1887

Abstract

We have proposed that hepatitis C virus should be classified into eleven genetic groups (types) which further divide into more than 80 genotypes (subtypes). However, only eight genetic groups (1–6, 10 and 11) have been defined on the basis of the full- length sequence. Hence, the entire nucleotide sequences of three HCV isolates in genetic groups 7–9 have now been determined. Phylogenetic analysis over the full-length sequences of these three isolates, along with 30 more in the other eight genetic groups, indicated that genetic groups 6–9 and 11 have bifurcated from a common branch and groups 3 and 10 from another. In the former branch groups 7 and 11, and groups 8 and 9, are closely related. Consequently, HCV can be classified into either eleven (1–11) or six groups (1; 2; 3 and 10;

4; 5; 6–9 and 11), allowing a clear separation of group and genotype similarity within the NS5b region or a subregion of 1093 nt. When pairwise comparison of 1093 nt in the NS5b sequence was performed on 106 HCV isolates of 36 genotypes in eleven genetic groups, they were classified into either eleven (1–11) or six (1; 2; 3 and 10; 4; 5; 6–9 and 11) genetic groups. However, group and genotype similarities were not clearly separable in either classification. The overlapping range was smaller using the classification into eleven genetic groups as compared to six genetic groups (2·7 vs 4·7%). These results indicate that HCV might not have evolved in the two-tiered fashion, at least in a strict sense.

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1998-08-01
2021-10-16
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References

