Taxonomy of genus Hepacivirus. Application of palindromic nucleotide substitutions for the determination of genotypes of human hepatitis C virus species

Journal of Virological Methods

Volumn 153, Issue 2, 2008, Pages 280-299

  Giangaspero, M ^a   Harasawa, R ^a   Zanetti, A ^b  

^a Faculty of Agriculture   (Japan)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

Genotypes; Hepatitis C virus; Palindromic nucleotide substitutions

Indexed keywords

ARTICLE; GENETIC VARIABILITY; GENOTYPE; GENUS; HEPATITIS C VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PESTIVIRUS; PRIORITY JOURNAL; UNINDEXED SEQUENCE; VIRUS DETECTION; VIRUS IDENTIFICATION; VIRUS STRAIN; VIRUS SURVIVAL;

5' UNTRANSLATED REGIONS; BASE PAIRING; GENETIC VARIATION; GENOTYPE; HEPACIVIRUS; INVERTED REPEAT SEQUENCES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, VIRAL; SPECIES SPECIFICITY;

HEPACIVIRUS; HEPATITIS C VIRUS; PESTIVIRUS;

EID: 53049087857     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2008.06.024     Document Type: Article

References (74)

1. Abdel Hamid M., El-Daly M., Molnegren V., El-Kafrawy S., Abdel-Latif S., Esmat G., Strickland G.T., Loffredo C., Albert J., and Widell A. Genetic diversity in hepatitis C virus in Egypt and possible association with hepatocellular carcinoma. J. Gen. Virol. 88 (2007) 1526-1531
2. Adams A., Chamberlain R.W., Taylor L.A., Davidson F., Lin C.K., Simmonds P., and Elliot R.M. Complete coding sequence of hepatitis C virus genotype 6a. Biochem. Biophys. Res. Commun. 234 (1997) 393-396
3. Aizaki H., Aoki Y., Harada T., Ishii K., Suzuki T., Nagamori S., Toda G., Matsuura Y., and Miyamura T. Full-length complementary DNA of hepatitis C virus genome from an infectious blood sample. Hepatology 27 (1998) 621-627
4. Beard M.R., Abell G., Honda M., Carroll A., Gartland M., Clarke B., Suzuki K., Lanford R., Sangar D.V., and Lemon S.M. An infectious molecular clone of a Japanese genotype 1b hepatitis C virus. Hepatology 30 (1999) 316-324
5. Bukh J., Apgar C.L., Engle R., Govindarajan S., Hegerich P.A., Tellier R., Wong D.C., Elkins R., and Kew M.C. Experimental infection of chimpanzees with hepatitis C virus of genotype 5a: genetic analysis of the virus and generation of a standardized challenge pool. J. Infect. Dis. 178 (1998) 1193-1197
6. Bukh J., Purcell R.H., and Miller R.H. Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 4942-4946
7. Chamberlain R.W., Adams N.J., Saeed A.A., Simmonds P., and Elliott R.M. Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J. Gen. Virol. 78 (1997) 1341-1347
8. Chamberlain R.W., Adams N.J., Taylor L.A., Simmonds P., and Elliot R.M. The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa. Biochem. Biophys. Res. Commun. 236 (1997) 44-49
9. Chayama, K., Kumada, H., 1996.Gene of type C hepatitis virus. Patent: JP 1996056672-A 2.
10. Chayama K., Tsubota A., Koida I., Arase Y., Saitoh S., Ikeda K., and Kumada H. Nucleotide sequence of hepatitis C virus (type 3b) isolated from a Japanese patient with chronic hepatitis C. J. Gen. Virol. 75 (1994) 3623-3628
11. Chen P.J., Lin M.H., Tai K.F., Liu P.C., Lin C.J., and Chen D.S. The Taiwanese hepatitis C virus genome: sequence determination and mapping the 5′ termini of viral genomic and antigenomic RNA. Virology 188 (1992) 102-113
