A new HCV genotype 6 subtype designated 6v was confirmed with three complete genome sequences

BackgroundAlthough hepatitis C virus (HCV) genotype 6 is classified into 21 subtypes, 6a–6u, new variants continue to be identified.ObjectiveTo characterize the full-length genomes of three novel HCV genotype 6 variants: KMN02, KM046 and KM181.Study designFrom sera of patients with HCV infection, the entire HCV genome was amplified by RT-PCR followed by direct DNA sequencing and phylogenetic analysis.ResultsThe sera contained HCV genomes of 9461, 9429, and 9461 nt in length, and each harboured a single ORF of 9051 nt. The genomes showed 95.3–98.1% nucleotide similarity to each other and 72.2–75.4% similarity to 23 genotype 6 reference sequences, which represent subtypes 6a–6u and unassigned variants km41 and gz52557. Phylogenetic analyses demonstrated that they were genotype 6, but were subtypically distinct. Based on the current criteria of HCV classification, they were designed to represent a new subtype, 6v. Analysis of E1 and NS5B region partial sequences revealed two additional related variants, CMBD-14 and CMBD-86 that had been previously reported in northern Thailand and sequences dropped into Genbank.ConclusionThree novel HCV genotype 6 variants were entirely sequenced and designated subtype 6v.