Abstract
Subtype analysis of hepatitis C viruses (HCVs) obtained from patients with chronic liver disease in Chiang Mai, Thailand, was performed. Of 46 HCV isolates, 13 (28%) were shown to belong to HCV subtype 3a (HCV-3a), 10 (22%) to belong to HCV-1a, 7 (15%) to belong to HCV-1b, 1 (2%) to belong to HCV-3b, and 1 (2%) to belong to a variant group, as determined from partial nucleotide sequences of the NS5B region of the viral genome. Analysis of 5' untranslated region sequences identified five other isolates (11%) of HCV type 1 and two other isolates (4%) of type 3. Detailed phylogenetic positions for the variant described above and those previously obtained from blood donors and drug addicts in Chiang Mai were determined by a six-parameter neighbor-joining method on the basis of core, E1, and NS5B region sequences. The results revealed that those sequence variants represent novel subtypes of HCV type 6. The HCV type 6 isolates appear to be antigenically different from isolates of HCV types 1 and 2, as determined by a serotyping method that utilizes recombinant peptides corresponding to a portion of the NS4 protein. The significance of subtype analysis around this area is discussed.
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- Apichartpiyakul C., Chittivudikarn C., Miyajima H., Homma M., Hotta H. Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai, Thailand. J Clin Microbiol. 1994 Sep;32(9):2276–2279. doi: 10.1128/jcm.32.9.2276-2279.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Apichartpiyakul C., Miyajima H., Doi H., Mizokami M., Homma M., Hotta H. Frequent detection of hepatitis C virus subtype 3a (HCV-3a) isolates in Thailand by PCR using subtype-specific primers. Microbiol Immunol. 1995;39(4):285–289. doi: 10.1111/j.1348-0421.1995.tb02203.x. [DOI] [PubMed] [Google Scholar]
- Bhattacherjee V., Prescott L. E., Pike I., Rodgers B., Bell H., El-Zayadi A. R., Kew M. C., Conradie J., Lin C. K., Marsden H. Use of NS-4 peptides to identify type-specific antibody to hepatitis C virus genotypes 1, 2, 3, 4, 5 and 6. J Gen Virol. 1995 Jul;76(Pt 7):1737–1748. doi: 10.1099/0022-1317-76-7-1737. [DOI] [PubMed] [Google Scholar]
- Bukh J., Miller R. H., Purcell R. H. Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Semin Liver Dis. 1995 Feb;15(1):41–63. doi: 10.1055/s-2007-1007262. [DOI] [PubMed] [Google Scholar]
- Davidson F., Simmonds P., Ferguson J. C., Jarvis L. M., Dow B. C., Follett E. A., Seed C. R., Krusius T., Lin C., Medgyesi G. A. Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5' non-coding region. J Gen Virol. 1995 May;76(Pt 5):1197–1204. doi: 10.1099/0022-1317-76-5-1197. [DOI] [PubMed] [Google Scholar]
- Doi H., Yoon S., Homma M., Hotta H. Identification of hepatitis C virus subtype 3b (HCV-3b) among Japanese patients with liver diseases using highly efficient primers for reverse transcription-polymerase chain reaction. Microbiol Immunol. 1994;38(2):159–163. doi: 10.1111/j.1348-0421.1994.tb01759.x. [DOI] [PubMed] [Google Scholar]
- Gojobori T., Ishii K., Nei M. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol. 1982;18(6):414–423. doi: 10.1007/BF01840889. [DOI] [PubMed] [Google Scholar]
- Grakoui A., McCourt D. W., Wychowski C., Feinstone S. M., Rice C. M. Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. J Virol. 1993 May;67(5):2832–2843. doi: 10.1128/jvi.67.5.2832-2843.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Greene W. K., Cheong M. K., Ng V., Yap K. W. Prevalence of hepatitis C virus sequence variants in South-East Asia. J Gen Virol. 1995 Jan;76(Pt 1):211–215. doi: 10.1099/0022-1317-76-1-211. [DOI] [PubMed] [Google Scholar]
- Hijikata M., Mizushima H., Akagi T., Mori S., Kakiuchi N., Kato N., Tanaka T., Kimura K., Shimotohno K. Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus. J Virol. 1993 Aug;67(8):4665–4675. doi: 10.1128/jvi.67.8.4665-4675.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hotta H., Doi H., Hayashi T., Purwanta M., Soemarto W., Mizokami M., Ohba K., Homma M. Analysis of the core and E1 envelope region sequences of a novel variant of hepatitis C virus obtained in Indonesia. Arch Virol. 1994;136(1-2):53–62. doi: 10.1007/BF01538816. [DOI] [PubMed] [Google Scholar]