12. Cho J.M., Park Y.-W., Lee Y.-B., Yang J.-Y., Kim C.-H., Choo S.-H., and Ryu W.-S. Molecular cloning of hepatitis C virus genome from a single Korean blood donor. Mol. Cells 5 (1995) 317-324
13. 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. Genetic organization and diversity of the hepatitis C virus. Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 2451-2455
14. Combet C., Garnier N., Charavay C., Grando D., Crisan D., Lopez J., Dehne-Garcia A., Geourjon C., Bettler E., Hulo C., Mercier P.L., Bartenschlager R., Diepolder H., Moradpour D., Pawlotsky J.M., Rice C.M., Trepo C., Penin F., and Deléage G. euHCVdb: the European hepatitis C virus database. Nucleic Acids Res. 35 (2007) D363-D366
15. Deng R., and Brock K.V. Molecular cloning and nucleotide sequence of the pestivirus genome, non-cytopathic bovine viral diarrhea virus strain SD-1. Virology 191 (1992) 867-879
16. Enomoto N., Sakuma I., Asahina Y., Kurosaki M., Murakami T., Yamamoto C., Izumi N., Marumo F., and Sato C. Comparison of full-length sequences of interferon-sensitive and resistant hepatitis C virus 1b. Sensitivity to interferon is conferred by amino acid substitutions in the NS5A region. J. Clin. Invest. 96 (1995) 224-230
17. Franco S., Tural C., Clotet B., and Martinez M.A. Complete nucleotide sequence of genotype 4 hepatitis C viruses isolated from patients co-infected with human immunodeficiency virus type 1. Virus Res. 123 (2007) 161-169
18. Freier S.M., Kierzek R., Jaeger J.A., Sugimoto N., Caruthers M.H., Nielson T., and Turner D.H. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. U.S.A. 83 (1986) 9373-9377
19. Giangaspero M., Harasawa R., Muschko K., and Büttner M. Characterisation of the 5′-untranslated region of wisent (Bison Bonasus) and reindeer (Rangifer tarandus). Vet. Ital. 42 (2006) 165-172
20. Giangaspero M., Harasawa R., and Verhulst A. Genotypic characteristics of the 5′ untranslated region of a pestivirus strain isolated from human leucocytes. Microbiol. Immunol. 40 (1997) 829-834
21. Giangaspero M., Vacirca G., Harasawa R., Büttner M., Panuccio A., De Giuli Morghen C., Zanetti A., Belloli A., and Verhulst A. Genotypes of pestivirus RNA detected in live virus vaccines for human use. J. Vet. Med. Sci. 63 (2001) 723-733
22. Harasawa R. Comparative analysis of the 5′ non-coding region of pestivirus RNA detected from live virus vaccines. J. Vet. Med. Sci. 56 (1994) 961-964
23. Harasawa R. Phylogenetic analysis of pestivirus based on the 5′ untranslated region. Acta Virol. 40 (1996) 49-54
24. Harasawa R., and Giangaspero M. A novel method for pestivirus genotyping based on palindromic nucleotide substitutions in the 5′-untranslated region. J. Virol. Methods 70 (1998) 225-230
25. Harasawa R., and Giangaspero M. Genetic variation in the 5′ end and NS5B regions of classical swine fever virus genome among Japanese isolates. Microbiol. Immunol. 43 (1999) 373-379
26. Harasawa R., and Giangaspero M. Bovine viral diarrhea virus 2: genotyping based on palindromic nucleotide substitutions. Proceedings of the XIIth International Congress of Virology The world of microbes (2002), International Union of Microbiological Societies, Paris, France 421
27. Honda M., Kaneko S., Unoura M., Kobayashi K., and Murakami S. Sequence comparisons for a hepatitis C virus genome RNA isolated from a patient with liver cirrhosis. Gene 120 (1992) 317-318
