Hepatitis C virus subtyping by a core-envelope 1-based reverse transcriptase PCR assay with sequencing and its use in determining subtype distribution among Danish patients

Journal of Clinical Microbiology

Volumn 41, Issue 3, 2003, Pages 1091-1100

  Corbet, Sylvie ^a   Bukh, Jens ^c   Heinsen, Anja ^a,b   Fomsgaard, Anders ^a  

^a STATENS SERUM INSTITUT   (Denmark)

^b AGILENT TECHNOLOGIES   (United States)

^c NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5' UNTRANSLATED REGION; ADOLESCENT; ADULT; AGED; ARTICLE; CHILD; CONTROLLED STUDY; DENMARK; ENVELOPE GENE; FEMALE; GENOTYPE; HEPATITIS C VIRUS; HUMAN; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MALE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PREVALENCE; PRIORITY JOURNAL; REFUGEE; RELIABILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS TYPING;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; DENMARK; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SEQUENCE HOMOLOGY, NUCLEIC ACID; VIRAL ENVELOPE PROTEINS;

HEPATITIS C VIRUS; RNA VIRUSES; SOMALIA; STAPHYLOCOCCUS PHAGE 3A;

EID: 0344406256     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.41.3.1091-1100.2003     Document Type: Article

References (43)

