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Identification and Molecular Characterisation of the Complete Genome of a Singapore Isolate of Hepatitis C Virus: Sequence Comparison with other Strains and Phylogenetic Analysis

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Abstract

The complete genomic sequence of a Singapore isolate of the hepatitis C virus (HCV) was obtained from serum of an individual chronically infected with HCV. Nine overlapping cDNA clones covering the entire viral genome was amplified by reverse-transcription–polymerase chain reaction (RT–PCR). This isolate (HCV-S1) comprised 9,609 nucleotides (nt), including 341 nt of the complete 5′ untranslated region (5′ UTR), a single open reading frame of 3,011 amino acids (aa) and 235 nt of the complete 3′ UTR. Its genotype was identified as type 1b from analyses of its sequences in the 5′ UTR, NS3 and NS5B regions. When compared against nine reported HCV isolates, the overall aa homology of HCV-S1 was closest with an Australian strain, HCV-A (94%) and a Japanese strain, HCV-JT (93.9%). Phylogenetic analysis revealed that it was most closely related to the Taiwan strain, HCV-TW and another Japanese strain, HCV-K1-R1.

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References

  1. Alter H.J., Purcell R.H., Shih J.W., Melpolder J.C, Houghton M., Choo Q.L., and Kuo G., N Engl J Med 321, 1491-1500, 1989.

    Google Scholar 

  2. Bukh J., Purcell R.H., and Miller R.H., Proc Natl Acad Sci USA 89, 187-191, 1992.

    PubMed  Google Scholar 

  3. Bukh J., Purcell R.H., and Miller R.H., Proc Natl Acad Sci USA 89, 4942-4946, 1992.

    PubMed  Google Scholar 

  4. Bukh J., Miller R.H., and Purcell R.H., Semin Liver Dis 15, 41-63, 1995.

    PubMed  Google Scholar 

  5. Chan S.W., McOmish F., Holmes E.C., Dow B., Peutherer J.F., Follett E.P., Yap P.L., and Simmonds P., J Gen Virol 73, 1131-1141, 1992.

    PubMed  Google Scholar 

  6. Chemello L., Cavalletto L., Noventa F., Bonetti., Casarin C., Bernardinello E., et al., J Viral Hepatol 2, 91-96, 1995.

    Google Scholar 

  7. Choo Q.L., Kuo G., Weiner A.J., Overly L.R., Bradley D.W., and Houghton M., Science 244, 359-362, 1989.

    PubMed  Google Scholar 

  8. Choo Q.L., Richman K.H., Han J.H., Berger K., Lee C., Dong C., Gallegos C., Coit D., Medina S.R., and Barr P.J., Proc Natl Acad Sci USA 88, 2451-2455, 1991.

    PubMed  Google Scholar 

  9. Chow W.C. and Ng H.S., Ann Acad Med Singapore 26(5), 682-686, 1997.

    PubMed  Google Scholar 

  10. Driesel G.D., Wirth D., Stark K., Baumgarten R., Sucker U., and Schrier E., Arch Virol 139, 379-388, 1994.

    PubMed  Google Scholar 

  11. Enomoto N., Sakuma I., Asahina Y., Kurosaki M., Murakami T., Yamamoto C., Izumi N., Marumo F., and Sato C., J Clin Invest 96, 224-230, 1995.

    PubMed  Google Scholar 

  12. Enomoto N., Sakuma I., Asahina Y., Kurosaki M., Murakami T., Yamamoto C., Ogura Y., Izumi N., Marumo F., and Sato C., N Engl J Med 334, 77-81, 1996.

    PubMed  Google Scholar 

  13. Francki R.I.B., Fauquet C.M., Knudson D.I., and Brown F., Springer, Wien New York, p. 223, Arch Virol (Suppl.) 2, 1991.

    Google Scholar 

  14. Greene W.K., Cheong M.K., Ng V., and Yap K.W., J Gen Virol 76(Pt 1), 211-215, 1995.

    PubMed  Google Scholar 

  15. Han J.H., Shyamala V., Richman K.H., Brauer M.J., Irvine B., Urdea M.S., Tekamp O.P., Kuo G., Choo Q.L., and Houghton M., Proc Natl Acad Sci USA 88, 1711-1715, 1991.

    PubMed  Google Scholar 

  16. Hayashi N., Hirokazu H., Kaminaka K., Sugimoto H., Esumi M., Komatsu K., Hayashi K., Sugitani M., Suzuki K., Tadao O., Nozaki C., Mizuno K., and Shikata T., J Hepat 17(Suppl. 3), S94-S107, 1993.

