Hcv clade and prototype sequences thereof

Abstract

The current invention relates to a previously unrecognized clade of HCV genotypes as well as to diagnostic, prophylactic and therapeutic applications of nucleic acids, proteins, and antibodies to said protein, derived of or based on the newly characterized hepatitis C viruses.

1 . An isolated nucleic acid comprising an HCV nucleic acid sequence of an HCV clade represented by any of the following HCV nucleic acid sequences which are prototype sequences of said HCV clade:
 (i) a nucleic acid sequence defined by SEQ ID NOs: 1, 2, 9, 10 or 16;   (ii) a nucleic acid sequence encoding a protein defined by SEQ ID NOs: 3, 4 or 17;   (iii) a nucleic acid sequence which is the complement of a nucleic acid sequence of (i) or (ii);   (iv) a nucleic acid sequence hybridizing to a nucleic acid sequence of (i), (ii) or (iii) under stringent conditions;   wherein said nucleic acid is DNA, cDNA or a synthetic nucleic acid, or wherein said nucleic acid is RNA and wherein “T” is replaced by “U”.   
     
     
         2 . An isolated nucleic acid comprising an HCV nucleic acid sequence of an HCV genotype represented by any of the following HCV nucleic acid sequences which are prototype sequences of said HCV genotype:
 (i) a nucleic acid sequence defined by SEQ ID NOs: 1, 2, 9, 10, or 16 wherein SEQ ID NOs: 1 and 9 and SEQ ID NOs:2, 10 and 16 each represent a different subtype of said HCV genotype;   (ii) a nucleic acid sequence encoding a protein defined by SEQ ID NOs: 3, 4 or 17;   (iii) a nucleic acid sequence which is the complement of a nucleic acid sequence of (i) or (ii);   (iv) a nucleic acid sequence hybridizing to a nucleic acid sequence of (i), (ii) or (iii) under stringent conditions;   wherein said nucleic acid is DNA, cDNA or a synthetic nucleic acid, or wherein said nucleic acid is RNA and wherein “T” is replaced by “U”.   
     
     
         3 - 7 . (canceled) 
     
     
         8 . An isolated protein comprising an HCV amino acid sequence encoded by an HCV nucleic acid sequence according to  claim 1 . 
     
     
         9 . The isolated protein according to  claim 8  wherein said HCV amino acid sequence is defined by SEQ ID NOs:3, 4 or 17. 
     
     
         10 . A peptide of at least 5 contiguous amino acids taken from an HCV amino acid sequence according to  claim 8  and wherein said peptide comprises at least one amino acid that is different from any HCV amino acid sequence of an HCV of clades 1 to 6 or different from any HCV amino acid sequence of an HCV genotype or subtype of clades 1 to 6. 
     
     
         11 . (canceled) 
     
     
         12 . A recombinant vector comprising a nucleic acid or oligonucleotide according to  claim 1 . 
     
     
         13 . The recombinant vector according to  claim 12  which is an expression vector capable of directing expression of an HCV protein encoded by the HCV nucleic acid sequence comprised in said vector. 
     
     
         14 . A host cell transformed with a nucleic acid or oligonucleotide according to  12 . 
     
     
         15 . (canceled) 
     
     
         16 . A method for determining the genotype of an HCV virus in a biological sample comprising the step of detecting the presence of a nucleic acid or oligonucleotide according to  claim 1 . 
     
     
         17 - 18 . (canceled) 
     
     
         19 . A method for detecting the presence of an HCV virus in a biological sample comprising the steps of:
 (i) obtaining a target HCV nucleic acid from a biological sample suspected to contain an HCV nucleic acid sequence according to  claim 1 ;   (ii) obtaining the nucleic acid sequence of the target HCV nucleic acid of (i);   (iii) inferring from the nucleic acid sequence obtained in (ii) the presence of an HCV nucleic acid sequence according to  claim 1  and, therefrom, the presence of an HCV virus in said biological sample.   
     
     
         20 - 22 . (canceled) 
     
     
         23 . A diagnostic kit for detecting the presence and/or for determining the genotype of an HCV virus in a biological sample, said kit comprising at least one of a nucleic acid according to  claim 1 . 
     
     
         24 . (canceled) 
     
     
         25 . A method for detecting antibodies to an HCV virus present in a biological sample comprising the step of detecting said antibodies with at least one protein or peptide according to  claim 8 . 
     
     
         26 - 27 . (canceled) 
     
     
         28 . A diagnostic kit for detecting antibodies to an HCV virus or for typing of an HCV virus, said kit comprising at least one protein or peptide according to  claim 8 . 
     
     
         29 . (canceled) 
     
     
         30 . An antibody raised upon immunization of a mammal with at least one protein or peptide according to  claim 8 . 
     
     
         31 . The antibody according to  claim 30  which is a monoclonal antibody or a humanized antibody. 
     
     
         32 - 39 . (canceled) 
     
     
         40 . An HCV vaccine composition comprising at least one of an nucleic acid or oligonucleotide according to  claim 1 . 
     
     
         41 - 51 . (canceled)