Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource

Authors

  • Donald B. Smith,

    Corresponding author
    1. Centre for Immunity, Infection and Evolution, University of Edinburgh, Scotland, UK
    • Address reprint requests to: Dr. Donald B. Smith or Professor Peter Simmonds, Centre for Immunity, Infection and Evolution, Ashworth Building, King's Buildings, West Mains Road, Edinburgh EH9 3JF, UK. E-mail: D.B.Smith@ed.ac.uk, Peter.Simmonds@ed.ac.uk; fax: +44 131 650 6564.

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  • Jens Bukh,

    1. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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  • Carla Kuiken,

    1. Theoretical Biology and Biophysics group, Los Alamos National Laboratory, Los Alamos, NM, USA
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  • A. Scott Muerhoff,

    1. Abbott Diagnostics Research and Development, Abbott Park, IL, USA
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  • Charles M. Rice,

    1. Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, USA
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  • Jack T. Stapleton,

    1. Medical Service, Iowa City Veterans Affairs Medical Center, Departments of Internal Medicine and Microbiology, University of Iowa, Iowa City, IA, USA
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  • Peter Simmonds

    Corresponding author
    1. Centre for Immunity, Infection and Evolution, University of Edinburgh, Scotland, UK
    • Address reprint requests to: Dr. Donald B. Smith or Professor Peter Simmonds, Centre for Immunity, Infection and Evolution, Ashworth Building, King's Buildings, West Mains Road, Edinburgh EH9 3JF, UK. E-mail: D.B.Smith@ed.ac.uk, Peter.Simmonds@ed.ac.uk; fax: +44 131 650 6564.

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  • Potential conflict of interest: Nothing to report.

  • Supported by a grant from the Wellcome Trust to the Centre for Immunity, Infection and Evolution at the University of Edinburgh, Scotland, UK.

Abstract

The 2005 consensus proposal for the classification of hepatitis C virus (HCV) presented an agreed and uniform nomenclature for HCV variants and the criteria for their assignment into genotypes and subtypes. Since its publication, the available dataset of HCV sequences has vastly expanded through advancement in nucleotide sequencing technologies and an increasing focus on the role of HCV genetic variation in disease and treatment outcomes. The current study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near-)complete genome sequences of HCV available on public databases in May 2013. Analysis resolved several nomenclature conflicts between genotype designations and using consensus criteria created a classification of HCV into seven confirmed genotypes and 67 subtypes. There are 21 additional complete coding region sequences of unassigned subtype. The study additionally describes the development of a Web resource hosted by the International Committee for Taxonomy of Viruses (ICTV) that maintains and regularly updates tables of reference isolates, accession numbers, and annotated alignments (http://talk.ictvonline.org/links/hcv/hcv-classification.htm). The Flaviviridae Study Group urges those who need to check or propose new genotypes or subtypes of HCV to contact the Study Group in advance of publication to avoid nomenclature conflicts appearing in the literature. While the criteria for assigning genotypes and subtypes remain unchanged from previous consensus proposals, changes are proposed in the assignment of provisional subtypes, subtype numbering beyond “w,” and the nomenclature of intergenotypic recombinant. Conclusion: This study represents an important reference point for the consensus classification of HCV variants that will be of value to researchers working in clinical and basic science fields. (Hepatology 2014;59:318-327)

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