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Complete genome sequencing and evolutionary analysis of HCV subtype 6xg from IDUs in Yunnan, China

PLoS Neglected Tropical Diseases May 24, 2019

Chen M, et al. - Given that hepatitis C virus (HCV) genotype 6 (HCV-6) usually displays the greatest genetic diversity among the eight HCV genotypes, researchers sought to further describe the previously identified group of HCV-6 sequences and investigate the evolutionary history of the HCV-6 family. From intravenous drug users (IDUs), blood samples from eight HCV seropositive samples were collected in 2014 in Yunnan Province, China. Data revealed the same coding region of 9,051 nucleotides in the eight genomes. From the previously assigned HCV-6 subtypes (6a-6xf), a distinct phylogenetic group was formed from the complete coding region sequences of the eight HCV isolates, which clustered with 6xg reference sequences found in Kachin State, Myanmar, and recently assigned and released. They created a timescaled phylogenetic tree based on the HCV-6 complete coding region sequences to unveil the HCV-6 evolutionary history, in which four HCV-6 phylogenetic subsets were there, whose median tMRCAs (time of most recent common ancestor) were 294.8, 388.5, 348.5 and 197.0 years ago, respectively. Subset I included subtype 6xg that had the most recent common ancestor with subtype 6n, which dated back to 101.2 (95% HPD: 78.7, 125.8) years ago. These findings suggest that the HCV-6 variant described belonged to newly assigned subtype 6xg. Furthermore, Southeast Asia has high diversity in HCV-6 family which has a complicated evolutionary history.

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