A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame

Journal of Medical Virology

Volumn 80, Issue 8, 2008, Pages 1370-1378

  Kuntzen, Thomas ^a   Berical, Andrew ^a   Ndjomou, Jean ^b   Bennett, Phil ^c   Schneidewind, Arne ^a   Lennon, Niall ^d   Birren, Bruce W ^d   Kuiken, Carla ^e   Henn, Matthew R ^d   Simmonds, Peter ^f   Allen, Todd M ^a  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WARWICK   (United Kingdom)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e LOS ALAMOS NATIONAL LABORATORY   (United States)

^f UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Hepatitis C virus; Long template PCR; Subtype

Indexed keywords

ARTICLE; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HEPATITIS C VIRUS GENOTYPE 4D; HEPATITIS C VIRUS GENOTYPE 4F; HEPATITIS C VIRUS GENOTYPE 4K; HUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; VIRUS INFECTION;

AMINO ACID SEQUENCE; BASE SEQUENCE; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HUMANS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; POLYMERASE CHAIN REACTION; RECOMBINATION, GENETIC; REFERENCE STANDARDS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

HEPATITIS C VIRUS;

EID: 46049119414     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.21240     Document Type: Article

References (41)

1. Airoldi A, Zavaglia C, Silini E, Tinelli C, Martinetti M, Asti M, Rossini A, Vangeli M, Salvaneschi L, Pinzello G. 2004. Lack of a strong association between HLA class II, tumour necrosis factor and transporter associated with antigen processing gene polymorphisms and virological response to alpha-interferon treatment in patients with chronic hepatitis C. Eur J Immunogenet 31:259-265.
2. Alfaleh FZ, Hadad Q, Khuroo MS, Aljumah A, Algamedi A, Alashgar H, Al-Ahdal MN, Mayet I, Khan MQ, Kessie G. 2004. Peginterferon alpha-2b plus ribavirin compared with interferon alpha-2b plus ribavirin for initial treatment of chronic hepatitis C in Saudi patients commonly infected with genotype 4. Liver Int 24:568-574.
3. Chamberlain RW, Adams N, Saeed AA, Simmonds P, Elliott RM. 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.
4. 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.
5. Chung RT, Monto A, Dienstag JL, Kaplan LM. 1999. Mutations in the NS5A region do not predict interferon-responsiveness in American patients infected with genotype 1b hepatitis C virus. J Med Virol 58:353-358.
6. Colina R, Casane D, Vasquez S, Garcia-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.
7. Davidson F, Simmonds P, Ferguson JC, Jarvis LM, Dow BC, Follett EA, Seed CR, Krusius T, Lin C, Medgyesi GA, et al. 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.
8. El-Zayadi AR, Attia M, Barakat EM, Badran HM, Hamdy H, El-Tawil A, El-Nakeeb A, Selim O, Saied A. 2005. Response of hepatitis C genotype-4 naive patients to 24 weeks of Peg-interferon-alpha2b/ribavirin or induction-dose interferon-alpha2b/ribavirin/amantadine: A non-randomized controlled study. Am J Gastroenterol 100:2447-2452.
9. Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, Ogura Y, Izumi N, Marumo F, Sato C. 1996. Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N Engl J Med 334:77-81.
10. Franco S, Tural C, Clotet B, Martinez MA. 2007. Complete nucleotide sequence of genotype 4 hepatitis C viruses isolated from patients co-infected with human immunodeficiency virus type 1. Virus Res 123: 161-169.
11. Fried MW, Shiffman ML, Reddy KR, Smith C, Marinos G, Goncales FL, Jr., Haussinger 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.
12. Hadziyannis SJ, Sette H, Jr., Morgan TR, Balan V, Diago M, Marcellin P, Ramadori G, Bodenheimer H, Jr., Bernstein D, Rizzetto M, Zeuzem S, Pockros PJ, Lin A, Ackrill AM. 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.
13. Halfon P, Halimi G, Bourliere M, Ouzan D, Durant J, Khiri H, Mercier L, Gerolami V, Cartouzou G. 2000. Integrity of the NS5A (amino acid 2209 to 2248) region in hepatitis C virus 1b patients non-responsive to interferon therapy. Liver 20:381-386.
14. Hasan F, Asker H, Al-Khaldi J, Siddique I, Al-Ajmi M, Owaid S, Varghese R, Al-Nakib B. 2004. Peginterferon alfa-2b plus ribavirin for the treatment of chronic hepatitis C genotype 4. Am J Gastroenterol 99:1733-1737.
15. Hung CH, Lee CM, Lu SN, Lee JF, Wang JH, Tung HD, Chen TM, Hu TH, Chen WJ, Changchien CS. 2003. Mutations in the NS5A and E2-PePHD region of hepatitis C virus type 1b and correlation with the response to combination therapy with interferon and ribavirin. J Viral Hepat 10:87-94.
16. 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.
