1887

Abstract

Hepatitis C virus (HCV) shows substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79% overall sequence similarity to one another. Phylogenetic analysis of nucleotide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5′ non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.

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1993-11-01
2024-03-19
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References

  1. Brown E. A., Zhang H., Ping H. -L., Lemon S. M. 1992; Secondary structure of the 5′ nontranslated region of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Research 20:5041–5045
    [Google Scholar]
  2. Bukh J., Purcell R. H., Miller R. H. 1992a; Importance of primer selection for the detection of hepatitis C virus RNA with the polymerase chain reaction assay. Proceedings of the National Academy of Sciences, U.S.A 89:187–191
    [Google Scholar]
  3. Bukh J., Purcell R. H., Miller R. H. 1992b; Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proceedings of the National Academy of Sciences, U.S.A 89:4942–4946
    [Google Scholar]
  4. Cha T. A., Kolberg J., Irvine B., Stempien M., Beall E., Yano M., Choo Q. L., Houghton M., Kuo G., Han J. H., Urdea M. S. 1991; Use of a signature nucleotide sequence of hepatitis C virus for detection of viral RNA in human serum and plasma. Journal of Clinical Microbiology 29:2528–2534
    [Google Scholar]
  5. Cha T. A., Beall E., Irvine B., Kolberg J., Chien D., Kuo G., Urdea M. S. 1992; At least five related, but distinct C viral genotypes exist. Proceedings of the National Academy of Sciences, U.S.A 89:7144–7148
    [Google Scholar]
  6. Chan S. -W., Simmonds P., McOmish F., Yap P. -L., Mitchell R., Dow B., Follett E. 1991; Serological reactivity of blood donors infected with three different types of hepatitis C virus. Lancet 338:1391
    [Google Scholar]
  7. Chan S. -W., McOmish F., Holmes E. C., Dow B., Peutherer J. F., Follett E., Yap P. L., Simmonds P. 1992; Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. Journal of General Virology 73:1131–1141
    [Google Scholar]
  8. Chen P. J., Lin M. H., Tai K. F., Liu P. C., Lin C. J., Chen D. S. 1992; The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5′ termini of viral genomic and antigenomic RNA. Virology 188:102–113
    [Google Scholar]
  9. Choo Q. L., Kuo G., Weiner A. J., Overby L. R., Bradley D. W., Houghton M. 1989; Isolation of a cDNA derived from a blood-borne non-A, non-B hepatitis genome. Science 244:359–362
    [Google Scholar]
  10. Choo Q. L., Richman K. H., Han J. H., Berger K., Lee C., Dong C., Gallegos C., Coit D., Medina Selby R., Barr P. J., Weiner A. J., Bradley D. W., Kuo G., Houghton M. 1991; Genetic organization and diversity of the hepatitis C virus. Proceedings of the National Academy of Sciences, U.S.A 88:2451–2455
    [Google Scholar]
  11. Enomoto N., Takada A., Nakao T., Date T. 1990; There are two major types of hepatitis C virus in Japan. Biochemical and Biophysical Research Communications 170:1021–1025
    [Google Scholar]
  12. Felsenstein J. 1991 PHYLIP Manual Version 3.4 Berkeley: University Herbarium, University of California;
    [Google Scholar]
  13. Han J. H., Shyamala V., Richman K. H., Brauer M. J., Irvine B., Urdea M. S., Tekamp Olson P., Kuo G., Choo Q. L., Houghton M. 1991; Characterization of the terminal regions of hepatitis C viral RNA: identification of conserved sequences in the 5′ untranslated region and poly(A) tails at the 3′ end. Proceedings of the National Academy of Sciences, U.S.A 88:1711–1715
    [Google Scholar]
  14. Higgins D. G., Bleasby A. J., Fuchs R. 1992; ClustaIV: improved software for multiple sequence alignments. CABIOS 8:189–191
    [Google Scholar]
  15. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., Ohkoshi S., Shimotohno K. 1991; Hypervariable regions in the putative glycoprotein of hepatitis C virus. Biochemical and Biophysical Research Communications 175:220–228
    [Google Scholar]
  16. Inchauspe G., Zebedee S., Lee D. H., Sugitani M., Nasoff M., Prince A. M. 1991; Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. Proceedings of the National Academy of Sciences, U.S.A 88:10292–10296
    [Google Scholar]
  17. Kanai K., Kako M., Okamoto H. 1992; HCV genotypes in chronic hepatitis-C and response to interferon. Lancet 339:1543
    [Google Scholar]
  18. Kato N., Huikata 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. Proceedings of the National Academy of Sciences, U.S.A 87:9524–9528
    [Google Scholar]
  19. Kato N., Ootsuyama Y., Ohkoshi S., Nakazawa T., Mori S., Hijikata M., Shimotohno K. 1991; Distribution of plural HCV types in Japan. Biochemical and Biophysical Research Communications 181:279–285
    [Google Scholar]
  20. Kubo Y., Takeuchi K., Boonmar S., Katayama T., Choo Q. L., Kuo G., Weiner A. J., Bradley D. W., 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 Research 17:10367–10372
    [Google Scholar]
  21. Kuo G., Choo Q. L., Alter H. J., Gitnick G. L., Redeker A. G., Purcell R. H., Miyamura T., Dienstag J. L., Alter M. J., Stevens C. E., Tegtmeier F., Bonino F., Columbo M., Lee W. -S., Kuo C., Berger K., Schuster J. R., Overby L. R., Bradley D. W., Houghton M. 1989; An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis. Science 244:362–364
    [Google Scholar]
