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Maunye TK, Gededzha MP, Blackard JT, Rakgole JN, Selabe SG. Hepatitis C Virus Genotype 5 Variability in Treatment-Naïve Patients in South Africa. Intervirology 2023; 66:77-87. [PMID: 37231989 PMCID: PMC10353306 DOI: 10.1159/000528178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/14/2022] [Indexed: 05/27/2023] Open
Abstract
INTRODUCTION Hepatitis C virus (HCV) genotype 5 was originally identified in South Africa, where it represents 35-60% of all HCV infections. There are limited data on resistance-associated variants (RAVs) in South Africa. Thus, we investigated variability within the NS3/NS4A, NS5A, and NS5B genes of treatment-naïve individuals with HCV genotype 5 infection at the Dr. George Mukhari Academic Hospital (DGMAH) in Pretoria, South Africa. METHODS Nested PCR was performed to amplify the NS3/4A, NS5A, and NS5B genes. RAVs were evaluated using the Geno2pheno tool. RESULTS In the NS3/4A gene, F56S and T122A were detected in one sample each. The D168E mutation was detected in 7 samples. Within the NS5A gene, the T62M mutation was detected in 2 individuals. In the NS5B gene, 8 of 12 individuals (67%) had the A421V mutation, while all 12 individuals (100%) had the S486A mutation. DISCUSSION RAVs were detected frequently among treatment-naïve individuals with HCV genotype 5 infection in South Africa. Thus, resistance testing may be prudent when initiating treatment of patients with genotype 5 infection. Additional population-based studies are needed to understand the prevalence of these RAVs during HCV genotype 5 infection.
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Affiliation(s)
- Tshegofatso K Maunye
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- National Health Laboratory Service, Pretoria, South Africa
| | - Maemu P Gededzha
- Department of Immunology, Faculty of Health Sciences, University of Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Jason T Blackard
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa,
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA,
| | - Johnny N Rakgole
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Selokela G Selabe
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- National Health Laboratory Service, Pretoria, South Africa
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Asselah T, Hassanein T, Waked I, Mansouri A, Dusheiko G, Gane E. Eliminating hepatitis C within low-income countries - The need to cure genotypes 4, 5, 6. J Hepatol 2018; 68:814-826. [PMID: 29229584 DOI: 10.1016/j.jhep.2017.11.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/01/2017] [Accepted: 11/13/2017] [Indexed: 12/19/2022]
Abstract
Around 70 to 100 million people are chronically infected with HCV worldwide. HCV antiviral drug development has revolutionised the treatment of HCV, with several direct-acting antiviral agents offering patients the chance of cure after only 8-12 weeks of treatment. Drug development was initially focussed on HCV genotype 1 (GT1) infection, since this was the most prevalent worldwide, although clinical trials included all genotypes prevalent in the US and Europe. Because the earliest in vitro assays utilised the GT1b and 2 replicons, the initial classes of direct-acting antivirals (protease inhibitors, non-nucleotide polymerase inhibitors) were GT1-specific, albeit they had an effect on other less prevalent genotypes. Epidemiological data has shown the regional importance of other HCV genotypes. More than 50% of all HCV infections around the globe are not with GT1. The prevalence of HCV genotype 4 (GT4), 5 (GT5), and 6 (GT6) is increasing in North America and Europe due to migration from the Middle East, Africa and South-East Asia. With the successful development of the multi and pan-genotypic non-structural protein 5A inhibitors, second generation protease inhibitors and nucleotide non-structural protein 5B inhibitors comes a unique opportunity to achieve global HCV elimination. The goal of this review is to summarise the available information pertaining to GT4, GT5 and GT6, with a specific focus on direct-acting antiviral agents.
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Affiliation(s)
- Tarik Asselah
- Centre de Recherche sur l'Inflammation, Viral Hepatitis INSERM UMR 1149, Université Paris Diderot, Department of Hepatology, AP-HP Hôpital Beaujon, Clichy, France.
| | - Tarek Hassanein
- Southern California GI and Liver Centers and Southern California Research Center, Coronado, CA, USA
| | - Imam Waked
- National Liver Institute, Menoufiya, Egypt
| | - Abdellah Mansouri
- Centre de Recherche sur l'Inflammation, Viral Hepatitis INSERM UMR 1149, Université Paris Diderot, Department of Hepatology, AP-HP Hôpital Beaujon, Clichy, France
| | - Geoffrey Dusheiko
- UCL Institute of Liver and Digestive Health, University College London Medical School, Kings College Hospital, London, UK
| | - Edward Gane
- Liver Unit, Auckland City Hospital, Auckland, New Zealand
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Prabdial-Sing N, Chirwa T, Thaver J, Smuts H, Vermeulen M, Suchard M, Puren AJ. Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008-2012. J Viral Hepat 2016; 23:881-888. [PMID: 27545625 DOI: 10.1111/jvh.12571] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/07/2016] [Indexed: 12/18/2022]
Abstract
There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease.
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Affiliation(s)
- N Prabdial-Sing
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa. .,Faculty of Health Sciences, Division of Virology and Communicable Diseases Surveillance, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
| | - T Chirwa
- Division of Epidemiology and Biostatistics, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - J Thaver
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - H Smuts
- Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | - M Vermeulen
- Donation Testing, South African National Blood Service, Roodepoort, South Africa
| | - M Suchard
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa.,Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A J Puren
- Faculty of Health Sciences, Division of Virology and Communicable Diseases Surveillance, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Centre for HIV and STI, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
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Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach. INFECTION GENETICS AND EVOLUTION 2016; 44:61-68. [DOI: 10.1016/j.meegid.2016.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 01/05/2023]
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Henquell C, Yameogo S, Sangaré L. First genome characterization of a novel hepatitis C virus genotype 5 variant. INFECTION GENETICS AND EVOLUTION 2016; 39:173-175. [PMID: 26807921 DOI: 10.1016/j.meegid.2016.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 12/14/2022]
Abstract
We report a new hepatitis C virus (HCV) genotype 5 variant from a woman living in Burkina Faso. Phylogenetic analysis of the near full-length genome sequence suggests that this isolate HCV5_BF16 could be the first reported strain belonging to a new HCV 5 subtype, distinct from the 5a subtype.
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Affiliation(s)
- Cécile Henquell
- CHU de Clermont-Ferrand, Laboratoire de Virologie, Centre National de Référence des Entérovirus et Parechovirus - Laboratoire Associé, 58 rue Montalembert, F-63003 Clermont-Ferrand, France; Université d'Auvergne, EA-4843, Faculté de Médecine, 28 place Henri Dunant, F-63000 Clermont-Ferrand, France.