28. Kalinina O., Norder H., and Magnius L.O. Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: proposed mechanism for its formation. J. Gen. Virol. 85 (2004) 1853-1857
29. Kato N., Hijikata M., Ootsuyama Y., Nakagawa M., Ohkoshi S., and Shimotohno K. A structural protein encoded by the 5′ region of the hepatitis C virus genome efficiently detects viral infection. Jpn. J. Cancer Res. 81 (1990) 1092-1094
30. Kato T., Furusaka A., Miyamoto M., Date T., Yasui K., Hiramoto J., Nagayama K., Tanaka T., and Wakita T. Sequence analysis of hepatitis C virus isolated from a fulminant hepatitis patient. J. Med. Virol. 64 (2001) 334-339
31. Kurihara C., Ishiyama N., Nishiyama Y., Fukushi S., Kageyama T., Katayama K., and Miura S. Molecular characterization of hepatitis C virus genotype 2a from the entire sequences of four isolates. J. Med. Virol. 64 (2001) 466-475
32. Li S.P., Khu Y.L., Hong W.J., Tay A., Ting A.E., Lim S.G., and Tan Y.H. Identification and molecular characterisation of the complete genome of a Singapore isolate of hepatitis C virus: sequence comparison with other strains and phylogenetic analysis. Virus Genes 23 (2001) 89-95
33. Lohmann V., Korner F., Koch J., Herian U., Theilmann L., and Bartenschlager R. Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285 (1999) 110-113
34. McOmish F., Yap P.L., Dow B.C., Follett E.A.C., 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., Fukuda K., Cuypers T., Saeed A.A., Al-Rasheed A.M., and Simmonds P. Geographical distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey. J. Clin. Microbiol. 32 (1994) 884-892
35. Murakami K., Abe M., Kageyama T., Kamoshita N., and Nomoto A. Down-regulation of translation driven by hepatitis C virus internal ribosomal entry site by the 3′ untranslated region of RNA. Arch. Virol. 146 (2001) 729-741
36. Murphy D.G., Willems B., Villeneuve J.P., and Delage G. Sequence analysis of the 5′ noncoding region reveals the existence of multiple hepatitis C virus genotypes in Quebec, Canada. In: Nishioka K., Suzuki H., Mishiro S., and Oda T. (Eds). Viral Hepatitis and Liver Disease (1994) 296-300
37. Nagayama K., Kurosaki M., Enomoto N., Maekawa S.Y., Miyasaka Y., Tazawa J., Izumi N., Marumo F., and Sato C. Time-related changes in full-length hepatitis C virus sequences and hepatitis activity. Virology 263 (1999) 244-253
38. Nakao H., Okamoto H., Tokita H., Inoue T., Iizuka H., Pozzato G., and Mishiro S. Full-length genomic sequence of a hepatitis C virus genotype 2c isolate (BEBE1) and the 2c-specific PCR primers. Arch. Virol. 141 (1996) 701-704
39. Okamoto H., Kanai N., and Mishiro S. Full-length nucleotide sequence of a Japanese hepatitis C virus isolate (HC-J1) with high homology to USA isolates. Nucleic Acids Res. 20 (1992) 6410
40. Okamoto H., Kojima M., Sakamoto M., Iizuka H., Hadiwandowo S., Suwignyo S., Miyakawa Y., and 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. 75 (1994) 629-635
41. Okamoto H., Kurai K., Okada S., Yamamoto K., Iizuka H., Tanaka T., Fukuda S., Tsuda F., and Mishiro S. Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188 (1992) 331-341
42. Okamoto, H., Nakamura, T., 1994. Hepatitis C viral gene, oligonucleotide and method for determining hepatitis C viral genotype. Patent: JP 1994319563-A 1.
43. Okamoto H., Okada S., Sugiyama Y., Kurai K., Iizuka H., Machida A., Miyakawa Y., and Mayumi M. Nucleotide sequences 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 (1991) 2697-2704
