A second-generation method of genotyping hepatitis C virus by the polymerase chain reaction with sense and antisense primers deduced from the core gene

Journal of Virological Methods

Volumn 57, Issue 1, 1996, Pages 31-45

  Okamoto, Hiroaki ^a   Kobata, Satoyuki ^b   Tokita, Hajime ^a   Inoue, Taisuke ^c   Woodfield, Graeme D ^d   Holland, Paul V ^e   Al Knawy, Bandar A ^f   Uzunalimoglu, Ozden ^g   Miyakawa, Yuzo ^h   Mayumi, Makoto ^a  

^a JICHI MEDICAL UNIVERSITY   (Japan)

^b Sumitomo Metal Industries Ltd   (Japan)

^c UNIVERSITY OF YAMANASHI   (Japan)

^d AUCKLAND CITY HOSPITAL   (New Zealand)

^e Sacramento Blood Centers   (United States)

^f KING SAUD UNIVERSITY   (Saudi Arabia)

^g ANKARA UNIVERSITY   (Turkey)

^h Mita Institute   (Japan)

Author keywords

Genotype; Hepatitis C; Hepatitis C viruses; Interferons; Polymerase chain reaction

Indexed keywords

PRIMER DNA;

ARTICLE; CONTROLLED STUDY; GENOTYPE; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; HUMAN TISSUE; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

HEPATITIS C VIRUS;

EID: 0029920947     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/0166-0934(95)01960-X     Document Type: Article

References (39)

