1887

Abstract

The entire nucleotide sequence of a hepatitis C virus (HCV) genome (NZL1) of genotype V/3a was determined from overlapping cDNA clones obtained from a human carrier in New Zealand. It comprised 9425 nucleotides (nt) including a 5-untranslated region of 339 nt, a single large open reading frame encoding a polyprotein of 3021 amino acids, a 3′-untranslated region of 23 nt, and 3 -terminal poly(U) stretches of variable lengths. The NZL1 genome was compared with 15 HCV isolates of other genotypes for which the full- length sequence has been determined. It differed from them by 31·1 to 34·3% in nucleotide sequence identity and by 24·5 to 29·1% in amino acid sequence identity, confirming the distinction of genotype V/3a from the other isolates.

The nucleotide sequence data reported in this paper are deposited in the DDBJ/GenBank/EMBL Data Libraries under the accession no. D17763.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-75-7-1761
1994-07-01
2021-10-18
Loading full text...

Full text loading...

/deliver/fulltext/jgv/75/7/JV0750071761.html?itemId=/content/journal/jgv/10.1099/0022-1317-75-7-1761&mimeType=html&fmt=ahah

References

  1. 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]
  2. Bukh J., Purcell R. H., Miller R. H. 1993; At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proceedings of the National Academy of Sciences, U.S.A 90:8234–8238
    [Google Scholar]
  3. Cha T. A., Beall E., Irvine B, Chien D., Kuo G., Urdea M. S. 1992; At least five related, but distinct, hepatitis C viral genotypes exist. Proceedings of the National Academy of Sciences, U.S.A 89:7144–7148
    [Google Scholar]
  4. Chan S.-W., Simmonds P., Mcomish F., Yap P.-L., Mitchell R., Dow B., Follett E. 1991; Serological responses to infection with three different types of hepatitis C virus. Lancet 338:1391
    [Google Scholar]
  5. 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]
  6. Chen P. J., Lin M. H., Tai K. F., Liu P. C., Lin C. J., Chen D. S. 1992; The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5′ termini of viral genomic and antigenomic RNA. Virology 188:102–113
    [Google Scholar]
  7. Choo Q.-L., Kuo G., Weiner A. J., Overby L. R., Bradley D. 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]
  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., 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]
  9. Grakoui A., Mccourt D. W., Wychowski C., Feinstone S. M., Rice C. M. 1993; Characterization of the hepatitis C virus- encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. Journal of Virology 67:2832–2843
    [Google Scholar]
  10. 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]
  11. 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]
  12. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., Ohkoshi S., Shimotohno K. 1991a; Hypervariable regions in the putative glycoprotein of hepatitis C virus. Biochemical and Biophysical Research Communications 175:220–228
    [Google Scholar]
  13. Hijikata M., Kato N., Ootsuyama Y., Nakagawa M., Shimotohno K. 1991b; Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis. Proceedings of the National Academy of Sciences, U.S.A 88:5547–5551
    [Google Scholar]
  14. Honda M., Kaneko S., Unoura M., Kobayashi K., Murakami S. 1992; Sequence comparisons for a hepatitis C virus genome RNA isolate from a patient with liver cirrhosis. Gene 120:317–318
    [Google Scholar]
  15. 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]
  16. Inchauspe G., Zebedee S., Lee D. H., Sugitani M., Nasoff M., Prince A. M. 1991; Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. Proceedings of the National Academy of Sciences, U.S.A 88:10292–10296
    [Google Scholar]
  17. 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, U.S.A 87:9524–9528
    [Google Scholar]
  18. Lee C.-H., Cheng C., Wang J., Lumeng L. 1992; Identification of hepatitis C viruses with a nonconserved sequence of the 5′ untranslated region. Journal of Clinical Microbiology 30:1602–1604
    [Google Scholar]
  19. Mcomish F., Chan S.-W., Dow B. C., Gillon J., Frame W. D., Crawford R. J., Yap P.-L., Follett E. A., Simmonds P. 1993; 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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 vims genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188:331–341
    [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. Okamoto H., Kojima M., Sakamoto M., Iizuka H., Hadiwandowo S., Suwignyo S., Miyakawa Y., Mayumi M. 1994; The entire nucleotide sequence and classification of a hepatitis C virus isolate of a novel genotype from an Indonesian patient with chronic liver disease. Journal of General Virology 75:629–635
    [Google Scholar]
  31. 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 14:661–668
    [Google Scholar]
  32. Stuyver L., van Arnhem W., Wyseur A., Deleys R., Maertens G. 1993a; Analysis of the putative El envelope and NS4a epitope regions of HCV type 3. Biochemical and Biophysical Research Communications 192:635–641
    [Google Scholar]
  33. Stuyver L., Rossau R., Wyseur A., Duhamel M., Vanderborght B., Van Heuverswyn H., Maertens G. 1993b; 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]
  34. 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]
  35. Tanaka T., Kato N., Nakagawa M., Ootsuyama Y., Cho M. J., Nakazawa T., Hijikata M., Ishimura Y., Shimotohno K. 1992; Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals. Virus Research 23:39–53
    [Google Scholar]
  36. 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 Virology 75:931–936
    [Google Scholar]
  37. Wang Y., Okamoto H., Tsuda F., Nagayama R., Tao Q.-M., Mishiro S. 1993; Prevalence, genotypes, and an isolate (HC-C2) of hepatitis C virus in Chinese patients with liver disease. Journal of Medical Virology 40:254–260
    [Google Scholar]
  38. Yoo B. J., Spaete R. R., Geballe A. P., Selby M., Houghton M., Han J. H. 1992; 5′ End-dependent translation initiation of hepatitis C viral RNA and the presence of putative positive and negative translational control elements within the 5′untranslated region. Virology 191:889–899
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-75-7-1761
Loading
/content/journal/jgv/10.1099/0022-1317-75-7-1761
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