44. Rispeter, K., 1998. Thesis. Universitaetsklinikum Essen, Institut fuer Virologie, Essen, Germany.
45. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
46. Samokhvalov E.I., Hijikata M., Gylka R.I., Lvov D.K., and Mishiro S. 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 (2000) 183-187
47. Seki M., and Honda Y. Phosphorothioate antisense oligodeoxynucleotides capable of inhibiting hepatitis C virus gene expression: in vitro translation assay. J. Biochem. 118 (1995) 1199-1204
48. Seki M., Honda Y., Kondo J., Fukuda K., Ohta K., Sugimoto J., and Yamada E. Effective production of the hepatitis C virus core antigen having high purity in Escherichia coli. J. Biotechnol. 38 (1995) 229-241
49. Simmonds P., Bukh J., Combet C., Deléage G., Enomoto N., Feinstone S., Halfon P., Inchauspé G., Kuiken C., Maertens G., Mizokami M., Murphy D.G., Okamoto H., Pawlotsky J.M., Penin F., Sablon E., Shin-I T., Stuyver L.J., Thiel H.J., Viazov S., Weiner A.J., and Widell A. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42 (2005) 962-973
50. Simmonds P., McOmish F., Yap P.L., Chan S.-W., Lin C.K., Dusheiko G., Saeed A.A., and Holmes E.C. Sequence variability in the 5′ non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. J. Gen. Virol. 74 (1993) 661-668
51. Smith, D. B., Mellor, J., Jarvis, L. M., Davidson, F., Kolberg, J., Urdea, M., Yap, P. L., Simmonds, P., and the International HCV Collaborative Study Group, 1995. Variation of the hepatitis C virus 5′ non-coding region: implications for secondary structure, virus detection and typing. The International HCV Collaborative Study Group. J. Gen. Virol. 76, 1749-1761.
52. Sominskaya I., Alekseeva E., Skrastina D., Mokhonov V., Starodubova E., Jansons J., Levi M., Prilipov A., Kozlovska T., Smirnov V., Pumpens P., and Isaguliants M.G. Signal sequences modulate the immunogenic performance of human hepatitis C virus E2 gene. Mol. Immunol. 43 (2006) 1941-1952
53. Takahashi K., Iwata K., Matsumoto M., Matsumoto H., Nakao K., Hatahara T., Ohta Y., Kanai K., Maruo H., Baba K., Hijikata M., and Mishiro S. Hepatitis C virus (HCV) genotype 1b sequences from fifteen patients with hepatocellular carcinoma: the 'progression score' revisited. Hepatol. Res. 20 (2001) 161-171
54. Takamizawa A., Mori C., Fuke I., Manabe S., Murakami S., Fujita J., Onishi E., Andoh T., Yoshida I., and Okayama H. Structure and organization of the hepatitis C virus genome isolated from human carriers. J. Virol. 65 (1991) 1105-1113
55. Tanabe Y., Nagayama K., Enomoto N., Izumi N., Tazawa J., Kurosaki M., Sakamoto N., Sato C., and Watanabe M. Characteristic sequence changes of hepatitis C virus genotype 2b associated with sustained biochemical response to IFN therapy. J. Viral Hepat. 12 (2005) 251-261
56. Tanaka T., Kato N., Nakagawa M., Ootsuyama Y., Cho M.J., Nakazawa T., Hijikata M., Ishimura Y., and Shimotohno K. Molecular cloning of hepatitis C virus genome from a single Japanese carrier: sequence variation within the same individual and among infected individuals. Virus Res. 23 (1992) 39-53
57. Thompson J.D., Gibson T.J., Plewniak F., Jaenmougin F., and Higgins D.G. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4867-4882
58. Thomson M., Nascimbeni M., Gonzales S., Murthy K.K., Rehermann B., and Liang T.J. Emergence of a distinct pattern of viral mutations in chimpanzees infected with a homogeneous inoculum of hepatitis C virus. Gastroenterology 121 (2001) 1226-1233
