is present whether the influenza A is pathogenic or seasonal.
• the invention provides diagnostic capture and detect reagents useful in assay methods for identifying influenza A and/or B viruses in a variety of different types of biological samples.
• Such formats include immunoprecipitation, Western blotting, ELISA, radioimmunoassay, competitive and immunometric assays. See Harlow & Lane, Antibodies ⁇ A Laboratory Manual (CSHP NY, 1988); U.S. Patent Nos.
• Immunometric or sandwich assays are a preferred format (see US 4,376,110, 4,486,530, 5,914,241, and 5,965,375). Such assays use one antibody or population of antibodies or a PDZ domain immobilized to a solid phase as a capture agent, and another antibody or population of antibodies or a PDZ domain in solution as detection agent. As discussed above, a combination of a capture PDZ domain and a detection antibody or vice versa is preferred for detection of influenza A. Typically, the detection agent is labeled. If an antibody population is used, the population typically contains antibodies binding to different epitope specificities within the target antigen. Accordingly, the same population can be used for both capture agent and detector agent.
• first and second monoclonal antibodies having different binding specificities are used for the solid and solution phase.
• Capture and detection agents can be contacted with target antigen in either order or simultaneously. If the capture agent is contacted first, the assay is referred to as being a forward assay. Conversely, if the detection agent is contacted first, the assay is referred to as being a reverse assay. If target is contacted with both capture agent and detection agent simultaneously, the assay is referred to as a simultaneous assay. After contacting the sample with capture and detection antibodies, a sample is incubated for a period that usually varies from about 10 min to about 24 hr and is usually about 1 hr.
• a wash step can then be performed to remove components of the sample not specifically bound to the detection agent.
• a wash can be performed after either or both binding steps.
• binding is quantified, typically by detecting label linked to the solid phase through binding of labeled solution antibody.
• a calibration curve is prepared from samples containing known concentrations of target antigen. Concentrations of antigen in samples being tested are then read by interpolation from the calibration curve. Analyte can be measured either from the amount of labeled solution antibody bound at equilibrium or by kinetic measurements of bound labeled solution antibody at a series of time points before equilibrium is reached. The slope of such a curve is a measure of the concentration of target in a sample.
• Target antigen in a sample competes with exogenously supplied labeled target antigen for binding to an antibody or PDZ detection reagent.
• the amount of labeled target antigen bound to the detection reagent is inversely proportional to the amount of target antigen in the sample.
• the detection reagent can be immobilized to facilitate separation of the bound complex from the sample prior to detection (heterogeneous assays) or separation may be unnecessary as practiced in homogeneous assay formats.
• the detection reagent is labeled.
• the detection reagent When the detection reagent is labeled, its binding sites compete for binding to the target antigen in the sample and an exogenously supplied form of the target antigen that can be, for example, the target antigen immobilized on a solid phase.
• Labeled detection reagent can also be used to detect antibodies in a sample that bind to the same target antigen as the labeled detection reagent in yet another competitive format. In each of the above formats, the detection reagent is present in limiting amounts roughly at the same concentration as the target that is being assayed.
• Lateral flow devices are a preferred format. Similar to a home pregnancy test, lateral flow devices work by applying fluid to a test strip that has been treated with specific biologicals. Carried by the liquid sample, phosphors labeled with corresponding biologicals flow through the strip and can be captured as they pass into specific zones. The amount of phosphor signal found on the strip is proportional to the amount of the target analyte.
• a sample suspected of containing influenza is added to a lateral flow device, the sample is allowed to move by diffusion and a line or colored zone indicates the presence of influenza .
• the lateral flow typically contains a solid support (for example nitrocellulose membrane) that contains three specific areas: a sample addition area, a capture area containing one or more antibodies to NS 1 , and a read-out area that contains one or more zones, each zone containing one or more labels.
• the lateral flow can also include positive and negative controls.
• a lateral flow device can be used as follows: an influenza A and/or B NSl protein is separated from other viral and cellular proteins in a biological sample by bringing an aliquot of the biological sample into contact with one end of a test strip, and then allowing the proteins to migrate on the test strip, e.g., by capillary action such as lateral flow.
• One or more antibodies, and/or aptamers are included as capture and/or detect reagents.
