title: Eight novel hepatitis C virus genomes reveal the changing taxonomic structure of genotype 6.
abstract: Analysis of partial hepatitis C virus sequences has revealed many novel genotype 6 variants that cannot be unambiguously classified, which obscure the distinctiveness of pre-existing subtypes. To explore this uncertainty, we obtained genomes of 98.0-98.8% full-length for eight such variants (KM35, QC273, TV257, TV476, TV533, L349, QC271 and DH027) and characterized them using phylogenetic analyses and per cent nucleotide similarities. The former four are closely related phylogenetically to subtype 6k, TV533 and L349 to subtype 6l, QC271 to subtypes 6i and 6j, and DH027 to subtypes 6m and 6n. The former six defined a high-level grouping that comprised subtypes 6k and 6l, plus related strains. The threshold between intra- and inter-subtype diversity in this group was indistinct. We propose that similar results would be seen elsewhere if more intermediate variants like QC271 and DH027 were sampled.
authors.affiliation: Vaccine Institute, 3rd Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China.
authors.forename: Hongren
authors.initials: H
authors.lastname: Wang
authors.affiliation: Vaccine Institute, 3rd Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China.
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, OX1 3SY, UK.
authors.forename: Eleanor
authors.initials: E
authors.lastname: Barnes
authors.affiliation: The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
authors.forename: Manqiong
authors.initials: M
authors.lastname: Yuan
authors.affiliation: The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Li
authors.affiliation: Guangzhou Blood Center, Guangzhou, Guangdong, PR China.
authors.forename: Yongshui
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, PR China.
authors.forename: Xueshan
authors.initials: X
authors.lastname: Xia
authors.affiliation: Vaccine Institute, 3rd Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China.
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.affiliation: Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.|Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK.|Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK.
authors.forename: Paul N
authors.initials: PN
authors.lastname: Newton
authors.affiliation: Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.
authors.forename: Manivanh
authors.initials: M
authors.lastname: Vongsouvath
authors.affiliation: The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, OX1 3SY, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Klenerman
authors.affiliation: Institut National de Santé Publique du Québec, Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan.
authors.forename: Donald
authors.initials: D
authors.lastname: Murphy
authors.affiliation: Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Abe
authors.affiliation: The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
authors.forename: Ling
authors.initials: L
authors.lastname: Lu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000097:blood / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*
chemical_list: D012367:RNA, Viral