Identification and Molecular Characterisation of the Complete Genome of a Singapore Isolate of Hepatitis C Virus: Sequence Comparison with other Strains and Phylogenetic Analysis

• Published in: Virus genes 2001-08, Vol.23 (1), p.89-95
• Main Authors: Lim, S P, Khu, Y L, Hong, W J, Tay, A, Ting, A E, Lim, S G, Tan, Y H
• Format: Article
• Language: English
• Subjects: 5' Untranslated Regions; Amino Acid Sequence; Base Sequence; DNA, Viral; Genome, Viral; Hepacivirus - classification; Hepacivirus - genetics; Hepacivirus - isolation & purification; Hepatitis C virus; Hepatitis C, Chronic - blood; Hepatitis C, Chronic - virology; Humans; Molecular Sequence Data; Phylogeny; Reverse Transcriptase Polymerase Chain Reaction; Sequence Homology, Amino Acid; Singapore
• ISSN: 0920-8569; 1572-994X
• DOI: 10.1023/A:1011143731677

The complete genomic sequence of a Singapore isolate of the hepatitis C virus (HCV) was obtained from serum of an individual chronically infected with HCV. Nine overlapping cDNA clones covering the entire viral genome was amplified by reverse-transcription–polymerase chain reaction (RT–PCR). This isolate (HCV-S1) comprised 9,609 nucleotides (nt), including 341 nt of the complete 5′ untranslated region (5′ UTR), a single open reading frame of 3,011 amino acids (aa) and 235 nt of the complete 3′ UTR. Its genotype was identified as type 1b from analyses of its sequences in the 5′ UTR, NS3 and NS5B 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 was most closely related to the Taiwan strain, HCV-TW and another Japanese strain, HCV-K1-R1.