Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: Proposals for standardization

Archives of Virology

Volumn 143, Issue 12, 1998, Pages 2493-2503

  Robertson, B ^a   Myers, G ^b   Howard, C ^c   Brettin, T ^b   Bukh, J ^d   Gaschen, B ^b   Gojobori, T ^e   Maertens, G ^f   Mizokami, M ^g   Nainan, O ^a   Netesov, S ^h   Nishioka, K ⁱ   Shin i, T ^e   Simmonds, P ^j   Smith, D ^j   Stuyver, L ^f   Weiner, A ^k  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c ROYAL VETERINARY COLLEGE   (United Kingdom)

^d NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^e NATIONAL INSTITUTE OF GENETICS   (Japan)

^f INNOGENETICS   (Belgium)

^g NAGOYA CITY UNIV MEDICAL SCHOOL   (Japan)

^h STATE RESEARCH CENTER OF VIROLOGY AND BIOTECHNOLOGY VECTOR   (Russian Federation)

ⁱ Viral Hepatitis Research Foundation of Japan   (Japan)

^j UNIVERSITY OF EDINBURGH   (United Kingdom)

^k NOVARTIS PHARMA AG   (Switzerland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DATA BASE; GENOTYPE; HEPATITIS C VIRUS; TAXONOMY;

DATABASES, FACTUAL; FLAVIVIRIDAE; GENOME, VIRAL; HEPACIVIRUS; HUMANS; PHYLOGENY; TERMINOLOGY;

HEPACIVIRUS; HEPATITIS C VIRUS;

EID: 0032408707     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s007050050479     Document Type: Article

References (59)