  1. Adams N. J., Chamberlain R. W., Taylor L. A., Davidson F., Lin C. K., Elliott R. M., Simmonds P. 1997; Complete coding sequence of hepatitis C virus genotype 6a. Biochemical and Biophysical Research Communications 234:393–396
    [Google Scholar]
  2. Bukh J., Miller R. H., Purcell R. H. 1995; Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Seminars in Liver Disease 15:41–63
    [Google Scholar]
  3. Chamberlain R. W., Adams N., Saeed A. A., Simmonds P., Elliott R. M. 1997; Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. Journal of General Virology 78:1341–1347
    [Google Scholar]
  4. Choo Q. L., Kuo G., Weiner A. J., Overby L. R., Bradley D. W., Houghton M. 1989; Isolation of a cDNA clone derived from a blood- borne non-A, non-B viral hepatitis genome. Science 244:359–362
    [Google Scholar]
  5. de Lamballerie X., Charrel R. N., Attoui H., de Micco P. 1997; Classification of hepatitis C virus variants in six major types based on analysis of the envelope 1 and nonstructural 5B genome regions and complete polyprotein sequences. Journal of General Virology 78:45–51
    [Google Scholar]
  6. Gojobori T., Ishii K., Nei M. 1982; Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. Journal ofMolecular Evolution 18:414–423
    [Google Scholar]
  7. Holland P. V., Barrera J. M., Ercilla M. G., Yoshida C. F. T., Wang Y., de Olim G. A. B., Betlach B., Kuramoto K., Okamoto H. 1996; Genotyping hepatitis C virus isolates from Spain, Brazil, China, and Macau by a simplified PCR method. Journal of Clinical Microbiology 34:2372–2378
    [Google Scholar]
  8. Kolykhalov A. A., Feinstone S. M., Rice C. M. 1996; Identification of a highly conserved sequence element at the 3′ terminus of hepatitis C virus genome RNA. Journal of Virology 70:3363–3371
    [Google Scholar]
  9. Lvov D. K., Samokhvalov E. I., Tsuda F., Selivanov N. A., Okamoto H., Stakhanova V. M., Stakhgildyan I. V., Doroshenko N. V., Yashina T. L., Kuzin S. N., Suetina I. A., Deryabin P. G., Ruzaeva L. A., Bezgodov V. N., Firsova L. A., Sorinson S. N., Mishiro S. 1996; Prevalence of hepatitis C virus and distribution of its genotypes in Northern Eurasia. Archives of Virology 141:1613–1622
    [Google Scholar]
  10. Mellor J., Walsh E. A., Prescott L. E., Jarvis L. M., Davidson F., Yap P. L., Simmonds P. 1996; Survey of type 6 group variants of hepatitis C virus in Southeast Asia by using a core-based genotyping assay. Journal of Clinical Microbiology 34:417–423
    [Google Scholar]
  11. Miyakawa Y., Okamoto H., Mayumi M. 1995; Classifying hepatitis C virus genotypes. Molecular Medicine Today 1:20–25
    [Google Scholar]
  12. Mizokami M., Gojobori T., Ohba K., Ikeo K., Ge X. M., Ohno T., Orito E., Lau J. Y. 1996; Hepatitis C virus types 7, 8 and 9 should be classified as type 6 subtypes. Journal of Hepatology 24:622–624
    [Google Scholar]
  13. Nakao H., Okamoto H., Tokita H., Inoue T., Iizuka H., Pozzato G., Mishiro S. 1996; Full-length genomic sequence of a hepatitis C virus genotype 2c isolate (BEBE1) and the 2c-specific PCR primers. Archives of Virology 141:701–704
    [Google Scholar]
  14. Okamoto H., Kojima M., Okada S., Yoshizawa H., Iizuka H., Tanaka T., Muchmore E. E., Peterson D. A., 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]
  15. Okamoto H., Kurai K., Okada S., Yamamoto K., Iizuka H., Tanaka T., Fukuda S., Tsuda F., Mishiro S. 1992b; 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]
  16. Okamoto H., Kobata S., Tokita H., Inoue T., Woodfield G. D., Holland P. V., Al-Knawy B. A., Uzunalimoglu O., Miyakawa Y., Mayumi M. 1996; A second-generation method of genotyping hepatitis C virus by the polymerase chain reaction with sense and antisense primers deduced from the core gene. Journal of Virological Methods 57:31–45
    [Google Scholar]
  17. 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]
  18. Simmonds P. 1995; Variability of hepatitis C virus. Hepatology 21:570–583
    [Google Scholar]
  19. Simmonds P., Holmes E. C., Cha T. A., Chan S. W., McOmish F., Irvine B., Beall E., Yap P. L., Kolberg J., Urdea M. S. 1993; Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. Journal of General Virology 74:2391–2399
    [Google Scholar]
  20. Simmonds P., Mellor J., Sakuldamrongpanich T., Nuchaprayoon C., Tanprasert S., Holmes E. C., Smith D. B. 1996; Evolutionary analysis of variants of hepatitis C virus found in South-East Asia : comparison with classifications based upon sequence similarity. Journal of General Virology 77:3013–3024
    [Google Scholar]
  21. Stuyver L., van Arnhem W., Wyseur A., Hernandez F., Delaporte E., Maertens G. 1994; Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes. Proceedings of the National Academy of Sciences, USA 91:10134–10138
    [Google Scholar]
  22. Stuyver L., Wyseur A., van Arnhem W., Lunel F., Laurent-Puig P., Pawlotsky J. M., Kleter B., Bassit L., Nkengasong J., van Doorn L. J., Maertens G. 1995; Hepatitis C virus genotyping by means of 5′-UR/core line probe assays and molecular analysis of untypeable samples. Virus Research 38:137–157
    [Google Scholar]
  23. Tanaka T., Kato N., Cho M. J., Sugiyama K., Shimotohno K. 1996; Structure of the 3′ terminus of the hepatitis C virus genome. Journal of Virology 70:3307–3312
    [Google Scholar]
  24. Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka H., Mishiro S., Miyakawa Y., Mayumi M. 1994a; Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proceedings of the National Academy of Sciences, USA 91:11022–11026
    [Google Scholar]
  25. Tokita H., Shrestha S. M., Okamoto H., Sakamoto M., Horikita M., lizuka H., Shrestha S., Miyakawa Y., Mayumi M. 1994b; Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. Journal of General Virology 75:931–936
    [Google Scholar]
  26. 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. Journal of General Virology 76:2329–2335
    [Google Scholar]
  27. Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Lesmana L. A., 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. Journal of General Virology 77:293–301
    [Google Scholar]
  28. Umlauft F., Wong D. T., Oefner P. J., Underhill P. A., Cheung R. C., Wright T. L., Kolykhalov A. A., Gruenewald K., Greenberg H. B. 1996; Hepatitis C virus detection by single-round PCR specific for the terminal 3′ noncoding region. Journal of Clinical Microbiology 34:2552–2558
    [Google Scholar]
  29. Yamada N., Tanihara K., Takada A., Yorihuzi T., Tsutsumi M., Shimomura H., Tsuji T., Date T. 1996; Genetic organization and diversity of the 3′ noncoding region of the hepatitis C virus genome. Virology 223:255–261
    [Google Scholar]
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