| | - Saydou Yameogo
- CHU Yalgado, avenue du Capitaine Thomas Sankara, 03 BP7022 Ouagadougou, Burkina Faso
| | - Lassana Sangaré
- CHU Yalgado, avenue du Capitaine Thomas Sankara, 03 BP7022 Ouagadougou, Burkina Faso
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Khan N, Akmal M, Hayat M, Umar M, Ullah A, Ahmed I, Rahim K, Ali S, Bahadar S, Saleha S. Geographic distribution of hepatitis C virus genotypes in pakistan. HEPATITIS MONTHLY 2014; 14:e20299. [PMID: 25477975 PMCID: PMC4250967 DOI: 10.5812/hepatmon.20299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 08/19/2014] [Accepted: 09/02/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND Distribution of Hepatitis C Virus (HCV) genotypes may be changed over time. Epidemiological Studies on distribution patterns of HCV genotypes in Pakistani population might assist for better treatment options and preventive strategies. OBJECTIVES This study was conducted to determine distribution patterns of HCV genotypes in different geographical regions of Pakistan. PATIENTS AND METHODS In this cross-sectional study, 1818 randomly selected patients from different geographical regions of Pakistan, diagnosed with HCV infection by the third generation Enzyme Linked Immunosorbent Assay (ELISA), were included between April 2011 and December 2013. HCV RNA was detected in serum samples of patients by Reverse Transcription Polymerase Chain Reaction (RT- PCR) of the core region. Qualitative PCR was performed to determine viral load. HCV genotyping was performed by RT-nested PCR using type-specific primers of the core region. Frequency of different genotypes among patients was assessed according to gender, age and geographical region at the time of sampling. RESULTS Of 1818 HCV RNA positive samples, HCV genotypes PCR fragments were detected in 1552 (85.5%) samples. HCV genotype 3a was the predominant genotype (39.4%) followed by genotype 2a (24.93%). HCV genotype 3 was the predominant genotype in Punjab and Sindh regions, while genotype 2 was the most predominant genotype in Khyber Pakhtunkhwa region and the second predominant genotype after genotype 3 in Sindh region. The incidence of genotype 2a is increasing in our country with decrease in the incidence of genotype 3a. A higher incidence of HCV various genotypes were observed among male patients and those younger than 45 years. CONCLUSIONS This study may facilitate treatment options and preventive strategies in Pakistan.
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Affiliation(s)
- Nasar Khan
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Muhammad Akmal
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Muhammad Hayat
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Muhammad Umar
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Atta Ullah
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Iqbal Ahmed
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Kashif Rahim
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Sadar Ali
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Sulaiman Bahadar
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
| | - Shamim Saleha
- Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan
- Corresponding Author: Shamim Saleha, Department of Microbiology, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa Kohat, Pakistan. Tel: +92-252915545, Fax: +92-3339642532, E-mail:
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Identification of Indian sub-continent as hotspot for HCV genotype 3a origin by Bayesian evolutionary reconstruction. INFECTION GENETICS AND EVOLUTION 2014; 28:87-94. [PMID: 25224661 DOI: 10.1016/j.meegid.2014.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 09/04/2014] [Accepted: 09/06/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recent emphasis in Hepatitis C virus (HCV) evolutionary biology has focused on analysis using Core, E1/E2 and/or NS5b regions, with limited appreciation of full length genome. While HCV genotypes have been described as endemic in the Indian subcontinent, there has been no confirmation at the molecular evolutionary level of these genotypes. We have attempted here to determine the status of Indian HCV genotype 3a sequences in relation to similar genotypes from other parts of the world. METHODS Cloning, sequencing and molecular characterization was performed on 9 Indian sequences and comparative analyses were performed with 46 sequences from other countries. Evolutionary-rate and molecular-clock hypothesis testing was addressed by Bayesian MCMC. RESULTS Genetic analysis of full length genome revealed two hypervariable regions (HVR) in E2 region - HVR496 and HVR576, with a variable 5-8 amino-acid insertion sequence and a putative N-glycosylation site. Phylogenetic analysis revealed a divergence resulting in 2 distinct clades: clade-1 represented by HCV 3a subtype and clade-2 represented by other 3 subtype genomes. Clade-2 shows earlier divergence than clade-1. Analysis revealed that genotype 3a genomes from India roots out first (∼99 years ago) in clade1. Bayesian skyline plot analysis revealed an increase in effective number of infections from 1940s to 1990s, followed by a gradual decrease after 2000. CONCLUSIONS Genotype 3a sequences appear to have originated in India and later dispersed to United Kingdom around mid 1940s, most likely around the time of Indian independence and World War II.
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Choudhary MC, Gupta E, Pandey P, Natarajan V, Sharma S, Vashishtha C, Sharma MK, Kazim SN, Sarin SK. Identification and full-length molecular characterization of rare hepatitis C virus genotype 5a from India. Arch Virol 2014; 160:329-33. [PMID: 25193070 DOI: 10.1007/s00705-014-2220-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/28/2014] [Indexed: 12/13/2022]
Abstract
This report presents a molecular characterization of the complete genome of a rare hepatitis C virus (HCV) genotype (GT5a) from India. Sequence homology of full genome revealed that the strain belonged to HCV GT5a. To trace the origin of this virus and to understand its evolutionary pattern, a phylogenetic reconstruction was carried out on full HCV genome sequences using Bayesian coalescent methods. The phylogenetic tree reconstruction revealed genotypic divergence, with formation of distinct clades. This analysis revealed that HCV genotype 5 might have originated from HCV genotype 3, as they have a recent common ancestor.
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Affiliation(s)
- Manish Chandra Choudhary
- Department of Research, Institute of Liver and Biliary Sciences (ILBS), Vasant Kunj, New Delhi, 110070, India
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Prevalence of hepatitis C virus genotypes in district bannu, khyber pakhtunkhwa, pakistan. HEPATITIS RESEARCH AND TREATMENT 2014; 2014:165826. [PMID: 25093120 PMCID: PMC4100271 DOI: 10.1155/2014/165826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 06/09/2014] [Indexed: 12/17/2022]
Abstract
Determination of an individual's hepatitis C virus (HCV) genotypes prior to antiviral therapy has become increasingly important for the clinical management and prognosis of HCV infection. Therefore, this study was conducted to investigate the prevalence of HCV genotypes in HCV infected patients of district Bannu in Khyber Pakhtunkhwa region of Pakistan. Serum samples of 117 seropositive patients were screened for HCV-RNA by using reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) and then PCR positive samples were subjected to HCV genotyping. Out of 117 seropositive samples, 110 samples were found positive by PCR analysis. Genotype 3a was the most prevalent one detected in 38% of patients, followed by genotype 3b in 21% of patients, and then genotype 2a in 12% of patients. However 21% of HCV-PCR positive samples could not be genotyped by method used in this study. Genotype 3a was the most prevalent genotype in patients of all age groups and its prevalence was found high among patients with increasing age (>34 years). Moreover, genotypes 3a and 3b were found to be the most prevalent genotypes in patients with history of shaving by barbers, receiving multiple injections, and dental procedures. In conclusion there is need of further investigation of genotypes of HCV by using more sensitive assays and considering large sample size in district Bannu.
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10
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Hepatitis C virus genotype 5a subgenomic replicons for evaluation of direct-acting antiviral agents. Antimicrob Agents Chemother 2014; 58:5386-94. [PMID: 24982066 DOI: 10.1128/aac.03534-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus (HCV) exists as six major genotypes that differ in geographical distribution, pathogenesis, and response to antiviral therapy. In vitro replication systems for all HCV genotypes except genotype 5 have been reported. In this study, we recovered genotype 5a full-length genomes from four infected voluntary blood donors in South Africa and established a G418-selectable subgenomic replicon system using one of these strains. The replicon derived from the wild-type sequence failed to replicate in Huh-7.5 cells. However, the inclusion of the S2205I amino acid substitution, a cell culture-adaptive change originally described for a genotype 1b replicon, resulted in a small number of G418-resistant cell colonies. HCV RNA replication in these cells was confirmed by quantification of viral RNA and detection of the nonstructural protein NS5A. Sequence analysis of the viral RNAs isolated from multiple independent cell clones revealed the presence of several nonsynonymous mutations, which were localized mainly in the NS3 protein. These mutations, when introduced back into the parental backbone, significantly increased colony formation. To facilitate convenient monitoring of HCV RNA replication levels, the mutant with the highest replication level was further modified to express a fusion protein of firefly luciferase and neomycin phosphotransferase. Using such replicons from genotypes 1a, 1b, 2a, 3a, 4a, and 5a, we compared the effects of various HCV inhibitors on their replication. In conclusion, we have established an in vitro replication system for HCV genotype 5a, which will be useful for the development of pan-genotype anti-HCV compounds.