• a test strip can comprise a proximal region for loading the sample (the sample-loading region) and a distal test region containing an antibody to an NS 1 protein and buffer reagents and additives suitable for establishing binding interactions between the antibody any influenza B NS 1 protein in the migrating biological sample.
• the test strip comprises two test regions that contain different antibodies to NSl from two different subtypes of influenza B i.e., each is capable of specifically interacting with a different influenza B analyte.
• Suitable detectable labels for use in the above methods include any moiety that is detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical, chemical, or other means.
• suitable labels include biotin for staining with labeled streptavidin conjugate, fluorescent dyes (e.g., fluorescein, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., .
• Radiolabels can be detected using photographic film or scintillation counters, fluorescent markers can be detected using a photodetector to detect emitted light.
• Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
• the level of influenza B NSl protein in a sample can be quantified and/or compared to controls.
• Suitable negative control samples are e.g. obtained from individuals known to be healthy, e.g., individuals known not to have an influenza viral infection. Specificity controls may be collected from individuals having known influenza A or influenza C infection, or individuals infected with viruses other than influenza. Control samples can be from individuals genetically related to the subject being tested, but can also be from genetically unrelated individuals.
• a suitable negative control sample can also be a sample collected from an individual at an earlier stage of infection, i.e., a time point earlier than the time point at which the test sample is taken. Recombinant NSl of influenza B can be used as a positive control.
• any biological sample from a subject can be used that contains or is thought might contain a detectable concentration of influenza proteins and preferably of NSl .
• samples are often obtain from humans having or suspected of or at elevated risk of having influenza (e.g., through contact with others having influenza).
• samples that can be used are lung exudates, cell extracts (respiratory, epithelial lining nose), blood, mucous, and nasal swabs, for example.
• a high concentration of NSl can be found in nasal swabs.
• a preferred sample for identification of NSl is nasal secretion.
• Binding of NSl to an antibody occurs in the presence of up to 0.05% SDS, including 0.03% and 0.01%. Therefore, when the nasal or other bodily secretion is not likely to easily be used in a lateral flow format, it can be treated with SDS.
• the amount of SDS added is up to a final concentration of 0.01%, more preferably 0.03% and even more preferably, 0.05%.
• kits are provided for carrying out the present methods.
• the kits include one or more binding agents, typically antibodies or PDZ domains that specifically bind to NSl of influenza A and/or B.
• the instant kit optionally contains one or more of the reagents, buffers or additive compositions or reagents disclosed in the examples.
• the kit can also include a means, such as a device or a system, for removing the influenza viral NSl from other potential interfering substances in the biological sample.
• the instant kit can further include, if desired, one or more of various components useful in conducting an assay: e.g., one or more assay containers; one or more control or calibration reagents; one or more solid phase surfaces on which to conduct the assay; or, one or more buffers, additives or detection reagents or antibodies; one or more printed instructions detailing how to use the kit to detect influenza A and/or B, e.g. as package inserts and/or container labels, for indicating the quantities of the respective components that are to be used in performing the assay, as well as, guidelines for assessing the results of the assay.
• the instant kit can contain components useful for conducting a variety of different types of assay formats, including e.g. test strips, sandwich ELISA, Western blot assays, latex agglutination and the like.
• the invention further provides arrays of antibodies and/or PDZ domains immobilized at different regions.
• Such arrays include a plurality of different antibodies and/or PDZ domains in different regions of the array, each with specificity for NSl of influenza A and/or B.
• the different antibodies can be selected to have specificity for different subtypes and/or strains of influenza A and/or B.
• Antibodies that are panspecific for influenza A and/or B NSl can also be included.
• Antibodies for influenza A or C NSl proteins can also be included.
• Such arrays are useful for detection of influenza A and/or influenza B, and/or influenza C and distinguishing between subtypes and strains of these viruses.
• US Patent No. 5,922,615 describes a device that utilizes multiple discrete zones of immobilized antibodies on membranes to detect multiple target antigens in an array.
• US Patent Nos. 5,458,852, 6,019,944, US 6,143,576 and US Patent Application Serial No. 08/902,775 describe diagnostic devices with multiple discrete antibody zones immobilized in a device but not on a membrane for the assay of multiple target antigens.
