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Volume 78, Issue 2

The origin of hepatitis C virus genotypes. Free

Abstract

For many RNA viruses, relatively recent times of origin of extant viruses are implied by the high rate of substitution observed in longitudinal studies. However, extrapolation of short-term rates of substitution can give misleading estimates of times of divergence. We show here that the common ancestor of different types of hepatitis C virus (HCV) is older than previously thought. The rate of HCV sequence change was measured amongst a cohort of individuals infected following administration of anti-D immunoglobulin. Virus sequences were obtained in the E1 and NS5B genes and compared with each other and with sequences from an infective batch. Taking account of the bias towards synonymous transition substitutions, the time of divergence of variants of subtype 1b is estimated to have occurred 70–80 years ago. The numerous subtypes of HCV are proposed to derive from more than 300 years of endemic infection in certain geographical regions, with recent spread of some subtypes to other parts of the world. Estimation of the time of origin of the major HCV genotypes (types 1–6) is problematic, but our data and analogy with other viruses suggest that divergence occurred at least 500–2000 years ago.

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© Society for General Microbiology 1997
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1997-02-01
2024-04-24
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References

  1. Abe K., Inchauspe G., Fujisawa K. 1992; Genomic characterization and mutation rate of hepatitis C virus isolated from a patient who contracted hepatitis during an epidemic of non-A, non-B hepatitis in Japan. Journal of General Virology 73:2725–2729
     [Google Scholar]
  2. 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]
  3. 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]
  4. Cuypers H. T. M., Winkel I. N., VanderPoel C. L., Reesink H. W., Lelie P. N., Houghton M., Weiner A. 1991; Analysis of genomic variability of hepatitis C virus. Journal of Hepatology 13:S15–S19
     [Google Scholar]
  5. Darwish M. A., Raouf T. A., Rushdy P., Constantine N. T., Rao M. R., Edelman R. 1993; Risk factors associated with a high seroprevalence of hepatitis C virus infection in Egyptian blood donors. American Journal of Tropical Medicine and Hygiene 49:440–447
     [Google Scholar]
  6. Dittmann S., Roggendorf M., Durkop J., Wiese M., Lorbeer B., Deinhardt F. 1991; Long -term persistence of hepatitis C virus antibodies in a single source outbreak. Journal of Hepatology 13:323–327
     [Google Scholar]
  7. Expert Group 1995 Report of the Expert Group on the Blood Transfusion Board Pn 1538 Stationery Office, Dublin, Ireland;
     [Google Scholar]
  8. Felsenstein J. 1993; PHYLIP Inference Package version 3.5. Department of Genetics, University of Washington, Seattle, Wash.; USA:
     [Google Scholar]
  9. Findlay G. M., MacCallum F. O. 1937; Note on acute hepatitis and yellow fever immunization. Transactions of the Royal Society of Tropical Medicine and Hygiene 31297–308
     [Google Scholar]
  10. Gessain A., Mauclere P., Froment A., Biglione M., Le Hesran J. Y., Tekaia F., Millan J., de Thé G. 1995; Isolation and molecular characterization of a human T-cell lymphotropic virus type II (HTLV-II), subtype B, from a healthy Pygmy living in a remote area of Cameroon: an ancient origin for HTLV-II in Africa. Proceedings of the National Academy of Sciences USA: 924041–4045
     [Google Scholar]
  11. Hirsch V. M., Dapolito G. A., Goldstein S., McClure H., Emau P., Fultz P. N., Isahakia M., Lenroot R., Myers G., Johnson P. R. 1993; A distinct African lentivirus from Syke’s monkeys. Journal of Virology 67:1517–1528
     [Google Scholar]
  12. Ina Y. 1995; New methods for estimating the numbers of synonymous and nonsynonymous substitutions. Journal of Molecular Evolution 40:190–226
     [Google Scholar]
  13. Ina Y., Mizokami M., Ohba K., Gojobori T. 1994; Reduction of synonymous substitutions in the core protein gene of hepatitis C virus. Journal of Molecular Evolution 38:50–56
     [Google Scholar]
  14. Kumar S., Tamura K., Nei M. 1993; MEGA: Molecular evolutionary genetics analysis, version 1.0. Pennsylvania State University, Pennsylvania; USA:
     [Google Scholar]
  15. Leary T. P., Desai S. M., Yamaguchi J., Chalmers M. L., Schlauder G. G., Dawson G. J., Mushawar I. K. 1996; Species-specific variants of BB virus A in captive monkeys. Journal of Virology 70:9028–9030
     [Google Scholar]
  16. Liu H. -F., Goubau P., Brussel M. V., Laethem K. V., Chen Y. -C., Desmyter J., Vandamme A. -M. 1996; The three human T- lymphotropic virus type I subtypes arose from three geographically distinct simian reservoirs. Journal of General Virology 77:359–368