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Wantuck JM, Ahmed A, Nguyen MH. Review article: the epidemiology and therapy of chronic hepatitis C genotypes 4, 5 and 6. Aliment Pharmacol Ther 2014; 39:137-47. [PMID: 24251930 DOI: 10.1111/apt.12551] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 06/23/2013] [Accepted: 10/27/2013] [Indexed: 02/06/2023]
Abstract
BACKGROUND The global burden of hepatitis C (HCV) infection is mostly found in Africa, the Middle East and Asia, where HCV genotypes 4, 5 and 6 are common. The literature on these genotypes is sparse and this synopsis will review characteristics of patients infected with these genotypes. AIM To review characteristics of patients infected with HCV genotypes 4, 5 and 6. METHODS PubMed search for 'hepatitis C' AND 'genotype 4', 'hepatitis C' AND 'genotype 5', and 'hepatitis C' AND 'genotype 6' was conducted and relevant articles were reviewed. RESULTS Intravenous drug use is generally responsible for HCV genotype 4 infection in developed countries, but unsafe medical practices cause most cases of HCV genotypes 4, 5 and 6 in endemic countries. The sustained virological response (SVR) rate for patients with HCV genotype 4 who receive pegylated interferon and ribavirin for 48 weeks ranges from 40% to 70% in various small studies. The SVR rate is in the 60-70% range for HCV genotype 5 and 70-80% range for HCV genotype 6 following 48 weeks with pegylated interferon and ribavirin. Preliminary data suggest that a shorter course of 24 weeks of pegylated interferon and ribavirin may be acceptable for HCV genotype 6, with an SVR rate of approximately 70%. CONCLUSIONS The current standard-of-care therapy for HCV genotypes 4, 5 and 6 is pegylated interferon and ribavirin for 48 weeks. A shorter course with 24 weeks of therapy may be considered for patients with genotype 6. Newer and much more effective therapies may be forthcoming in the next few years.
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Affiliation(s)
- J M Wantuck
- Department of Medicine, Stanford University Medical Center, Palo Alto, CA, USA
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Gededzha MP, Selabe SG, Blackard JT, Kyaw T, Mphahlele MJ. Near full-length genome analysis of HCV genotype 5 strains from South Africa. INFECTION GENETICS AND EVOLUTION 2013; 21:118-23. [PMID: 24220189 DOI: 10.1016/j.meegid.2013.10.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/25/2013] [Accepted: 10/27/2013] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) genotype 5 is the predominant genotype in South Africa. However, to date, only 2 full-length genotype 5 genomes have been sequenced and only one is from South Africa. This study characterized HCV genotype 5 sequences from South Africa, including six near full-length genomes, as well as the E1 region from an additional 12 genotype 5 samples. Phylogenetic analysis of these near full-length genome sequences revealed that all genotype 5 sequences formed a close cluster with high bootstrap support. Bayesian analysis of the E1 region was used to estimate the time of the most recent common ancestor (tMRCA). The tMRCA for HCV genotype 5a was estimated at 114-134 years before the last sampling date. In conclusion, this study provides six near full-length genotype 5 nucleotide sequences for use as references to design efficient vaccines and for the development of new antiviral agents, and provides further insight into the diversity of HCV genotypes circulating in South Africa.
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Affiliation(s)
- Maemu P Gededzha
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
| | - Selokela G Selabe
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
| | - Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Thanda Kyaw
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
| | - M Jeffrey Mphahlele
- HIV and Hepatitis Research Unit, Department of Virology, University of Limpopo, Medunsa Campus/National Health Laboratory Service, Pretoria, South Africa.
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Rubio-Lezama MA, López-Alférez R, Santillán-Arreygue L, Romero-Figueroa M. [Hepatitis C virus genotype 5 in Mexico: a case report with successful treatment and a literature review]. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2013; 78:191-5. [PMID: 23972822 DOI: 10.1016/j.rgmx.2012.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/16/2012] [Accepted: 12/26/2012] [Indexed: 10/26/2022]
Abstract
Hepatitis C virus (HCV) genotype 5 is extremely rare and there is very little reported on its management in the medical literature. We present herein the case of a patient with HCV genotype 5 that presumably acquired the disease through a blood transfusion during infancy. Sustained virologic response was achieved after 24 weeks of treatment. According to the available information on HCV genotype 5 treatment, it has a similar response to that of HCV genotype 1. Our patient presented with various favorable outcome factors. There is much less reported on the treatment of HCV genotype 5 than there is regarding HCV genotypes 1, 2, 3, and 4. This is mainly due to the low prevalence of genotype 5 in the Mexican environment.
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Affiliation(s)
- M A Rubio-Lezama
- Coordinación Clínica de Educación e Investigación en Salud, Hospital General de Zona N.° 58 «General Manuel Ávila Camacho», Instituto Mexicano del Seguro Social, Tlalnepantla de Baz, Estado de México, México.
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Petruzziello A, Coppola N, Diodato AM, Iervolino V, Azzaro R, Di Costanzo G, Di Macchia CA, Di Meo T, Loquercio G, Pasquale G, Cacciapuoti C. Age and gender distribution of hepatitis C virus genotypes in the metropolitan area of Naples. Intervirology 2013; 56:206-12. [PMID: 23594735 DOI: 10.1159/000348506] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/22/2013] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To assess any time-related variations in the distribution of hepatitis C virus (HCV) genotypes in the metropolitan area of Naples, Italy. METHODS HCV genotypes were analysed in 255 HCV RNA-positive patients with chronic HCV infection, observed from 2009 to 2011, and compared with data pertaining to a sample of 176 HCV RNA-positive patients observed from 2006 to 2008. RESULTS In both periods of analysis, genotype 1b was predominant (51.8 and 48.3%, respectively), followed by genotype 2 (27.9 and 31.7%, respectively). These HCV genotypes were particularly prevalent in older patients, whereas genotypes 3a and 1a were observed more frequently in the younger population. Genotype 1b was particularly common in females compared to males in both study periods (39.3% of 89 males vs. 64.3% of 87 females in the 3-year period 2006-2008, p < 0.001; 41.5% of 118 males vs. 54.0% of 137 females in the period 2009-2011, p < 0.05). The prevalence of patients with genotype 1b in the age range 51-60 years was higher in the 2006-2008 period than in 2009-2011 (76.9 vs. 37.7%; p < 0.0005) and lower in the over 60 year olds (55.1 vs. 59.6%; p = 0.5). CONCLUSION Genotype 1b, historically the most prevalent in Italy, is still predominant; however, when comparing the two time periods, a cohort effect evidencing the increasing prevalence of genotype 1b among elderly patients was revealed.
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Affiliation(s)
- Arnolfo Petruzziello
- Laboratory of Virology and Molecular Biology 'V. Tridente', Transfusion Service, Department of Haematology, Istituto Nazionale Tumori, Fondazione G. Pascale, Naples, Italy.
