Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group

• Published in: Journal of general virology 1994-04, Vol.75 (4), p.931-936
• Main Authors: Tokita, Hajime, Shrestha, Santosh Man, Okamoto, Hiroaki, Sakamoto, Minoru, Horikita, Minoru, Iizuka, Hisao, Shrestha, Shobhana, Miyakawa, Yuzo, Mayumi, Makoto
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Base Sequence; Biological and medical sciences; Chronic Disease; Consensus Sequence; Fundamental and applied biological sciences. Psychology; Genetic Variation - genetics; Genotype; Hepacivirus - classification; Hepacivirus - genetics; Hepatitis C - epidemiology; Hepatitis C - microbiology; hepatitis C virus; Humans; Microbiology; Molecular Epidemiology; Molecular Sequence Data; Nepal - epidemiology; Phylogeny; Replicative cycle, interference, host-virus relations, pathogenicity, miscellaneous strains; RNA, Viral - isolation & purification; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Virology
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/0022-1317-75-4-931

1 Immunology Division, Jichi Medical School, Tochigi-Ken 329-04, Japan, 2 Liver Unit, Bir Hospital, Kathmandu, Nepal, 3 First Department of Internal Medicine, Yamanashi Medical College, Yamanashi-Ken 409-38, 4 Second Department of Internal Medicine, The University of Tokushima School of Medicine, Tokushima-Ken 770, 5 Japanese Red Cross Saitama Blood Center, Saitama-Ken 338, and 6 Mita Institute, Tokyo 108, Japan Five isolates of hepatitis C virus (HCV) RNA from patients with chronic liver disease in Nepal were not classifiable into the known genotypes I/1a, II/1b, III/2a, IV/2b or V/3a using PCR with type-specific primers deduced from the HCV core gene. Their nucleotide sequences were determined for the 5'-terminal 1·5 kilobases and 3'-terminal 1·2 kilobases, covering 30% of the entire genome, and compared with each other and with reported sequences of HCV isolates of various genotypes. They were more similar to a reported HCV isolate (NZL1) of genotype V/3a (in 81·6 to 84·1% of their nucleotides and 85·7 to 88·7% of the deduced amino acid sequence) compared with the genotypes I/1a to IV/2b (in 69·3 to 74·7% and 72·3 to 77·4%, respectively). Hence they were considered to be variants of the third major group (group 3). The five HCV isolates shared 81·3 to 85·2% of nucleotide sequence and 85·4 to 89·3% of deduced amino acid sequence. Thus they were substantially different from each other. One of them was classified as genotype VI/3b due to an 88·2% similarity in nucleotide sequence to that of the reported HCV isolates of this genotype, whereas the remaining four were classified into provisional genotypes 3c, 3d, 3e and 3f. These HCV variants have evolved and remained in Nepal, and have not been observed in the other areas of the world. Received 8 September 1993; accepted 5 November 1993.