1887

Abstract

Sequences obtained in the 5′ non-coding region (5′NCR) of hepatitis C virus (HCV) were obtained from Scottish blood donors and compared with previously published HCV sequences. Phylogenetic analysis revealed the existence of three distinct groups of sequences; two of these corresponded to the recently described HCV types 1 and 2 variants, while viral sequences detected in around a third of the blood donors formed a separate phylogenetic group that probably represents infection with a novel virus species. Nucleotide sequences of this latter group differed from all previously published 5′NCR sequence variants by at least 9%. This new virus type also differed considerably from previously published variants in other regions of the viral genome (core, NS-3 and NS-5), with corrected nucleotide distances of 15, 43 and 49% respectively from the prototype HCV-1 sequence. Formal phylogenetic analysis of each of the coding regions confirmed that HCV type 1 variants could be clearly differentiated into regional variants (Far East and U.S.A./European), in contrast to the clearly overlapping geographical distributions of the main HCV types in U.K. blood donors. We discuss the evidence for and against the hypothesis that the three main phylogenetic groups identified in this study represent separate species of HCV.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-73-5-1131
1992-05-01
2022-01-24
Loading full text...

Full text loading...

/deliver/fulltext/jgv/73/5/JV0730051131.html?itemId=/content/journal/jgv/10.1099/0022-1317-73-5-1131&mimeType=html&fmt=ahah