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Identification of rare hepatitis C virus genotype 5a among Indian population. Virus Genes 2013; 47:152-5. [DOI: 10.1007/s11262-013-0905-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 03/14/2013] [Indexed: 10/27/2022]
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Prabdial-Sing N, Puren AJ, Bowyer SM. Sequence-based in silico analysis of well studied hepatitis C virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds. BMC Immunol 2012; 13:67. [PMID: 23227878 PMCID: PMC3552980 DOI: 10.1186/1471-2172-13-67] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/30/2012] [Indexed: 02/07/2023] Open
Abstract
Background Host genetics influence the outcome of HCV disease. HCV is also highly mutable and escapes host immunity. HCV genotypes are geographically distributed and HCV subtypes have been shown to have distinct repertoires of HLA-restricted viral epitopes which explains the lack of cross protection across genotypes observed in some studies. Despite this, immune databases and putative epitope vaccines concentrate almost exclusively on HCV genotype 1 class I-epitopes restricted by the HLA-A*02 allele. While both genotype and allele predominate in developed countries, we hypothesise that HCV variation and population genetics will affect the efficacy of proposed epitope vaccines in South Africa. This in silico study investigates HCV viral variability within well-studied epitopes identified in genotype 1 and uses algorithms to predict the immunogenicity of their variants from other less studied genotypes and thus rate the most promising vaccine candidates for the South African population. Six class I- and seven class II- restricted epitope sequences within the core, NS3, NS4B and NS5B regions were compared across the six HCV genotypes using local genotype 5a sequence data together with global data. Common HLA alleles in the South African population are A30:01, A02:01, B58:02, B07:02; DRB1*13:01 and DRB1*03:01. Epitope binding to 13 class I- and 8 class –II alleles were described using web-based prediction servers, Immune Epitope Database, (IEDB) and Propred. Online population coverage tools were used to assess vaccine efficacy. Results Despite the homogeneity of genotype 1 and genotype 5 over the epitopes, there was limited promiscuity to local HLA-alleles.Host differences will make a putative vaccine less effective in South Africa. Of the 6 well-characterized class I- epitopes, only 2 class I- epitopes were promiscuous and 3 of the 7 class-II epitopes were better conserved and promiscuous. By fine tuning the putative vaccine using an optimal cocktail of genotype 1 and 5a epitopes and local HLA data, the coverage was raised from 65.85% to 91.87% in South African Blacks. Conclusion While in vivo and in vitro studies are needed to confirm immunogenic epitopes, in silico HCV epitope vaccine design which takes into account HCV variation and host allele frequency will maximize population coverage in different ethnic groups.
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Affiliation(s)
- Nishi Prabdial-Sing
- Specialized Molecular Diagnostics, Hepatitis Unit, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.
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Antaki N, Abboud D, Antaki F, Craxi A. HCV genotype 5: an orphan virus. Antivir Ther 2012; 18:263-9. [PMID: 23111702 DOI: 10.3851/imp2449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2012] [Indexed: 12/23/2022]
Abstract
HCV genotype 5 (HCV-5) is the least known HCV genotype. It is found mainly in South Africa and in restricted areas of Belgium, Spain, France, Syria and Greece. Sporadic cases are reported worldwide. The main modes of transmission are blood transfusion and iatrogenic causes. Little is known about its origin, but various studies have elucidated its spread worldwide. In endemic areas, patients infected with HCV-5 are on average older and have a higher viral load and more advanced fibrosis than those infected with non-HCV-5 genotypes.The current standard of care for HCV-5 chronic infection is 48 weeks of dual therapy with pegylated interferon plus ribavirin. 'Favourable' Il28B polymorphisms are not associated with higher sustained viral response rates. Assessment of shorter duration of therapy is made difficult by the lack of identifiable baseline predictors of response. Whilst there are in vitro data showing good activity of some direct-acting antivirals and of host-targeted agents against HCV-5, no clinical trials of these molecules have yet started.
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Affiliation(s)
- Nabil Antaki
- Department of Gastroenterology and Hepatology, Saint Louis Hospital, Aleppo, Syria.
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Karatapanis S, Tsoplou P, Papastergiou V, Vasiageorgi A, Stampori M, Saitis I, Tsitsopoulos E, Lisgos P, Skorda L, Ketikoglou I, Goulis I. Hepatitis C virus genotyping in Greece: unexpected high prevalence of genotype 5a in a Greek island. J Med Virol 2012; 84:223-8. [PMID: 22170541 DOI: 10.1002/jmv.22249] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hepatitis C virus (HCV) genotype 5 (G5) is a rare genotype reported mainly in South Africa. However, increasing data suggest the sporadic presence of this genotype in different European countries. To assess the epidemiology of HCV-G5 in Greece, genotyping was performed in 973 consecutive patients infected with HCV, referred to 7 hepatology centers throughout Greece, from January 2005 to December 2009. Genotype 5a (19 patients, 1.9%) was the fifth most prevalent genotype after genotype 1 (408 patients, 41.9%), genotype 3 (318 patients, 32.7%), genotype 4 (158 patients, 16.2%), and genotype 2 (70 patients, 7.2%). The majority of patients infected with G5 (16/19,84.2%) were referred to the General Hospital of Rhodes, an island in south-east Greece. The HCV genotype distribution in that particular island, indicates a particularly high G5 prevalence of 12.8%, after genotype 1 (40%), genotype 3 (28%), and genotype 4 (15%). Among the patients from Rhodes infected with G5 (n = 16), 13 (81.2%) were females. The mean age was 62.3 ± 6.5 years, significantly older than the patients infected with other HCV genotypes (mean age 40.6 ± 7.2, P < 0.0001). Nine out of the 16 cases (56.2%) presented features of high pre-treatment viral loads. Advanced liver fibrosis (Metavir F3-F4) was found in four out of five performed liver biopsies. Ten patients received treatment with pegylated interferon plus ribavirin and a sustained viral response were achieved in six cases. The source of infection is unknown but parenteral iatrogenic routes of transmission seem to have contributed significantly to the spread of genotype 5a in this region.
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Gededzha MP, Selabe SG, Kyaw T, Rakgole JN, Blackard JT, Mphahlele MJ. Introduction of new subtypes and variants of hepatitis C virus genotype 4 in South Africa. J Med Virol 2012; 84:601-7. [PMID: 22337299 DOI: 10.1002/jmv.23215] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hepatitis C virus (HCV) genotype is an important predictor of disease progression and treatment response. This descriptive study investigated the sequence diversity and genotypes of HCV in South Africa based on comparative analysis of the 5' untranslated region (UTR), C/E1, and NS5B regions of 60 sequences from 52 patients. Genotype distribution in the studied population was as follows: 54% (28/52) were genotype 5, 19% (10/52) were genotype 1, 19% (10/52) were genotype 4, and 2% (1/52) were genotype 3. Three of 52 (6%) individuals were infected with multiple genotypes based on the 5'UTR. Phylogenetic analysis of the 5'UTR was accurate in determining genotypes, while the C/E1 and NS5B coding region was able to differentiate both genotypes and subtypes, including an outlier group. Furthermore, this study observed the existence of distinct variants of HCV which were divergent from confirmed genotype 4 subtypes. For the first time in South Africa, this analysis has shown the presence of HCV subtypes 4k, 4q, and 4r, as well as evidence of intragenotypic recombinant 4l/4q within NS5B. In conclusion, while genotype 5a remains the predominant genotype in South Africa, the current study indicates the introduction of new subtypes and existence of variants of genotype 4 in South Africa.
