Abstract
Previous studies in South African patients have shown that hepatitis C virus (HCV) prevalence is low (2.6%) and genotype 5 is the dominant genotype. This is the first sequence-based genotype study from this country on two different patient groups (haemophiliacs (H) and liver disease (LD) patients) over two time periods (2000–2002 and 2007). Genotype 5 was found to be the dominant genotype in the LD groups, but genotype 1 dominated in the H group. Genotype 2, and a higher prevalence of genotype 3a, was present in the H group when compared to previous South African studies. Genotypes 3 and 4 have been described here in the LD groups for the first time in South Africa, with subtypes 4c and 4g being identified. A separate cluster of genotype 5 sequences were found to have only one adenine at nucleotide position 107 of the 5′UTR, as previously reported. Subtyping in the less conserved NS5B region was used to further characterize the 2000–2002 isolates and validate 5′UTR typing. The study shows that by using reliable methods of genotyping, the prevalence and frequencies of HCV genotypes can be monitored in South Africa for better diagnosis and treatment of the disease.
Similar content being viewed by others
References
Bernier L, Willems B, Delage G, Murphy DG (1996) Identification of numerous hepatitis C virus genotypes in Montreal, Canada. J Clin Microbiol 34:2815–2818
Botha JF, Kassianides C, Schneider HR, Song E, Spearman CWN, Van der Merwe SW (2005) South African hepatitis C management guidelines. The SA Gastroenterol Rev 3:18–21
Chamberlain RW, Adams NJ, Taylor LA, Simmonds P, Elliott RM (1997) The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa. Biochem Biophys Res Commun 236:44–49
Chan SW, McOmish F, Holmes EC, Dow B, Peutherer JF, Follett E, Yap PL, Simmonds P (1992) Analysis of a new hepatitis C virus type and its phylogenetic relationship to existing variants. J Gen Virol 73:1131–1141
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
Choo QL, Richman KH, Han JH, Berger K, Lee C, Dong C, Gallegos C, Coit D, Medina-Selby R, Barr PJ (1991) Genetic organization and diversity of the hepatitis C virus. Proc Natl Acad Sci USA 88:2451–2455
EHRN, Eurasian Harm Reduction Network (formerly the Central and Eastern European Harm Reduction Network–CEEHRN) HCV infection in Europe, October 1st 2007. http://www.ceehrn.org
Ellis LA, Brown D, Conradie JD, Paterson A, Sher R, Millo J, Theodossiadou E, Dusheiko GM (1990) Prevalence of hepatitis C in South Africa: detection of anti-HCV in recent and stored serum. J Med Virol 32:249–251
Henquell C, Cartau C, Abergel A, Laurichesse H, Regagnon C, de Champs C, Bailly J-L, Peigue-Lafeuille H (2004) High prevalence of hepatitis C virus type 5 in central France evidenced by a prospective study from 1996 to 2002. J Clin Microbiol 42:3030–3035
Hissar SS, Goyal A, Kumar M, Pandey C, Suneetha PV, Sood A, Midha V, Sakhuja P, Malhotra V, Sarin SK (2006) Hepatitis C virus genotype 3 predominates in North and Central India and is associated with significant histopathologic liver disease. J Med Virol 78:452–458
Jover R, Perez-Serra J, de Vera F, Alamo JM, Munoz C, Yago C, Martinez-Ramirez R, Vidal JV (2001) Infection by genotype 5a of HCV in a district of Southeast Spain. Am J Gastroenterol 96:3042–3043
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis of sequence alignments. Brief Bioinform 5:2–3
Laperche S, Saune K, Deny P, Duverlie G, Alain S, Chaix M-L, Gaudy C, Lunel F, Pawlotsky J-M, Payan C, Pozzetto B, Tamalet C, Thibault V, Vallet S, Bouchardeau F, Izopet J, Lefrere J-J (2006) Unique NS5b hepatitis C virus gene sequence consensus database is essential for standardization of genotype determinations in multicenter epidemiological studies. J Clin Microbiol 44:614–616
Lee SC, Anthony A, Lee N, Leibow J, Yang JQ (2000) Improved version 2.0 qualitative and quantitative AMPLICOR RT-PCR tests for hepatitis C RNA: calibration of units, enhanced genotype reactivity and performance characteristics. J Clin Microbiol 38:4171–4179
Levi JE, Takaoka DT, Garrini RH, Fachini RM, Foccacia R, de Bortholi Santos E, Mitre HP, de Mendonca JS, de Paula Cavalheiro N, Barone AA, Wendel S (2002) Three cases of infection with hepatitis C virus genotype 5 among Brazilian hepatitis patients. J Clin Microbiol 40:2645–2647
