1
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Vo-Quang E, Pawlotsky JM. 'Unusual' HCV genotype subtypes: origin, distribution, sensitivity to direct-acting antiviral drugs and behaviour on antiviral treatment and retreatment. Gut 2024:gutjnl-2024-332177. [PMID: 38782565 DOI: 10.1136/gutjnl-2024-332177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
The high genetic diversity of hepatitis C virus (HCV) has led to the emergence of eight genotypes and a large number of subtypes in limited geographical areas. Currently approved pangenotypic DAA regimens have been designed and developed to be effective against the most common subtypes (1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a and 6a). However, large populations living in Africa and Asia, or who have migrated from these regions to industrialised countries, are infected with 'unusual', non-epidemic HCV subtypes, including some that are inherently resistant to currently available direct-acting antiviral (DAA) drugs due to the presence of natural polymorphisms at resistance-associated substitution positions. In this review article, we describe the origin and subsequent global spread of HCV genotypes and subtypes, the current global distribution of common and unusual HCV subtypes, the polymorphisms naturally present in the genome sequences of unusual HCV subtypes that may confer inherently reduced susceptibility to DAA drugs and the available data on the response of unusual HCV subtypes to first-line HCV therapy and retreatment. We conclude that the problem of unusual HCV subtypes that are inherently resistant to DAAs and its threat to the global efforts to eliminate viral hepatitis are largely underestimated and warrant vigorous action.
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Affiliation(s)
- Erwan Vo-Quang
- National Reference Centre for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale (INSERM U955), Créteil, France
- Department of Hepatology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Centre for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale (INSERM U955), Créteil, France
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2
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Adeboyejo K, King BJ, Tsoleridis T, Tarr AW, McLauchlan J, Irving WL, Ball JK, McClure CP. Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination. J Med Virol 2023; 95:e28178. [PMID: 36168235 PMCID: PMC10092547 DOI: 10.1002/jmv.28178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND AND AIMS: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of HCV naturally harbor drug resistance associated substitutions (RAS), these are often overlooked as "rarities." Furthermore, commercial subtyping assays and associated epidemiological findings are skewed towards Western cohorts and whole-genome sequencing can be problematic to deploy without significant infrastructure and training support. We thus aimed to develop a simple, robust and accurate HCV subtyping pipeline, to optimize and streamline molecular detection and sequence-based typing of diverse RAS-containing subtypes. METHODS HCV serum derived from 146 individuals, whose likely source of infection was from sub-Saharan Africa (SSA) was investigated with a novel panel of single round polymerase chain reaction (PCR) assays targeting NS5B and NS5A genomic regions. Virus subtype assignments were determined by pairwise-distance analysis and compared to both diagnostic laboratory assignments and free-to-use online typing tools. RESULTS Partial NS5A and NS5B sequences were respectively obtained from 131 to 135 HCV-positive patients born in 19 different countries from SSA but attending clinics in the UK. We determined that routine clinical diagnostic methods incorrectly subtyped 59.0% of samples, with a further 6.8% incorrectly genotyped. Of five commonly used online tools, Geno2Pheno performed most effectively in determining a subtype in agreement with pairwise distance analysis. CONCLUSION This study provides a simple low-cost pathway to accurately subtype in SSA, guide regional therapeutic choice and assist global surveillance and elimination initiatives.
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Affiliation(s)
- Kazeem Adeboyejo
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Barnabas J King
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Theocharis Tsoleridis
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William L Irving
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK.,Clinical Microbiology, Nottingham University Hospitals, Nottingham, UK.,Nottingham University Hospitals, Nottingham, UK
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
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3
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Nankya-Mutyoba J, Apica BS, Otekat G, Kyeyune DB, Nakyagaba L, Nabunje J, Nakafeero M, Seremba E, Ocama P. Hepatitis C in Uganda: Identification of infected blood donors for micro-elimination. J Virus Erad 2021; 7:100041. [PMID: 34188952 PMCID: PMC8219885 DOI: 10.1016/j.jve.2021.100041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background The drive to eliminate viral hepatitis by 2030 is underway. However, locally generated data on active infection is required to focus such efforts. We performed a regionally-inclusive survey to determine prevalence of active HCV, genotypes and related factors among Ugandan blood donors. Methods Participants from regional blood banks and blood collection centers were surveyed for information on demographic, clinical and lifestyle factors. Blood was assayed for HCV infection, HCV genotypes and subtypes. Logistic regression was performed to determine factors associated with active HCV infection. Results Of 1243 participants, 1041 (83.7%) were male, average age (SD), 27.7 (9.8). Prevalence of active HCV infection was 7.8% and we identified 3 genotypes. Median age (adj. OR (95% CI) = 1.03 (1.01-1.06), p-value = 0.040)), Northern region of birth versus Central or Eastern (adj. OR (95% CI) = 10.25 (2.65-39.68), p-value = 0.001)), Northern residence, versus Central or Eastern (adj. OR (95% CI) = 0.23 (0.08-0.65), p-value = 0.006)), and being married (versus single/divorced) adj. OR 2.49(1.3-4.79), p-value = 0.006 were associated with active HCV infection. Conclusion Targeted interventions in at-risk populations coupled with linkage to care and treatment will help achieve the WHO elimination goals in this setting.
