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Volume 76, Issue 3

Diversity of genotypes of hepatitis C virus in southern India Free

Abstract

A second generation assay for antibody to hepatitis C virus (anti-HCV) was used to screen 78 southern Indian individuals with a high risk of infection. RT-PCR targeted at the 5′ end untranslated region (5′UTR) of the HCV genome was used to evaluate evidence of viraemia in 32 anti-HCV positive sera. The PCR products amplified from the 5′UTR of the HCV genome from 24 patients were sequenced, revealing the existence of two distinct groups of sequences: 21 corresponded to HCV type 1 while the other three sequences had 95% to 99% identity to HCV type 3. Two of these three isolates had more than 90% nucleotide identity in the NS5 region to established 3b sequences whereas the other had less than 74% nucleotide identity to any of the published genotype 3 (3a, 3b, 3c, 3d, 3e and 3f) sequences. However, a search of the EMBL nucleotide database revealed 91% identity to the unpublished sequence of an isolate of HCV from Indonesia. We provide evidence that these two isolates may represent a novel subtype within genotype 3. Our data also suggest that HCV genotype 1 predominates over HCV genotype 3 in southern India.

  • Received:
  • Accepted:
  • Published Online:
© Journal of General Virology 1995
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1995-03-01
2024-04-19
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. Journal of Molecular Biology 215:403–110
     [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, USA 89:187–191
     [Google Scholar]
  3. Bukh J., Purcell R. H., Miller R. H. 1992b; Sequence analysis of the 5′ noncoding region of hepatitic C virus. Proceedings of the National Academy of Sciences, USA 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 5 related, but distinct, hepatitis C viral genotypes exist. Proceedings of the National Academy of Sciences, USA 89:7144–7148
     [Google Scholar]
  6. 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]
  7. Chemello L., Alberti A., Rose K., Simmonds P. 1994; Hepatitis C serotype and response to interferon therapy. New England Journal of Medicine 330:143
     [Google Scholar]
  8. Choo Q. L., Weiner A. J., Overby L. R., Kuo G., Houghton M., Bradley D. W. 1990; Hepatitis C virus–the major causative agent of viral non-A, non-Β hepatitis. British Medical Bulletin 46:423–441
     [Google Scholar]
  9. Choo Q. L., Richman K. H., Han J. H., Berger K., Lee C., Dong C., Gallegos C., Coit D., Medinaselby A., 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, USA 88:2451–2455
     [Google Scholar]
  10. Enomoto N., Takada A., Nakao T., Date T. 1990; There are two major types of hepatitic C virus in Japan. Biochemical & Biophysical Research Communications 170:1021–1025
     [Google Scholar]
  11. 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]
  12. Garson J. A., Clewley J. P., Simmonds P., Zhang L. Q., Mori J., Ring C., Follett E. A. C., Dow B. C., Martin S., Gunson H. 1992; Hepatitis C viraemia in United Kingdom blood donors - a multicentre study. Vox Sanguinis 62:218–223
     [Google Scholar]
  13. Han J. H., Shyamala V., Richman K. H., Brauer M. J., Irvine B., Urdea M. S., Tekampolson 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, USA 88:1711–1715
     [Google Scholar]
  14. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., Ohkoshi S., Shimotohno K. 1991; Hypervariable regions in the putative glycoprotein of hepatitis C virus. Biochemical & Biophysical Research Communications 175:220–228
     [Google Scholar]
  15. Houghton M., Weiner A., Han J., Kuo G., Choo Q. L. 1991; Molecular biology cf the hepatitis C viruses – implications for diagnosis, development and control of viral disease. Hepatology 14:381–388
     [Google Scholar]
  16. Kamel M. A., Ghaffar Y. A., Wasef M. A., Wright M., Clark L. C., Miller F. D. 1992; High HCV prevalence in Egyptian blood donors. Lancet 340:427
     [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. Karlin S., Altschul S. F. 1990; Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciences, USA 87:2264–2268
     [Google Scholar]
  19. Kato N., Hijikata 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, USA 87:9524–9528
     [Google Scholar]
  20. Kiyosawa K., Tanaka E., Sodeyama T., Yoshizawa K., Yabu K., Furuta K., Imai H., Nakano Y., Usuda S., Uemura K., Furuta S., Watanabe Y., Watanabe J., Fukuda Y., Takayama T., Urushibara A., Matsumoto A., Mori H., Kobayashi M., Suzuki T., Yamada S., Seki T., Shimizu S., Nakamura M., Sone H., Hara K., Ichijo T., Ohike Y., Gibo Y., Nakatsuji Y., Yoda H., Tsuchiya K., Hayata T., Imai Y., Hara N. 1994; Transmission of hepatitis C in an isolated area in Japan: community– acquired infection. Gastroenterology 106:1596–1602
     [Google Scholar]
  21. 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. 1992; Detection of three types of hepatitis C virus in blood donors - investigation of type-specific differences in serologic reactivity and rate of alanine aminotransferase abnormalities. Transfusion 33:7–13
     [Google Scholar]
  22. 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 & Biophysical Research Communications 183:334–342
     [Google Scholar]
  23. Ohto H., Terazawa S., Sasaki N., Hino K., Ishiwata C., Kako K., Ujiie N., Endo C., Matsui A., Okamoto H., Mishiro S., Kojima M., Aikawa T., Shimoda K., Sakamoto M., Akahane Y., Yoshizawa H., Tanaka T., Tokita H., Tsuda F. 1994; Transmission of hepatitis C virus from mothers to infants. New England Journal of Medicine 330:744–750
     [Google Scholar]
  24. 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]
  25. 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]
  26. Okamoto H., Kurai K., Okada S. I., Yamamoto K., Lizuka H., Tanaka T., Fukuda S., Tsuda F., Mishiro S. 1992; 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]
  27. Okamoto H., Tokita H., Sakamoto M., Horikita M., Kojima M., Iizuka H., Mishiro S. 1993; Characterization of the genomic sequence of type-v (or 3a) hepatitis C virus isolates and PCR primers for specific detection. Journal of General Virology 74:2385–2390
     [Google Scholar]
  28. Seeff L. B., Alter H. J. 1994; Spousal transmission of the hepatitis C virus. Annals of Internal Medicine 120:807–809
     [Google Scholar]
  29. 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. 1993a; 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]
  30. Simmonds P., McOmish F., Yap P. L., Chan S.-W., Lin C. K., Dusheiko G., Saeed A. A., Holmes E. C. 1993b; 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]
  31. Simmonds P., Smith D. B., McOmish F., Yap P. L., Kolberg J., Urdea M. S., Holmes E. C. 1994; Identification of genotypes of hepatitis C virus by sequence comparisons in the core, El and NS-5 regions. Journal of General Virology 75:1053–1061
     [Google Scholar]
  32. Stuyver L., Rossau R., Wyseur A., Duhamel M., Vanderborght B., Van Heuverswyn H., Maertens G. 1993; Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. Journal of General Virology 74:1093–1102
     [Google Scholar]
  33. 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]
  34. Tokita H., Shrestha S. M., Okamoto H., Sakamoto M., Horikita M., Iizuka H., Shrestha S., Miyakawa Y., Mayumi M. 1994; Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. Journal of General Virologv 75:931–936
     [Google Scholar]
  35. 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]
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Diversity of genotypes of hepatitis C virus in southern India
J. Gen. Virol. 76, 711 (1995); https://doi.org/10.1099/0022-1317-76-3-711
/content/journal/jgv/10.1099/0022-1317-76-3-711
/content/journal/jgv/10.1099/0022-1317-76-3-711
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