Methods and compositions for diagnosis and treatment of influenza

Abstract

The invention provides method and compositions for determining the presence and amount of an influenza virus in a sample including high risk strains of Influenza A. Also provided are methods for determining whether a subject is infected with a influenza virus, as well as, the type and strain of the influenza virus. The methods involve contacting a sample from the subject with a PDZ polypeptides (PDZ) and/or PDZ ligands (PL) and determining whether binding interactions occur between PDZ and PL. Assays for identifying anti-viral agents are also provided, as well as, methods for using the compositions to alter PDZ binding to PL in influenza infected cells.

1 - 89 . (canceled) 
     
     
         90 . A method for assessing the presence, amount and/or subtype of an influenza virus in a human or avian subject, comprising:
 (a) contacting a sample obtained from nasopharyngeal, tracheal and/or sputum fluids of the subject with a first reagent (“capture reagent”) that specifically binds to an influenza virus non-structural-1 (NS1) protein,   (b) contacting the sample with a detectable second reagent (“detector reagent”) that specifically binds to an influenza virus NS1 protein, and   (c) determining the presence, absence or amount of a complex formed between the detector agent and the capture agent as a result of both reagents specifically binding to any NS1 protein in the sample, by detecting the detector reagent in the complex,   wherein the presence, absence and/or amount of the complex is indicative of:   (i) the presence and/or amount of any influenza virus in the sample, and/or   (ii) the subtype of the influenza virus, if the capture or detector reagent specifically binds to NS1 in a subtype-specific manner.   
     
     
         91 . The method of  claim 90 , wherein the influenza virus is an influenza A virus, and the capture reagent and the detector reagent both bind specifically to an NS1 protein of at least one subtype of influenza A virus. 
     
     
         92 . The method of  claim 91 , wherein the capture reagent is immobilized upon a solid support before presence, absence or amount of the complex is determined. 
     
     
         93 . The method of  claim 91 , wherein the solid support is in the form of beads. 
     
     
         94 . The method of  claim 91 , wherein the solid support is part of a lateral flow assay device, and wherein the presence, absence or amount of the complex is determined by a lateral flow assay. 
     
     
         95 . The method of  claim 90 , wherein the detector reagent can be optically detected, and the presence, absence or amount of the complex is determined by optically detecting the detector reagent in the complex. 
     
     
         96 . The method of  claim 95 , wherein the colored label comprises gold or colored latex particles, and the presence, absence or amount of the complex is determined by a lateral flow assay. 
     
     
         97 . The method of  claim 95 , wherein the presence, absence or amount of complex is determined within about 90 minutes after the sample is contacted with a capture or detector reagent. 
     
     
         98 . The method of  claim 95 , wherein the specific binding is visualized by eye. 
     
     
         99 . The method of  claim 90 , wherein the capture reagent or detector reagent comprises at least one PDZ polypeptide and/or antibody that binds specifically to NS1. 
     
     
         100 . The method of  claim 99 , wherein the PDZ polypeptide or antibody specifically binds to a C-terminal PL site of NS1. 
     
     
         101 . The method of  claim 91 , wherein the capture reagent or detector reagent comprises one or more binding agents that specifically binds to an NS1 protein of at least one subtype of influenza A virus. 
     
     
         102 . The method of  claim 101 , wherein the capture reagent or detector reagent comprises at least one binding agent that specifically binds to NS1 in a subtype-specific manner. 
     
     
         103 . The method of  claim 102 , wherein said at least one particular subtype is pathogenic and said at least one other subtype is non-pathogenic, or vice versa. 
     
     
         104 . The method of  claim 103 , wherein the pathogenic subtype is H5N1 and/or the non-pathogenic subtype is H3N2. 
     
     
         105 . A method for assessing the presence, absence, amount and/or subtype of an influenza A virus in a subject, comprising:
 (a) contacting a sample obtained from nasopharyngeal fluids of the subject with a capture agent that specifically binds to an influenza A virus NS1 protein and is immobilized upon a solid substrate,   (b) contacting the sample with a optically detectable second reagent (“detector reagent”) that specifically binds to an NS1 protein and is in solution, and   (c) determining the presence, absence or amount of a complex formed between the detector agent and the capture agent as a result of both reagents specifically binding to any NS1 protein in the sample, by optically detecting the detector reagent in the complex using a lateral flow assay.   
     
     
         106 . The method of  claim 105 , wherein the capture reagent comprises said first and second binding agents that specifically bind to an NS1 protein organized in an array. 
     
     
         107 . The method of  claim 90 , further comprising comparing the presence or amount of the complex formed with the sample to the amount of complex formed with a similarly-treated positive or negative control sample. 
     
     
         108 . The method of  claim 90 , wherein the presence, absence or amount of complex is determined within about 90 minutes after the sample is contacted with a capture or detector reagent. 
     
     
         109 . The method of  claim 108 , wherein the specific binding is visualized by eye.