• WO 99/67641 describes an array of microspheres is generated with tags that enable the decoding and identification of the specific binders (including antibodies) immobilized on individual microspheres after the microspheres are immobilized on the ends of optical fibers.
• microspheres are again used to immobilize binders (including antibodies) and the microspheres are distinguished from one another without separating them from the sample by detecting the relative amounts of two different fluorophores that are contained in the microspheres in order to identify the specific binder attached to the microsphere.
• any feature, step or embodiment can be used in combination with any other feature, step or embodiment.
• Human nasal secretions were examined for the presence and amount of NSl from Influenza A.
• Human nasal aspirates were collected and stored in M4 viral transport media (Remel, Inc, Lenexa, KS) at -80° C. Stored material was thawed and run on 10% SDS- PAGE.
• Western blot analysis was performed with monoclonal antibodies to NSl, 3H3 and IAlO (Arbor Vita Corporation, Sunnyvale, CA). The results for six samples are shown in Figure 4. The results show that NSl is present in large amounts in nasal secretions.
• NSl was produced and secreted by cells infected with influenza A virus.
• MDCK cells were infected with human influenza A/PR/8 at a MOI of 0.1.
• Supernatant as well as cells were collected and lysed in 1% Triton X-IOO and subjected to SDS-PAGE and western analysis with monoclonal antibody 3H3 which is pan- reactive to NSl .
• NSl was detected in infected cells within 24 hours after infection and detected in the supernatant of infected cells within 48 hours (see Figure 5). This suggests that a NSl based diagnostic may be able to detect infection by influenza A within 48 hours and possibly within 24 hours.
• glutathione-sepharose-PDZ beads were prepared (40ug of INAD Ld8) and used to pulldown 150ug of lysate from 293ET cells transfected with H3N2. Following an overnight incubation at 4°C and multiple washes with PBS, a western blot was prepared and probed a-HA (1 :500) (Roche). INADL d8 successfully pulldown HA-H3N2 NSl from cell lysate ( Figure 7).
• NSl PL is functional within the cell and can interact with PDZ domains as determined by the MATRIX assay.
• Monoclonal antibodies were prepared to specifically bind to subtype NSl proteins (e.g., H5N1), NSl PL classes (e.g., ESEV) and for pan-specificity (influenza A).
• subtype NSl proteins e.g., H5N1
• NSl PL classes e.g., ESEV
• pan-specificity influenza A
• GST and MBP fusion proteins of NSl were generated.
• the cloning vectors were obtained from Pharmacia (GST) or New England Biolabs (MBP).
• the NSl coding regions were synthesized using overlapping oligonucleotides by DNA 2.0 (Menlo Park, CA).
• mice were immunized with MBP-NSl fusion proteins at doses ranging from 10-100 ug per dose in CFA then IFA and PBS.
• Splenocytes and lymphocytes were harvested 3 days after the last boost with the corresponding GST-NSl fusion protein and fused with FOX-NY myeloma cells according to Kohler and Milstein (Nature 1975).
• the hybridomas were screened first with MBP-NSl in an ELISA.
• the positive wells were cloned and rescreened with a panel of MBP and GST NSl and classified into pan- reactive or subtype reactive.
• Steps 5 and 6 were repeated with eukaryotic expressed NSl in the form of a cell lysate.
• the antibodies are checked for compatibility with a lateral flow format described in Example 4.
• Figure 8 provides a lateral flow using PDZ capture followed by monoclonal antibody detection.
• PDZ domain proteins or antibodies were deposited on RF 120 Millipore membrane using a striper.
• the PDZ proteins PSD95D1-3, and INADL D8 were deposited at a concentration of 0.5 mg/ml.
• a control band was also deposited composed of goat anti-mouse antibody (GAM) also at 0.5 mg/ml.
• GAM goat anti-mouse antibody
• NSl protein was combined with gold conjugated monoclonal anti-NSl such as 4B2 in 100 ul volume in TBS-T buffer.
• NSl proteins used were from HlNl, H3N2, H5N197, H5N1, and a control lane did not contain NSl .
• human nasal aspirates were diluted and stored in saline or M4, as indicated.
• the samples were directly mixed with gold conjugated antibody in the amounts described below.