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Affiliation(s)
- Joan Nankya-Mutyoba
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Betty S Apica
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda.,Mulago National Referral Hospital, Kampala, Uganda
| | - Grace Otekat
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda.,Mulago National Referral Hospital, Kampala, Uganda.,Uganda Uganda Blood Transfusion Service, Uganda
| | | | - Lourita Nakyagaba
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Joletta Nabunje
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Mary Nakafeero
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Emmanuel Seremba
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda
| | - Ponsiano Ocama
- Makerere University College of Health Sciences, School of Public Health, Kampala, Uganda.,Makerere Unversity College of Health Sciences, School of Medicine
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4
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Amougou-Atsama M, Jean Adrien Atangana P, Noah Noah D, Fewou Moundipa P, Pineau P, Njouom R. The role of hepatitis C virus genotypes and core mutations in hepatocellular carcinoma in Cameroon. J Viral Hepat 2020; 27:880-885. [PMID: 32301239 DOI: 10.1111/jvh.13303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is known to be an important risk factor for hepatocellular carcinoma (HCC) in Cameroon. However, the effect of HCV-related factors on HCC development still remains unknown in the Central Africa. In this study, we investigated the role of HCV genotypes and core mutations in HCC development in Cameroonian patients. METHODS A case-control study was conducted using patients with HCV-related HCC and matched controls individuals with chronic HCV infection but without HCC. HCV genotypes and mutations were determined using a hemi-nested amplification and sequencing analysis focus on the core and NS5B HCV regions. RESULTS We identify HCV genotype 1, 2 and 4 in both groups. Interestingly, genotype 4 was significantly more prevalent in HCC patients (53.3%). Overall, distribution of genotypes was very different between cases and controls (P = 4.2 E-7). The risk factors analysis showed that infection with HCV-4 is strongly associated with HCC development with odd ratio, 95% confidence interval and p-values of 7.4 (95% CI: 2.08-26.6; P = .001). Furthermore, the risk of developing HCC increased even more significantly in case of infection with HCV subtype 4f with the odd ratio of 20.8 (95% CI, 4.1-66.8; P < .001). Mutations K10R, T72E, K74R and G77A were significantly more frequent in patients with HCC. Remarkably, HCV-4f isolates from HCC patients carried significantly more mutations when compared to controls with HCV-4f or others genotypes (P = .0001). CONCLUSIONS Our results indicate that patients infected with HCV-4f or with selected variants affecting HCV core gene are at increased risk to develop HCC.
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Affiliation(s)
| | | | | | - Paul Fewou Moundipa
- Laboratory of Pharmacology and Toxicology of University of Yaoundé I, Yaoundé, Yaoundé, Cameroon
| | - Pascal Pineau
- Unité « Organisation nucléaire et Oncogenèse », INSERM U993, Institut Pasteur, Paris, France
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5
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Chen M, Ma Y, Chen H, Dai J, Luo H, Jia M, Song Z. Complete genome sequencing and evolutionary analysis of HCV subtype 6xg from IDUs in Yunnan, China. PLoS One 2019; 14:e0217010. [PMID: 31095618 PMCID: PMC6522032 DOI: 10.1371/journal.pone.0217010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Background HCV genotype 6 (HCV-6) typically circulates in Southeast Asia and exhibits the highest genetic diversity among the eight HCV genotypes. In our previous work, a group of HCV-6 sequences was not clearly classified. Here, we further characterized this HCV-6 variant and analyzed the evolutionary history of the enlarged HCV-6 family. Methods Blood samples from eight HCV seropositive samples collected from intravenous drug users (IDUs) in 2014 in Yunnan Province, China. The full-length HCV genome sequences were amplified by using reverse transcription PCR followed by DNA sequencing and phylogenetic analysis. Bayesian evolutionary analysis was performed with the complete coding region sequences of subtype 6a-6xh. Results The eight genomes had the same coding region of 9051 nucleotides. The complete coding region sequences of the eight HCV isolates formed a distinct phylogenetic group from the previously assigned HCV-6 subtypes (6a-6xf), however which clustered with 6xg reference sequences that were found in Kachin State, Myanmar, and recently assigned and released. The p-distances of the eight isolates to subtype 6a-6xf and 6xh ranged from 0.143 to 0.283. Based on the HCV-6 complete coding region sequences, we constructed a timescaled phylogenetic tree to reveal the HCV-6 evolutionary history, in which there were four HCV-6 phylogenetic subsets, whose median tMRCAs were 294.8, 388.5, 348.5 and 197.0 years ago, respectively. Subtype 6xg clustered into Subset I, and had the most recent common ancestor with subtype 6n, which dated back to 101.2 (95% HPD: 78.7, 125.8) years ago. The genetic evolutionary analysis further confirmed that subtype 6xg originated from Myanmar, and transmitted to Dehong through cross-border IDUs. Conclusion The HCV-6 variant characterized in this study belonged to newly assigned subtype 6xg. Our finding further confirmed the assignment of 6xg. HCV-6 family was highly divers and had a complicated evolutionary history in Southeast Asia. It is necessary to further characterize HCV-6 genetics in this region.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (ZS); (MJ)
| | - Zhizhong Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (ZS); (MJ)
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6
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Low prevalence of HCV infection with predominance of genotype 4 among HIV patients living in Libreville, Gabon. PLoS One 2018; 13:e0190529. [PMID: 29385148 PMCID: PMC5791959 DOI: 10.1371/journal.pone.0190529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 12/15/2017] [Indexed: 11/24/2022] Open
Abstract
Background Gabon is an endemic area for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) and the risk of co-infection is high. Method Between November 2015 and April 2016, we conducted retrospective study on HCV infection among people living with HIV/AIDS (PLHA). A total of 491 PLHA were included in this study and tested for the presence of HCV infection. HIV viral loads were obtained using the Generic HIV viral Load® assay and the CD4+ T cells count was performed using BD FACSCount™ CD4 reagents. HCV screening was performed using the MP Diagnostics HCV ELISA 4.0 kit. HCV genotypes were determined by sequence analysis of NS5B and Core regions. The Mann-Whitney test was used to compare the groups. Chi-2 test and Fisher's Exact Test were used to compare prevalence. Results HCV seroprevalence was 2.9% (14/491), (95% confidence interval (CI):1.4–4.3%). The percentage of HCV viremic patients, defined by the detection of HCV RNA in plasma, was 57% (8/14), representing 1.6% of the total population. HCV seroprevalence and replicative infection were not statistically differ with gender. The percentage of co-infection increased with age. No correlation with CD4+ T cells count and HIV viral load level was registered in this study. Identified HCV strains were predominantly of genotype 4 (87.5%) including 4k, 4e, 4g, 4p, 4f and 4c subtypes. Only one strain belonged to genotype 2 (subtype 2q). Analysis of the NS5B region did not reveal the presence of resistance-associated substitutions for sofosbuvir. Conclusion A systematic screening of hepatitis C is therefore strongly recommended as well as genotyping of HCV strains in order to adapt treatments for the specific case of people living with HIV/AIDS in Central Africa.
