Entire nucleotide sequence and characterization of a hepatitis C virus of genotype V/3a

1 First Department of Internal Medicine, Yamanashi Medical College, Yamanashi-Ken 409-38 2 Viral Hepatitis Research Foundation of Japan, Tokyo 113 3 Japanese Red Cross Saitama Blood Center, Saitama-Ken 338, Japan 4 Department of Transfusion Medicine, Regional Blood Center, Auckland, New Zealand and 5 Immunology Division, Jichi Medical School, Tochigi-Ken 329-04, Japan The entire nucleotide sequence of a hepatitis C virus (HCV) genome (NZL1) of genotype V/3a was determined from overlapping cDNA clones obtained from a human carrier in New Zealand. It comprised 9425 nucleotides (nt) including a 5'-untranslated region of 339 nt, a single large open reading frame encoding a polyprotein of 3021 amino acids, a 3'-untranslated region of 23 nt, and 3'-terminal poly(U) stretches of variable lengths. The NZL1 genome was compared with 15 HCV isolates of other genotypes for which the full-length sequence has been determined. It differed from them by 31.1 to 34.3% in nucleotide sequence identity and by 24.5 to 29.1% in amino acid sequence identity, confirming the distinction of genotype V/3a from the other isolates. Received 29 November 1993; accepted 12 January 1994.