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Affiliation(s)
- Maemu P Gededzha
- Department of Virology, Medunsa Campus, University of Limpopo/NHLS Dr George Mukhari Tertiary Laboratory, Pretoria, South Africa
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Nakano T, Lau GMG, Lau GML, Sugiyama M, Mizokami M. An updated analysis of hepatitis C virus genotypes and subtypes based on the complete coding region. Liver Int 2012; 32:339-45. [PMID: 22142261 DOI: 10.1111/j.1478-3231.2011.02684.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 10/09/2011] [Indexed: 12/23/2022]
Abstract
BACKGROUND The hepatitis C virus (HCV) genomic database is expanding rapidly. AIMS There is a need to provide an updated phylogenetic tree analysis based on the complete coding region of HCV. METHODS All available HCV complete genome sequences in the HCV databases available through October 2010 were analyzed. RESULTS The assignment of all known complete sequences up-to-date confirmed the previous six major genotypes and one new sequence, which have been provisionally assigned as subtype 7a. New recombinant forms of HCV, although uncommon, have been detected and were found to have different crossover points. CONCLUSION This updated analysis based on the complete region of HCV confirmed the validity of the previously assigned genotypes/subtypes and provided an up-to-date reference for future basic research and clinical studies.
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Affiliation(s)
- Tatsunori Nakano
- Department of Internal Medicine, Fujita Health University Nanakuri Sanatorium, Mie, Japan
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Hepatitis C virus infection in the Middle East and North Africa "MENA" region: injecting drug users (IDUs) is an under-investigated population. Infection 2012; 40:1-10. [PMID: 22237470 DOI: 10.1007/s15010-011-0236-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/08/2011] [Indexed: 01/06/2023]
Abstract
PURPOSE Investigation of the injecting drug users (IDUs) population is becoming extremely critical and timely in light of the recent evidence that IDUs now act as the core of hepatitis C virus (HCV) epidemics in developed countries. The purpose of this article, therefore, is not only to review the epidemiology of HCV in the Middle East and North Africa (MENA) region, but also to see whether IDUs were adequately studied and whether harm reduction strategies to be applied for their protection have been set. METHODS A literature review was carried out of articles published within the last decade on HCV infection. RESULTS The gathered data showed that the population of IDUs is severely under-investigated throughout the whole region, possibly due to religious and cultural impediments. CONCLUSION In order to reduce the risk of HCV infection in IDUs, a set of recommendations are advanced emphasizing the urgent need for bio-behavioral studies in this population in order to help identify the source and mode of transmission and the genotypes of HCV involved. These results may allow the development of effective and, yet, socially acceptable intervention strategies. We believe that the role which IDUs play in sustaining HCV infection is also an under-investigated topic in many developing countries. Similar reviews and, hence, interventions should be initiated in these regions.
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D'Heygere F, George C, Van Vlierberghe H, Decaestecker J, Nakad A, Adler M, Delwaide J, Laureys A, Nevens F. Efficacy of interferon-based antiviral therapy in patients with chronic hepatitis C infected with genotype 5: a meta-analysis of two large prospective clinical trials. J Med Virol 2011; 83:815-9. [PMID: 21412790 DOI: 10.1002/jmv.22049] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The characteristics and response rate to pegylated interferon and ribavirin (PEG-INF + RBV) of patients with chronic hepatitis C infected with genotype 5 are poorly documented. A meta-analysis of two large phase III/IV prospective randomized clinical trials conducted in Belgium in patients with chronic hepatitis C (n = 1,073 patients) was performed in order to compare the response to antiviral therapy of hepatitis C virus (HCV) genotype 5 with that of other HCV genotypes. A subset of HCV-1 infected patients selected from within the study database were selected to match the HCV-5 sample for known prognostic factors. In Belgium HCV-5 is responsible for a significant minority of cases of chronic hepatitis C CHC (4.5%) and is characterized by a more advanced age (58.4 years), a high frequency of cirrhosis (27.7%), a specific mode of HCV acquisition, and a particular geographic origin (66.7% of patients from West Flanders). The primary comparative analysis showed that response to treatment with PEG-INF + RBV of HCV-5 is similar to HCV-1 and lower compared to HCV-2/3. The analysis of the matched patient subgroup demonstrates that the HCV-5 "intrinsic sensitivity" to PEG-IFN + RBV therapy is identical to HCV-1, with a sustained virological response of 55% in both groups. In contrast to previous publications, this meta-analysis suggests that HCV-5 response to treatment is closer to HCV-1 than to HCV-2/3 and suggests that in Belgium HCV-5 infection should be treated with the same antiviral regimen as HCV-1.
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Cornberg M, Razavi HA, Alberti A, Bernasconi E, Buti M, Cooper C, Dalgard O, Dillion JF, Flisiak R, Forns X, Frankova S, Goldis A, Goulis I, Halota W, Hunyady B, Lagging M, Largen A, Makara M, Manolakopoulos S, Marcellin P, Marinho RT, Pol S, Poynard T, Puoti M, Sagalova O, Sibbel S, Simon K, Wallace C, Young K, Yurdaydin C, Zuckerman E, Negro F, Zeuzem S. A systematic review of hepatitis C virus epidemiology in Europe, Canada and Israel. Liver Int 2011; 31 Suppl 2:30-60. [PMID: 21651702 DOI: 10.1111/j.1478-3231.2011.02539.x] [Citation(s) in RCA: 304] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIM Decisions on public health issues are dependent on reliable epidemiological data. A comprehensive review of the literature was used to gather country-specific data on risk factors, prevalence, number of diagnosed individuals and genotype distribution of the hepatitis C virus (HCV) infection in selected European countries, Canada and Israel. METHODOLOGY Data references were identified through indexed journals and non-indexed sources. In this work, 13,000 articles were reviewed and 860 were selected based on their relevance. RESULTS Differences in prevalence were explained by local and regional variances in transmission routes or different public health measures. The lowest HCV prevalence (≤ 0.5%) estimates were from northern European countries and the highest (≥ 3%) were from Romania and rural areas in Greece, Italy and Russia. The main risk for HCV transmission in countries with well-established HCV screening programmes and lower HCV prevalence was injection drug use, which was associated with younger age at the time of infection and a higher infection rate among males. In other regions, contaminated glass syringes and nosocomial infections continue to play an important role in new infections. Immigration from endemic countries was another factor impacting the total number of infections and the genotype distribution. Approximately 70% of cases in Israel, 37% in Germany and 33% in Switzerland were not born in the country. In summary, HCV epidemiology shows a high variability across Europe, Canada and Israel. CONCLUSION Despite the eradication of transmission by blood products, HCV infection continues to be one of the leading blood-borne infections in the region.