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7
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Sonderup MW, Afihene M, Ally R, Apica B, Awuku Y, Cunha L, Dusheiko G, Gogela N, Lohouès-Kouacou MJ, Lam P, Lesi O, Mbaye PS, Musabeyezu E, Musau B, Ojo O, Rwegasha J, Scholz B, Shewaye AB, Tzeuton C, Kassianides C, Spearman CW. Hepatitis C in sub-Saharan Africa: the current status and recommendations for achieving elimination by 2030. Lancet Gastroenterol Hepatol 2017; 2:910-919. [DOI: 10.1016/s2468-1253(17)30249-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/18/2017] [Accepted: 07/27/2017] [Indexed: 12/16/2022]
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8
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Hundie GB, Raj VS, GebreMichael D, Pas SD, Haagmans BL. Genetic diversity of hepatitis C virus in Ethiopia. PLoS One 2017; 12:e0179064. [PMID: 28570623 PMCID: PMC5453619 DOI: 10.1371/journal.pone.0179064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatitis C virus (HCV) is genetically highly divergent and classified in seven major genotypes and approximately hundred subtypes. These genotypes/subtypes have different geographic distribution and response to antiviral therapy. In Ethiopia, however, little is known about their molecular epidemiology and genetic diversity. The aim of this study was to investigate the distribution and genetic diversity of HCV genotypes/subtypes in Ethiopia, using 49 HCV RNA positive samples. HCV genotypes and subtypes were determined based on the sequences of the core and the nonstructural protein 5B (NS5B) genomic regions. Phylogenetic analysis revealed that the predominant was genotype 4 (77.6%) followed by 2 (12.2%), 1 (8.2%), and 5 (2.0%). Seven subtypes were identified (1b, 1c, 2c, 4d, 4l, 4r and 4v), with 4d (34.7%), 4r (34.7%) and 2c (12.2%) as the most frequent subtypes. Consistent with the presence of these subtypes was the identification of a potential recombinant virus. One strain was typed as genotype 2c in the NS5B region sequence and genotype 4d in the core region. In conclusion, genotype 4 HCV viruses, subtypes 4d and 4r, are most prevalent in Ethiopia. This genotype is considered to be difficult to treat, thus, our finding has an important impact on the development of treatment strategies and patient management in Ethiopia.
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Affiliation(s)
| | - V. Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Suzan D. Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
- * E-mail:
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9
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Gürtler LG, Eberle J. Aspects on the history of transmission and favor of distribution of viruses by iatrogenic action: perhaps an example of a paradigm of the worldwide spread of HIV. Med Microbiol Immunol 2017; 206:287-293. [PMID: 28434128 PMCID: PMC5511299 DOI: 10.1007/s00430-017-0505-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 02/07/2023]
Abstract
Transmission of infectious agents might be associated with iatrogenic actions of charitable help in health care. An example is the vaccination against yellow fever in USA that transmitted hepatitis B virus. Another example is injections of praziquantel for treatment and cure of schistosomiasis in Central and Northern Africa, with a focus in Egypt that has spread hepatitis C virus. There is no indication that human T-lymphotropic virus type 1 was spread by injection treatment for African trypanosomiasis, syphilis and treponematosis, but these treatments might have contributed to the early spread of human immunodeficiency virus type 1 (HIV-1) in Central Africa. Slave trade contributed as well to the spread of viruses from Africa to the Americas; it was stopped in 1850. Until that date HIV-1 was not transported to the Americas. By analysis of nucleic acid sequence data it can be concluded that the continental spread of HCV and HIV-1 might have started around 1920 with an exponential phase from 1940 to 1970. Further iatrogenic actions that promoted the spread of HCV and HIV-1 might be vaccinations to prevent deadly diseases. The successful vaccination was followed by diminution of the infectious agent in the population such as small pox, yellow fever and measles. Measurements to reduce the spread of plague and cholera were further benefits increasing survival of diseased subjects in a population. Thus, the reduction of exposure to deadly infectious agents might have given a chance to HIV-1 infected subjects to survive and for HIV-1 to be distributed around the world starting from Central Africa in the 1950s.
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Affiliation(s)
- Lutz G. Gürtler
- Max von Pettenkofer Institute, National Reference Centre for Retroviruses, Ludwig-Maximilians-University of München, Pettenkofer Str 9A, 80336 Munich, Germany
| | - Josef Eberle
- Max von Pettenkofer Institute, National Reference Centre for Retroviruses, Ludwig-Maximilians-University of München, Pettenkofer Str 9A, 80336 Munich, Germany
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10
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Al-Qahtani AA, Baele G, Khalaf N, Suchard MA, Al-Anazi MR, Abdo AA, Sanai FM, Al-Ashgar HI, Khan MQ, Al-Ahdal MN, Lemey P, Vrancken B. The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia. Sci Rep 2017; 7:44947. [PMID: 28322313 PMCID: PMC5359580 DOI: 10.1038/srep44947] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023] Open
Abstract
The relatedness between viral variants sampled at different locations through time can provide information pertinent to public health that cannot readily be obtained through standard surveillance methods. Here, we use virus genetic data to identify the transmission dynamics that drive the hepatitis C virus subtypes 4a (HCV4a) and 4d (HCV4d) epidemics in Saudi Arabia. We use a comprehensive dataset of newly generated and publicly available sequence data to infer the HCV4a and HCV4d evolutionary histories in a Bayesian statistical framework. We also introduce a novel analytical method for an objective assessment of the migration intensity between locations. We find that international host mobility patterns dominate over within country spread in shaping the Saudi Arabia HCV4a epidemic, while this may be different for the HCV4d epidemic. This indicates that the subtypes 4a and 4d burden can be most effectively reduced by combining the prioritized screening and treatment of Egyptian immigrants with domestic prevention campaigns. Our results highlight that the joint investigation of evolutionary and epidemiological processes can provide valuable public health information, even in the absence of extensive metadata information.