1. Andonov, A. and Chaudhary, R.K. (1994) Genotyping of Canadian hepatitis C virus isolates by PCR. J. Clin. Microbiol. 32, 2031-2034.
2. 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., Saeed, A.A., Parker, D., Yap, P.-L. and Simmonds P. (1995) Use of NS-4 peptides to identify type-specific atibody to hepatitis C virus genotypes 1, 2, 3, 4, 5 and 6. J. Gen. Virol. 76, 1737-1748.
3. Bukh, J., Miller, R.H. and Purcell, R.H. (1995) Genetic heterogeneity of hepatitis C virus: Quasispecies and genotypes. Semin. Liver Dis. 15, 41-63.
4. Bukh, J., Purcell, R.H. and 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. Proc. Natl. Acad. Sci. USA 90, 8234-8238.
5. Bukh, J., Purcell, R.H. and Miller, R.H. (1994) Sequence analysis of the core gene of 14 hepatitis C virus genotypes. Proc. Natl. Acad. Sci. USA 91, 8239-8243.
6. Cha, T.-A., Beall, E., Irvine, B., Kolberg, J., Chien, D., Kuo, G. and Urdea, M.S. (1992) At least five related, but distinct, hepatitis C viral genotypes exist. Proc. Natl. Acad. Sci. USA 89, 7144-7148.
7. Chayama, K., Tsubota, A., Arase, Y., Saitoh, S., Koida, I., Ikeda, K., Matsumoto, T., Kobayashi, M., Iwasaki, S., Koyama, S., Morinaga, T. and Kumada, H. (1993) Genotypic subtyping of hepatitis C virus. J. Gastroenterol. Hepatol. 8, 150-156.
8. Davidson, F., Simmonds. P., Ferguson J.C., Jarvis, L.M., Dow, B.C., Follett, E.A.C., Seed, C.R.G., Krusius, T., Lin, C., Medgyesi, G.A., Kiyosawa, H., Olim, G., Duraisamy, G., Cuypers, T., Saeed, A.A., Teo, D., Conradie, J., Kew, M.C., Lin, M., Nuchaprayoon, C., Ndimbie, O.K. and Yap, P.L. (1995) Survey of major genotypes and subtypes of hepatitis C virus using RFLP of sequences amplified from the 5′ non-coding region. J. Gen. Virol. 76, 1197-1204.
9. Grakoui, A., McCourt, D.W., Wychowski, C., Feinstone, S.M. and Rice, C.M. (1993) Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. J. Virol. 67, 2832-2843.
10. Hino, K., Sainokami, S., Shimoda, K., Iino, S., Wang, Y., Okamoto, H., Miyakawa, Y. and Mayumi, M. (1994) Genotypes and titers of hepatitis C virus for predicting response to interferon in patients with chronic hepatitis C. J. Med. Virol. 42, 299-305.
11. Houghton, M., Weiner, A., Han, J., Kuo, G. and Choo, Q.L. (1991) Molecular biology of the hepatitis C viruses: implications for diagnosis, development and control of viral disease. Hepatology 14, 381-388.
12. Ina, Y., Mizokami, M., Ohba, K. and Gojobori, T. (1994) Reduction of synonymous substitutions in the core protein gene of hepatitis C virus. J. Mol. Evol. 38, 50-56.
13. Lau, J.Y., Mizokami, M., Kolberg, J.A., Davis, G.L., Prescott, L.E., Ohno, T., Perrillo, R.P., Lindsay, K.L., Gish, R.G., Qian, K.P., Kohara, M., Simmonds, P. and Urdea, M.S. (1995) Application of six hepatitis C virus genotyping systems to sera from chronic hepatitis C patients in the United States. J. Infect. Dis. 171, 281-289.
14. Mahaney, K., Tedeschi, V., Maertens, G., di Bisceglie, A.M., Vergalla, J., Hoofnagle, J.H. and Sallie, R. (1994) Genotypic analysis of hepatitis C virus in American patients. Hepatology 20, 1405-1411.
15. McOmish, F., Yap, P.L., Dow, B.C., Follett, E.A., Seed, C., Keller, A.J., Cobain, T.J., Krusius, T., Kolho, E., Naukkarinen, R. Lin, C., Lai, C., Leong, S., Medgyesi, G.A., Hejjas, M., Kiyokawa, H., Fukada, K., Cyuypers, T., Saeed, A.A., Al-Rasheed, A.M., Lin, M. and Simmonds, P. (1994) Geographical distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey. J. Clin. Microbiol. 32, 884-892.
16. Miyakawa, Y., Okamoto, H. and Mayumi, M. (1995) Classifying hepatitis C virus genotypes. Mol. Med. Today 1, 20-25.
17. Nakao, T., Enomoto, N., Takada, N., Takada, A. and Date, T. (1991) Typing of hepatitis C virus genomes by restriction fragment length polymorphism. J. Gen. Virol. 72, 2105-2112.
18. Newton, C.R., Graham, A., Heptinstall, L.E., Powell, S.J., Summers, C., Kalsheker, N., Smith, J.C. and Markham, A.F. (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17, 2503-2516.
19. Nousbaum, J.B., Pol, S., Nalpas, B., Landais, P., Berthelot, P., Brechet, C and the Collaborative Study Group. (1995) Hepatitis C virus type 1b (II) infection in France and Italy. Ann. Intern. Med. 122, 161-168.
20. Okamoto, H., Kurai, K., Okada, S., Yamamoto, K., Lizuka, H., Tanaka, T., Fukuda, S., Tsuda, F. and Mishiro, S. (1992a) Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188, 331-341.