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Affiliation(s)
- Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
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Henquell C, Guglielmini J, Verbeeck J, Mahul A, Thibault V, Lebray P, Laperche S, Trimoulet P, Foucher J, Le Guillou-Guillemette H, Fouchard-Hubert I, Legrand-Abravanel F, Métivier S, Gaudy C, D’Alteroche L, Rosenberg AR, Podevin P, Plantier JC, Riachi G, Saoudin H, Coppere H, André E, Gournay J, Feray C, Vallet S, Nousbaum JB, Baazia Y, Roulot D, Alain S, Loustaud-Ratti V, Schvoerer E, Habersetzer F, Pérez-Serra RJ, Gourari S, Mirand A, Odent-Malaure H, Garraud O, Izopet J, Bommelaer G, Peigue-Lafeuille H, van Ranst M, Abergel A, Bailly JL. Evolutionary history of hepatitis C virus genotype 5a in France, a multicenter ANRS study. INFECTION GENETICS AND EVOLUTION 2011; 11:496-503. [DOI: 10.1016/j.meegid.2010.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 12/22/2010] [Accepted: 12/29/2010] [Indexed: 01/01/2023]
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Elasifer HA, Agnnyia YM, Al-Alagi BA, Daw MA. Epidemiological manifestations of hepatitis C virus genotypes and its association with potential risk factors among Libyan patients. Virol J 2010; 7:317. [PMID: 21073743 PMCID: PMC2993674 DOI: 10.1186/1743-422x-7-317] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 11/13/2010] [Indexed: 12/23/2022] Open
Abstract
Background The information on hepatitis C virus genotypes and subtypes among Libyan population and its association with various risk factors is not known. The objectives of this study were to determine the epidemiological manifestations of HCV genotypes among Libyan patients and their association with certain potential risk factors. Methods A total of 1240 of HCV infected patients registered at Tripoli Medical Centre were studied in five years period from January 2005 to October 2009. The information were reviewed and the data were collected. A sample from each patient (785 male; 455 female) was analysed for genotyping and sub-typing using specific genotyping assay. The information was correlated with the risk factors studied and the statistical data were analyzed using SPSS version 11.5. Results Off the total patients studied, four different genotypes were reported, including genotypes 1, 2, 3, and 4. Genotype4 was the commonest (35.7%), followed by genotype1 (32.6%). According to subtypes 28% were unclassified genotype 4, 14.6% were genotype 1b and some patients infected with more than one subtype (2.3% genotype 4c/d, 1% genotype 2a/c). Genotypes 1 was the commonest among males, while genotype 4 among females. According to the risk factors studied, Genotype1 and genotype 4 were found with most of the risk factors. Though they were particularly evident surgical intervention, dental procedures and blood transfusion while genotype 1 was only followed by genotype 3 mainly which mainly associated with certain risk groups such as intravenous drug abusers. Conclusion Here in we report on a detailed description of HCV genotype among Libyans. The most common genotype was type 4 followed by genotype 1, other genotypes were also reported at a low rate. The distribution of such genotypes were also variable according to gender and age. The commonly prevalent genotypes found to be attributable to the medical -related transmission of HCV, such as blood, surgery and dental procedures when compared with other risk factors. This however, raises an alarming signal on the major steps to be taken to reduce such infection in Libya
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Affiliation(s)
- Hana A Elasifer
- Department of Medical Microbiology & Immunology, Faculty of Medicine and Department of Infectious Diseases Tripoli Medical Centre, Tripoli-Libya
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Abstract
Hepatitis C (HCV) is the disease that has affected around 200 million people globally. HCV is a life threatening human pathogen, not only because of its high prevalence and worldwide burden but also because of the potentially serious complications of persistent HCV infection. Chronicity of the disease leads to cirrhosis, hepatocellular carcinoma and end-stage liver disease. HCV positive hepatocytes vary between less than 5% and up to 100%, indicating the high rate of replication of viral RNA. HCV has a very high mutational rate that enables it to escape the immune system. Viral diversity has two levels; the genotypes and Quasiaspecies. Major HCV genotypes constitute genotype 1, 2, 3, 4, 5 and 6 while more than 50 subtypes are known. All HCV genotypes have their particular patterns of geographical distribution and a slight drift in viral population has been observed in some parts of the globe.
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Affiliation(s)
- Nazish Bostan
- Department of Biological Sciences, Quaid-i-Azam University, Islamabad-45320, Pakistan
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Antaki N, Craxi A, Kamal S, Moucari R, Van der Merwe S, Haffar S, Gadano A, Zein N, Lai CL, Pawlotsky JM, Heathcote EJ, Dusheiko G, Marcellin P. The neglected hepatitis C virus genotypes 4, 5 and 6: an international consensus report. Liver Int 2010; 30:342-55. [PMID: 20015149 DOI: 10.1111/j.1478-3231.2009.02188.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract Hepatitis C virus (HCV) genotypes 4, 5 and 6 represent >20% of all HCV cases worldwide. HCV-4 is mainly seen in Egypt, where it represents 90% of all HCV cases. Antischistosomal therapy was the main cause of contamination there, followed by procedures performed by informal providers and traditional healers such as dental care, wound treatment, circumcision, deliveries, excision and scarification. It is also highly prevalent in sub-Saharan Africa and in the Middle East. In Europe, its prevalence has recently increased particularly among intravenous drug users and in immigrants. HCV-5 is mainly found in South Africa, where it represents 40% of all HCV genotypes, but four pockets of HCV-5 were found in France, Spain, Syria and Belgium and sporadic cases were found elsewhere. The mode of transmission is mainly iatrogenic and transfusion. HCV-6 is found in Hong Kong, Vietnam, Thailand and Myanmar and also in American and Australian from Asian origin. The response to treatment in HCV-4 is intermediate between HCV-1 and HCV-2 and HCV-3. A sustained viral response is achieved in 43-70% with pegylated interferon and ribavirin. It is higher in Egyptians than Europeans and Africans and is negatively related to insulin resistance and to the severity of fibrosis. It increases to >80% with 24 weeks of therapy only if a rapid virological response is achieved. In HCV-5, a sustained virological response is achieved in >60% with 48 weeks of therapy. HCV-6 is also considered an easy-to-treat genotype, leading to a response in 60-85% of cases.
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Affiliation(s)
- Nabil Antaki
- Department of Gastroenterology and Hepatology, Saint Louis Hospital, Aleppo, Syria.
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Pizzillo P, Almasio PL, Ferraro D, Craxì A, Di Stefano R. HCV genotypes in Sicily: Is there any evidence of a shift? J Med Virol 2009; 81:1040-6. [DOI: 10.1002/jmv.21498] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Ribeiro LC, Souto FJD, do Espírito-Santo MP, G-Oliveira R, Lampe E. An autochthonous case of hepatitis C virus genotype 5a in Brazil: phylogenetic analysis. Arch Virol 2009; 154:665-70. [DOI: 10.1007/s00705-008-0279-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 11/11/2008] [Indexed: 10/21/2022]
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Demetriou VL, van de Vijver DAMC, Kostrikis LG. Molecular epidemiology of hepatitis C infection in Cyprus: evidence of polyphyletic infection. J Med Virol 2009; 81:238-48. [PMID: 19107977 DOI: 10.1002/jmv.21370] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The genetic diversity of the hepatitis C virus (HCV) in Cyprus is investigated for the first time in this study. Nucleotide sequence analysis of the CORE-E1 and NS5B regions of the HCV genome was performed on blood plasma samples obtained from 77 HCV patients in Cyprus, collected during 2005-2008. The amplified products were sequenced and compared to reference HCV strains of known genotype and subtype in order to classify the isolates found in this study. Genotype could be determined for all strains, and subtype for all but four isolates. Phylogenetic analysis revealed that 51 patients were genotype 1, of which 38 were subtype 1b, 9 were 1a, and 1 was unclassified, one patient was genotype 2c, 13 were genotype 3a, nine were genotype 4, of which six were subtype 4a, and three were of unclassified subtype, one was genotype 5a, two patients seem to carry a possible 2k/1b recombinant strain, and no genotype 6 strains were found. This study demonstrated a genetic heterogeneity of HCV infection in Cyprus, with five of the six known HCV genotypes on the island, including unclassified isolates in genotypes 1 and 4, and also the apparent introduction of the 2k/1b recombinant strain in intravenous drug users.