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Affiliation(s)
- Ahmed A Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Guy Baele
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Nisreen Khalaf
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, USA
| | - Mashael R Al-Anazi
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Ayman A Abdo
- Section of Gastroenterology, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal M Sanai
- Gastroenterology Unit, Department of Medicine, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Hamad I Al-Ashgar
- Gastroenterology Unit, Department of Medicine, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Mohammed Q Khan
- Gastroenterology Unit, Department of Medicine, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Philippe Lemey
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Bram Vrancken
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
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11
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Rajhi M, Ghedira K, Chouikha A, Djebbi A, Cheikh I, Ben Yahia A, Sadraoui A, Hammami W, Azouz M, Ben Mami N, Triki H. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa. PLoS One 2016; 11:e0153761. [PMID: 27100294 PMCID: PMC4839596 DOI: 10.1371/journal.pone.0153761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/04/2016] [Indexed: 01/06/2023] Open
Abstract
HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization.
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Affiliation(s)
- Mouna Rajhi
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
- University of Carthage, Faculty of Sciences, Bizerte, Tunisia
- * E-mail:
| | - Kais Ghedira
- Pasteur Institute, Tunis, Tunisia; Laboratory of Bioinformatics, Mathematics and Statistics, Tunis, Tunisia
- University of Tunis El Manar, Tunis, 1036, Tunisia
| | - Anissa Chouikha
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Ahlem Djebbi
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Imed Cheikh
- Department of Gastroenterology, Regional Hospital of Bizerte, Bizerte, Tunisia
| | - Ahlem Ben Yahia
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Amel Sadraoui
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Walid Hammami
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
| | - Msaddek Azouz
- Department of Gastroenterology, Regional Hospital of Nabeul, Nabeul, Tunisia
| | - Nabil Ben Mami
- Department of Gastroenterology, La Rabta Hospital, Tunis, Tunisia
| | - Henda Triki
- Pasteur Institute, Tunis, Tunisia; Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Tunis, Tunisia
- University of Tunis El Manar, Tunis, 1036, Tunisia
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12
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Riou J, Aït Ahmed M, Blake A, Vozlinsky S, Brichler S, Eholié S, Boëlle PY, Fontanet A. Hepatitis C virus seroprevalence in adults in Africa: a systematic review and meta-analysis. J Viral Hepat 2016; 23:244-55. [PMID: 26477881 DOI: 10.1111/jvh.12481] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022]
Abstract
With the introduction of more efficient treatments for hepatitis C virus (HCV), improved epidemiological information is required at the country level to allow evidence-based policymaking for elaboration of national strategies and HCV resources planning. We present a systematic review with meta-analysis of HCV seroprevalence data in adults in African countries. We conducted a systematic review of all HCV seroprevalence estimates reported in African countries from 2000 to 2014 in MEDLINE, AJOL and grey literature. We assessed studies performed in the general population and among blood donors, pregnant women and HIV-positive patients. A meta-regression analysis was used to provide adjusted estimates of HCV seroprevalence in the general adult population in each country, accounting for the heterogeneity in sample age structure and population types in the included studies. We identified 775 national-level estimations, among which 184 were included. Estimates of HCV seroprevalence were produced for 38 countries, in addition to the results from nationwide representative surveys available in Egypt and Libya. Next to Egypt, which clearly stands out, the highest levels of seroprevalence were found in Middle Africa (e.g. Cameroon, Gabon and Angola) and some West African countries (e.g. Burkina Faso, Benin), and the largest absolute numbers of infected adults were found in Nigeria, Ethiopia and Democratic Republic of Congo. This study exposes the diversity of HCV epidemiology among African countries. Egypt and several countries of West and Middle Africa present a HCV burden that will require strong governmental commitment to promote efficient preventive and curative interventions.
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Affiliation(s)
- J Riou
- Institut Pasteur, Unité d'Epidémiologie des Maladies Emergentes, Paris, France
| | - M Aït Ahmed
- Institut Pasteur, Unité d'Epidémiologie des Maladies Emergentes, Paris, France
| | - A Blake
- Institut Pasteur, Unité d'Epidémiologie des Maladies Emergentes, Paris, France
| | - S Vozlinsky
- Institut Pasteur, Unité d'Epidémiologie des Maladies Emergentes, Paris, France
| | - S Brichler
- Service de Bactériologie, Virologie, Hygiène, laboratoire associé au Centre National de Référence des Hépatites B, C et Delta, Assitance Publique-Hôpitaux de Paris, Université, Sorbonne Paris Cité, Hôpital Avicenne, Bobigny, France.,INSERM U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - S Eholié
- Service des Maladies Infectieuses et Tropicales, CHU de Treichville, Abidjan, Côte d'Ivoire
| | - P-Y Boëlle
- Sorbonne Universités, Université Pierre et Marie Curie, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - A Fontanet
- Institut Pasteur, Unité d'Epidémiologie des Maladies Emergentes, Paris, France.,Conservatoire National des Arts et Métiers, Chaire Santé et Développement, Paris, France
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13
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Ali-Mahamat M, Njouom R. High rate of infection with hepatitis C virus genotype 4 in Chad, Central Africa. Indian J Med Microbiol 2015; 33:608-9. [DOI: 10.4103/0255-0857.167343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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14
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Iles JC, Raghwani J, Harrison GLA, Pepin J, Djoko CF, Tamoufe U, LeBreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Simmonds P, Klenerman P, Pybus OG. Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa. Virology 2014; 464-465:233-243. [PMID: 25105489 PMCID: PMC4162651 DOI: 10.1016/j.virol.2014.07.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/04/2014] [Accepted: 07/05/2014] [Indexed: 12/18/2022]
Abstract
HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650-1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2.