1. Abid, K., R. Quadri, A.-L. Veuthey, A. Hadengue, and F. Negro. 2000. A novel hepatitis C virus (HCV) subtype from Somalia and its classification into HCV clade 3. J. Gen. Virol. 81:1485-1493.
2. Amoroso, P., M. Rapicetta, M. E. Tosti, A. Mele, E. Spada, S. Buonocore, G. Lettieri, P. Pierri, P. Chionne, A. R. Ciccaglione, and L. Sagliocca. 1998. Correlation between virus genotypes and chronicity rate in acute hepatitis C. J. Hepatol. 28:939-944.
3. Bukh, J., R. H. Miller, and R. H. Purcell. 1995. Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Semin. Liver Dis. 15:41-63.
4. Bukh, J., R. H. Purcell, and R. H. Miller. 1992. Importance of primer selection for the detection of hepatitis C virus RNA with the polymerase chain reaction assay. Proc. Natl. Acad. Sci. USA 89:187-191.
5. Bukh, J., R. H. Purcell, and R. H. Miller. 1992. Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proc. Natl. Acad. Sci. USA 89:4942-4946.
6. Bukh, J., R. H. Purcell, and R. H. Miller. 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.
7. Bukh, J., R. H. Purcell, and R. H. Miller. 1994. Sequence analysis of the core gene of 14 hepatitis C virus genotypes. Proc. Natl. Acad. Sci. USA 91:8239-8243.
8. Chamberlain, R. W., N. Adams, A. A. Saeed, P. Simmonds, and R. M. Elliott. 1997. Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J. Gen. Virol. 78:1341-1347.
9. Choo, Q.-L., G. Kuo, A. J. Weiner, L. R. Overby, D. W. Bradley, and M. Houghton. 1989. Isolation of a cDNA clone derived from a bloodborne non-A, non-B hepatitis genome. Science 244:359-362.
10. Davis, G. L., R. Esteban-Mur, V. Rustgi, J. Hoefs, S. C. Gordon, C. Trépo, M. L. Shiffman, S. Zeuzem, A. Craxi, M. H. Ling, J. Albrecht, and The International Hepatitis Interventional Therapy Group. 1998. Interferon alfa-2b alone or in combination with ribavirin for the treatment of relapse of chronic hepatitis C. N. Engl. J. Med. 339:1493-1499.
11. European Association for the Study of the Liver. 1999. EASL International Consensus Conference on hepatitis C. Consensus statement. J. Hepatol. 30:956-961.
12. Felsenstein, J. 1989. PHYLIP-phylogenetic interference package (version 3.2). Cladistics 5:164-166.
13. Furione, M., L. Simoncini, M. Gatti, F. Baldanti, M. G. Revello, and G. Gerna. 1999. HCV genotyping by three methods: analysis of discordant results based on sequencing. J. Clin. Virol. 3:121-130.
14. Han, J. H., V. Shyamala, K. H. Richman, M. J. Brauer, B. Irvine, M. S. Urdea, P. Tekamp-Olson, G. Kuo, Q. L. Choo, and M. Houghton. 1991. Characterization of the terminal regions of hepatitis C viral RNA: identification of conserved sequences in the 5′ untranslated region and poly(A) tails at the 3′ end. Proc. Natl Acad. Sci. USA 88:1711-1715.
15. Higgins, D., A. J. Bleasby, and R. Fuchs. 1992. CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8:189-191.
16. McHutchison, J. G., S. C. Gordon, E. R. Schiff, M. L. Shiffman, W. M. Lee, V. K. Rustgi, Z. D. Goodman, M. H. Ling, S. Cort, and J. K. Albrecht. 1998. Interferon alfa-2b alone or in combination with ribavirin as initial treatment for chronic hepatitis C. N. Engl. J. Med. 339:1485-1492.
17. Norder, H., Å. Bergström, I. Uhnoo, J. Aldén, L. Weiss, J. Czajkowski, and L. Magnius. 1998. Confirmation of nosocomial transmission of hepatitis C virus by phylogenetic analysis of the NS5-B region. J. Clin. Microbiol. 36:3066-3069.
18. Ohno, O., M. Mizokami, R. Wu, M. Saleh, K. Ohba, E. Orito, M. Mukaide, R. Williams, and J. Y. Lau. 1997. New hepatitis C virus (HCV) genotyping system that allows for identification of HCV genotypes 1a, 1b, 2a, 2b, 3b, 4, 5a, and 6a. J. Clin. Microbiol. 35:201-207.
19. Okamoto, H., N. Kanai, and S. Mishiro. 1992. Full-length nucleotide sequence of a Japanese hepatitis C virus isolate (HC-J1) with high homology to USA isolates. Nucleic Acids Res. 20:6410.
20. Okamoto, H., M. Kojima, M. Sakamoto, H. Iizuka, S. Hadiwandowo, S. Suwignyo, Y. Miyakawa, and M. Mayumi. 1994. 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.
21. Okamoto, H., K. Kurai, S.-I. Okada, K. Yamamoto, H. Iizuka, T. Tanaka, S. Fukuda, F. Tsuda, and S. Mishiro. 1992. 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.
22. Okamoto, H., S. Okada, Y. Sugiyama, K. Kurai, H. Iizuka, A. Machida, Y. Miyakawa, and M. Mayumi. 1991. Nucleotide sequence of the genomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. J. Gen. Virol. 72:2697-2704.
23. Okamoto, H., H. Tokita, M. Sakamoto, M. Horikita, M. Kojima, H. Iizuka, and S. Mishiro. 1993. Characterization of the genomic sequences of type V (or 3a) hepatitis C virus isolates and PCR primers for specific detection. J. Gen. Virol. 74:2385-2390.