    Google Scholar 

  17. Kato N., Hijikata M., Ootsuyama Y., Nakagawa M., Okoshi S., Sugimura T., and Shimotohno K., Proc Natl Acad Sci USA 87, 9524-9528, 1990.

    PubMed  Google Scholar 

  18. Kolykhalov A.A., Feinstone S.M., and Rice C.M., J Virol 70, 3363-3371, 1996.

    PubMed  Google Scholar 

  19. Lau J.Y., Davis G.L., Prescott L.E., Maertens G., Lindsay K.L., Qian K., Mizokami M., and Simmonds P., Ann Intern Med 124(10), 868-876, 1996.

    PubMed  Google Scholar 

  20. Lee A.S.G., Ng K.Y., Chee M.K.L., Vathsala A., Choong H.L., Ng H.S., et al., Biochem Biophys Res Comm 199, 37-40, 1994.

    PubMed  Google Scholar 

  21. Martell M., Esteban J.I., Quer J., Genesca J., Weiner A., Esteban R., Guardia J., and Gomez J., J Virol 66, 3225-3229, 1992.

    PubMed  Google Scholar 

  22. Martinot-Peignoux M., Marcellin P., Pouteau M., Castelnau C., Boyer N., Poliquin M., et al., Hepatology 22, 1050-1056, 1995.

    Article  PubMed  Google Scholar 

  23. Okamoto H., Okada S., Sugiyama Y., Kurai K., Iizuka H., Machida A., Miyakawa Y., and Mayumi M., J Gen Virol 72, 2697-2704, 1991.

    PubMed  Google Scholar 

  24. Saito I., Miyamura T., Ohbayashi A., Harada H., Katayama T., Kikuchi S., Watanbe Y., Koi S., Onji M., Ohta Y., et al., Proc Natl Acad Sci USA 7, 6547-6549, 1990.

    Google Scholar 

  25. Simmonds P., Hepatology 21, 570-583, 1990.

    Google Scholar 

  26. Simmonds P., Alberti A., Alter H.J., Bonino F., Bradley D.W., Brechot C., Brouwer J.T., Chan S.W., Chayama K., Chen D.S., et al., Hepatology 19(5), 1321-1324, 1994.

    PubMed  Google Scholar 

  27. Takamizawa A., Mori C., Fuke I., Manabe S., Murakami S., Fujita J., Onishi E., Andoh T., Yoshida I., and Okayama H., J Virol 65, 1105-1113, 1991.

    PubMed  Google Scholar 

  28. Tanaka T., Kato N., Cho M.J., and Shimotohno, K., Biochem and Biophy Res Comm 215, 744-749, 1995.

    Google Scholar 

  29. Tanaka T., Kato N., Nakagawa M., Ootsuyama Y., Cho M.J., Nakazawa T., Jijikata M., Ishimura Y., and Shimotohno K.,Virus Res 23(1–2), 39-53, 1992.

    PubMed  Google Scholar 

  30. Trowbridge R. and Gowans E.J., 1998. ArchVirol 143, 501-511, 1998.

    Google Scholar 

  31. Wang Y., Okamoto H., Tsuda F., Nagayama R., Tao Q.M., and Mishiro S., J Med Virol 40, 254-260, 1993.

    PubMed  Google Scholar 

Download references

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Authors and Affiliations

  1. Collaborative anti-viral research, Institute of Molecular and Cell Biology, National University of Singapore, 30 Medical Dr, Singapore, 117609

    Siew Pheng Lim, Yee Ling Khu, Alice Tay & Yin Hwee Tan

  2. Protein Trafficking in Mammalian Cells, Institute of Molecular and Cell Biology, National University of Singapore, 30 Medical Dr, Singapore, 117609

    Wan Jin Hong

  3. Screening for novel inhibitors, Institute of Molecular and Cell Biology, National University of Singapore, 30 Medical Dr, Singapore, 117609

    Anthony Eugene Ting

  4. Department of Medicine, National, University of Hospital, 5 Lower Kent Ridge Road, Singapore, 119074

    Seng Gee Lim

Authors
  1. Siew Pheng Lim
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  2. Yee Ling Khu
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  3. Wan Jin Hong
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  4. Alice Tay
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  5. Anthony Eugene Ting
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  6. Seng Gee Lim
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  7. Yin Hwee Tan
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Correspondence to Siew Pheng Lim.

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Lim, S.P., Khu, Y.L., Hong, W.J. et al. Identification and Molecular Characterisation of the Complete Genome of a Singapore Isolate of Hepatitis C Virus: Sequence Comparison with other Strains and Phylogenetic Analysis. Virus Genes 23, 89–95 (2001). https://doi.org/10.1023/A:1011143731677

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  • DOI: https://doi.org/10.1023/A:1011143731677

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