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Affiliation(s)
- James C Iles
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - G L Abby Harrison
- Department of Infection & Immunity, Walter & Eliza Hall Institute, Victoria 3052, Australia
| | - Jacques Pepin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada
| | | | | | | | | | | | - Felix M Tshala
- Department of Military Health, Ministry of Defense, Kinshasa, Democratic Republic of the Congo
| | - Patrick K Kayembe
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Jean Jacques Muyembe
- National Institute of Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Samuel Edidi-Basepeo
- National AIDS Control Program, Reference Laboratory, Kinshasa, Democratic Republic of the Congo
| | - Nathan D Wolfe
- Metabiota, San Francisco, USA; Stanford University Program in Human Biology, Stanford, USA
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Melo IC, Ferraz MLG, Perez RM, Emori CT, Uehara SNDO, de Carvalho-Filho RJ, Silva AEB, de Souza e Silva IS. Do differences exist between chronic hepatitis C genotypes 2 and 3? Rev Soc Bras Med Trop 2014; 47:143-8. [PMID: 24861286 DOI: 10.1590/0037-8682-0269-2013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/14/2014] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Six genotypes of the hepatitis C virus (HCV) have been identified thus far, and their distribution is well defined. Genotype 1, which is the most prevalent worldwide, is always compared to genotypes 2 and 3, particularly in terms of treatment response. However, little is known about the differences between genotypes 2 and 3 because these genotypes are analyzed together in most studies. Therefore, the aim of this study was to evaluate differences in the clinical, epidemiological, laboratory, and histological parameters between HCV-2 and HCV-3. METHODS Patients with chronic hepatitis C infected with genotypes 2 and 3 were studied retrospectively and compared according to clinical, laboratory, and histological aspects. Hepatitis C virus-ribonucleic acid (HCV-RNA) was analyzed quantitatively by TaqMan® real-time PCR, and the HCV genotype was determined by sequencing the 5'-untranslated region. RESULTS A total of 306 patients with chronic HCV-2 (n=50) and HCV-3 (n = 256) were studied. Subtype 2b (n=17/50) and subtype 3a (n=244/256) were the most prevalent among patients infected with HCV-2 and HCV-3, respectively. The mean age was 47 ± 10 years, and there was a predominance of men in the group studied (61%). Comparative analysis between HCV-2 and HCV-3 showed a younger age (p=0.002), less prevalence of arterial hypertension (p=0.03), higher serum albumin levels (p=0.01), more advanced stage of liver fibrosis (p=0.03), and higher frequency of steatosis in patients with HCV-3 (p=0.001). After multivariate regression analysis, all the variables, except serum albumin, remained as variables associated with HCV-3 in the final model. CONCLUSIONS Clinical and histological differences exist between HCV-2 and HVC-3, which suggests the need for separate analyses of these genotypes.
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Affiliation(s)
- Isaura Cunha Melo
- Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Lucia Gomes Ferraz
- Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Renata Mello Perez
- Departamento de Medicina Interna, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Christine Takemi Emori
- Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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An Y, Wu T, Wang M, Lu L, Li C, Zhou Y, Fu Y, Chen G. Conservation in China of a novel group of HCV variants dating to six centuries ago. Virology 2014; 464-465:21-25. [PMID: 25043585 DOI: 10.1016/j.virol.2014.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/15/2014] [Accepted: 06/10/2014] [Indexed: 12/18/2022]
Abstract
UNLABELLED We characterized a novel group of HCV variants that are genetically related but distinct from each other belonging to genotype 6 (HCV-6). From 26 infected Austronesian-descended aborigines on Hainan Island, China, HCV sequences were determined followed by genetic analyses. Six nearly full-length genomes and 20 E1 sequences of HCV were obtained, which differ from each other and from all known HCV lineages by nucleotides above the intra-subtype level of 13%. Together with subtypes 6g and 6w, they constitute a phylogenetic group sharing a common ancestor dating from the end of the 12th century. CONCLUSION Our data indicate the maintenance of an isolated HCV-6 indigenous circulation on Hainan Island at least for six centuries.
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Affiliation(s)
- Yuling An
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Tao Wu
- Department of Infectious Disease, Southern Medical University, Guangzhou, Guangdong 510515, China; Department of Infectious Disease, Hainan General Hospital, Haikou, Hainan 570311, China
| | - Min Wang
- Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Ling Lu
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China; Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yuanpin Zhou
- Department of Infectious Disease, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Guihua Chen
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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17
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Golemba MD, Culasso ACA, Villamil FG, Bare P, Gadano A, Ridruejo E, Martinez A, Di Lello FA, Campos RH. Hepatitis C virus diversification in Argentina: comparative analysis between the large city of Buenos Aires and the small rural town of O'Brien. PLoS One 2013; 8:e84007. [PMID: 24386322 PMCID: PMC3875501 DOI: 10.1371/journal.pone.0084007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/11/2013] [Indexed: 01/19/2023] Open
Abstract
Background The estimated prevalence of HCV infection in Argentina is around 2%. However, higher rates of infection have been described in population studies of small urban and rural communities. The aim of this work was to compare the origin and diversification of HCV-1b in samples from two different epidemiological scenarios: Buenos Aires, a large cosmopolitan city, and O'Brien, a small rural town with a high prevalence of HCV infection. Patients and Methods The E1/E2 and NS5B regions of the viral genome from 83 patients infected with HCV-1b were sequenced. Phylogenetic analysis and Bayesian Coalescent methods were used to study the origin and diversification of HCV-1b in both patient populations. Results Samples from Buenos Aires showed a polyphyletic behavior with a tMRCA around 1887–1900 and a time of spread of infection approximately 60 years ago. In contrast, samples from ÓBrien showed a monophyletic behavior with a tMRCA around 1950–1960 and a time of spread of infection more recent than in Buenos Aires, around 20–30 years ago. Conclusion Phylogenetic and coalescence analysis revealed a different behavior in the epidemiological histories of Buenos Aires and ÓBrien. HCV infection in Buenos Aires shows a polyphyletic behavior and an exponential growth in two phases, whereas that in O'Brien shows a monophyletic cluster and an exponential growth in one single step with a more recent tMRCA. The polyphyletic origin and the probability of encountering susceptible individuals in a large cosmopolitan city like Buenos Aires are in agreement with a longer period of expansion. In contrast, in less populated areas such as O'Brien, the chances of HCV transmission are strongly restricted. Furthermore, the monophyletic character and the most recent time of emergence suggest that different HCV-1b ancestors (variants) that were in expansion in Buenos Aires had the opportunity to colonize and expand in O’Brien.