24. Pawlotsky, Y. M., L. Tsakiris, F. Roudot-Thoraval, C. Pellet, L. Stuyver, J. Duval, and D. Dhumeaux. 1995. Relationship between hepatitis C virus genotypes and sources of infection in patients with chronic hepatitis C. J. Infect. Dis. 171:1607-1610.
25. Pistello, M., F. Maggi, L. Vatteroni, N. Cecconi, F. Panicucci, G. P. Bresci, L. Gambordella, M. Taddei, A. Bionda, and M. Tuoni. 1994. Prevalence of hepatitis C virus genotypes in Italy. J. Clin. Microbiol. 32:232-234.
26. Pogam, S. L., D. L. Chapois, R. Christen, F. Dubois, F. Barin, and A. Goudeau. 1998. Hepatitis C in a hemodialysis unit: molecular evidence for nosocomial transmission. J. Clin. Microbiol. 36:3040-3043.
27. Pohjanpelto, P., M. Lappalainen, A. Widell, K. Asikainen, and M. Paunio. 1996. Hepatitis C genotypes in Finland determined by RFLP. Clin. Diagn. Virol. 7:7-16.
28. Prescott, L. E., A. Berger, J.-M. Pawlotsky, P. Conjeevaram, I. Pike, and P. Simmonds. 1997. Sequence analysis of hepatitis C virus variants producing discrepant results with two different genotyping assays. J. Med. Virol. 53:237-244.
29. Qu, D., O. Hantz, M. Gouy, L. Vitvitski, J. S. Li, F. Berby, S. P. Tong, and C. Trepo. 1994. Heterogeneity of hepatitis C virus genotypes in France. J. Gen. Virol. 75:1063-1070.
30. Robertson, B., G. Meyers, C. Howard, T. Brettin, J. Bukh, B. Gaschen, T. Gojobori, G. Maertens, M. Mizokami, O. Nainan, S. Netesov, K. Nishioka, T. Shin-I, P. Simmonds, D. Smith, L. Stuyver, and A. Weiner. 1998. Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. Arch. Virol. 143:2493-2503.
31. Samakhvalov, E. I., M. Hijikata, R. I. Gylka, D. K. Lvov, and S. Mishiro. 2000. 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.
32. Silini, E., F. Bono, A. Cividini, A. Cerino, S. Bruno, S. Rossi, G. Belloni, B. Brugnetti, E. Civardi, L. Salvaneschi, and M. U. Mondelli. 1995. Differential distribution of hepatitis C virus genotypes in patients with and without liver function abnormalities. Hepatology 21:285-290.
33. Smith, D. B., S. Pathirana, F. Davidson, E. Lawlor, J. Power, P. L. Yap, and P. Simmonds. 1997. The origin of hepatitis C virus genotypes. J. Gen. Virol. 78:321-328.
34. Stuyver, L., R. Rossau, A. Wyseur, M. Duhamel, B. Vanderborght, H. Van Heuverswyn, and G. Maertens. 1993. Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J. Gen. Virol. 74:1093-1102.
35. Tokita, H., H. Okamoto, M. Sakamoto, M. Horikita, H. Iizuka, S. Shrestha, Y. Miyakawa, and M. Mayumi. 1994. Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group. J. Gen. Virol. 75:931-936.
36. Tokita, H., H. Okamoto, H. Iizuka, J. Kishimoto, F. Tsuda, L. A. Lesmana, Y. Miyakawa, and M. Mayumi. 1996. Hepatitis C virus variants from Jakarta, Indonesia classifiable into novel genotypes in the second (2e and 2f), tenth (10a) and eleventh (11a) genetic groups. J. Gen. Virol. 77:293-301.
37. Tokita, H., H. Okamoto, H. Iizuka, J. Kishimoto, F. Tsuda, Y. Miyakawa, and M. Mayumi. 1998. The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7-9 and comparison with those in the other eight genetic groups. J. Gen. Virol. 79:1847-1857.
38. Tokita, H., H. Okamoto, P. Luengrojanakul, K. Vareesangthip, T. Chainuvati, H. Iizuka, F. Tsuda, Y. Miyakawa, and M. Mayumi. 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. 75:2329-2335.
39. Tokita, H., H. Okamoto, F. Tsuda, P. Song, S. Nakata, T. Chosa, H. Iizuka, S. Mishiro, Y. Miyakawa, and M. Mayumi. 1994. 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.
40. Viazov, S., S. Kuzin, N. Paladi, M. Tchernovetsky, E. Isaeva, L. Mazhul, F. Vasychova, A. Widell, and M. Roggendorf. 1997. Hepatitis C virus genotypes in different regions of the former Soviet Union (Russia, Belarus, Moldova, and Uzbekistan). J. Med. Virol. 53:36-40.
41. White, P. A., X. Zhai, I. Carter, and Y. Zhao. 2000. Simplified hepatitis C virus genotyping by heteroduplex mobility analysis. J. Clin. Microbiol. 38:477-482.
42. Widell, A., S. Shev, S. Månsson, Y.-Y. Zhang, U. Foberg, G. Norkrans, A. Frydon, O. Weilana, J. Kurkus, and E. Nordenfelt. 1994. Genotyping of hepatitis C virus isolates by a modified polymerase chain reaction assay using type specific primers: epidemiological applications. J. Med. Virol. 44:272-279.
43. Zein, N. N., J. Rakela, E. L. Krawitt, K. R. Reddy, T. Tominaga, D. H. Persing, et al. 1996. Hepatitis C virus genotypes in the United States: epidemiology, pathogenicity, and response to interferon therapy. Ann. Intern. Med. 125:634-639.