Methods and compositions for identifying and characterizing hepatitis c

Abstract

The invention provides novel methods and compositions for amplifying portions of the HCV genome. The nucleic acid sequences set forth as SEQ ID NOS:1-64 derived from HCV cDNA and functional equivalents thereof, kits containing same, and methods employing same, are useful for the identification and characterization of HCV in biological samples.

1 . A set of primers comprising:
 (a) an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 80% identical to either SEQ ID NO: 4; and   (b) an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 80% identical to either SEQ ID NO: 7,   wherein each isolated nucleic acid molecule is 4 to 100 nucleotides in length.   
     
     
         2 . An isolated nucleic acid molecule comprising a nucleotide sequence which is at least 80% identical to either SEQ ID NO: 4 or SEQ ID NO: 7, wherein the isolated nucleic acid molecule is 4 to 100 nucleotides in length. 
     
     
         3 . The isolated nucleic acid molecule of  claim 2 , wherein the nucleotide sequence is at least 80% identical to SEQ ID NO: 4. 
     
     
         4 . The isolated nucleic acid molecule of  claim 3 , wherein the nucleotide sequence is at least 80% identical to SEQ ID NO: 7. 
     
     
         5 . The isolated nucleic acid molecule of  claim 3 , wherein the isolated nucleic acid molecule is 17 to 30 nucleotides in length. 
     
     
         6 . The isolated nucleic acid molecule of  claim 4 , wherein the isolated nucleic acid molecule is 17 to 30 nucleotides in length. 
     
     
         7 . The isolated nucleic acid molecule of  claim 2 , wherein the isolated nucleic acid molecule comprises a nucleotide sequence identical to SEQ ID NO: 4. 
     
     
         8 . The isolated nucleic acid molecule of  claim 2 , wherein the isolated nucleic acid molecule comprises a nucleotide sequence identical to SEQ ID NO: 7. 
     
     
         9 . The isolated nucleic acid molecule of  claim 7 , wherein the isolated nucleic acid molecule is 17 to 30 nucleotides in length. 
     
     
         10 . The isolated nucleic acid molecule of  claim 8 , wherein the isolated nucleic acid molecule is 17 to 30 nucleotides in length. 
     
     
         11 . The isolated nucleic acid molecule of  claim 3 , wherein the nucleotide sequence consists of SEQ ID NO: 4. 
     
     
         12 . The isolated nucleic acid molecule of  claim 4 , wherein the nucleotide sequence consists of SEQ ID NO: 7. 
     
     
         13 . A kit for the detection of HCV, comprising an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 80% identical to either SEQ ID NO: 4 or SEQ ID NO: 7, wherein the isolated nucleic acid molecule is 4 to 100 nucleotides in length. 
     
     
         14 . A method for detecting HCV infection in a patient, comprising:
 (a) combining a DNA sample from the patient with a set of primers comprising:
 (i) an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 80% identical to either SEQ ID NO: 4; and 
 (ii) an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 80% identical to either SEQ ID NO: 7, 
 wherein each isolated nucleic acid molecule is 4 to 100 nucleotides in length; and 
   (b) amplifying a target nucleic acid under conditions which allow for an amplification reaction to occur,   wherein the presence of amplified target nucleic acid is indicative of HCV infection.   
     
     
         15 . The method of  claim 14 , wherein the target nucleic acid is from the HCV genome. 
     
     
         16 . The method of  claim 14 , further comprising sequencing the amplified target nucleic acid. 
     
     
         17 . The method of  claim 16 , further comprising evaluating the sequence for mutations.