Hepatitis C virus subtyping based on sequencing of the C/E1 and NS5B genomic regions in comparison to a commercially available line probe assay

Journal of Medical Virology

Volumn 85, Issue 5, 2013, Pages 815-822

  Avó, Ana Patrícia ^a   Água Doce, Ivone ^a   Andrade, Ana ^b   Pádua, Elizabeth ^a  

^a NATIONAL INSTITUTE OF HEALTH DR RICARDO JORGE   (Portugal)

^b Department of Ophthalmology   (Portugal)

Author keywords

C E1 and NS5B regions; Commercial line probe assay; Genotyping and sub typing; Hepatitis C virus; Phylogenetic analysis; Recombinants forms

Indexed keywords

NONSTRUCTURAL PROTEIN 5B;

ARTICLE; ASSAY; COMPARATIVE STUDY; GENOTYPE; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; LINE PROBE ASSAY; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRISONER; SEQUENCE ANALYSIS; VIRAL GENETICS; VIRUS FORMS;

GENOTYPE; HEPACIVIRUS; HEPATITIS C, CHRONIC; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PORTUGAL; PRISONERS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; VIRAL CORE PROTEINS; VIRAL ENVELOPE PROTEINS; VIRAL NONSTRUCTURAL PROTEINS;

HEPATITIS C VIRUS;

EID: 84875660709     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.23545     Document Type: Article

References (42)