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Affiliation(s)
- Marcelo D. Golemba
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrés C. A. Culasso
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico G. Villamil
- Unidad de Trasplante Hepático, Hospital Británico de Buenos Aires, Argentina y Unidad de Trasplante Hepático, Hospital El Cruce, Buenos Aires, Argentina
| | - Patricia Bare
- Sección Virología, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Adrián Gadano
- Hepatology Unit, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno, CEMIC, Buenos Aires, Argentina
| | - Alfredo Martinez
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno, CEMIC, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rodolfo H. Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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Iles JC, Abby Harrison G, Lyons S, Djoko CF, Tamoufe U, Lebreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Klenerman P, Simmonds P, Pybus OG. Hepatitis C virus infections in the Democratic Republic of Congo exhibit a cohort effect. INFECTION GENETICS AND EVOLUTION 2013; 19:386-94. [DOI: 10.1016/j.meegid.2013.01.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 12/26/2022]
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The current hepatitis C virus prevalence in China may have resulted mainly from an officially encouraged plasma campaign in the 1990s: a coalescence inference with genetic sequences. J Virol 2013; 87:12041-50. [PMID: 23986603 DOI: 10.1128/jvi.01773-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In this study, we investigated hepatitis C virus (HCV) molecular epidemiology and evolutionary dynamics. Both E1 and NS5B sequences were characterized in 379 of 433 patients in southern China and classified into five major subtypes: 1b in 256 patients, 6a in 67 patients, 2a in 29 patients, 3a in 14 patients, and 3b in 13 patients. Using the E1 sequences obtained, along with those from other studies using samples from China, we inferred the HCV epidemic history by means of coalescence strategies. Five Bayesian skyline plots (BSPs) were estimated for the five subtypes. They concurrently highlighted the rapid growth in the HCV-infected population size from 1993 to 2000, followed by an abrupt slowing. Although flanked on both sides by variable population sizes, the plots showed distinct patterns of rapid HCV growth. Coincidently, 1993 to 2000 was a period when contaminated blood transfusions were common in China due to a procedural error in an officially encouraged plasma campaign. The abrupt slowing in 1998 to 2000 corresponded to the central government outlawing paid blood donations in 1998. Using a parametric model, the HCV population growth rates were estimated during 1993 to 2000. It was revealed that the 6a rate was the highest, followed by those of 1b, 2a, 3b, and 3a. Because these rates differed significantly (P < 1e-9) from each other, they may help explain why 6a is increasingly prevalent in southern China and 1b is predominant nationwide. These rates are approximately 10-fold higher than those reported elsewhere. These findings suggested that during the plasma campaign, certain barriers to efficient viral transmission were removed, allowing wide HCV dissemination.
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Yuan M, Lu T, Li C, Lu L. The evolutionary rates of HCV estimated with subtype 1a and 1b sequences over the ORF length and in different genomic regions. PLoS One 2013; 8:e64698. [PMID: 23762247 PMCID: PMC3675120 DOI: 10.1371/journal.pone.0064698] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 04/17/2013] [Indexed: 01/06/2023] Open
Abstract
Background Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance. Methods/Results 176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10−3 substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure. Conclusion Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.
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Affiliation(s)
- Manqiong Yuan
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Teng Lu
- University of Southern California, Los Angeles, California, United States of America
| | - Chunhua Li
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Ling Lu
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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21
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[The different epidemic and evolution of HCV genotypes]. YI CHUAN = HEREDITAS 2012; 34:666-72. [PMID: 22698736 DOI: 10.3724/sp.j.1005.2012.00666] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepatitis C virus (HCV) is a prevalent and globally distributed human pathogen that currently infects an estimated 170 million people. Chronic HCV infection significantly increases the risk of chronic hepatitis. The virus exhibits a very high degree of genetic diversity that is classified six genotypes and sub-classified more than 80 subtypes by phylogenetic analysis. The various genotypes and subtypes of HCV have been associated with different epidemiological and geographical spread patterns. Genotypes 1 and 2 are globally distributed; genotype 3 is predominant in Asia, North America and parts of Europe; similar regional patterns of endemic diversity have been found for genotype 4 in Europe, Middle East and Central Africa, for genotype 5 in parts of Africa and Europe, and for genotype 6 in Southeast Asia and North America. Up to date, four HCV genotypes, including genotype 1, 2, 3 and 6, were identified in China. Genotypes 1b and 2a were mainly found in Northern China. The fast spreading of genotypes 3 and 6 in Southern and South-Western China was reported by recent studies. It's deduced that Yunnan may become an important source of HCV epidemic and spread, which will cause great changes in the distribution of HCV genotypes and subtypes, and a variety of transmission. With the development of evolution theory and related analysis methods, such as coalescent theory and evolutionary molecular, it is possible to understand the characters of virus evolution and migration. For HCV, the further understanding on the prevalence and evolution characters of various genotypes is very important for the deep investigation of HCV epidemic and the development of prevention strategy.
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Njouom R, Caron M, Besson G, Ndong-Atome GR, Makuwa M, Pouillot R, Nkoghé D, Leroy E, Kazanji M. Phylogeography, risk factors and genetic history of hepatitis C virus in Gabon, central Africa. PLoS One 2012; 7:e42002. [PMID: 22870274 PMCID: PMC3411564 DOI: 10.1371/journal.pone.0042002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/28/2012] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The epidemiological and molecular characteristics of hepatitis C virus (HCV) infection in the general population have been poorly investigated in Africa. The aim of this study was to determine the prevalence, genotype distribution and epidemic history of HCV in the Gabonese general population. METHODS/PRINCIPAL FINDINGS A total of 4042 sera collected from adults in 220 villages in all nine administrative areas of the country were screened for antibodies to HCV. HCV NS5B region sequencing was performed for molecular characterization and population genetic analyses. Of 4042 tested sera, 455 (11.2%) were positive. The seroprevalence of HCV varied significantly by administrative area, with the highest rate in Ogooué-Lolo province (20.4%) and the lowest in Ogooué-Maritine province (3.7%). History of parenteral injections, past hospital admission and age over 55 years were independent risk factors for HCV infection (p<0.0001). Phylogenetic analyses showed that 91.9% of the strains were genotype 4 (HCV-4), 5.7% genotype 1 and 2.2% genotype 2. HCV-4 strains were highly heterogeneous, with more than eight subtypes; subtype 4e predominated (57.3%). Coalescence analyses indicated that subtype 4e was the oldest, with an estimated most recent common ancestor of 1702 [95% CI, 1418-1884]. The epidemic profile indicated that it spread exponentially during the first part of the 20th century, probably by iatrogenic transmission. CONCLUSIONS/SIGNIFICANCE These results confirm the endemicity of HCV subtype 4e in Gabon and show that its spread is due to a cohort effect, with previous, possibly iatrogenic events. More extensive epidemiological studies are needed to better characterize the route of transmission and the dissemination of HCV in Gabon.