• the PDZ striped membrane was inserted into the NS 1/anti-NS 1 protein solution and flow initiated by capillary action and a wicking pad.
• NSl was subtyped based on the pattern of PDZ reactivity; HlNl binds to both PSD95 and INADL d8; H3N2 binds to INADL d8 only; H5N1 binds to PSD95 only. Influenza A subtyping was performed based on the results of the NSl lateral flow using reactivity to PDZ and detection with a gold conjugated pan- reactive anti-NS 1 monoclonal antibody.
• FIG. 9 13 different monoclonal antibodies were deposited on the lateral flow device.
• the 13 antibodies used were F64-1A0, F64-3H3, F64-6G12, F64-7A8, F64-7D1, F68-1D10, F68-4B2, F68-4H9, F68-6A12, F68-6B7, F68-6D6, F68-7B10.
• a subtype specific gold conjugated pan-NSl antibody was added to a sample containing HlNl influenza virus. The sample was applied to the lateral flow device and the results are shown in Figure 9. The results show that a pan-specific antibody can be used for the test and the assay identified which antibodies were the best for binding to HlNl.
• the binding strength is quantified by using the following symbols: (-) for no binding, (+) for weak binding, (+++) for strong binding and (++) for moderate binding.
• a lateral flow assay to identify pathogenic Influenza A in a patient sample is produced having pan-specific antibodies deposited on the membrane.
• the patient sample is admixed with a mixture of gold-labeled antibodies that recognize all NSl PL's.
• the sample is applied to the lateral flow test strip and if a pathogenic strain of influenza A is present a line is formed on the strip.
• the strip tests were run using the following protocol and materials: strips previously striped with goat anti-mouse/ PSD95 dl,2,3/ INADL d8; TBST/ 2% BSA/ 0.25% Tween 20 buffer; Stocks of NSl proteins MBP-HlNl, MBP-H3N2, MBP-H5N1 A, and MBP-H5N1B "old" (Jon's) fast gold-conjugated F68-4B2 antibody; and Maxisorp ELISA plates. The procedure was performed as follows:
• test provided in Figures 1OA and 1OB was prepared as follows: a GST-PSD95 dl,2,3 protein was striped onto the membrane at 3mg/mL for the avian test, or alternatively a mixture of two monoclonal antibodies can be used (1.1 mg/mL F64-3H3 and 0.075 mg/mL F68-4H9 for the pan-flu A test. A second line of 1 mg/mL polyclonal goat anti-mouse antibody was used for the test capture line. The steps are set out below.
• FIG. 10a both test are positives.
• Figure 1OC shows three of twenty human samples that were tested with the format shown in Figures 1OA and 1OB.
• Sample 1 was positive for Flu A, but negative for Avian Flu A (i.e., H5N1) and Sample 14 was negative for both (i.e., FIuA and H5N1).
• Figure 1Od shows the same test for HlNl, H3N2, and H5N1 recombinant proteins.
• the Pan-FluA test was positive for all three.
• the Avian Flu test was positive for only H5N1.
• Figure 1OE Gold-conjugated PDZs were used as detectors and single or multiple mAbs were used for capture.
• Figure 1OE had liquid gold added in the form of Au-PSD95 dl.2,3 with a F68-4B2 mAb capture.
• 1.7 ng of NSl H5N1 protein tested positively. This was an Avian Flu (i.e., H5N1) specific test.
• a lateral flow test was developed to detect Influenza B NSl .
• Monoclonal anti- influenza B NSl antibodies were deposited on an HF075 Millipore membrane at a concentration of ⁇ 0.7 mg/ml using a striper.
• Some examples of antibodies deposited as capture agents are among the following: F89 1F4, F94 3Al, F89 4D5.
• a control band was also deposited composed of goat anti-mouse antibody (GAM) also at 1 mg/ml.
• Flu B NSl protein was combined with gold conjugated monoclonal anti-NSl such as F94 3Al (when F94 3Al is not used as capture) in 100 ⁇ l volume of AVC Flu B buffer.
• the FIuB NSl proteins used were either recombinant AVC ID 522 (B/BA/78 NSl) and AVC ID 523 (B/YM/222/2002) or clinical samples of from patients known to be infected with influenza B.
