Phylogenetic analysis of Hepatitis C virus isolates from Tunisian patients

European Journal of Epidemiology

Volumn 19, Issue 6, 2004, Pages 555-562

  Djebbi, Ahlem ^a   Mejri, Selma ^a   Thiers, Valerie ^b   Triki, Henda ^a  

^a PASTEUR INSTITUTE OF TUNIS   (Tunisia)

^b INSTITUT PASTEUR   (France)

Author keywords

Epidemiology; Genotype; Hepatitis C virus; Phylogeny; Tunisia

Indexed keywords

NUCLEIC ACID;

5' UNTRANSLATED REGION; ADOLESCENT; ADULT; AGED; ARTICLE; BLOOD DONOR; CHRONIC HEPATITIS; CONTROLLED STUDY; EGYPT; EUROPE; FEMALE; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HEMOPHILIA; HEPATITIS C VIRUS; HUMAN; MALE; NUCLEOTIDE SEQUENCE; PHYLOGENY; TUNISIA; UNINDEXED SEQUENCE; VIRUS ISOLATION;

5' UNTRANSLATED REGIONS; ADOLESCENT; ADULT; AGED; BASE SEQUENCE; CASE-CONTROL STUDIES; DNA, VIRAL; FEMALE; HEMOPHILIA A; HEPACIVIRUS; HEPATITIS C; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; TUNISIA;

EID: 3442885627     PISSN: 03932990     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:EJEP.0000032348.83087.01     Document Type: Article

References (47)

1. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M: Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral genome. Science 1989; 244: 359-362.
2. Morris JA Jr, Wilcox TR, Reed GW, et al. Safety of the blood supply. Surrogate testing and transmission of hepatitis C in patients after massive transfusion. Ann Surg 1994; 219: 517-525; discussion 525-526.
3. Alter MJ, Margolis SH, Krawczynki K, et al. The natural history of community required hepatitis C in United States. N Engl J Med 1992; 327: 1899-1905.
4. Simmonds P, Holmes EC, Cha TA, et al. 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 1993; 74(Pt 11): 2391-2399.
5. Buck J, Purcell RH, Miller RH. 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 1993; 90: 8234-8238.
6. Stuyver L, van Arnhem W, Wyseur A, Hernandez F, Delaporte E, Maertens G. Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and non-structural 5B regions and identification of five additional subtypes. Proc Natl Acad Sci USA 1994; 91: 10134-10138.
7. Tokita H, Okamoto H, Tsuda F, et al. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc Natl Acad Sci USA 1994; 91: 11022-11026.
8. Tokita H, Okamoto H, Iizuka H, et al. 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 1996; 77(Pt 2): 293-301.
9. Robertson B, Myers G, Howard C, et al. Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: Proposals for standardization. International Committee on Virus Taxonomy. Arch Virol 1998; 143: 2493-2503.
10. Chamberlain RW, Adams N, Saeed AA, Simmonds P, 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(Pt 6): 1341-1347.
11. Xu LZ, Larzul D, Delaporte E, Brechot C, Kremsdorf D. Hepatitis C virus genotype 4 is highly prevalent in central Africa (Gabon). J Gen Virol 1994; 75(Pt 9): 2393-2398.
12. Abdulkarim AS, Zein NN, Germer JJ, et al. Hepatitis C virus genotypes and hepatitis G virus in hemodialysis patients from Syria: Identification of two novel hepatitis C virus subtypes. Am J Trop Med Hyg 1998; 59: 571-576.
13. Cha TA, Beall E, Irvine B, et al. At least five related, but distinct, hepatitis C viral genotypes exist. Proc Natl Acad Sci USA 1992; 89: 7144-7148.
14. Simmonds P, McOmish F, Yap PL, et al. 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 1993; 74(Pt 4): 661-668.
15. Yoshioka K, Kakumu S, Wakita T, Ishikawa T, et al. Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: Relationship to genotypes of hepatitis C virus. Hepatology 1992; 16: 293-299.
16. Davis GL. Prediction of response to interferon treatment of chronic hepatitis C. J Hepatol 1994; 21: 1-3.
17. Tsubota A, Chayama K, Ikeda K, et al. Factors predictive of response to interferon-alpha therapy in hepatitis C virus infection. Hepatology 1994; 19: 1088-1094.
18. Maggi F, Vatteroni ML, Pistello M, et al. Serological reactivity and viral genotypes in hepatitis C virus infection. J Clin Microbiol 1995; 35: 209-211.
19. Gorgi Y, Ben Nejma HL, Azouz MM. Detection of hepatitis C virus in the general population of Tunisia. Bull Soc Pathol Exot 1998; 91: 177.
20. Triki H, Said N, Salah SB, et al. Seroepidemiology of hepatitis B, C and Delta viruses in Tunisia. Trans Roy Soc Trop Med Hyg 1997; 91: 11-14.
21. Djebbi A, Triki H, Bahri O, et al. Genotypes of hepatitis C virus circulating in Tunisia. Epidemiol Infect 2003; 130: 501-505.
22. Smith DB, Mellor J, Jarvis LM, et al. Variation of the hepatitis C virus 5′ non coding-region: Implications for secondary structure, virus detection and typing. J Gen Virol 1995; 76: 749-761.
23. Thiers V, Jaffredo F, Tuveri R, Chodan N, Brechot C. Development of a simple restriction fragment length polymorphism (RFLP) based assay for HCV genotyping and comparative analysis with genotyping and serotyping tests. J Virol Meth 1997; 65: 9-17.
24. Desenclos JC, Bourdiol-Razes M, Rolin B, et al. Hepatitis C in a ward for cystic fibrosis and diabetic patients: Possible transmission by spring-loaded fingerstick devices for self-monitoring of capillary blood glucose. Infect Control Hosp Epidemiol 2001; 22: 701-707.
25. Higgins DG, Sharp PM. CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 1988; 73: 237-244.
26. Kumar S, Tamura K, Nei M. MEGA: Molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci 1994; 10: 189-191.
27. Felsenstein, J. Phylogeny Inference Package (PHYLIP). Version 3.5. University of Washington, Seattle, 1993.
28. Kimura, M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111-120.
29. Saitou N, Nei M. The neighbor-joining method: A new method for 7 reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406-425.
30. Page, RDM. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996; 12: 357-358.
31. Stuyver L, Wyseur A, Arnhem WV, Hernandez F, Maertens G. Second-generation line probe assay for Hepatitis C virus genotyping. J Clin Microbiol, 1996; (Sept): 2259-2266.
32. Qu D, Hantz O, Gouy M, et al. Heterogeneity of hepatitis C virus genotypes in France. J Gen Virol 1994; 75 (Pt 5): 1063-1070.
33. Jeannel D, Fretz C, Traore Y, et al. Evidence for high genetic diversity and long-term endemicity of hepatitis C virus genotypes 1 and 2 in West Africa. J Med Virol 1998; 55: 92-97.
34. Ray SC, Arthur RR, Carella A, Bukh J, Thomas DL. Genetic epidemiology of hepatitis C virus throughout Egypt. J Infect Dis 2000; 182: 698-707.
35. 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(Pt 5): 1001-1012.
36. Kalinina O, Norder H, Mukomolov S, et al. A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersbourg. J Virol 2002; (Apr): 4034-4043.
37. Stuyver L, Wyseur A, van Arnhem W, et al. Hepatitis C virus genotyping by means of 5′-UR/core line probe assays and molecular analysis of untypeable samples. Virus Res 1995; 38: 137-157.
38. Smithg Db, Pathirana S, Davidson F, et al. The origin of hepatitis C virus genotypes. J Gen Virol 1997; 78: 321-328.
39. Fujimura Y, Ishimoto S, Shimoyama T, et al. Genotypes and multiple infections with hepatitis C virus in patients with haemophilia A in Japan. J Viral Hepat 1996; 3: 79-84.
40. Mellor J, Holmes EC, Jarvis LM, Yap PL, Simmonds P. 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 1995; 76(Pt 10): 2493-2507.
41. Ruggieri A, Argentini C, Kouruma F, et al. Heterogeneity of hepatitis C virus genotype 2 variants in West Central Africa (Guinea Conakry). J Gen Virol 1996; 77(Pt 9): 2073-2076.
42. Argentini C, Dettori S, Villano U, et al. Molecular characterisation of HCV genotype 4 isolates circulating in Italy. J Med Virol 2000; 62: 84-90.
43. Cacoub P, Ohayon VV, Sekkat S, et al. Epidemiologic and virologie study of hepatitis C virus infection in Morocco. Gastroenterol Clin Biol 2000; 24: 169-73.
44. Saleh MG, Pereira LM, Tibbs CJ, et al. High prevalence of hepatitis C virus in the normal Libyan population. Trans R Soc Trop Med Hyg 1994; 88: 292-294.
45. Kamel MA, Ghaffer YA, Wasef MA, Wright M, Clark LC, Miller FD. High HCV prevalence in Egyptian blood donors. Lancet 1992; 340-427.
46. Waked IA, Saleh SM, Moustapha MS, Raouf AA, Thomas DL, Strickland GT. High prevalence of hepatitis c in egyptian patients with chronic liver disease. Gut 1995; 37: 105-107.
47. Ayed Z, Houinato D, Hocine M, Ranger-Rogez S, Denis F. Prevalence of serum Markers of hepatitis B and C in blood donors and pregnant women in Algeria Bull Soc Pathol Exot 1995; 88: 225-228.