Phylogenetic analysis of isolated HCV strains from tunisian hemodialysis patients

Viral Immunology

Volumn 26, Issue 1, 2013, Pages 40-48

  Kchouk, Fatma Houissa ^a   Gorgi, Yousr ^a   Bouslama, Lamjed ^b   Sfar, Imen ^a   Ayari, Rym ^a   Khiri, Hacene ^c   Halfon, Phillipe ^c   Aouadi, Houda ^a   Jendoubi Ayed, Saloua ^a   Ayed, Khaled ^a   Ben Abdallah, Taieb ^a  

^a CHARLES NICOLLE HOSPITAL   (Tunisia)

^b CENTRE DE BIOTECHNOLOGIE DE BORJ CÉDRIA   (Tunisia)

^c Laboratoire Alphabio   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; CLINICAL ARTICLE; FEMALE; GENOTYPE; HEMODIALYSIS PATIENT; HEPATITIS C VIRUS; HUMAN; MALE; MOLECULAR PHYLOGENY; NONHUMAN; NS5B GENE; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TUNISIA; UNINDEXED SEQUENCE; VIRUS GENE; VIRUS ISOLATION; VIRUS STRAIN;

ADULT; CLUSTER ANALYSIS; FEMALE; GENETIC VARIATION; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; RENAL DIALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; TUNISIA; VIRAL NONSTRUCTURAL PROTEINS;

EID: 84874078991     PISSN: 08828245     EISSN: 15578976     Source Type: Journal    
DOI: 10.1089/vim.2012.0043     Document Type: Article

References (45)

