title: An expanded taxonomy of hepatitis C virus genotype 6: Characterization of 22 new full-length viral genomes.
abstract: We characterized the full-length genomes of 22 hepatitis C virus genotype 6 (HCV-6) isolates: 10 from Vietnam (classified into subtypes 6e, 6h, 6p, 6r, 6s, and 6u), one from China (confirmed as a new subtype 6xd), and 11 from the Lao PDR (representing a new subtype 6xe plus eight novel variants). With these 22 new genomes, HCV-6 now has a diverse and extended taxonomic structure, comprised of 28 assigned subtypes (denoted 6a-6xe) and 27 unassigned lineages, all of which have been represented by full-length genomes. Our phylogenetic analyses also included many partially-sequenced novel variants of HCV-6 from Lao PDR. This revealed that Lao HCV isolates are genetically very diverse and are phylogenetically distributed in multiple lineages within genotype 6. Our results suggest that HCV-6 has been maintained in Laos, a landlocked country, since the common ancestor of genotype 6 and indicates historical dispersal of HCV-6 across Southeast Asia.
authors.affiliation: The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Li
authors.affiliation: The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road and Oxford NIHR Biomedical Research Centre, OX1 3SY, UK.
authors.forename: Eleanor
authors.initials: E
authors.lastname: Barnes
authors.affiliation: Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine and Global Health, Churchill Hospital, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
authors.forename: Paul N
authors.initials: PN
authors.lastname: Newton
authors.affiliation: Guangzhou Blood Center, Guangzhou 510095, China.
authors.forename: Yongshui
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic.
authors.forename: Manivanh
authors.initials: M
authors.lastname: Vongsouvath
authors.affiliation: The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road and Oxford NIHR Biomedical Research Centre, OX1 3SY, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Klenerman
authors.affiliation: Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi Tochigi 329-0498, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Okamoto
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: Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA. Electronic address: llu@kumc.edu.
authors.forename: Ling
authors.initials: L
authors.lastname: Lu
mesh_terms: D000818:Animals; D002681:China; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D007812:Laos; D008969:Molecular Sequence Data; D010802:Phylogeny; D014744:Vietnam; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: Full-length genome; Genotype 6; HCV; Laos; Sequence