Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for st
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Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization B. Robertson1, G. Myers2, C. Howard3, T. Brettin2, J. Bukh4, B. Gaschen 2, T. Gojobori5, G. Maertens6, M. Mizokami7, O. Nainan1, S. Netesov8, K. Nishioka9, T. Shin-i5, P. Simmonds10, D. Smith10, L. Stuyver6, and A. Weiner11 1
Hepatitis Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, U.S.A. 2 Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, U.S.A. 3 Royal Veterinary College, Royal College Street, London, U.K. 4 Hepatitis Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, U.S.A. 5 Center of Informatics Biology, National Institute of Genetics, Mishima, Japan 6 Innogenetics, Hepatitis Program, Gent, Belgium 7 Second Department of Medicine, Nagoya City University Medical School, Nagoya, Japan 8 State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Novosibirsk, Russia 9 Viral Hepatitis Research Foundation of Japan, Tokyo, Japan 10 Department of Medical Microbiology, University of Edinburgh, Edinburgh, Scotland, U.K. 11 Chiron Corporation, Emeryville, California, U.S.A.
Summary. This paper presents a summary of the recommendations that were formulated for the purposes of unifying the nomenclature for hepatitis C virus (HCV), based upon guidelines of the International Committee on Virus Taxonomy (ICTV), and provides guidelines for the incorporation of sequence data into an HCV database that will be available to researchers through the internet. Based upon the available data, the genus Hepacivirus should be regarded as comprising a single species with HCV-1 as the prototype. All currently known isolates of HCV can be divided into six phylogenetically distinct groups, and we recommend that these groups are described as clades 1 to 6. Whether or not these should be regarded as different species within the Hepacivirus genus requires additional clinical, virological, and immunological information. Clades 1, 2, 4, and 5 would correspond to genotype 1, 2, 4, and 5 while clade 3 would comprise genotype 3 and genotype 10, and clade 6 comprise genotypes 6, 7, 8, 9, and 11. We propose that existing subtype designations are reassigned within these clades based upon publication priority, the existence of a complete genome sequence and prevalence. The assignment of isolates to new clades and subtypes should be confined to isolates characterized from epidemiologically unlinked individuals. Comparisons should be based on nucleotide sequences of at least two coding regions and preferably of complete genome sequences, and should be based on phylogenetic analysis rather than percent identity. A forum for discussion and contributions to these recommendations will be made available at the international HCV database at http://s2as02.genes.nig.ac.jp.
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