Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses

Abstract

In this study, the first complete genome sequences for hepatitis C virus (HCV) subtypes 6f, 6i, 6j and 6m, obtained from infected blood donors in Chiang Mai, Thailand, are reported. Pairwise genome-wide nucleotide similarities between some of these isolates were higher than the 75-80 % value used previously to define different HCV subtypes. To investigate further, the entire genomes of four prototype isolates, Th602 (6i), Th553 (6j), B4/92 (6m) and D86/93 (6n), were sequenced. Pairwise comparison of these sequences gave a similar range of nucleotide similarities, thereby providing new information for HCV subtype classification. In order to study the hypothesis of interspousal HCV transmission, four additional complete HCV genome sequences were obtained from two infected Thai blood donors and their spouses, C-0044 and C-0046 (6f), and C-0192 and C-0185 (6m). Pairwise comparison of the sequences revealed that C-0044 and C-0046 share a nucleotide similarity of 98.1 %, whilst C-0185 and C-0192 have a similarity of 97.8 %. Several other studies of partial HCV sequences of different genomic regions from HCV-infected couples have shown nucleotide similarities ranging from 96.3 to 100 %. The similarities of the complete genome sequences from the two couples in the current study are consistent with HCV transmission between spouses.

Complete genome analysis of hepatitis C virus subtypes 6t and 6u

“…Complete genome analysis of HCV subtypes 6t and 6u subtype found only in Thailand, have been sequenced recently (Lu et al, 2007b). TH24 complete genome and core, E1 and NS5B phylogenetic trees showed 99-100 % bootstrap support related to the C-0159 sequence (Fig.…”

Complete genomes of three subtype 6t isolates and analysis of many novel hepatitis C virus variants within genotype 6

“…However, the genetic diversity is a variable that has shown clear discontinuities between HCV genotypes, subtypes and isolates. The discontinuities are possibly due to the missing detection of some HCV variants or incomplete sampling (Lu et al, 2007a). It is likely that this second group of variants may partially fill the discontinuities between subtypes and isolates when their complete genomes are sequenced.…”

“…Potential genetic recombination events were examined using the RDP2 software (Martin et al, 2005) and the bootscanning approach. All these procedures were performed as described previously (Lu et al, 2007a).…”

“…Previously, we characterized the complete genome sequences for 11 assigned subtypes and two novel variants (km41 and gz52557), using samples from patients in southeast Asia or immigrants from this region. These studies have completed a full panel of genomes for subtypes 6a-6q Lu et al, 2006Lu et al, , 2007a. In the present study, we further describe the complete genomes of three novel HCV variants.…”

“…The main transmission routes are injection drug use, unsafe medical practices and blood transfusion prior to the introduction of screening assays. Transmission is also associated with other parenteral exposures such as sexual contacts (Lu et al, 2007a).…”