1. Abdel-Hamid M, El-Daly M, Molnegren V, et al. Genetic diversity in hepatitis C virus in Egypt and possible association with hepatocellular carcinoma. J Gen Virol 2007;88:1526-1531.
2. Ashfaq UA, Javed T, Rehman S, Nawaz Z, and Riazuddin S. An overview of HCV molecular biology, replication and immune responses. Virol J 2011;8:161-170.
3. Ayed K, Gorgi Y, Ben Abdallah T, et al. Hepatitis C virus infection in hemodialysis patients from Tunisia: National survey by serological and molecular methods. Transplant Proc 2003;35:2573-2575.
4. Ben Moussa M, Barguellil Ben Moussa M, Barguellil F, Bouziani A, and Amor A. Comparison of two hepatitis C virus typing assays in a Tunisian population. Ann Biol Clin 2003;61:234-238.
5. Bruguera M, Saiz JC, Franco S, et al. Outbreak of nosocomial hepatitis C infection resolved by genetic analysis of HCV RNA. J Clin Microbiol 2002;40:4363-4366.
6. Bukh J, Miller RH, and Purcell RH. Genetic heterogeneity of hepatitis C virus : Quasispecies and genotypes. Semin Liver Dis 1995;15:41-63.
7. Chamberlain RW, Chamberlain RW, Adams N, Saeed AA, Simmonds P, and Elliott RM. Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. J Gen Virol 1997;78:1341-1347.
8. Chen Z, and Weck KE. Hepatitis C virus genotyping: Interrogation of the 5' untranslated region cannot accurately distinguish genotypes 1a and 1b. J Clin Microbiol 2002;40: 3127-3134.
9. Demetriou VL, and Kostrikis LG. Near-full genome characterization of unclassified hepatitis C virus strains relating to genotypes 1 and 4. J Med Virol 2011:83:2119-2127.
10. Djebbi A, Triki H, Bahri O, et al. Genotypes of hepatitis C virus circulating in Tunisia. Epidemiol Infect 2003;130:501-505.
11. Djebbi A, Mejri S, Thiers V, and Triki H. Phylogenetic analysis of hepatitis C virus isolates from Tunisian patients. Eur J Epidemiol 2004;19:555-562.
12. Djebbi A, Bahri O, Langar H, Sadraoui A,Mejri S, and Triki H. Genetic variability of genotype 1 hepatitis C virus isolates from Tunisian haemophiliacs. New Microbiol 2008;31:473-480.
13. Frank C, Mohamed MK, Strickland GT, et al. The role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt. Lancet 2000;355:887-891.
14. Gaudieri S, Rauch A, Pfafferott K, et al. Hepatitis C virus drug resistance and immune-driven adaptations: Relevance to new antiviral therapy. Hepatology 2009;49:1069-1082.
15. Genovese D, Dettori S, Argentini C, et al. Molecular epidemiology of hepatitis C virus genotype 4 isolates in Egypt and analysis of the variability of envelope proteins E1 and E2 in patients with chronic hepatitis. J Clin Microbiol 2005; 43:1902-1909.
16. Halfon P, Roubicek C, Gerolami V, et al. Use of phylogenetic analysis of hepatitis C virus (HCV) hypervariable region 1 sequences to trace on outbreak of HCV in autodialysis unit. J Clin Microbiol 2002;40:1541-1545.
17. Hmida S, Mojaat N, Chaouachi E, Mahjoub T, Abid S, and Boukef K. HCV antibodies in hemodialyzed patients in Tunisia. Pathol Biol 1995;43:581-583.
18. Kamal SM, and Nasser IA. Hepatitis C genotype 4: What we know and what we don't yet know. Hepatology 2008;47: 1371-1383.
19. Khattab MA, Ferenci P, Hadziyannis SJ, et al. Management of hepatitis C virus genotype 4: Recommandations of an international expert panel. J Hepatol 2011;54:1250-1262.
20. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111-120.
21. Koletzki D, Dumont S, Vermeiren H, Fevery B, De Smet P, and Stuyver LJ. Development and evaluation of an automated hepatitis C virus NS5B sequence-based subtyping assay. Clin Chem Lab Med 2010;48:1095-1102.
22. Kumar S, Tamura K, Jakobsen IB, and Nei M. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 2001;17:1244-1245.
23. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947-2948.
24. Li C, Lu L, Wu X, et al. Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r, and 4t. J Gen Virol 2009;90:1820-1826.
25. McOmish F, Yap PL, Dow BC, et al. Geographical distribution of hepatitis C virus genotypes in blood donors: An international collaborative survey. J Clin Microbiol 1994;32: 884-892.
26. Mejri S, Salah AB, Triki H, Alaya NB, Djebbi A, and Dellagi K. Contrasting patterns of hepatitis C virus infection in two regions from Tunisia. J Med Virol 2005;76:185-193.
27. Merani S, Petrovic D, James I, et al. Effect of immune pressure on hepatitis C virus evolution: Insights from a singlesource outbreak. Hepatology 2011;53:396-405.
28. Morice Y, Roulot D, Grando V, et al. Phylogenetic analyses confirm the high prevalence of hepatitis C virus (HCV) type 4 in the Seine-Saint-Denis district (France) and indicate seven different HCV-4 subtypes linked to two different epidemiological patterns. J Gen Virol 2001;82:1001-1012.
29. Murphy DG, Willems B, Deschenes M, Hilzenrat N, Mousseau R, and Sabbah S. 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 2007;45:1102-1112.
30. Natov SN, and Pereira BJ. Hepatitis C virus in chronic dialysis patients. Minerva Urol Nefrol 2005;57:175-197.
31. Ndjomou J, Pybus OG, and Matz B. Phylogenetic analysis of hepatitis C virus isolates indicates a unique pattern of endemic infection in Cameroon. J Gen Virol 2003;84:2333-2341.
32. Nguyen MH, and Keeffe EB. Prevalence and treatment of hepatitis C virus genotypes 4, 5, and 6. Clin Gastroenterol Hepatol 2005;3:S97-S101.
33. Nicot F, Legrand-Abravanel F, Sandres-Saune K, et al. Heterogeneity of hepatitis C virus genotype 4 strains circulating in south-western France. J Gen Virol 2005;86:107-114.
34. Patel PR, Thompson ND, Kallen AJ, and Arduino MJ. Epidemiology, surveillance, and prevention of hepatitis C virus infections in hemodialysis patients. Am J Kidney Dis 2010; 56:371-378.
35. Rahnavardi M, Hosseini Moghaddam SM, and Alavian SM. Hepatitis C in hemodialysis patients: Current global magnitude, natural history, diagnostic difficulties, and preventive measures. Am J Nephrol 2008;28:628-640.
36. Ramirez S, Perez-del-Pulgar S, Carrion JA, et al. Hepatitis C virus superinfection of liver grafts: A detailed analysis of early exclusion of non-dominant virus strains. J Gen Virol 2010;91:1183-1188.
37. Ray SC, Ray SC, Arthur RR, Carella A, Bukh J, and Thomas DL. Genetic epidemiology of hepatitis C virus throughout Egypt. J Infect Dis 2000;182:698-707.
38. Saitou N, and Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-425.
39. Sandres-Saune K, Deny P, Pasquier C, Thibaut V, Duverlie G, and Izopet J. Determining hepatitis C genotype by analyzing the sequence of the NS5b region. J Virol Methods 2003;109:187-193.
40. Schreier E, Roggendorf M, Driesel G, Hoihne M, and Viazov S. Genotypes of hepatitis C virus isolates from different parts of the world. Arch Virol Suppl 1996;11:185-193.
41. Scott JD, and Gretch DR. Molecular diagnostics of hepatitis C virus infection. JAMA 2007;297:724-732.
42. Stuyver L, van Arnhem W, Wyseur A, Hernandez F, Delaporte E and Maertens G. 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 1994;91:10134-10138.
43. Tanaka Y, Agha S, Saudy N, et al. Exponential spread of hepatitis C virus genotype 4a in Egypt. J Mol Evol 2004; 58:191-195.
44. Timm J, Neukamm M, Kuntzen T, et al. Characterization of full-length hepatitis C virus genotype 4 sequences. J Virol Hepat 2007;14:330-337.
45. 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 1998;8:1847-1857.