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Molecular Characterization of a Full Genome Turkish Hepatitis C Virus 1b Isolate (HCV-TR1): A Predominant Viral Form in Turkey

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Abstract

Based on direct sequencing information from 5′UTR and NS5B regions, we identified subtype 1b as a predominant hepatitis C virus genome in Turkey, which affected more than 91% of 79 patients studied. Next, the full genome sequence of a Turkish 1b isolate was obtained by the cloning of polypeptide-encoding region into 7 overlapping fragments. Turkish 1b isolate, which was named HCV-TR1, comprises 9361 nucleotides, including 306 nucleotides of 5′UTR, a single long open reading frame of 9033 nucleotides, and 22 nucleotides of 3′UTR. When compared to HCV 1b polypeptide sequences available at GenBank, the predicted polypeptide displayed a total of 36 amino acid substitutions, of which 16 was specific for HCV-TR1 isolate. Despite these changes, major structural and functional motifs of HCV proteins were maintained in HCV-TR1. In contrast, HCV-TR1 displayed amino acid substitutions in 6 out of 9 major cytotoxic T-cell epitopes. These data suggest that HCV-TR1 encodes functionally intact viral proteins, but it also encodes altered viral epitopes, which may affect host immune-response.

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References

  1. Sarbah S.A., and Younossi Z.M., J Clin Gastroenterol 31(1), 79-79, 2000.

    Google Scholar 

  2. Forns X. and Bukh J., Clin Liver Dis 3(4), 693-716, 1999.

    Google Scholar 

  3. Brechot C., Jaffredo F., Lagorce D., Gerken G., Meyer zum Buschenfelde K., Papakonstontinou A., Hadziyannis S., Romeo R., Colombo M., Rodes J., Bruix J., Williams R., and Namaoumov N., J Hepatology 29, 173-183, 1998.

    Google Scholar 

  4. Benvegnu L., Pontisso P., Cavalletto D., Noventa F., Chemello L. and Alberti A., Hepatology 25, 211-215, 1997.

    Google Scholar 

  5. Amoroso P., Rapicetta M., Tosti M.E., Mele A., Spada E., Buonocore S., Lettieri G., Pierri P., Chionne P., Ciccaglione A.R., and Sagliocca L., J Hepatology 28, 939-944, 1998.

    Google Scholar 

  6. Fine L.G., Soni P., Dusheiko G.M., Harrison T.J., and Dhillon A.P., Lancet 345, 562-566, 1995.

    Google Scholar 

  7. Silini E., Bottelli R., Asti M., Bruno S., Candusso M.E., Brambilla S., Bono F., Iamoni G., Tinelli C., Mondelli M.U., and Ideo G., Gastroenterology 111, 199-205, 1996.

    Google Scholar 

  8. Ray S.C., Arthur R.R., Carella A., Bukh J., and Thomas D.L., J Infect Dis 182, 698-707, 2000.

    Google Scholar 

  9. Shemer-Avni Y., el Astal Z., Kemper O., el Najjar K.J., Yaari A., Hanuka N., Margalith., and Sikuler E., J Med Virol 56, 230-233, 1998.

    Google Scholar 

  10. Abdulkarim A.S., Zein N.N., Germer J.J., Kolbert C.P., Kabbani L., Krajnik K.L., Hola A., Agha M.N., Tourogman M., and Persing D.H., Am J Trop Med Hyg 59(4), 571-576, 1998.

    Google Scholar 

  11. Viazov S., Kuzin S., Paladi N., Tchernovetsky M., Isaeva E., Mazhul L., Vasychova F., Widell A., and Roggendorf M., J Med Virol 53(1), 36-40, 1997.

    Google Scholar 

  12. Simmonds P., Hepatology 21, 570, 1995.

    Google Scholar 

  13. Andonov A., Teoharov P., and Bakalova S., Eur J Clin Microbiol Infect Dis 15(6), 521-523, 1996.

    Google Scholar 

  14. Abacioglu Y.H., Davidson F., Tuncer S., Yap P.L., Ustacelebi S., Yulug N., and Simmonds P., J Viral Hepat 2, 297-301, 1995.

    Google Scholar 

  15. Simsek H., Tatar G., Savas C., and Telatar H.J., Int Med Res 24(1), 132-137, 1996.

    Google Scholar 

  16. Shah H.A., Jafri W., Malik I., Prescott L., and Simmonds P., J Gastroenterol Hepatol 12(11), 758-761, 1997.

    Google Scholar 

  17. Ausubel F.M., Current Protocols in Molecular Biology. Green Pub. Associates and Wily-Interscience, Cold Spring Harbor, USA 1987.

