1887

Abstract

Five isolates of hepatitis C virus (HCV) RNA from patients with chronic liver disease in Nepal were not classifiable into the known genotypes I/1a, Il/lb, III/2a, IV/2b or V/3a using PCR with type-specific primers deduced from the HCV core gene. Their nucleotide sequences were determined for the 5′ -terminal 1·5 ldlobases and 3′ -terminal 1·2 kilobases, covering 30% of the entire genome, and compared with each other and with reported sequences of HCV isolates of various genotypes. They were more similar to a reported HCV isolate (NZL1) of genotype V/3a (in 81·6 to 84T % of their nucleotides and 85·7 to 88·7% of the deduced amino acid sequence) compared with the genotypes I/1a to IV/2b (in 69·3 to 74·7% and 72·3 to 77·4%, respectively). Hence they were considered to be variants of the third major group (group 3). The five HCV isolates shared 81·3 to 85·2% of nucleotide sequence and 85·4 to 89·3 % of deduced amino acid sequence. Thus they were substantially different from each other. One of them was classified as genotype VI/3b due to an 88·2 % similarity in nucleotide sequence to that of the reported HCV isolates of this genotype, whereas the remaining four were classified into provisional genotypes 3c, 3d, 3e and 3f. These HCV variants have evolved and remained in Nepal, and have not been observed in the other areas of the world.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-75-4-931
1994-04-01
2021-10-18
Loading full text...

Full text loading...

/deliver/fulltext/jgv/75/4/JV0750040931.html?itemId=/content/journal/jgv/10.1099/0022-1317-75-4-931&mimeType=html&fmt=ahah

References

  1. Alter H. J., Purcell R. H., Shih J. W., Melpolder J. C., Houghton M., Choo Q.-L., Kuo G. 1989; Detection of antibody to hepatitis C virus in prospectively followed transfusion recipients with acute and chronic non-A, non-B hepatitis. New England Journal of Medicine 321:1494–1500
    [Google Scholar]
  2. Bukh J., Purcell R. H., Miller R. H. 1992; Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proceedings of the National Academy of Sciences, U.S.A 89:4942–4946
    [Google Scholar]
  3. 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]
  4. 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]
  5. Han J. H., Houghton M. 1992; Group specific sequences and conserved secondary structures at the 3′ end of HCV genome and its implication for viral replication. Nucleic Acids Research 20:3520
    [Google Scholar]
  6. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., Ohkoshi S., Shimotohno K. 1991; Hypervariable regions in the putative glycoprotein of hepatitis C virus. Biochemical and Biophysical Research Communications 175:220–228
    [Google Scholar]
  7. 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 and Biophysical Research Communications 183:334–342
    [Google Scholar]
  8. Nagayama R., Tsuda F., Okamoto H., Wang Y., Mitsui T., Tanaka T., Miyakawa Y., Mayumi M. 1993; Genotype dependence of hepatitis C virus antibodies detectable by the first-generation enzyme-linked immunosorbent assay with C100-3 protein. Journal of Clinical Investigation 92:1529–1533
    [Google Scholar]
  9. Nei M., Gojobori T. 1986; Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3:418–426
    [Google Scholar]
  10. Okamoto H., Okada S., Sugiyama Y., Tanaka T., Sugai Y., Akahane Y., Machida A., Mishiro S, Miyakawa Y., Mayumi M. 1990; 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]
  11. 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]
  12. Okamoto H., Kanai N., Mishiro S. 1992a; Full-length nucleotide sequence of a Japanese hepatitis C virus isolate (HC-J1) with high homology to USA isolates. Nucleic Acids Research 20:6410
    [Google Scholar]
  13. Okamoto H., Kurai K., Okada S., Yamamoto K., Iizuka H., Tanaka T., Fukuda S., Tsuda F., Mishiro S. 1992b; 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]
  14. Okamoto H., Kojima M., Okada S., Yoshizawa H., Iizuka H., Tanaka T., Muchmore E. E., Peterson D. A., Ito Y., Mishiro S. 1992c; Genetic drift of hepatitis C virus during an 8·2-year infection in a chimpanzee: variability and stability. Virology 190:894–899
    [Google Scholar]
  15. Okamoto H., Sugiyama Y., Okada S., Kurai K., Akahane Y., Sugai Y., Tanaka T., Sato K., Tsuda F., Miyakawa Y., Mayumi M. 1992d; Typing hepatitis C virus by polymerase chain reaction with type-specific primers: application to clinical surveys and tracing infectious sources. Journal of General Virology 73:673–679
    [Google Scholar]
  16. 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]
  17. Simmonds P., Mcomish F., Yap P.-L., Chan S.-W., Lin C. K., Dusheiko G., Saeed A. A., Holmes E. C. 1993; 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]
  18. Stuyver L., Rossau T., Wyseur A., Duhamel M., Vanderrorght 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]
  19. Takada N., Takase S., Enomoto N., Takada A., Date T. 1992; Clinical backgrounds of the patients having different types of hepatitis C virus genomes. Journal of Hepatology 14:35–40
    [Google Scholar]
  20. 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]
  21. Yoshioka K., Kakumu S., Wakita T., Ishikawa T., Itoh Y., Takayanagi M., Higashi Y., Shibata M., Morishima T. 1992; Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: relationship to genotypes of hepatitis C virus. Hepatology 16:293–299
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-75-4-931
Loading
/content/journal/jgv/10.1099/0022-1317-75-4-931
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