1. Bouchardeau F, Cantaloube J, Chevaliez S, Portal C, Razer A, Lefrère J, Pawlotsky J, De Micco P, Laperche S. 2007. Improvement of hepatitis C virus (HCV) genotype determination with the new version of the INNO-LiPA HCV assay. J Clin Microbiol 45:1140-1145.
2. Calado RA, Rocha MR, Parreira R, Piedade J, Venenno T, Esteves A. 2011. Hepatitis C virus subtypes circulating among intravenous drug users in Lisbon, Portugal. J Med Virol 83:608-615.
3. Cannon NA, Donlin MJ, Fan X, Aurora R, Tavis JE. Group V-CS. 2008. Hepatitis C virus diversity and evolution in the full open-reading frame during antiviral therapy. PLoS ONE 3:e2123.
4. Cantaloube JF, Laperche S, Gallian P, Bouchardeau F, de Lamballerie X, de Micco P. 2006. Analysis of the 5′ noncoding region versus the NS5b region in genotyping hepatitis C virus isolates from blood donors in France. J Clin Microbiol 44:2051-2056.
5. Chen Z, Weck KE. 2002. Hepatitis C virus genotyping: Interrogation of the 5′ untranslated region cannot accurately distinguish genotypes 1a and 1b. J Clin Microbiol 40:3127-3134.
6. Chevaliez S, Bouvier-Alias M, Brillet R, Pawlotsky JM. 2009. Hepatitis C virus (HCV) genotype 1 subtype identification in new HCV drug development and future clinical practice. PLoS One 4:e8209.
7. Chinchai T, Labout J, Noppornpanth S, Theamboonlers A, Haagmans BL, Osterhaus AD, Poovorawan Y. 2003. Comparative study of different methods to genotype hepatitis C virus type 6 variants. J Virol Methods 109:195-201.
8. Colina R, Casane D, Vasquez S, García-Aguirre L, Chunga A, Romero H, Khan B, Cristina J. 2004. Evidence of intratypic recombination in natural populations of hepatitis C virus. J Gen Virol 85:31-37.
9. EMCDDA - European Monitoring Centre for Drugs and Drug Addiction. 2011. The state of the drugs problem in Europe. Available at: http://www.emcdda.europa.eu/attachements.cfm/att_143743_EN_EMCDDA_AR2011_EN.pdf. Accessed on 18-05-2012.
10. Esteban JI, Sauleda S, Quer J. 2008. The changing epidemiology of hepatitis C virus infection in Europe. J Hepatol 48:148-162.
11. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
12. Fried MW, Shiffman ML, Reddy KR, Smith C, Marinos G, Gonçales FJ, Häussinger D, Diago M, Carosi G, Dhumeaux D, Craxi A, Lin A, Hoffman J, Yu J. 2002. Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N Engl J Med 347:975-982.
13. Hadziyannis SJ, Sette H, Jr., Morgan TR, Balan V, Diago M, Marcellin P, Ramadori G, Bodenheimer HJ, Bernstein D, Rizzetto M, Zeuzem S, Pockros P, Lin A, Ackrill A, Group PIS. 2004. Peginterferon-alpha2a and ribavirin combination therapy in chronic hepatitis C: A randomized study of treatment duration and ribavirin dose. Ann Intern Med 140:346-355.
14. Hall T. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
15. Hézode C, Forestier N, Dusheiko G, Ferenci P, Pol S, Goeser T, Bronowicki JP, Bourlière M, Gharakhanian S, Bengtsson L, McNair L, George S, Kieffer T, Kwong A, Kauffman RS, Alam J, Pawlotsky JM, Zeuzem S, for the PROVE2 Study Team. 2009. Telaprevir and peginterferon with or without ribavirin for chronic HCV infection. N Engl J Med 360:1839-1850.
16. Irshad M, Ansari MA, Singh A, Nag P, Raghvendra L, Singh S, Badhal SS. 2010. HCV genotypes: A review on their origin global status, assay system, pathogenecity and response to treatment. Hepato-Gastroenterology 57:1529-1538.
17. Kalinina O, Norder H, Mukomolov S, Magnius LO. 2002. A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J Virol 76:4034-4043.
18. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
19. Kumar U, Brown J, Monjardino J, Thomas H. 1993. Sequence variation in the large envelope glycoprotein (E2/NS1) of hepatitis C virus during chronic infection. J Infect Dis 167:726-730.
20. Lange CM, Sarrazin C, Zeuzema S. 2010. Review article: specifically targeted anti-viral therapy for hepatitis C-a new era in therapy. Aliment Pharmacol Ther 32:14-28.
21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
22. Lavanchy D. 2009. The global burden of hepatitis C. Liver Int 29:74-81.
23. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152-160.
24. Manns M, McHutchison J, Gordon S, Rustgi V, Shiffman M, Reindollar R, Goodman Z, Koury K, Ling M, Albrecht J. 2001. Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: A randomised trial. Lancet 358:958-965.
25. Marinho RT. 2008. A hepatite C mata em Portugal? In: Liver Today, Boletim informativo da APEF, 3rd edition. Available at: http://www.hsm.min-saude.pt/contents/pdfs/Divulgacao/Liver%20Today%20APEF%203.pdf. Accessed on 18-05-2012.
26. Marinho R, Moura M, Giria J, Ferrinho P. 2001. Epidemiological aspects of hepatitis C in Portugal. J Gastroenterol Hepatol 16:1076-1077.
27. McHutchison JC, Everson GT, Gordon SC, Jacobson IM, Sulkowski M, Kauffman R, McNair L, Alam J, Muir AJ, PROVE1 Study Team. 2009. Telaprevir with peginterferon and ribavirin for chronic HCV genotype 1 infection. N Engl J Med 360:1827-1838.
28. Mühlberger N, Schwarzer R, Lettmeier B, Sroczynski G, Zeuzem S, Siebert U. 2009. HCV-related burden of disease in Europe: A systematic assessment of incidence, prevalence, morbidity, and mortality. BMC Public Health 9:34.
29. Murphy DG, Willems B, Deschênes M, Hilzenrat N, Mousseau R, Sabbah S. 2007. Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 5′ untranslated region sequences. J Clin Microbiol 45:1102-1112.
30. Pawlotsky JM. 2009. Therapeutic implications of hepatitis C virus resistance to antiviral drugs. Ther Adv Gastroenterol 2:205-219.
31. Ross RS, Verbeeck J, Viazov S, Lemey P, Van Ranst M, Roggendorf M. 2008. Evidence for a complex mosaic genome pattern in a full-length hepatitis C virus sequence. Evol Bioinform Online 4:249-254.
32. Shepard CW, Finelli L, Alter MJ. 2005. Global epidemiology of hepatitis C virus infection. Lancet Infect Dis 5:558-567.
33. Simmonds P. 2004. Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 85:3173-3188.
34. Simmonds P, Holmes EC, Cha TA, Chan SW, McOmish F, Irvine B, Beall E, Yap PL, Kolberg J, Urdea MS. 1993. 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.
35. Simmonds P, Mellor J, Sakuldamrongpanich T, Nuchaprayoon C, Tanprasert S, Holmes EC, Smith DB. 1996. Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: Comparison with classifications based upon sequence similarity. J Gen Virol 77:3013-3024.
36. Simmonds P, Bukh J, Combert C, Deléage G, Enomoto N, Feinstone S, Halfon P, Inchauspé G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shin-I T, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A. 2005. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotype. Hepathology 42:962-973.
37. Smith DB, Mellor J, Jarvis LM, Davidson F, Kolberg J, Urdea M, Yap PL, Simmonds P. 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.
38. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEG A4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
39. Thompson WD, Walter SD. 1988. Kappa and the concept of independent errors. J Clin Epidemiol 41:969-970.
40. Verbeeck J, Stanley MJ, Shieh J, Celis L, Huyck E, Wollants E, Morimoto J, Farrior A, Sablon E, Jankowski-Hennig M, Schaper C, Johnson P, Van Ranst M, Van Brussel M. 2008. Evaluation of Versant hepatitis C virus genotype assay (LiPA) 2.0. J Clin Microbiol 46:1901-1906.
41. Vieira A, Freire R, Mangualde J, Pinho C, Fernandes V, Alves A, Augusto F, Lobato C, Oliveira A. 2007. Hepatitie C-Casuística da consulta de hepatologia de um hospital distrital. J Port Gastrenterol 14:134-140.
42. Wasley A, Alter M. 2000. Epidemiology of hepatitis C: Geographic differences and temporal trends. Semin Liver Dis 20:1-16.