    Google Scholar 

  18. Enomoto N., Sakuma I., Asahina Y., Kurosaki M., Murakami T., Yamamoto C., Izumi N., Marumo F., and Sato C.J., Clin Invest 96(1), 224-230, 1995.

    Google Scholar 

  19. Reed K.E., and Rice C.M., in Hagedorn C.H., and Rice C.M., (eds), The Hepatitis C Virus. Springer Publishing, Berlin, Germany 2000, pp. 55-85.

    Google Scholar 

  20. Okamoto H., Kurai K., Okada S., Yamamoto K., Lizuka H., Tanaka T., Fukuda S., Tsuda F., and Mishiro S., Virology 188, 331-341, 1992c.

    Google Scholar 

  21. Dubuisson J., Duvet S., Meunier J.C., Op De Beeck A., Cacan R., Wychowski C., and Cocquerel L., J Biol Chem 29:275(39), 30605-30609, 2000.

    Google Scholar 

  22. Kim D.W., Kim J., Gwack Y., Han J.H., and Choe J., J Virol 71(12), 9400-9409, 1997.

    Google Scholar 

  23. De Francesco R., Urbani A., Nardi M.C., Tomei L., Steinkuhler C., and Tramontano A., Biochemistry 35, 13282-13287, 1996.

    Google Scholar 

  24. Kim J.L., Morgenstern K.A., Lin C., Fox T., Dwyer M.D., Landro J.A., Chambers S.P., Markland W., Lepre C.A., O'Malley E.T., Harbeson S.L., Rice C.M., Murcko M.A., Caron P.R., and Thomson J.A., Cell 18:87(2), 343-355, 1996.

    Google Scholar 

  25. Kwong A.D., Kim J.L., and Lin C., in The Hepatitis C Virus. Hagedorn C.H., and Rice C.M., (eds), Springer Publishing, Berlin, Germany 2000, pp. 171-197.

    Google Scholar 

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

    Google Scholar 

  27. Puntoriero G., Meola A., Lahm A., Zucchelli S., Ercole B.B., Tafi R., Pezzanera M., Mondelli M.U., Cortese R., Tramontano A., Galfre G., and Nicosia A., EMBO J 17(13), 3521-3533, 1998.

    Google Scholar 

  28. Rehermann B., and Chisari F.V., in The Hepatitis C Virus. Hagedorn C.H., and Rice C.M. (eds), Springer Publishing, Berlin, Germany 2000, pp. 299-327.

    Google Scholar 

  29. Urbani S., Uggeri J., Matsuura Y., Miyamura T., Penna A., Boni C., and Ferrari C., Hepatology 33, 1533-1543, 2001.

    Google Scholar 

  30. Maertens G. and Stuyver L., in The Molecular Medicine of Viral Hepatitis. Harrison T.J. and Zuckerman A.J. (eds), Wiley and Sons Publishing, Chichefter, UK 1997 pp. 183-235.

    Google Scholar 

  31. Smith B.D., Pathirana S., Davidson F., Lawlor E., Power J., Yap L.P., and Simmonds P., J Gen Virol 78, 321-328, 1997.

    Google Scholar 

  32. Simmonds P. and Smith D.B., J Viral Hepat 4(suppl), 69-74, 1997.

    Google Scholar 

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

    Google Scholar 

  34. Kato N., Hijikata M., Ootsuyama Y., Nakagawa M., Ohkoshi S., Sugimura T., and Shimotohno K., Proc Natl Acad Sci USA 87(24), 9524-9528, 1990.

    Google Scholar 

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

    Google Scholar 

  36. Dayhoff M.O., Schwartz R.M., and Orcutt B.C., in Atlas of Protein Sequence and Structure Dayhoff M.O. (ed.), National Biomedical Research Foundation, Washington, DC, 1978, pp. 345-352.

    Google Scholar 

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Authors and Affiliations

  1. Department of Molecular Biology and Genetics and BilGen Genetics and Biotechnology, Research and Development Center, Bilkent University, Ankara, Turkey

    Esra Yildiz, Asli Oztan, Funda Sar, Ergun Pinarbasi, Rengul Cetin-Atalay & Mehmet Ozturk

  2. Department of Medical Biology and Genetics, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey

    Ergun Pinarbasi

  3. Department of Hepatology, Faculty of Medicine, Cukurova University, Adana, Turkey

    Hikmet Akkiz

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  1. Esra Yildiz
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  2. Asli Oztan
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  3. Funda Sar
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Correspondence to Mehmet Ozturk.

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Yildiz, E., Oztan, A., Sar, F. et al. Molecular Characterization of a Full Genome Turkish Hepatitis C Virus 1b Isolate (HCV-TR1): A Predominant Viral Form in Turkey. Virus Genes 25, 169–177 (2002). https://doi.org/10.1023/A:1020161818764

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