21. Okamoto, H., Sugiyama, Y., Okada, S., Kurai, K., Akahane, Y., Sugai, Y., Tanaka, T., Sato, K., Tsuda, F., Miyakawa, Y. and Mayumi, M. (1992b) Typing hepatitis C virus by polymerase chain reaction with type-specific primers: application to clinical surveys and tracing infectious sources. J. Gen. Virol. 73, 673-678.
22. Okamoto, H., Tokita, H., Sakamoto, M., Horikita, M., Kojima, M., Iizuka, H. and Mishiro, S. (1993) Characterization of the genomic sequence of type V (or 3a) hepatitis C virus isolates and PCR primers for specific detection. J. Gen. Virol. 74, 2385-2390.
23. Okamoto, H., Kojima, M., Sakamoto, M., Iizuka, H., Hadiwandowo, S., Suwignyo, S., Miyakawa, Y. and Mayumi, M. (1994a) 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. 75, 629-635.
24. Okamoto, H., Mishiro, S., Tokita, H., Tsuda, F., Miyakawa, Y. and Mayumi, M. (1994b) Superinfection of chimpanzees carrying hepatitis C virus of genotype II/1b with that of genotype III/2a or I/1a. Hepatology 20, 1131-1136.
25. Okamoto, H., Crovatto, M., Pozzatto, G., Feray, C., Brechot, C. and Mishiro, S. (1995) Molecular and clinical characteristics of the hepatitis C virus genotype '2c' found in Italians in Italy and France. Int. Hepatol. Commun. 3, 161-165.
26. Qu, D., Li, J.S., Vitvitski, L., Mechai, S., Berby, F., Tong, S.P., Bailly, F., Wang. Q.S., Martin, J.L. and Trepo, C. (1994) Hepatits C virus genotypes in France: comparison of clinical features of patients with HCV type I and type II. J. Hepatol. 21, 70-75.
27. Sakamoto, M., Akahane, Y., Tsuda, F., Tanaka, T., Woodfield, D.G. and Okamoto, H. (1994) Entire nucleotide sequence and characterization of a hepatitis C virus of genotype V/3a. J. Gen. Virol. 75, 1761-1768.
28. Simmonds, P. (1995) Variability of hepatitis C virus. Hepatology 21, 570-583.
29. Simmonds, P., Holmes, E.C., Cha, T.A., Chan, S.W., McOmish, F., Irvine, B., Beall, E., Yap, P.L., Kolberg, J. and Urdea, M.S. (1993a) 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. 74, 2391-2399.
30. Simmonds, P., Rose, K.A., Graham, S., Chan, S.W., McOmish, F., Dow, B.C., Follett, E.A., Yap, P.L. and Marsden, H. (1993b) Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV): use of type-specific peptides to serologically differentiate infections with HCV types 1, 2, and 3. J. Clin. Microbiol. 31, 1493-1503.
31. Stuyver, L., Rossau, R., Wyseur, A., Duhamel, M., Vanderborght, B., Van, H.H. and Maertens, G. (1993) Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J. Gen. Virol. 74, 1093-1102.
32. Stuyver, L., van Arnhem, W., Wyseur, A., Hernandez, F., Delaporte, E. and Maertens, G. (1994) Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes. Proc. Natl. Acad. Sci. USA 91, 10134-10138.
33. Tokita, H., Okamoto, H., Luengrojanakul, P., Vareesagnthip, K., Chainuvati, T., Iizuka, H., Tsuda, F., Miyakawa, Y. and Mayumi, M. (1995) Hepatitis C virus variants from Thailand classifiable into five novel genotypes in the sixth (6b), seventh (7c, 7d) and ninth (9b, 9c) major genetic groups. J. Gen. Virol. 76, 2329-2335.
34. Tokita, H., Okamoto, H., Tsuda, F., Song, P., Nakata, S., Chosa, T., Iizuka, H., Mishiro, S., Miyakawa, Y. and Mayumi, M. (1994a) Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc. Natl. Acad. Sci. USA 91, 11022-11026.
35. Tokita, H., Shrestha, S.M., Okamoto, H., Sakamoto, M., Horikita, M., Iizuka, H., Shrestha, S., Miyakawa, Y. and Mayumi, M. (1994b) Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. J. Gen. Virol. 75, 931-936.
36. Tsubota, A., Chayama, K., Ikeda, K., Yasuji, A., Koida, I., Saitoh, S., Hashimoto, M., Iwasaki, S., Kobayashi, M. and Kumada, H. (1994) Factors predictive of response to interferon-alpha therapy in hepatitis C virus infection. Hepatology 19, 1088-1094.
37. Viazov, S., Zibert, A., Ramakrishnan, K., Widell, A., Cavicchini, A., Schreier, E. and Roggendorf, M. (1994) Typing of hepatitis C virus isolates by DNA enzyme immunoassay. J. Virol. Methods 48, 81-91.
38. Xu, L.Z., Larzul, D., Delaporte, E., Brechot, C. and Kremsdorf, D. (1994) Hepatitis C virus genotype 4 is highly prevalent in central Africa (Gabon). J. Gen. Virol. 75, 2393-2398.
39. Yoshioka, K., Kakumu, S., Wakita, T., Ishikawa, T., Itoh, Y., Takayanagi, M., Higashi, Y., Shibata, M. and Morishima, T. (1992) Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: relationship to genotypes of hepatitis C virus. Hepatology 16, 293-299.