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

Abstract

Five isolates of hepatitis C virus (HCV) RNA from patients with chronic liver disease in Nepal were not classifiable into the known genotypes I/la, II/lb, II1/2a, 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/la 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 Vl/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.

Variation of the hepatitis C virus 5' non-coding region: implications for secondary structure, virus detection and typing

“…2). Single examples of several other subtypes of type 3 have been documented (Tokita et al, 1994b;van Doorn, 1994, J. Mellor, unpublished results), but the significance of 5'NCR sequence differences between these subtypes is uncertain.…”

“…Nucleotide sequences of the HCV 5'NCR and corresponding sequences from coding regions of the genome were obtained from published sources (Chan et al, 1992;Bukh et al, 1992Bukh et al, a, 1993Bukh et al, , 1994Stuyver et al, 1993Stuyver et al, , 1994Simmonds et al, 1993a, b, c;Honda et al, 1993;Okamoto et al, 1993Okamoto et al, , 1994Tokita et al, 1994b;van Doorn, 1994;Bhattacherjee et al, 1995), from GenBank (accession nos D13406, D10074, M96362, U01214, D10934, X65924, D10075, D 10077, D 17763, D00830, D16433, D16434, D28917, D11443, X76918, Z36522-Z36527, M86779, M86765, L12353-L12355 and L29585), and new sequence information for viruses from a variety of HCV infected individuals. RNA was extracted from sera, reverse transcribed and amplified by PCR using 5'NCR specific primers 939, 209, 940 and 211 as described previously (Chan et al, 1992).…”

Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification

“…2). As previously described (Tokita et al, 1994 a), the range of percentage sequence similarity values upon comparison of 16 complete genomic sequences was highly restricted; pairwise similarity values range from 65.7-68.8 for different genotypes (1, 2 and 3), from 76.9-80.11 between subtypes [la/lb/lc(O) and 2a/2b], and from 90-8-99 % within subtypes (la and lb). Surprisingly, analysis of subgenomic sequences of the same 16 HCV variants produced similarly restricted distributions of sequence similarity ( Fig.…”

Evidence of Hepatitis C Virus Infection and Associated Treatment in Nepal

“…Each participant was informed of their test individually. In study, the past medical history of patients was taken since 2002 to 2012 till now, and regarding Nepal Blood Bank, Annual Progress Report of medical year 2011/012 is accessed for reference [19][20][21][22].…”