1887

Abstract

Recently, we reported that hepatitis C virus (HCV) can be classified genetically into two types, HCV-K1 and HCV-K2, which show 67% and 71% identity at the nucleotide and amino acid sequence levels in a 340 bp region which encodes the NS5 gene Gly-Asp-Asp motif. To develop a rapid method to classify the genomes of HCV isolates, we identified restriction fragment length polymorphisms (RFLPs) in reverse transcriptase-polymerase chain reaction products encoding a portion of the NS5 gene. I and II enabled HCV to be classified into the K1 and K2 types, and 96I enabled classification into the K1 type, and the K2a and K2b subtypes. These RFLPs also generally allow Japanese isolates to be distinguished from the prototype (PT, an isolate from the U.S.A.), which is a K1 type. Sequence analysis of the 5′-untranslated regions of Japanese isolates revealed near identity between the K1 type and PT, and 93 to 94% identity between the K1 and K2 types, indicating that there are type K1- and K2-specific RFLPs in this region. Our results suggest that the nucleotide sequences of the K1 and K2 types are different throughout the HCV genome. The incidence of HCV types K1, K2a and K2b, and PT in 50 samples was 74%, 16%, 8% and 2%, respectively.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-72-9-2105
1991-09-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/jgv/72/9/JV0720092105.html?itemId=/content/journal/jgv/10.1099/0022-1317-72-9-2105&mimeType=html&fmt=ahah

References

  1. Argos P. 1988; A sequence motif in many polymerases. Nucleic Acids Research 16:9909–9916
    [Google Scholar]
  2. Chomszynski P., Sacchi N. 1987; Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry 162:156–159
    [Google Scholar]
  3. Choo Q. -L., Weiner A. J., Overby L. R., Bradley K. 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]
  4. 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]
  5. Enomoto N., Takada N., Takase S., Takada A., Date T. 1991; Hepatitis C virus RNA genome in plasma of patients with non-A, non-B hepatitis. Gastroenterologia Japonica 26:42–46
    [Google Scholar]
  6. Gyllensten U. B., Erlich H. A. 1988; Generation of singlestranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proceedings of the National Academy of Sciences, U.S.A. 85:7652–7656
    [Google Scholar]
  7. Hijikata M., Kato N., Mori S., Ootsuyama S., Nakagawa M., Sugimura T., Ohkoshi S., Kojima H., Meguro T., Taki M., Takayama S., Yamada K., Shimotohno K. 1990; Frequent detection of hepatitis C virus US strain in Japanese hemophiliacs. Japanese Journal of Cancer Research 81:1195–1197
    [Google Scholar]
  8. Houghton M., Choo Q.-L., Kuo G. 1988; NANB diagnostics and vaccines; European Patent Application 88, 310, 9225.5 and Published. 318:216.
    [Google Scholar]
  9. Kanai K., Iwata K., Nakako K., Kako M., Okamoto H. 1990; Suppression of hepatitis C virus RNA by interferon-α. Lancet i:245
    [Google Scholar]
  10. Kaneko S., Unoura M., Kobayashi K., Kuno K., Murakami S., Hattori N. 1990; Detection of serum hepatitis C virus RNA. Lancet i:976.
    [Google Scholar]
  11. Kato N., Ohkoshi S., Shimotohno K. 1989; Japanese isolates of the non-A, non-B hepatitis viral genome show sequence variations from the original isolate in the U.S.A. Proceedings of the Japan Academy 65:219–223
    [Google Scholar]
  12. Kato N., Hijikata M., Ootsuyama Y., Nakagawa M., Ohnishi 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]
  13. 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 Japan. Nucleic Acids Research 24:10367–10372
    [Google Scholar]
  14. 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., Tegtmer G. E., Bonino F., Colombo M., Lee W. -S., Kio C., Berger K., Shuster 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]
  15. Maeno M., Kaminaka K., Sugimoto H., Esumi M., Hayashi N., Komatsu K., Abe K., Sekiguchi S., Yano M., Mizuno K., Shikata T. 1990; A cDNA clone closely associated with non-A, non-B hepatitis. Nucleic Acids Research 18:2685–2689
    [Google Scholar]
  16. Okamoto H., Imai M., Tsuda F., Miyakawa Y., Mayumi M. 1987; Point mutation in the S gene of hepatitis B virus for d/y or w/r subtypic change in two blood donors carrying a surface antigen of compound subtypes adyt or adwt. Journal of Virology 61:3030–3034
    [Google Scholar]
  17. Okamoto H., Okada S., Sugiyama Y., Yotsumoto S., Tanaka T., Yoshizawa H., Tsuda F., Miyakawa Y., Mayumi M. 1990a; The 5′-terminal sequence of the hepatitis C virus genome. Japanese Journal of Experimental Medicine 60:167–177
    [Google Scholar]
  18. Okamoto H., Okada S., Sugiyama Y., Tanaka T., Sugai Y., Akahane Y., Machida A., Mishiro S., Yoshizawa H., Miyakawa Y., Mayumi M. 1990b; Detection of hepatitis C virus RNA by 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]
  19. Pletnev A. G., Yamshchikov V. F., Blinov V. M. 1990; Nucleotide sequence of the genome and complete amino acid sequence of the polyprotein of tick-borne encephalitis virus. Virology 174:250–263
    [Google Scholar]
  20. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. 1988; Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
    [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, U.S.A. 74:5463–5467
    [Google Scholar]
  22. 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]
  23. Takeuchi K., Kubo Y., Watanabe Y., Katayama T., Choo Q. -L., Kuo G., Houghton M., Saito I., Miyamura T. 1990a; 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]
  24. Takeuchi K., Boonmar S., Kubo Y., Katayama T., Harada H., Ohbayashi A., Choo Q. -L., Kuo G., Houghton M., Saito I., Miyamura T. 1990b; Hepatitis C viral cDNA clones isolated from a healthy carrier donor implicated in post-transfusion non-A, non-B hepatitis. Gene 91:287–291
    [Google Scholar]
  25. Takeuchi K., Kubo Y., Boonmar S., Watanabe Y., Katayama T., Choo Q. -L., Kuo G., Houghton M., Saito I., Miyamura T. 1990c; The putative nucleocapsid and envelope protein genes of hepatitis C virus determined by comparison of the nucleotide sequences of two isolates derived from an experimentally infected chimpanzee and healthy human carriers. Journal of General Virology 71:3027–3033
    [Google Scholar]
  26. Ulrich P. P., Romeo J. M., Lane P. K., Kelly I., Daniel L. J., Vyas G. N. 1990; Detection, semiquantitation, and genetic variation in hepatitis C virus sequences amplified from the plasma of blood donors with elevated alanine aminotransferase. Journal of Clinical Investigation 86:1609–1614
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-72-9-2105
Loading
/content/journal/jgv/10.1099/0022-1317-72-9-2105
Loading

Data & Media loading...

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