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Affiliation(s)
- Richard Njouom
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur, Yaoundé, Cameroon
| | - Mélanie Caron
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Guillaume Besson
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Division of Infectious Diseases, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | | | - Maria Makuwa
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Régis Pouillot
- Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur, Yaoundé, Cameroon
| | - Dieudonné Nkoghé
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Ministère de la Santé, Libreville, Gabon
| | - Eric Leroy
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Mirdad Kazanji
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Institut Pasteur de Bangui, Réseau International des Instituts Pasteur, Bangui, Central African Republic
- * E-mail:
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Forbi JC, Purdy MA, Campo DS, Vaughan G, Dimitrova ZE, Ganova-Raeva LM, Xia GL, Khudyakov YE. Epidemic history of hepatitis C virus infection in two remote communities in Nigeria, West Africa. J Gen Virol 2012; 93:1410-1421. [PMID: 22456613 DOI: 10.1099/vir.0.042184-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We investigated the molecular epidemiology and population dynamics of HCV infection among indigenes of two semi-isolated communities in North-Central Nigeria. Despite remoteness and isolation, ~15% of the population had serological or molecular markers of hepatitis C virus (HCV) infection. Phylogenetic analysis of the NS5b sequences obtained from 60 HCV-infected residents showed that HCV variants belonged to genotype 1 (n=51; 85%) and genotype 2 (n=9; 15%). All sequences were unique and intermixed in the phylogenetic tree with HCV sequences from people infected from other West African countries. The high-throughput 454 pyrosequencing of the HCV hypervariable region 1 and an empirical threshold error correction algorithm were used to evaluate intra-host heterogeneity of HCV strains of genotype 1 (n=43) and genotype 2 (n=6) from residents of the communities. Analysis revealed a rare detectable intermixing of HCV intra-host variants among residents. Identification of genetically close HCV variants among all known groups of relatives suggests a common intra-familial HCV transmission in the communities. Applying Bayesian coalescent analysis to the NS5b sequences, the most recent common ancestors for genotype 1 and 2 variants were estimated to have existed 675 and 286 years ago, respectively. Bayesian skyline plots suggest that HCV lineages of both genotypes identified in the Nigerian communities experienced epidemic growth for 200-300 years until the mid-20th century. The data suggest a massive introduction of numerous HCV variants to the communities during the 20th century in the background of a dynamic evolutionary history of the hepatitis C epidemic in Nigeria over the past three centuries.
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MESH Headings
- Adult
- Africa, Western/epidemiology
- Cluster Analysis
- Epidemics/history
- Female
- Genotype
- Hepacivirus/classification
- Hepacivirus/genetics
- Hepacivirus/isolation & purification
- Hepatitis C/epidemiology
- Hepatitis C/history
- Hepatitis C/virology
- High-Throughput Nucleotide Sequencing
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Male
- Molecular Epidemiology
- Molecular Sequence Data
- Nigeria/epidemiology
- Phylogeny
- Polymorphism, Genetic
- Population Groups
- Prevalence
- RNA, Viral/genetics
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- Joseph C Forbi
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael A Purdy
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - David S Campo
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Gilberto Vaughan
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Zoya E Dimitrova
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lilia M Ganova-Raeva
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Guo-Liang Xia
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Yury E Khudyakov
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Brahim I, Akil A, Mtairag EM, Pouillot R, Malki AE, Nadir S, Alaoui R, Njouom R, Pineau P, Ezzikouri S, Benjelloun S. Morocco underwent a drift of circulating hepatitis C virus subtypes in recent decades. Arch Virol 2011; 157:515-20. [PMID: 22160625 DOI: 10.1007/s00705-011-1193-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 12/01/2011] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) isolates circulating in Morocco are poorly documented. To determine the subgenotype distribution of HCV in chronically infected patients, serum samples from 185 anti-HCV-positive patients were analyzed. Determination of the HCV genotype and subtype was performed by sequencing the 5'UTR, NS5B and core regions. According to the NS5B phylogeny, the HCV strains primarily belonged to subtypes 1b (75.2%), 2i (19.1%) and 2k (2.8%). Using a Bayesian approach, the mean date of appearance of the most recent common ancestor was estimated to be 1910 for HCV-1b and 1854 for HCV-2i. Although it is currently the most frequent genotype in Morocco and the dominant form in hepatocellular carcinoma, it thus appears that HCV-1b was introduced into the population subsequently to HCV-2i.
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Affiliation(s)
- Ikram Brahim
- Virology Unit, Viral Hepatitis Laboratory, Pasteur Institute of Morocco, 1, Place Louis Pasteur, 20360 Casablanca, Morocco
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25
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Njouom R, Lavoie M, Foupouapouognigni Y, Frost E, Deslandes S, Mamadou-Yaya F, Mbélesso P, Mbadingai S, Pépin J. Transmission of Hepatitis C virus among spouses in Cameroon and the Central African Republic. J Med Virol 2011; 83:2113-8. [DOI: 10.1002/jmv.22225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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26
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Goumba AI, Konamna X, Komas NP. Clinical and epidemiological aspects of a hepatitis E outbreak in Bangui, Central African Republic. BMC Infect Dis 2011; 11:93. [PMID: 21492477 PMCID: PMC3089785 DOI: 10.1186/1471-2334-11-93] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 04/14/2011] [Indexed: 01/27/2023] Open
Abstract
Background Outbreaks of hepatitis E frequently occur in tropical developing countries during the rainy season due to overflowing drains, short-circuiting of networks of clean water and use of contaminated water from wells. Hepatitis E virus (HEV) infections are usually accompanied by general symptoms of acute liver disease. This study was conducted to define the clinical and epidemiological aspects of the HEV outbreak that occurred in May 2004 in Bangui. Methods Blood samples were collected from 411 patients aged 1-87 years, most of whom presented with jaundice, asthenia or signs of uncomplicated malaria, for a transversal study from June 2004 to September 2005. Patients were recruited at 11 health care centres, including two referral hospitals, after they had given informed consent. The diagnosis of HEV was made with a commercial ELISA test to detect IgM and/or IgG antibodies. HEV RNA was amplified by RT-PCR to confirm the presence of the viral genome. Results The most frequent clinical signs found were jaundice (93.4%), vomiting (50.7%), hepatalgia (47.4%), hepatomegaly (30.9%) and asthenia (26.8%), which are the general clinical signs of hepatic disease. Acute hepatitis E was found in 213 patients (51.8%) who were positive for HEV IgM antibodies. The IgG anti-HEV seroprevalence during this outbreak was high (79.5%). The age group 18-34 years was more frequently infected (91.2%) than those aged 1-17 (78.0%) or over 34 (64.9%) (p < 10-6). RT-PCR performed on 127 sera from the 213 IgM-HEV-positive patients was amplified, and the presence of the viral genome was found in 65 samples. Conclusion Although no specific clinical signs exist for hepatitis E infection, people presenting with jaundice, vomiting, hepatalgia, asthenia, hepatomegaly or distended abdomen with no signs of uncomplicated malaria in tropical developing countries should be sent to a laboratory for testing for hepatitis E.
