Cloned genome of infectious hepatitis c virus strain hc-tn and uses thereof

Abstract

Embodiments described herein include nucleic acid sequences, which encode hepatitis C virus of strain HC-TN, genotype 1a, proteins and polypeptides and fragments thereof. Use of these compositions, and diagnostics for HCV and in the development of screening assays for the identification of antiviral agents for HCV are also contemplated.

1 .- 7 . (canceled) 
     
     
         8 . An isolated or purified polypeptide comprising the amino acid sequence of SEQ ID NO: 2 or an antigenic fragment thereof comprising at least 9 consecutive amino acids. 
     
     
         9 . The polypeptide of  claim 8 , wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 2. 
     
     
         10 . The polypeptide of  claim 8 , wherein said polypeptide is a fragment of SEQ ID NO: 2 at least 100 consecutive amino acids in length. 
     
     
         11 . The polypeptide of  claim 10 , wherein said polypeptide is a fragment of SEQ ID NO: 2 at least 300 consecutive amino acids in length. 
     
     
         12 . A method for producing a hepatitis C virus comprising transfecting a host cell with a recombinant nucleic acid that encodes a human hepatitis C virus of genotype 1a and strain HC-TN, said molecule capable of expressing said virus when transfected into cells. 
     
     
         13 . The method of  claim 12 , wherein the recombinant nucleic acid encodes a polypeptide having the amino acid sequence of SEQ NO:2. 
     
     
         14 . A method for assaying candidate antiviral agents for activity against HCV, comprising:
 a) exposing a cell comprising a nucleic acid that encodes a polypeptide of  claim 8  or a fragment thereof to a candidate antiviral agent; and   b) measuring the presence or absence of hepatitis C virus replication or NS3 protease activity in the cell of step (a); and/or measuring the presence or absence of hepatitis C virus helicase or polymerase activity in the cell of step (a).   
     
     
         15 . The method of  claim 14 , wherein said replication activity in step (b) is measured by at least one of the following: negative strand RT-PCR, quantitative RT-PCR, Western blot, immunofluorescence, or infectivity in a susceptible animal. 
     
     
         16 . (canceled) 
     
     
         17 . A method for assaying candidate antiviral agents for activity against HCV, comprising:
 a) exposing an HCV protease encoded by a nucleic acid sequence that encodes a polypeptide according to  8  or a fragment thereof that contains protease activity to a candidate antiviral agent in the presence of a protease substrate; and   b) measuring the protease activity of said protease.   
     
     
         18 . The method of  claim 17 , wherein said HCV protease is selected from the group consisting of an NS3 domain protease, an NS3-NS4A fusion polypeptide, or an NS2-NS3 protease. 
     
     
         19 . A method of inducing an immune response to HCV comprising:
 identifying an animal in need of an immune response to HCV; and   providing to said animal a composition that comprises the polypeptide encoded by the nucleic acid of SEQ ID NO: 1 or a nucleic acid that encodes a polypeptide comprising the sequence of SEQ ID NO: 2.   
     
     
         20 . The method of  claim 19 , further comprising measuring the immune response to said polypeptide encoded by SEQ ID NO: 1 or a fragment thereof.