Identification and molecular characterisation of the complete genome of a singapore isolate of hepatitis C virus: Sequence comparison with other strains and phylogenetic analysis

The complete genomic sequence of a Singapore isolate of the hepatitis C vir us (HCV) was obtained from serum of an individual chronically infected with HCV. Nine overlapping cDNA clones covering the entire viral genome was amp lified by reverse-transcription-polymerase chain reaction (RT-PCR). This is olate (HCV-S1) comprised 9,609 nucleotides (nt), including 341 nt of the co mplete 5' untranslated region (5' UTR), a single open reading frame of 3,01 1 amino acids (aa) and 235 nt of the complete 3' UTR. Its genotype was iden tified as type 1b from analyses of its sequences in the 5' UTR, NS3 and NS5 B regions. When compared against nine reported HCV isolates, the overall aa homology of HCV-S1 was closest with an Australian strain, HCV-A (94%) and a Japanese strain, HCV-JT (93.9%). Phylogenetic analysis revealed that it w as most closely related to the Taiwan strain, HCV-TW and another Japanese s train, HCV-K1-R1.