References

  1. 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]
  2. Chen P. J., Lin M.-H., Tu S.-J., Chen D.-S. 1991; Isolation of a complementary DNA fragment of hepatitis C virus in Taiwan revealed significant sequence variations compared with other isolates. Hepatology 14:73–78
    [Google Scholar]
  3. Chomczynski P., Sacchi N. 1987; Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry 162:156–159
    [Google Scholar]
  4. Choo Q. L., Kuo G., Weiner A. J., Overby L. R., Bradley D. W., Houghton M. 1989; Isolation of a cDNA derived from a bloodborne non-A, non-B hepatitis genome. Science 244:359–362
    [Google Scholar]
  5. 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]
  6. Coelen R. J., Mackenzie J. S. 1990; The 5′-terminal non-coding region of Murray Valley encephalitis virus RNA is highly conserved. Journal of General Virology 71:241–245
    [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12:387–395
    [Google Scholar]
  8. 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]
  9. Esteban A., L J., Gonzalez A., Hernandez J. M., Viladomiu L., Sanchez C., Lopez Talavera J. C., Lucea D., Martin Vega C., Vidal X., Esteban R., Guardia J. 1990; Evaluation of antibodies to hepatitis C virus in a study of transfusion-associated hepatitis. New England Journal of Medicine 323:1107–1112
    [Google Scholar]
  10. Felsenstein J. 1988; Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 22:521–565
    [Google Scholar]
  11. Follett E. A. C., Dow B. C., McOmish F., Yap P. L., Hughes W., Mitchell R., Simmonds P. 1991; HCV confirmatory testing of blood donors. Iancet 338:1024
    [Google Scholar]
  12. Fuchs K., Motz M., Schreier E., Zachoval R., Deinhardt F., Roggendorf M. 1991; Characterization of nucleotide sequences from European hepatitis C virus isolates. Gene 103:163–169
    [Google Scholar]
  13. Garson J. A., Ring C., Tuke P., Tedder R. S. 1990; Enhanced detection by PCR of hepatitis C virus RNA. Lancet 336:878–879
    [Google Scholar]
  14. 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]
  15. Hosein B., Fang C. T., Popovsky M. A., Ye J., Zhang M., Wang C. Y. 1991; Improved serodiagnosis of hepatitis C virus infection with synthetic peptide antigen from capsid protein. Proceedings of the National Academy of Sciences, U.S.A. 88:3647–3651
    [Google Scholar]
  16. Houghton M., Weiner A., Han J., Kuo G., Choo Q. L. 1991; Molecular biology of the hepatitis C viruses’, implications for diagnosis, development and control of viral disease. Hepatology 14:381–388
    [Google Scholar]
  17. Japanese Red Cross Non-A, Non-B Hepatitis Research Group 1991; Effect of screening for hepatitis C virus antibody and hepatitis B virus core antibody on the incidence of post-transfusion hepatitis. Lancet 338:1040–1041
    [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. Koonin E. V. 1991; The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Journal of General Virology 72:2197–2206
    [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., Colombo 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. Mandl C. W., Heinz F. X., Kunz C. 1988; Sequence of the structural proteins of tick-borne encephalitis virus (Western subtype) and comparative analysis with other flaviviruses. Virology 166:197–205
    [Google Scholar]
  23. Miller R. H., Purcell R. H. 1990; Hepatitis C virus shares amino acid sequence similarity with pestiviruses and flaviviruses as well as members of two plant virus supergroups. Proceedings of the National Academy of Sciences, U.S.A. 87:2057–2061
    [Google Scholar]
  24. Muraiso K., Huikata M., Ohkoshi S., Cho M. J., Kikuchi M., Kato N., Shimotohno K. 1990; A structural protein of hepatitis C virus expressed in E. coli facilitates accurate detection of hepatitis C virus. Biochemical and Biophysical Research Communications 172:511–516
    [Google Scholar]
  25. Nakao T., Enomoto N., Takada N., Takada A., Date T. 1991; Typing of hepatitis C virus genomes by restriction fragment length polymorphism. Journal of General Virology 72:2105–2112
    [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., Tanaka T., Sugai Y., Akahane Y., Machida A., Mishiro S., Yoshizawa H., Miyakawa Y., Mayumi M. 1990a; Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5′-noncoding region. Japanese Journal of Experimental Medicine 60:215–222
    [Google Scholar]
  28. Okamoto H., Okada S., Sugiyama Y., Yotsumoto S., Tanaka T., Yoshizawa H., Tsuda F., Miyakawa Y., Mayumi M. 1990b; The 5′-terminal sequence of the hepatitis C virus genome. Japanese Journal of Experimental Medicine 60:167–177
    [Google Scholar]
  29. 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]
  30. 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]
  31. Saitou N., Imanishi T. 1989; Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Molecular Biological Evolution 6:514–525
    [Google Scholar]
  32. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biological Evolution 4:406–425
    [Google Scholar]
  33. Simmonds P., Balfe P., Peutherer J. F., Ludlam C. A., Bishop J. O., Brown A. J. 1990a; Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. Journal of Virology 64:864–872
    [Google Scholar]
  34. Simmonds P., Zhang L. Q., Watson H. G., Rebus S., Ferguson E. D., Balfe P., Leadbetter G. H., Yap P. L., Peutherer J. F., Ludlam C. A. 1990b; Hepatitis C quantification and sequencing in blood products, haemophiliacs, and drug users. Lancet 336:1469–1472
    [Google Scholar]
  35. Staden R. 1984; Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Research 12:521–538
    [Google Scholar]
  36. Takamizawa A., Mori C., Fuke L., 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]
  37. Takeuchi K., Kubo Y., Boonmar S., Watanabe Y., Katayama T., Choo Q. L., Kuo G., Houghton M., Saito I., Miyamura T. 1990; Nucleotide sequence of core and envelope genes of the hepatitis C virus genome derived directly from human healthy carriers. Nucleic Acids Research 18:4626
    [Google Scholar]
  38. 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 virus. Virus Genes 5:243–254
    [Google Scholar]
  39. VAN DER Poel C. L., Cuypers H. T., Reesink H. W., Weiner A. J., Quan S., di Nello R., van Boven J. J., Winkel L., Mulder Folkerts D., Exel Oehlers P. J., Schaasberg W., Leentvaar Kuypers A., Polito A., Houghton M., Lelie P. N. 1991; Confirmation of hepatitis C virus infection by new four-antigen recombinant immunoblot assay. Lancet 337:317–319
    [Google Scholar]
  40. Weiner A. J., Kuo G., Bradley D. W., Bonino F., Saracco G., Lee C., Rosenblatt J., Choo Q. L., Houghton M. 1990; Detection of hepatitis C viral sequences in non-A, non-B hepatitis. Lancet 335:1–3
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-73-5-1131
Loading
/content/journal/jgv/10.1099/0022-1317-73-5-1131
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error