  22. Lee C., Cheng C., Wang J., Lumeng L. 1992; Identification of hepatitis C viruses with a nonconserved sequence of the 5′ untranslated region. Journal of Clinical Microbiology 30:1602–1604
    [Google Scholar]
  23. Li J., Tong S., Vitvitski L., Lepot D., Trepo C. 1991; Two French genotypes of hepatitis C virus: homology of the predominant genotype with the prototype American strain. Gene 105:167–172
    [Google Scholar]
  24. McOmish F., Chan S. -W., Dow B. C., Gillon J., Frame W. D., Crawford R. J., Yap P. L., Follett E. A. C., Simmonds P. 1993; Detection of three types of hepatitis C virus in blood donors: investigation of type-specific differences in serological reactivity and rate of alanine aminotransferase abnormalities. Transfusion 33:7–13
    [Google Scholar]
  25. Mori S., Kato N., Yagyu A., Tanaka T., Ikeda Y., Petchclai B., Chiewsilp P., Kurimura T., Shimotohno K. 1992; A new type of hepatitis C virus in patients in Thailand. Biochemical and Biophysical Research Communications 183:334–342
    [Google Scholar]
  26. Ogata N., Alter H. J., Miller R. H., Purcell R. H. 1991; Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proceedings of the National Academy of Sciences, U.S.A 88:3392–3396
    [Google Scholar]
  27. Okamoto H., Okada S., Sugiyama Y., Yotsumoto S., Tanaka T., Yoshizawa H., Tsuda F., Miyakawa Y., Mayumi M. 1990; The 5′-terminal sequence of the hepatitis C virus genome. Japanese Journal of Experimental Medicine 60:167–177
    [Google Scholar]
  28. Okamoto H., Okada S., Sugiyama Y., Kurai K., Iizuka H., Machida A., Miyakawa Y., Mayumi M. 1991; Nucleotide sequence of the genomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. Journal of General Virology 72:2697–2704
    [Google Scholar]
  29. Okamoto H., Kojima M., Okada S. -L., Yoshizawa H., Iizuka H., Tanaka T., Muchmore E. E., Ito Y., Mishiro S. 1992a; Genetic drift of hepatitis C virus during an 8.2 year infection in a chimpanzee: variability and stability. Virology 190:894–899
    [Google Scholar]
  30. Okamoto H., Kurai K., Okada S., Yamamoto K., Iizuka H., Tanaka T., Fukuda S., Tsuda F., Mishiro S. 19926; 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
    [Google Scholar]
  31. Pozzato G., Moretti M., Franzin F., Croce L. S., Tiribelli C., Masayu T., Kaneko S., Unoura M., Kobayashi K. 1991; Severity of liver disease with different hepatitis C viral clones. Lancet 338:509
    [Google Scholar]
  32. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406–425
    [Google Scholar]
  33. Simmonds P., Chan S. -W. 1993; Analysis of viral sequence variation by PCR. In Molecular Virology: A Practical Approach pp 109–138 Edited by Davison A. J., Elliott R. M. Oxford: IRL Press;
    [Google Scholar]
  34. Simmonds P., Balfe P., Ludlam C. A., Bishop J. O., Brown A. J. 1990; Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. Journal of Virology 64:5840–5850
    [Google Scholar]
  35. Simmonds P., McOmish F., Yap P. L., Chan S.-W., Lin C. K., Dusheiko G., Saeed A. A, Holmes E. C. 1993a; Sequence variability in the 5′ non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. Journal of General Virology 74:661–668
    [Google Scholar]
  36. Simmonds P., Rose K. A., Graham S., Chan S. W., McOmish F., Dow B. C., Follett E. A. C., Yap P. L., Marsden H. 1993b; Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV) – use of type-specific peptides to serologically differentiate infections with HCV type 1, type 2, and type 3. Journal of Clinical Microbiology 31:1493–1503
    [Google Scholar]
  37. Takada N., Takase S., Enomoto N., Takada A., Date T. 1992a; Clinical backgrounds of the. patients having different types of hepatitis C virus genomes. Journal of Hepatology 14:35–40
    [Google Scholar]
  38. Takada N., Takase S., Takada A., Date T. 1992b; HCV genotypes in different countries. Lancet 339:808
    [Google Scholar]
  39. Takamizawa A., Mori C., Fuke I., Manabe S., Murakami S., Fujita J., Onishi E., Andoh T., Yoshida I., Okayama H. 1991; Structure and organization of the hepatitis C virus genome isolated from human carriers. Journal of Virology 65:1105–1113
    [Google Scholar]
  40. Tanaka T., Kato N., Nakagawa M., Ootsuyama Y., Cho M. J., Nakazawa T., Huikata M., Ishimura Y., Shimotohno K. 1992; Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals. Virus Research 23:39–53
    [Google Scholar]
  41. Tsukiyama Kohara K., Kohara M., Yamaguchi K., Maki N., Toyoshima A., Miki K., Tanaka S., Hattori N., Nomoto A. 1991; A second group of hepatitis C viruses. Virus Genes 5:243–254
    [Google Scholar]
  42. Weiner A. J., Brauer M. J., Rosenblatt J., Richman K. H., Tung J., Crawford K., Bonino F., Saracco G., Choo Q. L., Houghton M., Han J. H. 1991; Variable and hypervariable domains are found in the regions of HCV corresponding to the flavivirus envelope and NS1 proteins and the pestivirus envelope glycoproteins. Virology 180:842–848
    [Google Scholar]
  43. Yanisch-Perron C., Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–107
    [Google Scholar]
  44. Yoshioka K., Kakumu S., Wakita T., Ishikawa T., Itoh Y., Takayanagi M., Higashi Y., Shibata M., Morishima T. 1992; Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: relationship to genotypes of hepatitis C virus. Hepatology 16:293–299
    [Google Scholar]
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