1. Adams NJ, Chamberlain RW, Taylor LA, Davidson F, Lin CK, Elliot RM, Simmonds P (1997) Complete coding sequence of hepatitis C virus genotype 6a. Biochem Biophys Res Commun 234: 393-396
2. Bukh J, Purcell RH, Miller RH (1992) Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proc Natl Acad Sci USA 89: 4942-4946
3. Bukh J, Purcell RH, Miller RH (1993) At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proc Natl Acad Sci USA 90: 8234-8238
4. Bukh J, Purcell RH, Miller RH (1994) Sequence analysis of the core gene of 14 hepatitis C virus genotypes. Proc Natl Acad Sci USA 91: 8239-8243
5. Bukh J, Miller RH, Purcell RH (1995) Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Semin Liver Dis 15: 41-63
6. Bukh J, Apgar CL (1997) Five new or recently discovered (GBV-A) virus species are indigenous to New World Monkeys and may constitute a separate genus of Flaviviridae. Virology 229: 429-436
7. Cha T-A, Beall E, Irvine B, Kolberg J, Chien D, Kuo G, Urdea MS (1992) At least five related, but distinct, hepatitis C viral genotypes exist. Proc Natl Acad Sci USA 89: 77144-7148
8. Chamberlain RW, Adams N, Saeed AA, Simmonds P, Elliott RM (1997) Complete nucleotide sequence of a type 4 hepatitis C virus vairant, the predominant gnotype in the Middle East. J Gen Virol 78: 1341-1340
9. Chamberlain RW, Adams NJ, Taylor LA, Simmonds P, Elliott RM (1997) The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa. Biochem Biophys Res Commun 236: 44-49
10. Chan SW, McOmish F, Holmes EC, Dow B, Peutherer JF, Follett E, Yap PL, Simmonds P (1992) Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. J Gen Virol 73: 1131-1141
11. Choo Q-L, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M (1989) Isolation of a c DNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244: 359-362
12. Enomoto N, Takada A, Nakao T, Date T (1990) There are two major types of hepatitis C in Japan. Biochem Biophys Res Commun 170: 1021-1025
13. Felsenstien J (1991) PHYLIP Manual Version 3.4. University of California, Berkeley
14. Felsenstein, J (1993) PHYLIP, Phylogeny Inference Package, Version 3.5c. University of Washington, Seattle
15. Gojobori T, Ishii K, Nei M (1982) Estimation of average number of nueleotide substitutions when the rate of substitution varies with nueleotide. J Mol Evol 18: 414-123
16. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method of assessing confidence in phylogenetic analysis. Syst Biol 42: 182-192
17. Hillis DM, Huelsenbeck JP, Cunningham CW (1994) Application and accuracy of molecular phylogenies. Science 264: 671-677
18. Hotta H, Handajani R, Luida MI, Soemarto W, Doi H, Miyajima H, Homma M (1994) Subtype analysis of hepatitis C virus in Indonesia on the basis of NS5b region sequences. J Clin Microbiol 32: 3049-3051
19. Kato N, Ohkoshi S, Shimotohno K (1989) Japanese isolates of the non-A, non-B hepatitis viral genome show sequences variations from the original isolate in the USA. Proc Jpn Acad 665: 219-223
20. Kato N, Hijikata M, Ootsuyama Y, Nakagawa M, Ohkoshi S, Sugimura T, Shimotohno K (1990) Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-a, non-B hepatitis. Proc Natl Acad Sci USA 87: 9524-9528
21. Korber BTM, Smith RF, MacInnes K, Myers G (1994) Mutational trends in V3 loop protein sequences observed in different genetic lineages of human immunodeficiency virus type 1. J Virol 68: 6730-6744
22. Kubo Y, Takeuchi K, Boonmar S, Katayama T, Choo QL, Kuo G, Weiner AJ, Bradley DW, Houghton M, Saito I, Miyamura T (1989) A cDNA fragment of hepatitis C virus isolated from an implicated donor of post-transfusion non-A, non-B hepatitis in Japan. Nucleic Acids Res 17: 10367-10372
23. Leary TP, Muerhoff AS, Simons JN, Pilot-Matias TJ Erker JC, Chalmers MS, Schaluder GG, Dawson GJ, Desai SM, Mushahwar IK (1996) Sequence and genomic organization of GBV-C: a novel member of the Flaviviridae associated with human non-A-E hepatitis. J Med Virol 48: 60-67
24. Leary TP, Desai SM, Yamaguchi J Chalmers ML, Schlauder GG, Dawson GJ, Mushahwar IK (1996) Species-specific variants of GB virus A in captive monkeys. J Virol 70: 9028-9030
