Abstract
Hepatitis C virus (HCV), a single-stranded RNA virus of the family Flaviviridae, has a wide range of genetic heterogeneity: 6–11 genotypes (or 6 clades) have been known and each genotype comprises multiple subtypes. Here we report the entire nucleotide sequence of an HCV isolate from a patient in Moldova with chronic hepatitis (isolate name VAT96). The genetic organization of VAT96 was, from 5′ to 3′ ends, 5′UTR (341 nt), polyprotein ORF (9099 nt), 3′UTR (38 nt except for the poly-U and poly-pyrimidine stretch), and X-tail (98 nt). Comparison of the polyprotein amino acid sequence of VAT96 with those of known full-genome isolates assigned VAT96 to the genotype 2 (or clade 2), and further phylogenetic analysis based on a 447-nt sequence that covers part of the C and E1 regions suggested that VAT96 represents a new subtype within the genotype 2, arbitrarily designated “2k” VAT96 was unique in that it possessed a U residue prior to GCC at the 5′ end of its genome while all the other full-genome HCV sequences start with GCC or ACC. In addition, the polyprotein ORF of HCV-VAT96, like HCV-BEBE1 of 2c, encoded several additional amino acids in excess, compared to 2a and 2b sequences. Despite these characteristics that may be unique to VAT96, the 98-nt sequence of the X-tail of VAT96 was highly homologous to those of other isolates with different genotypes so far reported.
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Choo Q.-L., Kuo G., Weiner A.J., Overby L.R., Bradley D.W., and Houghton M., Science 244, 359-362, 1989.
Okamoto H., Kojima M., Okada S., Yoshizawa H., Iizuka H., Tanaka T., Muchmore E.E., Peterson D.A., Ito Y., and Mishiro S., Virology 190, 894-899, 1992.
Okamoto H. and Mishiro S., Intervirology 37, 68-76, 1994.
Simmonds P., Holmes E.C., Cha T.A, Cahn S.W., McOmish F., Irvine B., Beall E., Yap P.L., Kplberg J., and Urdea M.S., J Gen Virol 74, 2391-2399, 1993.
Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Lesmana L.A., Miyakawa Y., and Mayumi M., J Gen Virol 77, 293-301, 1996.
Robertson B., Myers G., Howard C., Brettin T., Bukh J., Gaschen B., Gojobori T., Maertens G., Mizokami M., Nainan O., Netesov S., Nishioka K., Shin-i T., Simmonds P., Smith D., Stuyver L., and Weiner A., Arch Virol 143, 2493-2503, 1998.
Lvov D.K., Samokhvalov E.I., Tsuda F., Selivanov N.A., Okamoto H., Stakhanova V.M., Stakhgildyan I.V., Doroshenko N.V., Yashina T.L., Kuzin S.N., Suetina I.A., Deryabin P.G., Ruzaeva L.A., Bezgodov V.N., Firsova L.A., Sorinson S.N., and Mishiro S., Arch Virol 141, 1613-1622, 1996.
Okamoto H., Kurai K., Okada S.-I., Yamamoto K., Iizuka H., Tanaka T., Fukuda S., Tsuda F., and Mishiro S., Virology 188, 331-341, 1992.
Tanaka T., Kato N., Cho M.J., Sugiyama K., and Shimotohno K., J Virol 70, 3307-3312, 1996.
Choo Q.-L., Richman K., Han J.H., Berger K., Lee C., Dong C., Gallegos C., Coit D., Medina-Selby A., Barr P.J., Weiner A., Bradley D.W., Kuo G., and Houghton M., Proc Natl Acad Sci U.S.A. 88, 2451-2455, 1991.
Okamoto H., Kojima M., Sakamoto M., Iizuka H., Hadiwandowo S., Suwignyo S., Miyakawa Y., and Mayumi M., J Gen Virol 75, 629-635, 1994.
Okamoto H., Okada S., Sugiyama Y., Kurai K., Iizuka H., Machida A., Miyakawa Y., and Mayumi M., J Gen Virol 72, 2697-2704, 1991.
Nakao T., Okamoto H., Tokita H., Inoue T., Iizuka H., Pozzato G., and Mishiro S., Arch Virol 141, 701-704, 1996.
Sakamoto M., Akahane Y., Tsuda F., Tanaka T., Woodfield D.G., and Okamoto H., J Gen Virol 75, 1761-1768, 1994.
Chayama K., Tsubota A., Koida I., Arase Y., Saitoh S., Ikeda K., and Kumada H., J Gen Virol 75, 3623-3628, 1994.
Chamberlaln R.W., Adams N., Saeed A.A., Simmonds P., and Elliott R.M., J Gen Virol 78, 1341-1347, 1997.
Chamberlain R.W., Adams N.J., Taylor L.A., Simmonds P., and Elliott R.M., Biochem Biophys Res Commun 236, 44-49, 1997.
Adams N.J., Chamberlain R.W., Taylor L.A., Davidson F., Lin C.K., Elliott R.M., and Simmonds P., Biochem Biophys Res Commun 234, 393-396, 1997.
Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Miyakawa Y., and Mayumi M., J Gen Virol 79, 1847-1857, 1998.
Stuyver L., Wyseur A., van Arnhem W., Lunel F., Laurent-Puig P., Pawlotsky J.-M., Kleter B., Bassit L., Nkengasong J., van Doorn L.-J., and Maertens G., Virus Res 38, 137-157, 1995.
Van Doorn L.-J., Kleter B.G.E.M., Stuyver L., Maertens G., Brouwer J.T., Schalm S.W., Heijtink R.A., and Quint W.G.V., J Gen Virol 76, 1871-1876, 1995.
Okamoto H., Crovatto M., Pozzato G., Feray C., Brechot C., and Mishiro S., Int Hepatol Commun 3, 161-165, 1995.
Weiner A.J., Brauer M.J., Rosenblatt J., Richman K.H., Tung J., Crawford K., Bonino F., Saracco G., Choo Q.-L., Houghton M., and Han J.-H., Virology 180, 842-848, 1991.
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.
Kolykhalov A.A., Feinstone S.M., and Rice C.M., J Virol 70, 3363-3371, 1996.
Yanagi M., Purcell R.H., Emerson S.U., and Bukh J., Proc Natl Acad Sci USA 94, 8738-8743, 1997.
Yamada N., Tanihara K., Takada A., Yorihuzi T., Tsutsumi M., Shimomura H., Tsuji T., and Date T., Virology 223, 255-261, 1996.
Sugiyama K., Kato N., Mizutani T., Ikeda M., Tanaka T., and Shimotohno K., J Gen Virol 78, 329-336, 1997.
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Samokhvalov, E.I., Hijikata, M., Gylka, R.I. et al. Full-genome Nucleotide Sequence of a Hepatitis C Virus Variant (Isolate Name VAT96) Representing a New Subtype within the Genotype 2 (Arbitrarily 2k). Virus Genes 20, 183–187 (2000). https://doi.org/10.1023/A:1008182901274
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DOI: https://doi.org/10.1023/A:1008182901274