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Affiliation(s)
- Alice I Goumba
- Viral Hepatitis Laboratory, Institut Pasteur de Bangui, PO Box 923, Bangui, Central African Republic
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27
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Eriksen MB, Jørgensen LB, Krarup H, Laursen AL, Christensen PB, Møller A, Schlichting P, Kuiken C, Bukh J, Weis N. Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark. J Med Virol 2011; 82:1869-77. [PMID: 20872713 DOI: 10.1002/jmv.21896] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The prevalence of hepatitis C virus (HCV) genotype 4 has increased throughout Europe. This is an epidemiological study of patients infected chronically with HCV genotype 4 in Denmark. The HCV strains analyzed originated from patient samples collected between 1999 and 2007 as part of the national Danish hepatitis B and C network, DANHEP. Sequence analyses were based on the envelope 1 region of HCV. Results from a total of 72 patients indicated a high degree of genetic heterogeneity. Fifty-six patients (78%) were infected with one of the three dominating subtypes: 4d, 4a, or 4r. The remaining 16 patients (22%) were infected with subtypes 4h, 4k, 4l, 4n, 4o, or 4Unclassified. Three epidemiological profiles were identified: (1) patients infected with HCV by intravenous drug use were infected solely with subtype 4d. They were all of European origin, and 15 of the 16 patients were ethnic Danes. No single transmission event could be confirmed, but the pairwise nucleotide identity within the patients of Danish origin was relatively high (∼95%), suggesting a recent introduction into Denmark. (2) The 21 patients infected with subtype 4a all came from Northern Africa, Egypt, Pakistan, or the Middle East. (3) Patients from Southern Africa dominated among patients infected with subtype 4r (10 of 12 patients). This study demonstrates that HCV genotype 4d has been introduced in and spread among Danish intravenous drug users. The remaining subtypes show restricted distribution, infecting almost exclusively patients from geographical areas with a relatively high prevalence of HCV genotype 4 infections.
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High prevalence and predominance of hepatitis delta virus genotype 1 infection in Cameroon. J Clin Microbiol 2011; 49:1162-4. [PMID: 21209162 DOI: 10.1128/jcm.01822-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibodies to the hepatitis delta virus (HDV) were found in 17.6% of 233 hepatitis B virus surface antigen-positive subjects in Cameroon. Phylogenetic analyses showed the presence of HDV-1, HDV-5, HDV-6, and HDV-7 genotypes. These results enrich the limited data on HDV prevalence and molecular diversity in Cameroon.
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Mujtaba G, Jahan S, Khaliq S, Mahmood N, Javed F, Choudhry N, Aslam A, Bashir T, Faiz M. Current Status of Transmission Risk Factors and Genotypes of Hepatitis C Virus, In Punjabi Population of Pakistan. ACTA ACUST UNITED AC 2011. [DOI: 10.5455/ijavms.20110526102003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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30
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Abstract
The hepatitis C virus genotype 4 (HCV-4) is prevalent in Egypt, the Middle East and Africa. Recently, the epidemiology of HCV-4 has changed and this genotype has begun to cross borders and spread to several regions in Europe through immigration and injection drug use. HCV-4 has been considered a difficult-to-treat genotype based on the low sustained virological response (SVR) rates obtained with conventional interferon (IFN)-based regimens. Pegylated interferons (PEG-IFN) plus ribavirin therapy for chronic HCV-4 has been associated with increased SVR rates of more than 60%. Shorter treatment of chronic HCV-4 patients with rapid and early virological responses has been associated with high SVR rates, better compliance, fewer adverse events and lower costs. Despite this progress, the treatment of HCV-4 non-responders, injection drug users, patients coinfected with human immunodeficiency virus, thalassaemic patients, patients on haemodialysis and patients with HCV-4 recurrence after liver transplantation still represents a significant therapeutic challenge. Treatment of HCV-4 has markedly improved, with higher sustained response rates and the possibility of shorter regimens. Despite the recent progress in the treatment of HCV-4, more research is required to optimize current therapy and include genotype 4 patients in clinical trials on emerging therapies such as specifically targeted antiviral therapy for HCV with protease and/or polymerase inhibitors.
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Affiliation(s)
- Sanaa M Kamal
- Department of Gastroenterology and Liver Disease, Ain Shams Faculty of Medicine, Cairo, Egypt.
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31
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Lampe E, Espirito-Santo MP, Martins RM, Bello G. Epidemic history of Hepatitis C virus in Brazil. INFECTION GENETICS AND EVOLUTION 2010; 10:886-95. [DOI: 10.1016/j.meegid.2010.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/15/2010] [Accepted: 05/18/2010] [Indexed: 02/07/2023]
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32
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Frost SDW, Volz EM. Viral phylodynamics and the search for an 'effective number of infections'. Philos Trans R Soc Lond B Biol Sci 2010; 365:1879-90. [PMID: 20478883 PMCID: PMC2880113 DOI: 10.1098/rstb.2010.0060] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK.
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