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Jensen T, Gottwein J, Scheel T, Hoegh A, Eugen‐Olsen J, Bukh J. Highly Efficient JFH1‐Based Cell‐Culture System for Hepatitis C Virus Genotype 5a: Failure of Homologous Neutralizing‐Antibody Treatment to Control Infection. J Infect Dis 2008; 198:1756-65. [DOI: 10.1086/593021] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Koletzki D, Dumont S, Vermeiren H, Peixe P, Nina J, Camacho RJ, Stuyver LJ. Full genome sequence of three isolates of hepatitis C virus subtype 4b from Portugal. Arch Virol 2008; 154:127-32. [PMID: 19050819 DOI: 10.1007/s00705-008-0270-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 11/09/2008] [Indexed: 02/05/2023]
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Prabdial-Sing N, Puren AJ, Mahlangu J, Barrow P, Bowyer SM. Hepatitis C virus genotypes in two different patient cohorts in Johannesburg, South Africa. Arch Virol 2008; 153:2049-58. [DOI: 10.1007/s00705-008-0227-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 09/24/2008] [Indexed: 12/24/2022]
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Gottwein JM, Bukh J. Cutting the gordian knot-development and biological relevance of hepatitis C virus cell culture systems. Adv Virus Res 2008; 71:51-133. [PMID: 18585527 DOI: 10.1016/s0065-3527(08)00002-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Worldwide approximately 180 million people are chronically infected with hepatitis C virus (HCV). HCV isolates exhibit extensive genetic heterogeneity and have been grouped in six genotypes and various subtypes. Additionally, several naturally occurring intergenotypic recombinants have been described. Research on the viral life cycle, efficient therapeutics, and a vaccine has been hampered by the absence of suitable cell culture systems. The first system permitting studies of the full viral life cycle was intrahepatic transfection of RNA transcripts of HCV consensus complementary DNA (cDNA) clones into chimpanzees. However, such full-length clones were not infectious in vitro. The development of the replicon system and HCV pseudo-particles allowed in vitro studies of certain aspects of the viral life cycle, RNA replication, and viral entry, respectively. Identification of the genotype 2 isolate JFH1, which for unknown reasons showed an exceptional replication capability and resulted in formation of infectious viral particles in the human hepatoma cell line Huh7, led in 2005 to the development of the first full viral life cycle in vitro systems. JFH1-based systems now enable in vitro studies of the function of viral proteins, their interaction with each other and host proteins, new antivirals, and neutralizing antibodies in the context of the full viral life cycle. However, several challenges remain, including development of cell culture systems for all major HCV genotypes and identification of other susceptible cell lines.
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Affiliation(s)
- Judith M Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
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HCV genotype 5: Epidemiology and spread of an uncommon genotype. J Clin Virol 2008; 41:170-1. [DOI: 10.1016/j.jcv.2007.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 11/01/2007] [Indexed: 02/05/2023]
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Esteban JI, Sauleda S, Quer J. The changing epidemiology of hepatitis C virus infection in Europe. J Hepatol 2008; 48:148-62. [PMID: 18022726 DOI: 10.1016/j.jhep.2007.07.033] [Citation(s) in RCA: 334] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 07/30/2007] [Indexed: 02/07/2023]
Abstract
The epidemic of hepatitis C virus (HCV) infection in Europe is continuously evolving and epidemiological parameters (prevalence, incidence, disease transmission patterns and genotype distribution) have changed substantially during the last 15 years. Four main factors contribute to such changes: increased blood transfusion safety, improvement of healthcare conditions, continuous expansion of intravenous drug use and immigration to Europe from endemic areas. As a result, intravenous drug use has become the main risk factor for HCV transmission, prevalent infections have increased and genotype distribution has changed and diversified. Hence, prevalence data from studies conducted a decade ago may not be useful to estimate the current and future burden of HCV infection and additional epidemiological studies should be conducted, as well as new preventive strategies implemented to control the silent epidemic. This review summarizes recently published data on the epidemiology of HCV infection in Europe focusing on the factors currently shaping the epidemic.
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Affiliation(s)
- Juan I Esteban
- Liver Unit, Department of Medicine, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain.
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Abergel A, Ughetto S, Dubost S, Bonny C, Aublet-Cuvelier B, Delarocque-Astagneau E, Bailly JL, Bommelaer G, Casanova S, Delteil J, Deny P, Laurichesse H, Odent-Malaure H, Roussel J, Peigue-Lafeuille H, Henquell C. The epidemiology and virology of hepatitis C virus genotype 5 in central France. Aliment Pharmacol Ther 2007; 26:1437-46. [PMID: 17900267 DOI: 10.1111/j.1365-2036.2007.03530.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND We previously reported high prevalence of hepatitis C virus genotype 5a (HCV 5) (14%) in Central France. AIM To identify the risk factors associated with HCV5 infection and to characterize local HCV5 lineages. METHOD A case-control study and phylogenetic analysis were conducted. RESULTS In all, 131 HCV5 and 343 HCV non 5 infected patients were enrolled. No HCV5 patient was born in sub-Saharan Africa and only two were injection drug user. HCV5 contamination was associated with living in a rural area called Vic le Comte (VLC) in non-transfused patients (OR = 17.7), with transfusion in patients living outside VLC (OR = 3.8) and with receiving injections in patients from VLC (OR = 3.1). More than 80% of the patients from outside VLC were contaminated by transfusion and those from VLC mainly by an iatrogenic factor - injections performed before 1972 by the local physician. Phylogenetic analysis of HCV5 isolates evidenced no distinct genetic cluster, but close relationships between the isolates of spouse pairs and between blood donors and recipients. CONCLUSIONS Our results suggest that HCV5 spread in our district by iatrogenic route before 1972 and then via transfusion to the whole district. Collaborative studies are underway to study viral sequences from different parts of Africa and Europe to estimate the origin of our HCV 5a strains.
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Affiliation(s)
- A Abergel
- CHU de Clermont-Ferrand, Service d'Hépato-Gastro-Entérologie, Hôtel-Dieu, Clermont-Ferrand, France.