17. Kalinina O, Norder H, Magnius LO. 2004. Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: Proposed mechanism for its formation. J Gen Virol 85:1853-1857.
18. Kuiken C, Combet C, Bukh J, Shin IT, Deleage G, Mizokami M, Richardson R, Sablon E, Yusim K, Pawlotsky JM, Simmonds P. 2006. A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes. Hepatology 44:1355-1361.
19. Lauer GM, Walker BD. 2001. Hepatitis C virus infection. N Engl J Med 345:41-52.
20. Legrand-Abravanel F, Claudinon J, Nicot F, Dubois M, Chapuy-Regaud S, Sandres-Saune K, Pasquier C, Izopet J. 2007. New natural intergenotypic (2/5) recombinant of hepatitis C virus. J Virol 81:4357-4362.
21. 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.
22. Manns MP, McHutchison JG, Gordon SC, Rustgi VK, Shiffman M, Reindollar R, Goodman ZD, Koury K, Ling M, Albrecht JK. 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.
23. Mellor J, Holmes EC, Jarvis LM, Yap PL, Simmonds P. 1995. Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: Implications for virus classification. The International HCV Collaborative Study Group. J Gen Virol 76:2493-2507.
24. Mellor J, Walsh EA, Prescott LE, Jarvis LM, Davidson F, Yap PL, Simmonds P. 1996. Survey of type 6 group variants of hepatitis C virus in Southeast Asia by using a core-based genotyping assay. J Clin Microbiol 34:417-423.
25. Murphy DG, Chamberland J, Dandavino R, Sablon E. 2007a. A new genotype of Hepatitis C Virus originating from Central Africa. Hepatology 46:623A.
26. Murphy DG, Willems B, Deschenes M, Hilzenrat N, Mousseau R, Sabbah S. 2007b. 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.
27. Ndjomou J, Pybus OG, Matz B. 2003. Phylogenetic analysis of hepatitis C virus isolates indicates a unique pattern of endemic infection in Cameroon. J Gen Virol 84:2333-2341.
28. Nguyen MH, Keeffe EB. 2005. Prevalence and treatment of hepatitis C virus genotypes 4, 5 and 6. Clin Gastroenterol Hepatol 3:S97-S101.
29. Noppornpanth S, Lien TX, Poovorawan Y, Smits SL, Osterhaus AD, Haagmans BL. 2006. Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus. J Virol 80:7569-7577.
30. Pascu M, Martus P, Hohne M, Wiedenmann B, Hopf U, Schreier E, Berg T. 2004. Sustained virological response in hepatitis C virus type 1b infected patients is predicted by the number of mutations within the NS5A-ISDR: A meta-analysis focused on geographical differences. Gut 53:1345-1351.
31. Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, Feinstone S, Halfon P, Inchauspe G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shin IT, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A. 2005. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962-973.
32. Squadrito G, Leone F, Sartori M, Nalpas B, Berthelot P, Raimondo G, Pol S, Brechot C. 1997. Mutations in the nonstructural 5A region of hepatitis C virus and response of chronic hepatitis C to interferon alfa. Gastroenterology 113:567-572.
33. Squadrito G, Orlando ME, Cacciola I, Rumi MG, Artini M, Picciotto A, Loiacono O, Siciliano R, Levrero M, Raimondo G. 1999. Long-term response to interferon alpha is unrelated to "interferon sensitivity determining region" variability in patients with chronic hepatitis C virus-1b infection. J Hepatol 30:1023-1027.
34. Squadrito G, Raffa G, Restuccia T, Pollicino T, Brancatelli S, Raimondo G. 2002. Is investigation of hepatitis C virus NS5A gene heterogeneity a tool for predicting long-lasting response to interferon therapy in patients with HCV-1b chronic hepatitis? J Viral Hepat 9:360-369.
35. Stuyver L, Wyseur A, van Arnhem W, Hernandez F, Maertens G. 1996. Second-generation line probe assay for hepatitis C virus genotyping. J Clin Microbiol 34:2259-2266.
36. 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.
37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882.
38. Timm J, Neukamm M, Kuntzen T, Kim AY, Chung RT, Brander C, Lauer GM, Walker BD, Allen TM. 2007. Characterization of full-length hepatitis C virus genotype 4 sequences. J Viral Hepat 14: 330-337.
39. Veillon P, Payan C, Gaudy C, Goudeau A, Lunel F. 2004. Mutation analysis of ISDR and V3 domains of hepatitis C virus NS5A region before interferon therapy with or without ribavirin. Pathol Biol (Paris) 52:505-510.
40. Viazov S, Kuzin S, Paladi N, Tchernovetsky M, Isaeva E, Mazhul L, Vasychova F, Widell A, Roggendorf M. 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. Watanabe H, Enomoto N, Nagayama K, Izumi N, Marumo F, Sato C, Watanabe M. 2001. Number and position of mutations in the Interferon (IFN) sensitivity-determining region of the gene for nonstructural protein 5A correlate with IFN efficacy in hepatitis C virus genotype 1b infection. J Infect Dis 183:1195-1203.