Conservation in China of a novel group of HCV variants dating to six centuries ago

•We characterized 26 novel variants of HCV genotype 6 on Hainan Island in China.•They were from Austronesian aborigines living in the central southern mountains.•They differ from each other and from all known HCV members by nucleotides over 13%.•Grouped with subtypes 6g and 6w, they may represent an ancient geographic lineage.•They indicate an isolated HCV ecosystem maintained on the island for many centuries.

We characterized a novel group of HCV variants that are genetically related but distinct from each other belonging to genotype 6 (HCV-6). From 26 infected Austronesian-descended aborigines on Hainan Island, China, HCV sequences were determined followed by genetic analyses. Six nearly full-length genomes and 20 E1 sequences of HCV were obtained, which differ from each other and from all known HCV lineages by nucleotides above the intra-subtype level of 13%. Together with subtypes 6g and 6w, they constitute a phylogenetic group sharing a common ancestor dating from the end of the 12th century.ConclusionOur data indicate the maintenance of an isolated HCV-6 indigenous circulation on Hainan Island at least for six centuries.