Skip to main content
NCBI home page
Journal of Clinical Microbiology logoLink to Journal of Clinical Microbiology
. 1996 Feb;34(2):417–423. doi: 10.1128/jcm.34.2.417-423.1996

Survey of type 6 group variants of hepatitis C virus in Southeast Asia by using a core-based genotyping assay.

J Mellor 1, E A Walsh 1, L E Prescott 1, L M Jarvis 1, F Davidson 1, P L Yap 1, P Simmonds 1
PMCID: PMC228809  PMID: 8789027

Abstract

Previous surveys of the prevalences of genotypes of hepatitis C virus (HCV) in different populations have often used genotyping assays based upon analysis of amplified sequences from the 5' noncoding region (5'NCR), such as restriction fragment length polymorphism (RFLP) or hybridization with type-specific probes (e.g., InnoLipa). Although highly conserved, this region contains several type-specific nucleotide polymorphisms that allow major genotypes 1 to 6 to be reliably identified. Recently, however, novel HCV variants found in Vietnam and Thailand that are distantly related to the type 6a genotype (type 6 group) by phylogenetic analysis of coding regions of the genome often have sequences in the 5'NCR that are similar or identical to those of type 1 and could therefore not be identified by an assay of sequences in this region. We developed a new genotyping assay based upon RFLP of sequences amplified from the more variable core region to investigate their distribution elsewhere in southeast (SE) Asia. Among 108 samples from blood donors in seven areas that were identified as type 1 by RFLP in the 5'NCR, type 6 group variants were found in Thailand (7 from 28 samples originally identified as type 1) and Burma (Myanmar) (1 of 3) but were not found in Hong Kong (n = 43), Macau (n = 8), Taiwan (n = 6), Singapore (n = 2), or Malaysia (n = 18). Although this small survey suggests a relatively limited distribution for type 6 group variants in SE Asia, larger studies will be required to explore their distribution in other geographical regions and the extent to which their presence would limit the practical usefulness of 5'NCR-based genotyping assays for clinical or epidemiological purposes.