     [Google Scholar]
  17. McGeoch D. J., Cook S., Dolan A., Jamieson F. E., Telford E. A. R. 1995; Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses. Journal of Molecular Biology 247:443–458
     [Google Scholar]
  18. Martinez M. A., Dopazo J., Hernandez J., Mateu M. G., Sobrino F., Domingo E., Knowles N. J. 1992; Evolution of the capsid protein genes of foot-and-mouth disease virus : antigenic variation without accumulation of amino acid substitutions over six decades. Journal of Virology 66:3557–3565
     [Google Scholar]
  19. Mellor J., Holmes E. C., Jarvis L. M., Yap P. L., Simmonds P. TheInternational HCV Collaborative Study Group 1995; Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. Journal of General Virology 762493–2507
     [Google Scholar]
  20. Mortimer P. P. 1995; Arsphenamine jaundice and the recognition of instrument-borne virus infection. Genitourinary Medicine 71:109–119
     [Google Scholar]
  21. 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 USA: 883392–3396
     [Google Scholar]
  22. Okamoto H., Kojima M., Okada S. -I., Yoshizawa H., Iizuka H., Tanaka T., Muchmore E. E., Ito Y., Mishiro S. 1992; Genetic drift of hepatitis C virus during an 8·2 year infection in a chimpanzee: variability and stability. Virology 190:894–899
     [Google Scholar]
  23. Okamoto H., Crovatto M., Pozzato G., Feray C., Brechot C., Mishiro S. 1995; Molecular and clinical characteristics of the hepatitis C virus genotype ‘2c’ found in Italians in Italy and France. International Hepatological Communications 3:161–165
     [Google Scholar]
  24. Orito E., Mizokami M., Ina Y., Moriyama E. N., Kameshima N., Yamamoto M., Gojobori T. 1989; Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. Proceedings of the National Academy of Sciences USA: 867059–7062
     [Google Scholar]
  25. Pawlotsky J. M., Tsakiris L., Roudotthoraval F., Pellet C., Stuyver L., Duval J., Dhumeaux D. 1995; Relationship between hepatitis C virus genotypes and sources of infection in patients with chronic hepatitis C. Journal of Infectious Diseases 171:1607–1610
     [Google Scholar]
  26. Power J. P., Lawlor E., Davidson F., Holmes E. C., Yap P. L., Simmonds P. 1995; Molecular epidemiology of an outbreak of infection with hepatitis C virus in recipients of anti-D immunoglobulin. Lancet 345:1211–1213
     [Google Scholar]
  27. Querat G., Audoly G., Sonigo P., Vigne R. 1990; Nucleotide sequence analysis of SA-OMVV, a visna-related ovine lentivirus : phylogenetic history of lentiviruses. Virology 175:434–447
     [Google Scholar]
  28. Sawyer W. A., Meyer K. F., Eaton M. D., Bauer J. H., Putnam P., Schwentker F. F. 1944; Jaundice in army personnel in western region of United States and its relation to vaccination against yellow fever. American Journal of Hygiene 39:337–430
     [Google Scholar]
  29. Shadan F. F., Villarreal L. P. 1993; Coevolution of persistently infecting small DNA viruses and their hosts linked to host-interactive regulatory domains. Proceedings of the National Academy of Sciences USA: 904117–4121
     [Google Scholar]
  30. Simmonds P. 1995; Variability of hepatitis C virus. Hepatology 21:570–583
     [Google Scholar]
  31. Stuyver L., Wyseur A., Vanarnhem W., Lunel F., Laurentpuig P., Pawlotsky J. M., Kleter B., Bassit L., Nkengasong J., Vandoorn 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]
  32. Tanaka T., Kato N., Hijikata M., Shimotohno K. 1993; Base transitions and base transversions seen in mutations among various types of the hepatitis C viral genome. FEBS Letters 315:201–203
     [Google Scholar]
  33. Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka H., Mishiro S., Miyakawa Y., Mayumi M. 1994; Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proceedings ofthe National Academy ofSciences, USA 9111022–11026
     [Google Scholar]
  34. 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]
  35. 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]
  36. Zanotto P. M. D., Gould E. A., Gao G. F., Harvey P. H., Holmes E. C. 1996; Population dynamics of flaviviruses revealed by molecular phylogenies. Proceedings of the National Academy of Sciences USA: 93548–553
     [Google Scholar]
  37. Zeuzem S., Ruster B., Lee J. H., Stripf T., Roth W. K. 1995; .Evaluation of a reverse hybridization assay for genotyping of hepatitis C virus. Journal of Hepatology 23:654–661
     [Google Scholar]
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The origin of hepatitis C virus genotypes.
J. Gen. Virol. 78, 321 (1997); https://doi.org/10.1099/0022-1317-78-2-321
/content/journal/jgv/10.1099/0022-1317-78-2-321
/content/journal/jgv/10.1099/0022-1317-78-2-321
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