Sequence analysis of nucleocapsid and partial envelope genes of the hepatitis C virus derived from an aboriginal...

Two overlapping cDNA fragments of the 5'-terminal region of the hepatitis C virus (named as HCV-B) were cloned by reverse transcription-polymerase chain reaction (RT-PCR). The consensus nucleotide sequence of the 1101 nucleotide length was constructed from the sequences of at least three independent clones of each one of these two amplified overlapping HCV cDNA fragments. By comparison with other HCV strains isolated from different countries, the 5' non-coding region was almost identical, with only 1 difference in 90 nucleotides, and the homology of the putative nucleocapsid gene was found to be quite conservative, with a similarity of 90-96% and 96-97% at the nucleotide and amino acid levels, respectively. The homology of the down-stream region which encodes a putative envelope protein showed a low degree of identities (71.5% and 76.7% compared with American HCV-1 strain) at the levels of nucleotide and amino acid. On the other hand, it was similar to the Taiwanese HCV-T strain and the Japanese major J1 strain; the homology was about 93% at both levels of nucleotide and amino acid. This finding led to a conclusion that the HCV-B strain is closely related to the major HCV genotypes as HCV-J1 and HCV-T, isolated in Asian area.