59. Timm J., Neukamm M., Kuntzen T., Kim A.Y., Chung R.T., Brander C., Lauer G.M., Walker B.D., and Allen T.M. Characterization of full-length hepatitis C virus genotype 4 sequences. J. Viral Hepat. 14 (2007) 330-337
60. Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Lesmana L.A., Miyakawa Y., and Mayumi M. 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 (1996) 293-301
61. Tokita H., Okamoto H., Iizuka H., Kishimoto J., Tsuda F., Miyakawa Y., and Mayumi M. 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 (1998) 1847-1857
62. Tokita H., Okamoto H., Tsuda F., Song P., Nakata S., Chosa T., Iizuka H., Mishiro S., Miyakawa Y., and 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. 91 (1994) 11022-11026
63. Topliff C.L., and Kelling C.L. Virulence markers in the 5′ untranslated region of genotype 2 bovine viral diarrhea virus isolates. Virology 250 (1998) 164-172
64. Trowbridge R., and Gowans E.J. Molecular cloning of an Australian isolate of hepatitis C virus. Arch. Virol. 143 (1998) 501-511
65. Tsukiyama-Kohara K., Tone S., Maruyama I., Inoue K., Katsume A., Nuriya H., Ohmori H., Ohkawa J., Taira K., Hoshikawa Y., Shibasaki F., Reth M., Minatogawa Y., and Kohara M. Activation of the CKI-cdk-Rb-E2F pathway in full genome hepatitis C virus-expressing cells. J. Biol. Chem. 279 (2004) 14531-14541
66. Van Regenmortal M.H.V., Fauquet C.M., Bishop D.H.L., Carstens E., Estes M.K., Lemon S., Maniloff J., Mayo M.A., McGeoch D.J., Pringle C.R., and Wickner R. Virus taxonomy. Classification and Nomenclature of Viruses (2000), Academic Press, New York
67. Wang Y., Okamoto H., Tsuda F., Nagayama R., Tao Q.M., and Mishiro S. Prevalence, genotypes, and an isolate (HC-C2) of hepatitis C virus in Chinese patients with liver disease. J. Med. Virol. 40 (1993) 254-260
68. Yamada N., Tanihara K., Mizokami M., Ohba K., Takada A., Tsutsumi M., and Date T. Full-length sequence of the genome of hepatitis C virus type 3a: comparative study with different genotypes. J. Gen. Virol. 75 (1994) 3279-3284
69. Yanagi M., Purcell R.H., Emerson S.U., and Bukh J. Hepatitis C virus: an infectious molecular clone of a second major genotype (2a) and lack of viability of intertypic 1a and 2a chimeras. Virology 262 (1999) 250-263
70. Yanagi M., St Claire M., Shapiro M., Emerson S.U., Purcell R.H., and Bukh J. Transcripts of a chimeric cDNA clone of hepatitis C virus genotype 1b are infectious in vivo. Virology 244 (1998) 161-172
71. Yeh C.T., Chu C.M., and Liaw Y.F. Distinct composition of viral quasispecies between ascites and serum samples from patients with late stage chronic hepatitis C. Biochem. Biophys. Res. Commun. 227 (1996) 524-529
72. Zhang J., Yamada O., Ito T., Akiyama M., Hashimoto Y., Yoshida H., Makino R., Masago A., Uemura H., and Araki H. A single nucleotide insertion in the 5′-untranslated region of hepatitis C virus leads to enhanced cap-independent translation. Virology 261 (1999) 263-270
73. Zheng W.Z. Genotype identification of hepatitis c virus (HCV) isolated from a single Japanese carrier in Nagasaki prefecture and genome analysis of E1 and E2/NS1 envelope glycoprotein regions. Jpn. J. Trop. Med. Hyg. 22 (1994) 169-177
74. Zuker M., and Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary. Nucleic Acids Res. 9 (1981) 133-148