25. Li W-H, Graur D (1991) Fundamentals of molecular evolution. Sinauer Publishers, Sunderland
26. Linnen J, Wages J, Zhang-Keck Z-Y, Fry KE, Krawczynski KZ, Alter H, Koonin E, Gallagher M, Alter M, Hadziyannis S, Karayiannis P, Fung K, Nakatsuji Y, Shih JW, Young L, Piatak M Jr, Hoover C, Fernandes J, Chen S, Zou JC, Morris T, Hyams KC, Ismay S, Lifson JD, Kim JP (1996) Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent. Sicence 271: 505-508
27. Maertens G, Stuyver L (1997) Genotypes and genetic variation of hepatitis C virus. In: Harrison TJ, Zuckerman AJ (eds) The molecular medicine of viral hepatitis. Wiley, New York, pp 183-233
28. Mellor J, Holmes EC, Jarvis LM, Yap PL, Simmonds P (1995) Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. J Gen Virol 76: 2493-2507
29. Miyakawa Y, Okamoto H, Mayumi M (1995) Classifying hepatitis C virus genotypes. Mol Med Today 1: 20-25
30. Mizokami M, Gojobori T, Lau JYN (1994) Molecular evolutionary virology: its application to hepatitis C virus. Gastroenterology 107: 1181-1182
31. Mizokami M, Gojobori T, Ohba K, Ikeo K, Orito E, Lau JYN (1996) Hepatitis C virus type 7, 8, and 9 should be classified as type 6 subtypes. J Hepatol 24: 622-624
32. Muerhoff AS, Leary TP, Simons JN, Pilot-Matias TJ, Dawson GJ, Erker JC, Chalmers ML, Schlauder GG, Desai SM, Mushahwar IK (1995) Genomic organization of GB viruses A and B: two members of the Flaviviridae associated with GB agent hepatitis. J Virol 69: 5621-5630
33. Muerhoff AS, Simonds JN, Leary TP, Erker JC, Chalmers ML, Pilot-Matias TJ, Dawson GJ, Desai SM, Mushahwar IK (1996) Sequence heterogeneity within the 5′-terminal region of the hepatitis GB virus C genome and evidence for genotypes. Hepatology 25: 379-384
34. Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers MD (1995) Introduction to the universal system of virus taxonomy. In: Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers MD (eds) Virus Taxonomy. Classification and Nomenclature of Viruses. Sixth Report of the International Committee on Taxonomy of Viruses. Springer, Wien New York, pp 1-13 (Arch Virol [Suppl] 10)
35. Myers G, Korber B, Foley B, Jeang K-T, Mellors JW, Wain-Hobson S (eds) (1996) Human retroviruses and AIDS 1996, III-108-III-112. Theoretical Division, Los Alamos National Laboratory, Los Alamos
36. Ohba K, Mizokami M, Ohno T, Suzuki K, Orito E, Ina Y, Lau JYN, Gojobori T (1995) Classification of hepatitis C virus into major types and subtypes based on molecular phylogenetic tree analysis. Virus Res 36: 201-214
37. Ohba K, Mizokami M, Lau JY, Orito E, Ikeo K, Gojobori T (1996) Evolutionary relationship of hepatitis C, pesti-, flavi-, plantviruses, and newly discovered GB hepatitis agents. FEBS Lett 378: 232-234
38. Okamoto H, Okada, S, Sugiyama Y, Kurai K, Iizuka H, Machida A, Miyakawa Y, Mayumi M (1991) Nucleotide sequence of the gnomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. J Gen Virol 72: 2697-2704
39. Okamoto H, Kurai K, Okada S, Yamamoto K, Lizuka H, Tanaka T, Fukuda S, Tsuda F, Mishiro S (1992) Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188: 331-341
40. Okamoto H, Kojima M, Sakamoto M, Iizuka H, Hadiwandowo S, Suwignyo S, Miyakawa Y, Mayumi M (1994) The entire nucleotide sequence and classification of a hepatitis C virus iolates of a novel genotype from an Indonesian patient with chronic liver disease. J Gen Virol 75: 629-635
41. Okamoto H, Nakao H, Inoue T, Fukuda M, Kishimoto J, Iizuka H, Tsuda F, Miyakawa Y, Mayumi MJ (1997) The entire nucleotide sequences of two GB virus C/hepatitis G virus isolates of distinct genotypes from Japan. J Gen Virol 78: 737-745
42. Sakamoto M, Akahane Y, Tsuda F, Tanaka T, Woodfield DG, Okamoto H (1994) Entire nucleotide sequence and characterization of a hepatitis C virus of genotype V/3a. J Gen Virol 75: 1761-1768.
43. Schlauder GG, Dawson GJ, Simons JN, Pilot-Matias TJ, Gutierrez RA, Heynen CA, Knigge MF, Kurpiewski GS, Buijk SL, Leary TP, Muerhoff AS, Desai SM, Mushahwar IK (1995) Molecular and serologic analysis in the transmission of the GB hepatitis agents. J Med Virol 46: 81-90