• the anti-Flu B NSl antibody striped membrane was inserted into the FIuB NSl/anti-NSl protein solution and flow initiated by capillary action and a wicking pad.
• the ELISA plate was tapped several times to mix the contents of the wells 15.) The pre-striped strips were added to the wells and observed during development.
• Fig. 11 shows results from testing various pairs of monoclonal antibodies as capture and detection reagent on two strains of influenza B, B/BA78 (also known as strain 522), and B/Yagamata ⁇ 222 ⁇ 2002, also known as strain 523).
• the four different panels show four combinations of antibodies.
• tracks 3 and 6 are negative controls.
• Tracks 1 and 2 are recombinant NSl from strain 522 and tracks 4 and 5 are recombinant NSl from strain 523.
• the presence of additional bands in tracks 4 and 5 but not tracks 1 and 2 of the first panel shows that the F89-F4 capture antibody F89-4G12 detection antibody combination detects the 523 strain but does not detect the 522 strains.
• the other panels can be analyzed in the same way.
• Table 13 shows which antibodies can serve as a capture antibody and which as a detection antibody and whether the antibodies are panspecific for both strains of influenza B (522 and 523) or monospecific to 522 or 523.
• the F89-1F4 antibody can serve as either a capture or detection antibody and is panspecific.
• F94-4C10 works as a detection antibody but not as a capture antibody and is specific for influenza B 523.
• F89-1F4 and F94-3A1 are preferred antibodies for use in lateral flow format.
• a lateral flow assay was used to identify Influenza B in a patient sample is produced having pan-specific antibodies deposited on the membrane.
• the patient sample was admixed with a mixture of gold-labeled antibodies that recognize all Influenza B NSIs.
• the sample was applied to the lateral flow test strip. Presence of influenza B is present a line is shown by a line formed on the strip.
• Fig. 12 shows the results from different dilutions of a patient sample compared with positive and negative controls. The upper part of the figure shows the actual appearance of lines indicating presence of influenza B. The lower part of the figure indicates the relative intensity of the bands. Influenza B was easily detectable up to a dilution of at least 400 fold.
• EXAMPLE 6 BINDING OF A POLYPEPTIDE COMPRISING 3 COPIES OF PSD95 DOMAIN 2 TO NSl
• a lateral flow assay was used to detect the presence of H5N1 protein in a sample.
• recombinant PDZ domain proteins or antibodies were deposited on RF 120 Millipore membrane using a striper.
• Increasing amounts (0, 25, 100 or 500 picograms) of a polypeptide comprising a single copy of PSD95 domain 2 were deposited as a band onto a membrane.
• Equal amounts of a polypeptide comprising three copies of PSD95 domain 2 in which natural PDZ domains 1 and 3 of PSD95 were each replaced with a copy of PSD95 PDZ domain 2 (Fig. 14A) were also deposited.
• Fig. 14A also shows in italics the sequence of an optional GST sequence that can be used for immobilization.
• a polypeptide comprising three copies of PSD95 domains 1, 2 and 3 were also deposited.
• a 3 mg/ml protein solution was printed at 0.05 ⁇ l/mm strip, wherein the strip was 4.26 mm wide.
• a goat anti-mouse antibody (GAM) was deposited as a control band.
• NSl protein was combined with gold conjugated monoclonal anti-NSl antibody (of mouse sequence) in 100 ⁇ l volume buffer. The striped membranes were inserted into the NSl/anti-NSl solution and flow was initiated by capillary action and a wi eking pad.
• the polypeptide comprising three copies of PSD95 domain 2 and the peptide comprising a single copy of PSD95 domain 2 both generated a detectable signal when contacted with H5N1 NSl. However, at a given concentration of H5N1 NSl, the signal was stronger for the polypeptide comprising three copies of PSD95 domain 2.
• a polypeptide comprising PSD95 domains 1, 2 and 3 also generated a detectable signal at the same concentration of H5N1 NSl, although this signal was not as strong as that of the polypeptide comprising three copies of PSD95 domain 2.
• the negative control included a buffer solution containing gold-conjugated anti NSl antibody but no NSl analyte. The negative control yields a dark control band line of GAM indicating that the excess gold- conjugated anti-NSl antibody, indicating that the unbound gold-conjugated anti -NSl antibody has indeed flowed past the control band.

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