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38
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Bonny C, Fontaine H, Poynard T, Hézode C, Larrey D, Marcellin P, Bourlière M, Bronowicki JP, Merle P, Zarski JP, Sapey T, Guillemard C, Ughetto S, Henquell C, Nicolas C, Roche C, Randl K, Bommelaer G, Abergel A. Effectiveness of interferon plus ribavirin combination in the treatment of naive patients with hepatitis C virus type 5. A French multicentre retrospective study. Aliment Pharmacol Ther 2006; 24:593-600. [PMID: 16907892 DOI: 10.1111/j.1365-2036.2006.03018.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AIM To assess the rate of sustained virological response in naïve hepatitis C virus-type 5 patients treated by standard interferon or pegylated-interferon [corrected] (peg-interferon) and ribavirin combination for 48 weeks. PATIENTS AND METHODS A total of 87 hepatitis C virus patients were included from 12 centres in France; 28 patients received interferon plus ribavirin and 59 were treated with peg-interferon plus ribavirin. RESULTS Baseline characteristics were: mean age 58 +/- 11 years, sex ratio 1, 66% had metavir fibrosis score >or=F2, 21% were cirrhotics and 53% had pretherapeutic viral load >or=800,000 IU/mL. Sustained virological response was achieved in 64% and 58% of hepatitis C virus-5 patients treated with interferon and peg-interferon, respectively (NS). In adherent patients, sustained virological response was obtained in 75% of patients. Sustained virological response in hepatitis C virus-5 patients (60%) was significantly higher than sustained virological response in hepatitis C virus-1 patients (37%) (P = 0.0499) and not significantly different from sustained virological response in hepatitis C virus-2-3 patients (63%) (P = 0.8098). CONCLUSIONS Combination therapy is effective in 60% of hepatitis C virus-5-infected patients. Sustained virological response seems better in hepatitis C virus-5 patients than in hepatitis C virus-1 patients, and is similar to that of hepatitis C virus-2-3 patients. More studies are needed to determine optimal duration of treatment in hepatitis C virus-5 patients.
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Affiliation(s)
- C Bonny
- Service d'Hépato-Gastroentérologie, Hôtel-Dieu, Clermont-Ferrand, France.
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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. Investigating the origin and spread of hepatitis C virus genotype 5a. J Virol 2006; 80:4220-6. [PMID: 16611881 PMCID: PMC1472033 DOI: 10.1128/jvi.80.9.4220-4226.2006] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 01/16/2006] [Indexed: 02/07/2023] Open
Abstract
Epidemiological and phylogenetic studies of hepatitis C virus (HCV) have identified six major HCV genotypes and have attempted to characterize their origin and spread worldwide. Putative regions of endemic infection have been identified for all HCV genotypes except HCV genotype 5a. Although HCV genotype 5a was previously thought to be largely restricted to the northern part of South Africa, this study reports an unexpected cluster of the genotype in West Flanders Province in Belgium. To investigate the molecular epidemiology of this cluster and of HCV genotype 5a in general, a rigorous phylogenetic analysis of Belgian and South African HCV genotype 5a samples was performed. Remarkably, the Belgian and South African strains form two distinct clusters of similar diversity. We used a Bayesian coalescent method to estimate the rate of virus spread through time for HCV genotype 5a in both regions. Our results indicate that HCV genotype 5a strains have been spreading independently in Belgium and South Africa for more than 100 years, with a rate of spread characteristic of an epidemic genotype. These findings have major implications for tracing the origin of HCV genotype 5a. Here, we speculate about the possible origins of these clusters.
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Affiliation(s)
- Jannick Verbeeck
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, BE-3000 Leuven, Belgium
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Verbeeck J, Maes P, Wollants E, Van der Merwe S, Song E, Nevens F, Van Ranst M. Use of a commercially available line probe assay for genotyping of hepatitis C virus 5a strains. J Clin Microbiol 2006; 43:6117-9. [PMID: 16333107 PMCID: PMC1317178 DOI: 10.1128/jcm.43.12.6117-6119.2005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To validate a commercially available line probe assay for samples containing the infrequently found hepatitis C virus (HCV) genotype 5a, we sequenced a 511-nucleotide fragment of the NS4b region of Belgian and South African HCV genotype 5a samples. Phylogenetic analysis of the sequence data was performed. For the 77 HCV genotype 5a samples collected, there was 100% concordance between the genotype assignment by the line probe assay and the genotyping based on nucleotide sequencing, despite sequence heterogeneity in the probe binding sites of some samples.
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Affiliation(s)
- Jannick Verbeeck
- Laboratory of Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Thomas F, Nicot F, Sandres-Sauné K, Dubois M, Legrand-Abravanel F, Alric L, Peron JM, Pasquier C, Izopet J. Genetic diversity of HCV genotype 2 strains in South Western France. J Med Virol 2006; 79:26-34. [PMID: 17133555 DOI: 10.1002/jmv.20765] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of chronic hepatitis and liver disease worldwide. The genetic heterogeneity of HCV and its spread among infected patients can be examined accurately by nucleotide sequencing. The diversity of HCV genotype 2 strains (HCV-2) was studied in a large cohort of patients in the Midi Pyrénées area of southern France. Phylogenetic analysis was performed on 344 NS5B sequences from patients infected with HCV-2. These included 145 strains whose E2 region was also analyzed, and epidemiological data were collected for the corresponding patients. HCV-2 accounts for 11.3% of HCV infections in this area. Phylogenetic analysis of NS5B sequences revealed eight subtypes, while that of the E2 region provided congruent results for 100% of strains. The most frequent subtypes were 2i (24.7%), 2k (22.4%) 2c (17.4%), and 2a (10.8%). The mean age of HCV-2-infected patients was 55.5 years. Epidemiological data showed that blood transfusion is the major route of infection, but it was not associated with any particular subtype. By contrast, intravenous drug users were infected predominantly with genotype 2a. HCV-2a-infected patients were younger than patients infected with other subtypes (48 vs. 56.5 years, P < 0.01). This study shows substantial genetic diversity of HCV-2 subtypes in the south of France and the spread of 2a strains via intravenous drug users.
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Affiliation(s)
- Fabienne Thomas
- Service de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse Cedex, France
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Delwaide J, Gerard C, Reenaers C, Vaira D, Bastens B, Bataille C, Servais B, Maes B, Belaiche J, Hepatotropes GLDDV. Hepatitis C virus genotype 5 in southern belgium: epidemiological characteristics and response to therapy. Dig Dis Sci 2005; 50:2348-51. [PMID: 16416187 DOI: 10.1007/s10620-005-3060-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2004] [Accepted: 04/11/2005] [Indexed: 01/02/2023]
Abstract
Data are scarce on patients infected with hepatitis C virus of genotype 5, due to the low prevalence of this genotype around the world. To better define the characteristics of these patients, we reviewed the files of 16 genotype 5 patients. Mean age was 38 +/- 14. All patients were of European origin. Most of them (75%) had been contaminated by transfusion within a short time period (between 1980 and 1991). There were no intravenous drug addicts. Seven patients received treatment. One patient did not respond to interferon (IFN) monotherapy. Of four patients treated with IFN and ribavirin, three became sustained viral responders. Two patients treated with pegylated IFN and ribavirin became sustained viral responders. In our region, genotype 5 patients seem to have been contaminated within a relatively short time period. Treatment with IFN or pegylated IFN and ribavirin gave a high rate (83%) of sustained viral responses.
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Affiliation(s)
- Jean Delwaide
- Department of Hepato-Gastroenterology, CHU Sart Tilman, Liège, Belgium.
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Abstract
Infection with hepatitis C virus (HCV) genotypes 1, 2, or 3 is widely distributed throughout the world and has been the focus of the majority of studies on the epidemiology and treatment of chronic hepatitis C. Infection with HCV genotypes 4 through 9 is prevalent in some geographic areas where the disease burden of chronic hepatitis C approaches endemic levels (eg, HCV genotype 4 in Egypt where there is an HCV infection prevalence of approximately 18%). This article reviews the existing literature, which suggests that chronic hepatitis C with genotypes 4 through 9 may exhibit epidemiologic, clinical, and treatment outcome differences from infection with genotypes 1, 2, or 3.
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Affiliation(s)
- Mindie H Nguyen
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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