44. Simmonds P, Holmes EC, Cha T-A, Chan SW, McOmish F, Irvine B, Beall E, Yap PL, Kolberg J, Urdea MS (1993) Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol 74: 2391-2399
45. Simmonds P, Smith DB, McOmish F, Yap PL, Kolberg J, Urdea MS, Holmes EC (1994) Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1, and NS-5 regions. J Gen Virol 75: 1053-1061
46. Simmonds P, Alberti A, Alter HJ, Bonino F, Bradley DW, Brechot C, Brouwer JT, Chan S-W, Chayama K, Chen D-S, Choo Q-L, Colombo M, Cuypers HTM, Date T, Dusheiko GM, Esteban JI, Fay O, Hadziyannis SJ, Han H, Hatzakis A, Holmes EC, Hotta H, Houghton M, Irvine B, Khoara M, Kolberg JA, Kuo G, Lau JYN, Lelie PN, Maertens G, McOmish F, Miyamura T, Mizokumi M, Nomoto A, Prince AM, Reesnik HW, Rice C, Roggendorf, M, Schalm SW, Shikata T, Shimotohno K, Stuyver L, Trepo C, Weiner A, Yap PL, Urdea MS (1994) A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19: 1321-1324
47. Simmonds P (1995) Variability of hepatitis C virus. Hepatology 21: 570-583
48. Simmonds P, Mellor J, Sakuldamrongpanich T, Nuchaprayoon C, Tanprasert S, Holmes EC, Smith DB (1996) Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity. J Gen Virol 77: 3013-3024
49. Simons JN, Leary TP, Dawson GJ, Pilot-Matias TJ, Muerhoff AS, Schlauder GG, Desai SM, Mushahwar IK (1995) Isolation of novel virus-like sequences associated with human hepatitis. Nat Med 1: 564-569
50. Simons JN, Pilot-Matias TJ, Leary TP, Dawson GJ, Desai SM, Schlauder GG, Muerhoff AS, Erker JC, Buijk SL, Chalmers ML, Van Sant CL, Mushahwar IK (1995) Identification of two flavivirus-like genomes in the GB hepatitis agent. Proc Natl Acad Sci USA 92: 3401-3405
51. Smith DB, Cuceanu N, Davidson F, Jarvis LM, Mikili JL, Hamid S, Ludlam CA, Simmonds P (1997) Discrimination of hepatitis G virus/GBV-C geographical variants by analysis of the 5′ non-coding region. J Gen Virol 78: 1533-1542
52. Smith DB, Simmonds P (1988) Characteristics of nucleotide substitution in the hepatitis C virus genome: constraints on sequence change in coding regions at both ends of the genome. J Mol Evol (in press)
53. Stuyver L, Arnhem WV, Wyseur A, Hernandez F, Delaporte E, Maertens G (1994) Classification of hepatitis C viruses based on phylogenetic analysis of the envelope E1 and nonstructural 5B regions and identification of five additional subtypes. Proc Natl Acad Sci USA 91: 10134-10138
54. Takahashi K, Hijikata M, Hino K, Mishiro S (1997) Entire polyprotein-ORF sequences of Japanese GBV-C/ HGV isolates: implications for new genotypes. Hepatology Res 8: 139-148
55. Tokita H, Shrestha SM, Okamoto H, Sakamoto M, Horikita M, Iizuka H, Shrestha S, Miyakawa Y, Mayumi M (1994a) Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. J Gen Virol 75: 931-936
56. Tokita H, Okamoto H, Tsuda F, Song P, Nakata S, Chosa T, Iizuka H, Mishiro S, Miyakawa Y, Mayumi M (1994b) Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth and ninth major genetic groups. Proc Natl Acad Sci USA 91: 11022-11026
57. Tokita H, Okamoto H, Luengrojanakul P, Vareesangthip K, Chainuvati T, Iizuka H, Tsuda F, Miyakawa Y, Mayumi M (1995) Hepatitis C virus variants from Thailand classifiable into five novel genotypes in the sixth (6b), seventh (7c, 7d) and ninth (9b, 9c) major genetic groups. J Gen Virol 76: 2329-2335
58. Tokita H, Okamoto H, Iizuka H, Kishimoto J, Tsuda F, Lesmana LA, Miyakawa Y, Mayumi M (1996) Hepatitis C virus variants from Jakarta, Indonesia classifiable into novel genotypes in the second (2e and 2f), tenth (10a) and eleventh (11a) genetic groups. J Gen Virol 77: 293-301
59. Wengler G, Bradley DW, Collett MS, Heinz FX, Schlesinger RW, Strass JH. (1995) Flaviviridae. In: Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers MD (eds) Virus Taxonomy. Classification and Nomenclature of Viruses. Sixth Report of the International Committee on Taxonomy of Viruses. Springer, Wien New York, pp 415-427 (Arch Virol [Suppl] 10)