Lodenyo H, Schoub B, Ally R, Kairu S, Segal I (2000) Hepatitis B and C virus infections and liver functions in AIDS patients at Chris Hani Baragwanath Hospital, Johannesburg. East Afr Med J 77:13–15
Morbidity and Mortality Weekly Report (1998) Recommendations for prevention and control of Hepatitis C virus (HCV) infection and HCV-related chronic disease 47(RR-19): 1–39
Muerhoff AS, Smith DB, Leary TP, Erker LC, Desai SM, Mushahwar IK (1997) Identification of GB virus C variants by phylogenetic analysis of untranslated and coding region sequences. J Virol 71:6501–6508
Nguyen MH, Keeffe EB (2005) Prevalence and treatment of hepatitis C virus genotypes 4, 5, and 6. Clin Gastroenterol Hepatol 10:S97–S100
Ohno T, Mizokami M, Tibbs CJ, Ohba K, Suzuki K, Wu RR, Nouri-Aria KT, Williams R (1994) New genotype of hepatitis C virus in South Africa. J Med Virol 42:409–413
Pasquier C, Njouom R, Ayouba A, Dubois M, Sartre MT, Vessière A, Timba I, Thonnon J, Izopet J, Nerrienet E (2005) Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon. J Med Virol 77:390–398
Sandres-Saune K, Deny P, Pasquier C, Thibaut V, Duverlie G, Izopet J (2003) Determining hepatitis C genotype by analyzing the sequence of the NS5b region. J Virol Methods 109:187–193
Simmonds P, Holmes EC, Cha T-A, Chan S-W, McOmish F, Irvine B, Beall E, Yap BL, 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
Simmonds P, Smith DB, McOmish F, Yap PL, Kolberg J, Urdea MS, Holmes EC (1994) Identification of genotypes of hepatitis C virus by sequence comparison in the core, E1 and NS5 regions. J Gen Virol 75:1053–1061
Sithebe NP, Aspinall S, Smuts H (1996) Molecular epidemiology of hepatitis C virus infection at Ga-Rankuwa Hospital. SAMJ 86:1543–1544
Smuts HEM, Kannemeyer J (1995) Genotyping of hepatitis C virus in South Africa. J Clin Microbiol 33:1679–1681
Soni PN, Tait DR, Gopaul W, Sathar MA, Simjee AE (1996) Hepatitis C virus infection in chronic liver disease in Natal. SAMJ 86:80–83
Stuyver L, Van Arnhem W, Wyseur A, Hernandez F, Delaporte E, Maertens G (1994) Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes. PNAS 91:10134–10138
Tamalet C, Colson P, Tissot-Dupont H, Henry M, Tourres C, Tivoli N, Botta D, Ravaux I, Poizot-Martin I, Yahi N (2003) Genomic and phylogenetic analysis of hepatitis C virus isolates: a survey of 535 strains circulating in southern France. J Med Virol 71:391–398
Thakur A, Guptan RC, Arankale V, Sarin SK (2003) Low specificity of the third generation ELISA for HCV detection in voluntary blood donors in India. eJIFCC 14:4
Tucker TJ, Voigt M, Bird A, Robson S, Gibbs B, Kannemeyer J, Galloway M, Kirsch RE, Smuts H (1997) Hepatitis C virus infection rate in volunteer blood donors from the western cape-comparison of screening tests and PCR. SAMJ 87:603–605
Vandenbroucke JP, von Elm E, Altman DG (2007) Strengthening the reporting of observational studies in epidemiology (STROBE): explanation and elaboration. Ann Intern Med 147:163–192
Vardas E, Ross MH, Sharp G, McAnerney J, Sim J (2002) Viral hepatitis in South African healthcare workers at increased risk of occupational exposure to blood-borne viruses. J Hosp Infect 50:6–12
Verbeeck J, Maes P, Lemey P, Pybus OG, Wollants E, Song E, Nevens F, Fevery J, Delport W, Van der Merwe S, Van Ranst M (2006) Investigating the origin and spread of hepatitis C virus genotype 5a. J Virol 80:4220–4226
Verbeeck J, Peigue-Lafeuille H, Stefan Ross R, Abergel A, Nevens F, Van Der Merwe S, Van Ranst M, Henquell C (2008) HCV genotype 5: epidemiology and spread of an uncommon genotype. J Clin Virol 41:170–171
Acknowledgments
Financial support for this study was provided by The Poliomyelitis Foundation Research Grant, South Africa (93718). Statistical analysis and help was provided by Professor Geoff Candy, Department of Surgery, WITS Medical School, Johannesburg.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Prabdial-Sing, N., Puren, A.J., Mahlangu, J. et al. Hepatitis C virus genotypes in two different patient cohorts in Johannesburg, South Africa. Arch Virol 153, 2049–2058 (2008). https://doi.org/10.1007/s00705-008-0227-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-008-0227-2