Phylogenetic Analysis of the HCV NS5B Gene.

Vietnamese HCV gene sequences from the present study (n = 259 NS5B) are presented with reference sequences (n = 74) downloaded from the Los Alamos database. Analysis was based on a 329-bp of the HCV NS5B gene (nucleotides 8282–8610 relative to H77 NC004102). “A” depicts a midpoint rooted radial phylogenetic tree constructed using the neighbour joining distance method under a Kimura-2-paramter model of evolution. Bootstrap values >70% were obtained for all major nodes separating the confirmed genotypes (not shown). The scale bar indicates an evolutionary distance of 0.08 nucleotide substitutions per site. Branches and annotations are colour coded for all HCV subtypes identified in this study, with reference sequences shown in black. Sequences are annotated by the study cohort from which they were obtained, namely: IDU, intravenous drug user; SW, commercial sex worker; DIA, dialysis patient; MT, multi-transfused patient; ES, elective surgery patient; MR, military recruit. Reference sequences are annotated by subtype name. “B” represents all obtained HCV genotypes/subtypes in the varying risk groups. In total, genotypes were identified for 282 specimens - 201 based on both the NS5B and core/E1 regions, 58 from the NS5B region alone and 23 from the core/E1 region only. Genbank accession numbers are JX102664–JX103137.