- Hotta H., Handajani R., Lusida M. I., Soemarto W., Doi H., Miyajima H., Homma M. Subtype analysis of hepatitis C virus in Indonesia on the basis of NS5b region sequences. J Clin Microbiol. 1994 Dec;32(12):3049–3051. doi: 10.1128/jcm.32.12.3049-3051.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Houghton M., Weiner A., Han J., Kuo G., Choo Q. L. Molecular biology of the hepatitis C viruses: implications for diagnosis, development and control of viral disease. Hepatology. 1991 Aug;14(2):381–388. [PubMed] [Google Scholar]
- Kanai K., Kako M., Okamoto H. HCV genotypes in chronic hepatitis C and response to interferon. Lancet. 1992 Jun 20;339(8808):1543–1543. doi: 10.1016/0140-6736(92)91311-u. [DOI] [PubMed] [Google Scholar]
- Kleter G. E., van Doorn L. J., Brouwer J. T., Schalm S. W., Heijtink R. A., Quint W. G. Sequence analysis of the 5' untranslated region in isolates of at least four genotypes of hepatitis C virus in The Netherlands. J Clin Microbiol. 1994 Feb;32(2):306–310. doi: 10.1128/jcm.32.2.306-310.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Luengrojanakul P., Vareesangthip K., Chainuvati T., Murata K., Tsuda F., Tokita H., Okamoto H., Miyakawa Y., Mayumi M. Hepatitis C virus infection in patients with chronic liver disease or chronic renal failure and blood donors in Thailand. J Med Virol. 1994 Nov;44(3):287–292. doi: 10.1002/jmv.1890440313. [DOI] [PubMed] [Google Scholar]
- Mizushima H., Hijikata M., Asabe S., Hirota M., Kimura K., Shimotohno K. Two hepatitis C virus glycoprotein E2 products with different C termini. J Virol. 1994 Oct;68(10):6215–6222. doi: 10.1128/jvi.68.10.6215-6222.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ohba K., Mizokami M., Ohno T., Suzuki K., Orito E., Ina Y., Lau J. Y., Gojobori T. Classification of hepatitis C virus into major types and subtypes based on molecular evolutionary analysis. Virus Res. 1995 May;36(2-3):201–214. doi: 10.1016/0168-1702(95)00007-d. [DOI] [PubMed] [Google Scholar]
- Okamoto H., Kojima M., Sakamoto M., Iizuka H., Hadiwandowo S., Suwignyo S., Miyakawa Y., Mayumi M. The entire nucleotide sequence and classification of a hepatitis C virus isolate of a novel genotype from an Indonesian patient with chronic liver disease. J Gen Virol. 1994 Mar;75(Pt 3):629–635. doi: 10.1099/0022-1317-75-3-629. [DOI] [PubMed] [Google Scholar]
- Pistello M., Maggi F., Vatteroni L., Cecconi N., Panicucci F., Bresci G. P., Gambardella L., Taddei M., Bionda A., Tuoni M. Prevalence of hepatitis C virus genotypes in Italy. J Clin Microbiol. 1994 Jan;32(1):232–234. doi: 10.1128/jcm.32.1.232-234.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pozzato G., Moretti M., Franzin F., Crocè L. S., Tiribelli C., Masayu T., Kaneko S., Unoura M., Kobayashi K. Severity of liver disease with different hepatitis C viral clones. Lancet. 1991 Aug 24;338(8765):509–509. doi: 10.1016/0140-6736(91)90578-d. [DOI] [PubMed] [Google Scholar]
- Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
- 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. A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology. 1994 May;19(5):1321–1324. [PubMed] [Google Scholar]
- Simmonds P., Holmes E. C., Cha T. A., Chan S. W., McOmish F., Irvine B., Beall E., Yap P. L., Kolberg J., Urdea M. S. Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J Gen Virol. 1993 Nov;74(Pt 11):2391–2399. doi: 10.1099/0022-1317-74-11-2391. [DOI] [PubMed] [Google Scholar]
- Simmonds P., Smith D. B., McOmish F., Yap P. L., Kolberg J., Urdea M. S., Holmes E. C. Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions. J Gen Virol. 1994 May;75(Pt 5):1053–1061. doi: 10.1099/0022-1317-75-5-1053. [DOI] [PubMed] [Google Scholar]
- Tanaka T., Tsukiyama-Kohara K., Yamaguchi K., Yagi S., Tanaka S., Hasegawa A., Ohta Y., Hattori N., Kohara M. Significance of specific antibody assay for genotyping of hepatitis C virus. Hepatology. 1994 Jun;19(6):1347–1353. [PubMed] [Google Scholar]
- Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka H., Mishiro S., Miyakawa Y., Mayumi M. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11022–11026. doi: 10.1073/pnas.91.23.11022. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tokita H., Shrestha S. M., Okamoto H., Sakamoto M., Horikita M., Iizuka H., Shrestha S., Miyakawa Y., Mayumi M. Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. J Gen Virol. 1994 Apr;75(Pt 4):931–936. doi: 10.1099/0022-1317-75-4-931. [DOI] [PubMed] [Google Scholar]