Full Text

The Full Text of this article is available as a PDF (243.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Apichartpiyakul C., Chittivudikarn C., Miyajima H., Homma M., Hotta H. Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai, Thailand. J Clin Microbiol. 1994 Sep;32(9):2276–2279. doi: 10.1128/jcm.32.9.2276-2279.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bhattacherjee V., Prescott L. E., Pike I., Rodgers B., Bell H., El-Zayadi A. R., Kew M. C., Conradie J., Lin C. K., Marsden H. Use of NS-4 peptides to identify type-specific antibody to hepatitis C virus genotypes 1, 2, 3, 4, 5 and 6. J Gen Virol. 1995 Jul;76(Pt 7):1737–1748. doi: 10.1099/0022-1317-76-7-1737. [DOI] [PubMed] [Google Scholar]
  3. Brown E. A., Zhang H., Ping L. H., Lemon S. M. Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Res. 1992 Oct 11;20(19):5041–5045. doi: 10.1093/nar/20.19.5041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bukh J., Miller R. H., Purcell R. H. Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Semin Liver Dis. 1995 Feb;15(1):41–63. doi: 10.1055/s-2007-1007262. [DOI] [PubMed] [Google Scholar]
  5. Bukh J., Purcell R. H., Miller R. H. At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):8234–8238. doi: 10.1073/pnas.90.17.8234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bukh J., Purcell R. H., Miller R. H. Sequence analysis of the core gene of 14 hepatitis C virus genotypes. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8239–8243. doi: 10.1073/pnas.91.17.8239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Choo Q. L., Kuo G., Weiner A. J., Overby L. R., Bradley D. W., Houghton M. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science. 1989 Apr 21;244(4902):359–362. doi: 10.1126/science.2523562. [DOI] [PubMed] [Google Scholar]
  8. 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. Genetic organization and diversity of the hepatitis C virus. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2451–2455. doi: 10.1073/pnas.88.6.2451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Davidson F., Simmonds P., Ferguson J. C., Jarvis L. M., Dow B. C., Follett E. A., Seed C. R., Krusius T., Lin C., Medgyesi G. A. Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5' non-coding region. J Gen Virol. 1995 May;76(Pt 5):1197–1204. doi: 10.1099/0022-1317-76-5-1197. [DOI] [PubMed] [Google Scholar]
  10. Greene W. K., Cheong M. K., Ng V., Yap K. W. Prevalence of hepatitis C virus sequence variants in South-East Asia. J Gen Virol. 1995 Jan;76(Pt 1):211–215. doi: 10.1099/0022-1317-76-1-211. [DOI] [PubMed] [Google Scholar]
  11. Kleter G. E., van Doorn L. J., Brouwer J. T., Schalm S. W., Heijtink R. A., Quint W. G. Sequence analysis of the 5' untranslated region in isolates of at least four genotypes of hepatitis C virus in The Netherlands. J Clin Microbiol. 1994 Feb;32(2):306–310. doi: 10.1128/jcm.32.2.306-310.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Luengrojanakul P., Vareesangthip K., Chainuvati T., Murata K., Tsuda F., Tokita H., Okamoto H., Miyakawa Y., Mayumi M. Hepatitis C virus infection in patients with chronic liver disease or chronic renal failure and blood donors in Thailand. J Med Virol. 1994 Nov;44(3):287–292. doi: 10.1002/jmv.1890440313. [DOI] [PubMed] [Google Scholar]
  13. Machida A., Ohnuma H., Tsuda F., Munekata E., Tanaka T., Akahane Y., Okamoto H., Mishiro S. Two distinct subtypes of hepatitis C virus defined by antibodies directed to the putative core protein. Hepatology. 1992 Oct;16(4):886–891. doi: 10.1002/hep.1840160406. [DOI] [PubMed] [Google Scholar]
  14. Mellor J., Holmes E. C., Jarvis L. M., Yap P. L., Simmonds P. Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification. The International HCV Collaborative Study Group. J Gen Virol. 1995 Oct;76(Pt 10):2493–2507. doi: 10.1099/0022-1317-76-10-2493. [DOI] [PubMed] [Google Scholar]
  15. Okamoto H., Kurai K., Okada S., Yamamoto K., Lizuka H., Tanaka T., Fukuda S., Tsuda F., Mishiro S. Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology. 1992 May;188(1):331–341. doi: 10.1016/0042-6822(92)90762-e. [DOI] [PubMed] [Google Scholar]
  16. Okamoto H., Tokita H., Sakamoto M., Horikita M., Kojima M., Iizuka H., Mishiro S. Characterization of the genomic sequence of type V (or 3a) hepatitis C virus isolates and PCR primers for specific detection. J Gen Virol. 1993 Nov;74(Pt 11):2385–2390. doi: 10.1099/0022-1317-74-11-2385. [DOI] [PubMed] [Google Scholar]
  17. Sakamoto M., Akahane Y., Tsuda F., Tanaka T., Woodfield D. G., Okamoto H. Entire nucleotide sequence and characterization of a hepatitis C virus of genotype V/3a. J Gen Virol. 1994 Jul;75(Pt 7):1761–1768. doi: 10.1099/0022-1317-75-7-1761. [DOI] [PubMed] [Google Scholar]
  18. 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. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol. 1993 Nov;74(Pt 11):2391–2399. doi: 10.1099/0022-1317-74-11-2391. [DOI] [PubMed] [Google Scholar]
  19. Simmonds P., Rose K. A., Graham S., Chan S. W., McOmish F., Dow B. C., Follett E. A., Yap P. L., Marsden H. Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV): use of type-specific peptides to serologically differentiate infections with HCV types 1, 2, and 3. J Clin Microbiol. 1993 Jun;31(6):1493–1503. doi: 10.1128/jcm.31.6.1493-1503.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Simmonds P. Variability of hepatitis C virus. Hepatology. 1995 Feb;21(2):570–583. doi: 10.1002/hep.1840210243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Smith D. B., Mellor J., Jarvis L. M., Davidson F., Kolberg J., Urdea M., Yap P. L., Simmonds P. Variation of the hepatitis C virus 5' non-coding region: implications for secondary structure, virus detection and typing. The International HCV Collaborative Study Group. J Gen Virol. 1995 Jul;76(Pt 7):1749–1761. doi: 10.1099/0022-1317-76-7-1749. [DOI] [PubMed] [Google Scholar]
  22. Stuyver L., Rossau R., Wyseur A., Duhamel M., Vanderborght B., Van Heuverswyn H., Maertens G. Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J Gen Virol. 1993 Jun;74(Pt 6):1093–1102. doi: 10.1099/0022-1317-74-6-1093. [DOI] [PubMed] [Google Scholar]
  23. Stuyver L., van Arnhem W., Wyseur A., Hernandez F., Delaporte E., Maertens G. Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes. Proc Natl Acad Sci U S A. 1994 Oct 11;91(21):10134–10138. doi: 10.1073/pnas.91.21.10134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tanaka T., Tsukiyama-Kohara K., Yamaguchi K., Yagi S., Tanaka S., Hasegawa A., Ohta Y., Hattori N., Kohara M. Significance of specific antibody assay for genotyping of hepatitis C virus. Hepatology. 1994 Jun;19(6):1347–1353. [PubMed] [Google Scholar]
  25. Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka H., Mishiro S., Miyakawa Y., Mayumi M. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11022–11026. doi: 10.1073/pnas.91.23.11022. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Clinical Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES