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Tung HD, Chen JJ. Genetic history of hepatitis C virus genotype 6 in Taiwan. J Formos Med Assoc 2023:S0929-6646(23)00431-X. [PMID: 37996321 DOI: 10.1016/j.jfma.2023.10.013] [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: 05/08/2022] [Revised: 03/09/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023] Open
Abstract
Unlike hepatitis C virus (HCV) genotype (GT) 6, which is widely circulated in Southeast Asia and South China, GT 6 was not reported in Taiwan until 2006. GT 1b and 2a, also known as global HCV subtypes, have been reported as major GTs circulating in Taiwan. Because of improvement in genotyping kits and sequencing techniques for the subtyping of HCV, an increasing number of GT 6 subtypes have been reported, especially subtype 6a among intravenous drug users with human immunodeficiency virus infection after an outbreak since 2003. Thus, HCV GT 6 infection is regarded to be closely associated with injection drug use. However, recently, we found an unexpectedly high GT 6 prevalence in the general population in Tainan, southern Taiwan. Most of these GT 6 samples belonged to a putative novel subtype closely related to 6g and 6w instead of 6a. Phylogenetic analyses indicated that this putative 6g-related novel subtype and 6w could be indigenous in southern Taiwan for centuries. Southern Taiwan could be the origin of HCV subtype 6w. This finding might change the perspective of HCV epidemiology in Taiwan.
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Affiliation(s)
- Hung-Da Tung
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chi-Mei Hospital, Liouying, Tainan, Taiwan
| | - Jyh-Jou Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chi-Mei Hospital, Liouying, Tainan, Taiwan.
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2
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Xu R, Aranday-Cortes E, Leitch ECM, Hughes J, Singer JB, Sreenu V, Tong L, da Silva Filipe A, Bamford CGG, Rong X, Huang J, Wang M, Fu Y, McLauchlan J. The Evolutionary Dynamics and Epidemiological History of Hepatitis C Virus Genotype 6, Including Unique Strains from the Li Community of Hainan Island, China. Virus Evol 2022; 8:veac012. [PMID: 35600095 PMCID: PMC9115904 DOI: 10.1093/ve/veac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/17/2022] [Accepted: 02/15/2022] [Indexed: 12/09/2022] Open
Abstract
Abstract
Hepatitis C virus (HCV) is a highly diverse pathogen that frequently establishes a chronic long-term infection, but the origins and drivers of HCV diversity in the human population remain unclear. Previously unidentified strains of HCV genotype 6 (gt6) were recently discovered in chronically infected individuals of the Li ethnic group living in Baisha County, Hainan Island, China. The Li community, who were early settlers on Hainan Island, have a distinct host genetic background and cultural identity compared to other ethnic groups on the island and mainland China. In this report, we generated 33 whole virus genome sequences to conduct a comprehensive molecular epidemiological analysis of these novel gt6 strains in the context of gt6 isolates present in Southeast Asia. With the exception of one gt6a isolate, the Li gt6 sequences formed 3 novel clades from two lineages which constituted 3 newly assigned gt6 subtypes and 30 unassigned strains. Using Bayesian inference methods, we dated the most recent common ancestor for all available gt6 whole virus genome sequences to approximately 2767 BCE (95% HPD intervals, 3670 to 1397 BCE), which is far earlier than previous estimates. The substitution rate was 1.20 x 10-4 substitutions/site/year (s/s/y) and this rate varied across the genome regions, from 1.02 x 10-5 s/s/y in the 5ʹUTR region to 3.07 x 10-4 s/s/y in E2. Thus, our study on an isolated ethnic minority group within a small geographical area of Hainan Island has substantially increased the known diversity of HCV gt6, already acknowledged as the most diverse HCV genotype. The extant HCV gt6 sequences from this study were probably transmitted to the Li through at least three independent events dating perhaps from around 4000 years ago. This analysis describes deeper insight into basic aspects of HCV gt6 molecular evolution including the extensive diversity of gt6 sequences in the isolated Li ethnic group.
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Affiliation(s)
- Ru Xu
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | | | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | - Xia Rong
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Jieting Huang
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Min Wang
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Yongshui Fu
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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3
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Black AP, Khounvisith V, Xaydalasouk K, Sayasinh K, Sausy A, Muller CP, Hübschen JM. Unexpectedly High Prevalence of Hepatitis C Virus Infection, Southern Laos. Emerg Infect Dis 2022; 28:256-259. [PMID: 34932463 PMCID: PMC8714196 DOI: 10.3201/eid2801.211307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
During 2017-2019, a total of 88/753 (11.7%) of patients 5-90 years of age in hospitals in Saravan Province, Laos, were seropositive for hepatitis C virus antibodies. Viral RNA was found in 44 samples. Sequencing showed high diversity within genotype 6. We recommend exposure-risk investigations and targeted testing and treatment.
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Affiliation(s)
| | | | | | - Kong Sayasinh
- Institut Pasteur du Laos, Vientiane, Laos (A.P. Black, V. Khounvisith, K. Xaydalasouk)
- Saravan Provincial Hospital, Saravan, Laos (K. Sayasinh)
- Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg (A. Sausy, C.P. Muller, J.M. Hübschen)
| | - Aurelie Sausy
- Institut Pasteur du Laos, Vientiane, Laos (A.P. Black, V. Khounvisith, K. Xaydalasouk)
- Saravan Provincial Hospital, Saravan, Laos (K. Sayasinh)
- Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg (A. Sausy, C.P. Muller, J.M. Hübschen)
| | - Claude P. Muller
- Institut Pasteur du Laos, Vientiane, Laos (A.P. Black, V. Khounvisith, K. Xaydalasouk)
- Saravan Provincial Hospital, Saravan, Laos (K. Sayasinh)
- Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg (A. Sausy, C.P. Muller, J.M. Hübschen)
| | - Judith M. Hübschen
- Institut Pasteur du Laos, Vientiane, Laos (A.P. Black, V. Khounvisith, K. Xaydalasouk)
- Saravan Provincial Hospital, Saravan, Laos (K. Sayasinh)
- Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg (A. Sausy, C.P. Muller, J.M. Hübschen)
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4
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Shah R, Ahovegbe L, Niebel M, Shepherd J, Thomson EC. Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. J Hepatol 2021; 75:462-473. [PMID: 33974951 PMCID: PMC8310923 DOI: 10.1016/j.jhep.2021.04.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/12/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
The hepatitis C virus (HCV) is an extremely diverse virus, subtypes of which are distributed variably around the world. Viral genotypes may be divided into epidemic subtypes; those that have become prevalent globally, and endemic subtypes that have a more limited distribution, mainly in Africa and Asia. The high variability of endemic strains reflects evolutionary origins in the locations where they are found. This increased genetic diversity raises the possibility of resistance to pan-genotypic direct-acting antiviral regimens. While many endemic subtypes respond well to direct-acting antiviral therapies, others, for example genotypes 1l, 3b and 4r, do not respond as well as predicted. Many genotypes that are rare in high-income countries but common in other parts of the world have not yet been fully assessed in clinical trials. Further sequencing and clinical studies in sub-Saharan Africa and Asia are indicated to monitor response to treatment and to facilitate the World Health Organization's 2030 elimination strategy.
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Affiliation(s)
- Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lucrece Ahovegbe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Mbarara University of Science and Technology, Mbarara, Uganda
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; London School of Hygiene and Tropical Medicine, London, UK.
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Irekeola AA, Malek NA, Wada Y, Mustaffa N, Muhamad NI, Shueb RH. Prevalence of HCV genotypes and subtypes in Southeast Asia: A systematic review and meta-analysis. PLoS One 2021; 16:e0251673. [PMID: 34014997 PMCID: PMC8136688 DOI: 10.1371/journal.pone.0251673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Known for its high genetic diversity and variation in genotypic presence in different regions of the world, hepatitis C virus (HCV) is estimated to infect about 71 million people globally. Selection of an appropriate therapeutic regimen largely depends on the identification of the genotype responsible for the infection. This systematic review and meta-analysis was conducted to provide a comprehensive view of HCV genotype and subtype distribution in Southeast Asia (SEA). The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA). We searched five databases without year and language restrictions. Data from 90 eligible studies involving 15,089 genotypes and 9,646 subtypes representing 10 SEA countries were analyzed. The pooled estimates showed that genotype 1 (46.8%) [95% CI, 43.2–50.4; I2 = 92.77%; p < 0.001] was the most dominant HCV genotype in the region, followed by genotype 3 (23.1%) [95% CI, 19.4–27.2; I2 = 93.03%; p < 0.001], genotype 6 (16.5%) [95% CI, 13.8–19.6], genotype 2 (4.6%) [95% CI, 3.5–5.9], genotype 4 (1.1%) [95% CI, 0.7–1.5] and genotype 5 (0.8%) [95% CI, 0.4–1.3]. Philippines had the highest prevalence of genotypes 1 and 2. Genotype 6 became more prevalent after year 2000. Over 40 different subtypes were identified, with subtypes 1b (26.3%), 1a (21.3%), and 3a (14.3%) being the most prevalent of all the reported subtypes. Although on a global scale, genotype 6 is considered highly prevalent in SEA, evidence from this study reveals that it is the third most prevalent genotype within the region.
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Affiliation(s)
- Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa Kwara State, Nigeria
| | - Nurul Adila Malek
- Department of Pathology, Hospital Sultanah Nur Zahirah, Kuala Terengganu, Terengganu, Malaysia
| | - Yusuf Wada
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
- Department of Zoology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Nazri Mustaffa
- Department of Medicine, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Nur Izat Muhamad
- Department of Medicine, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
- * E-mail:
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Abstract
Laos is a landlocked country in South East Asia, ranking fifth for primary liver cancer incidence worldwide. Risk factors that might explain this worrying situation are poorly known. We conducted a review of the literature concerning the etiologies of terminal liver diseases in Laos. A double infectious burden with hepatitis B and C viruses and the liver fluke Opisthorchis viverrini seems to be the main cause of the high liver cancer incidence. Moreover, it was also suggested that mutagenic substances frequently found in tobacco, alcoholic beverages, fermented fish, and mold-contaminated cereals or nuts, which are all substances heavily consumed by Lao people, lead to the accumulation of DNA mutations in the liver cell genome causing tumor processes. However, the respective proportions of liver cancer cases attributable to each category of infections and substances consumed, as well as the histological nature of the neoplasia are still not precisely documented in Laos. The international medical and scientific communities as well as public health stakeholders should urgently consider the alarming situation of liver health in Laos to stimulate both research and subsequent implementation of prevention policies.
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Qi M, Yang M, Xu L, Ma C, Huang P, Sun J, Shi J, Hu Y. Complete genome analysis identifies recombinant events and positive selection sites of hepatitis C virus from mainland China during 2010-2019. Virus Res 2021; 296:198354. [PMID: 33639223 DOI: 10.1016/j.virusres.2021.198354] [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: 01/13/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 11/18/2022]
Abstract
Identification of new recombinant HCV strains and positive selection sites are crucially important for the formulation of virus intervention measures. However, little is known about the recombinant variant information and positive selection sites of circulating HCV strains in mainland China. In this study, we systematically identified recombinant variants and positive selection sites of HCV in mainland China during the 2010-2019. Phylogenetic analysis results indicated that HCV-6 was one of the dominant genotypes in mainland China during 2010-2019, whereas genotypes 7 and 8 were not detected. Recombinant analysis based on 102 full-length genome sequences of Chinese epidemic strains of HCV identified four intra-genotypic recombinants (strains WYHCV286, GB28, GZ2983, and HCV156) and one inter-genotypic recombinant (strain HH075). Specifically, two breakpoints in the 5' UTR of two recombinants, the strains HH075 and WYHCV286, are rather unusual and has not been described before. Further, selection pressure analyses revealed five positive selective sites, which were located in the core, E2, and NS5B protein. Notably, positive selective sites in NS5B and core protein may be partially responsible for the drug resistance and immune evasion. To the best of our knowledge, this study firstly reported five specific intertypic and intratypic recombinants of Chinese epidemic strains of HCV, which highlight their significance for anti-HCV treatment and vaccine development.
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Affiliation(s)
- Mengdi Qi
- Kunming Medical University, Kunming, Yunnan, China; Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Mengmei Yang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Liangzi Xu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Chunli Ma
- Kunming Medical University, Kunming, Yunnan, China; Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Pu Huang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
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Efficacy of NS5A inhibitors against unusual and potentially difficult-to-treat HCV subtypes commonly found in sub-Saharan Africa and South East Asia. J Hepatol 2020; 73:794-799. [PMID: 32470499 DOI: 10.1016/j.jhep.2020.05.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/22/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The efficacy of NS5A inhibitors against several less common subtypes of hepatitis C virus (HCV) is poorly characterised. Some subtypes including 3b, 3g, 6u and 6v commonly harbour amino acid residues in NS5A that may confer resistance to direct-acting antivirals (DAAs) in other common subtypes. Data from patients also suggest that 1l and 4r with amino acid substitutions at positions 28-31 and 93 in NS5A are relatively resistant to DAA therapy. METHODS In this study, we tested the efficacy of daclatasvir, elbasvir, ledipasvir, pibrentasvir and velpatasvir against these subtypes using the SGR-JFH1 replicon backbone. RESULTS NS5A inhibitors showed different levels of efficacy with only pibrentasvir effective against all tested subtypes. Daclatasvir and ledipasvir were ineffective against 6u and 6v (half maximal effective concentration [EC50] values of 239-321 nM) while 3b and 3g were only susceptible to pibrentasvir. Analysis of effects of individual mutations indicated that Q30R in 1l increased the EC50 of ledipasvir by 18-fold, conferring intermediate resistance, while those of L31M and Y93H in 4r induced increases in EC50 values of 2,100- and 3,575-fold (high-level resistance). CONCLUSION The high ledipasvir EC50 values of 1l with the Q30R substitution, 4r L31M and 4r Y93H may explain the treatment failure in patients who were infected with these viruses and treated with ledipasvir + sofosbuvir. This study also shows the ineffectiveness of the first generation NS5A inhibitors against 6u and 6v, and confirms the inherent resistance of 3b and 3g to most NS5A inhibitors. Clinical studies to confirm in vivo sensitivity to NS5A inhibitors are urgently needed so that rational, effective treatment strategies may be developed for unusual subtypes. LAY SUMMARY Little is known about the efficacy of NS5A inhibitors against some "unusual" hepatitis C virus (HCV) subtypes including 1l, 3b, 3g, 4r, 6u and 6v. In this study, we manufactured HCV replicons which express the NS5A protein from the unusual HCV subtypes 1l, 3b, 3g, 4r, 6u, 6v. We then tested the effect of the NS5A inhibitors daclatasvir, elbasvir, ledipasvir, pibrentasvir and velpatasvir on blocking replication, using these replicons. We show that these replicons are resistant at some level to all NS5A inhibitors other than pibrentasvir.
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Wasitthankasem R, Pimsingh N, Treesun K, Posuwan N, Vichaiwattana P, Auphimai C, Thongpan I, Tongsima S, Vongpunsawad S, Poovorawan Y. Prevalence of Hepatitis C Virus in an Endemic Area of Thailand: Burden Assessment toward HCV Elimination. Am J Trop Med Hyg 2020; 103:175-182. [PMID: 32394881 DOI: 10.4269/ajtmh.19-0817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Chronic hepatitis C virus (HCV) infection can lead to liver cirrhosis and hepatocellular carcinoma. To eliminate HCV infection in an endemic area, an epidemiological baseline of the current HCV infection in the population is required. We therefore aimed to evaluate the HCV burden in the Thai Province of Phetchabun, which has the highest HCV infection rate in the country. Toward this, a province-wide district-based representative sampling of 4,769 individuals ages 35-64 years previously shown to represent high-risk age-groups were tested for anti-HCV antibodies using the automated chemiluminescent microparticle assays. Active HCV infection and subsequent genotyping were determined from serologically reactive samples by amplification of the HCV core gene. We found that 6.9% (327/4,769) were anti-HCV positive, of which 75.8% (248/327) had detectable HCV RNA and 5.8% (19/327) were in the presence of hepatitis B virus coinfection. Nucleotide sequencing and phylogenetic analysis revealed that HCV genotype 6 was the most prevalent (41%, 101/248), followed by genotype 3 (31%, 78/248), and genotype 1 (28%, 69/248). Socioeconomic and demographic factors including male gender, education, and agricultural work were associated with HCV seropositivity. From these results, we defined the regional HCV genotypes and estimated the HCV burden necessary toward the implementation of pan-genotypic direct-acting antivirals, which may be appropriate and effective toward the diversity of genotypes identified in this study. Micro-elimination of HCV in Phetchabun may serve as a model for a more comprehensive coverage of HCV treatment in Thailand.
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Affiliation(s)
- Rujipat Wasitthankasem
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand.,National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand.,Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Napaporn Pimsingh
- Non-Communicable Disease Control Group, Phetchabun Provincial Health Office, Phetchabun, Thailand
| | - Khuandao Treesun
- Non-Communicable Disease Control Group, Phetchabun Provincial Health Office, Phetchabun, Thailand
| | - Nawarat Posuwan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Preeyaporn Vichaiwattana
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chompoonut Auphimai
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ilada Thongpan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand.,National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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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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11
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Ye M, Chen X, Wang Y, Duo L, Zhang C, Zheng YT. Identification of a New HCV Subtype 6xg Among Injection Drug Users in Kachin, Myanmar. Front Microbiol 2019; 10:814. [PMID: 31057519 PMCID: PMC6482298 DOI: 10.3389/fmicb.2019.00814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
Characterizing hepatitis C virus (HCV) genetic diversity not only allows us to trace its origin and evolutionary history, but also provides valuable insights into diagnosis, prevention and therapy of HCV infection. Although eight HCV genotypes and 86 subtypes have been classified, there are still some HCV variants that need to be assigned. The genotype 6 is the most diverse HCV genotype and mainly prevalent in Southeast Asia. In this study, we identified a new HCV subtype 6xg from injection drug users (IDUs) in Kachin, Myanmar. A distinctive feature of 6xg from other subtypes of the genotype 6 was a Lys insertion in NS5A gene, which changes the RRKR/K motif into RRKKR/K. Bayesian analyses showed that HCV 6xg originated during 1984–1988, and experienced a rapid population expansion during 2005–2009. We characterized HCV subtype profile among IDUs in this region, and detected six HCV subtypes, including 1a (12.0%), 3a (12.0%), 3b (24.0%), 6n (16.0%), 6xa (20.0%), and 6xg (12.0%). Importantly, we found that HCV subtype distribution in Kachin was very similar to that in Dehong prefecture of Yunnan, but very distinct from those in other regions of Myanmar and Yunnan, indicating that the China–Myanmar border region shared a unique HCV subtype pattern. The appearance of 6xg and the unique HCV subtype profile among IDUs in the China–Myanmar border region have significant epidemiological and public health implications.
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Affiliation(s)
- Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, The National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, The National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Yu Wang
- KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Lin Duo
- Yunnan Fuwai Cardiovascular Hospital, Kunming, China
| | - Chiyu Zhang
- Pathogen Discovery and Big Data Center, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, The National Kunming High Level Biosafety Research Center for Nonhuman Primate, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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12
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Le Ngoc C, Tran Thi Thanh T, Tran Thi Lan P, Nguyen Mai T, Nguyen Hoa T, Nghiem My N, Le Van T, Le Manh H, Le Thanh P, Nguyen Van Vinh C, Thwaites G, Cooke G, Heilek GM, Shikuma C, Le T, Baker S, Rahman M. Differential prevalence and geographic distribution of hepatitis C virus genotypes in acute and chronic hepatitis C patients in Vietnam. PLoS One 2019; 14:e0212734. [PMID: 30865664 PMCID: PMC6415813 DOI: 10.1371/journal.pone.0212734] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The highest burden of disease from hepatitis C virus (HCV) is found in Southeast Asia, but our understanding of the epidemiology of infection in many heavily burdened countries is still limited. In particular, there is relatively little data on acute HCV infection, the outcome of which can be influenced by both viral and host genetics which differ within the region. We studied HCV genotype and IL28B gene polymorphism in a cohort of acute HCV-infected patients in Southern Vietnam alongside two other cohorts of chronic HCV-infected patients to better understand the epidemiology of HCV infection locally and inform the development of programs for therapy with the increasing availability of directly acting antiviral therapy (DAAs). METHODS We analysed plasma samples from patients with acute and chronic HCV infection, including chronic HCV mono-infection and chronic Human Immunodeficiency Virus (HIV)-HCV coinfection, who enrolled in four epidemiological or clinical research studies. HCV infection was confirmed with RNA testing. The 5' UTR, core and NSB5 regions of HCV RNA positive samples were sequenced, and the genotype and subtype of the viral strains were determined. Host DNA from all HCV positive patients and age- and sex-matched non-HCV-infected control individuals were analysed for IL28B single nucleotide polymorphism (SNP) (rs12979860 and rs8099917). Geolocation of the patients were mapped using QGIS. RESULTS 355 HCV antibody positive patients were analysed; 54.6% (194/355) and 46.4% (161/355) were acute and chronic infections, respectively. 50.4% (81/161) and 49.6.4% (80/161) of chronic infections had HCV mono-infection and HIV-HCV coinfection, respectively. 88.7% (315/355) and 10.1% (36/355) of the patients were from southern and central regions of Vietnam, respectively. 92.4% (328/355) of patients were HCV RNA positive, including 86.1% (167/194) acute and 100% (161/161) chronic infections. Genotype could be determined in 98.4% (322/328) patients. Genotypes 1 (56.5%; 182/322) and 6 (33.9%; 109/322) predominated. Genotype 1 including genotype 1a was significantly higher in HIV-HCV coinfected patients compared to acute HCV patients [43.8% (35/80) versus 20.5% (33/167)], (p = <0.001), while genotype 6 was significantly higher in chronic HCV mono-infected patients [(44.4% (36/81) versus 20.0% (16/80)] (p = < 0.004) compared to HIV-HCV coinfected patients. The prevalence of IL28B SNP (rs12979860) homozygous CC was 86.46% (83/96) in control individuals and was significantly higher in acutely-infected compared to chronically-infected patients [93.2 (82/88) versus 76.1% (35/46)] (p = < 0.005). CONCLUSION HCV genotype 6 is highly prevalent in Vietnam and the high prevalence in treatment naïve chronic HCV patients may results from poor spontaneous clearance of acute HCV infection with genotype 6.
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Affiliation(s)
- Chau Le Ngoc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Trinh Nguyen Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Trang Nguyen Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ngoc Nghiem My
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tan Le Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hung Le Manh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Phuong Le Thanh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Chau Nguyen Van Vinh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | | | - Gabrielle M. Heilek
- Roche Molecular Systems, Inc., Pleasanton, California, United States of America
| | - Cecilia Shikuma
- Hawaii Center for AIDS, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Thuy Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Hawaii Center for AIDS, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Duke University School of Medicine, Durham, NC, United States of America
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- * E-mail:
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13
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Mettikanont P, Bunchorntavakul C, Reddy KR. Systematic review: epidemiology and response to direct-acting antiviral therapy in genotype 6 chronic hepatitis C virus infection. Aliment Pharmacol Ther 2019; 49:492-505. [PMID: 30687952 DOI: 10.1111/apt.15100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/07/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) genotype 6 (GT6) is predominantly encountered in Southeast Asia and data on GT6 response to direct-acting antiviral (DAA) therapy are relatively limited. AIM To review the epidemiology and virologic outcome of DAA regimens in HCV GT6 patients. METHODS Electronic literature search of PubMed, EMBASE, and The Cochrane Library databases were conducted. RESULTS Hepatitis C virus genotype 6 is the most genetically diverse, has a prevalence of 19.9%-95.6% in HCV infected patients in Southeast Asia and has been associated with a higher risk of HCC in those with cirrhosis. After an extensive literature review, a total of 20 studies were selected to assess study population and treatment outcomes (total of 938 GT6 patients were included); 12 were clinical trials and eight were observational studies. Sustained virologic response at week 12 (SVR 12) following glecaprevir/pibrentasvir (n = 4; 108 patients), ledipasvir/sofosbuvir (n = 8; 427 patients), sofosbuvir/velpatasvir with or without voxilaprevir (n = 5; 171 patients), sofosbuvir/daclatasvir (n = 3; 172 patients) and sofosbuvir with ribavirin (n = 3; 60 patients) was 98%-100%, 64%-100%, 100%, 88%-94% and 100%, respectively. Failure was mostly in those with cirrhosis and prior treatment experience. DAA therapy was well tolerated and with a serious adverse event rate of <5%. CONCLUSIONS Hepatitis C virus genotype 6 is genetically diverse and is highly prevalent in Asia. While SVR rates have been high, cirrhosis and prior treatment experience marginally compromise response to DAAs. Large scale and exclusive studies in HCV genotype 6 prevalent areas are needed, while the current evidence suggests that DAAs are highly effective and safe.
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Affiliation(s)
| | - Chalermrat Bunchorntavakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok, Thailand
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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14
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Chen M, Zheng F, Yuan G, Duan X, Rong L, Liu J, Feng S, Wang Z, Wang M, Feng Y, Zhou Q, Li J, Deng K, Li C, Xia J, Rao G, Zhou Y, Fu Y, Li YP. Development of an Infectious Cell Culture System for Hepatitis C Virus Genotype 6a Clinical Isolate Using a Novel Strategy and Its Sensitivity to Direct-Acting Antivirals. Front Microbiol 2018; 9:2950. [PMID: 30564209 PMCID: PMC6288186 DOI: 10.3389/fmicb.2018.02950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus (HCV) is classified into seven major genotypes, and genotype 6 is commonly prevalent in Asia, thus reverse genetic system representing genotype 6 isolates in prevalence is required. Here, we developed an infectious clone for a Chinese HCV 6a isolate (CH6a) using a novel strategy. We determined CH6a consensus sequence from patient serum and assembled a CH6a full-length (CH6aFL) cDNA using overlapped PCR product-derived clones that shared the highest homology with the consensus. CH6aFL was non-infectious in hepatoma Huh7.5 cells. Next, we constructed recombinants containing Core-NS5A or 5′UTR-NS5A from CH6a and the remaining sequences from JFH1 (genotype 2a), and both were engineered with 7 mutations identified previously. However, they replicated inefficiently without virus spread in Huh7.5 cells. Addition of adaptive mutations from CH6a Core-NS2 recombinant, with JFH1 5′UTR and NS3-3′UTR, enhanced the viability of Core-NS5A recombinant and acquired replication-enhancing mutations. Combination of 22 mutations in CH6a recombinant with JFH1 5′UTR and 3′UTR (CH6aORF) enabled virus replication and recovered additional four mutations. Adding these four mutations, we generated two efficient recombinants containing 26 mutations (26m), CH6aORF_26m and CH6aFL_26m (designated “CH6acc”), releasing HCV of 104.3–104.5 focus-forming units (FFU)/ml in Huh7.5.1-VISI-mCherry and Huh7.5 cells. Seven newly identified mutations were important for HCV replication, assembly, and release. The CH6aORF_26m virus was inhibited in a dose- and genotype-dependent manner by direct-acting-antivirals targeting NS3/4A, NS5A, and NS5B. The CH6acc enriches the toolbox of HCV culture systems, and the strategy and mutations applied here will facilitate the culture development of other HCV isolates and related viruses.
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Affiliation(s)
- Mingxiao Chen
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Fuxiang Zheng
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Guosheng Yuan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaobing Duan
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Liang Rong
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Junwei Liu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shengjun Feng
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Ziting Wang
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Min Wang
- Guangzhou Blood Center, Guangzhou, China
| | - Yetong Feng
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Qing Zhou
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Jinqian Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Kai Deng
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Chunna Li
- Program of Pathobiology, The Fifth Affiliated Hospital and Zhongshan School of Medicine, Sun Yat-sen University, Guangdong, China
| | - Jinyu Xia
- Program of Pathobiology, The Fifth Affiliated Hospital and Zhongshan School of Medicine, Sun Yat-sen University, Guangdong, China
| | - Guirong Rao
- Key Laboratory of Liver Disease, Center of Infectious Diseases, PLA 458 Hospital, Guangzhou, China
| | - Yuanping Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Program of Pathobiology, The Fifth Affiliated Hospital and Zhongshan School of Medicine, Sun Yat-sen University, Guangdong, China
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15
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Hepatitis B, C and D virus genotypes detected in HBsAg- or anti-HCV-positive people from the Republic of Moldova. Arch Virol 2017; 163:431-438. [PMID: 29119358 DOI: 10.1007/s00705-017-3632-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/14/2017] [Indexed: 10/18/2022]
Abstract
In the Republic of Moldova, little is known about hepatitis B, C and D virus (HBV, HCV, HDV) genotypes, although the genetic variant may influence the course and outcome of disease. For HBV genotyping, 301 hepatitis B surface antigen (HBsAg)-positive sera collected in 2010 and 2011 from drug users, prison inmates, commercial sex workers, and the general population in different geographical regions were investigated. The 31 HBsAg-positive sera collected in 2011 were also tested for HDV. Eighty-eight anti-HCV-positive sera collected between 2010 and 2011 from the general population and health care workers were used for HCV genotyping. Phylogenetic analysis of 84 HBV sequences showed that most of the viruses belonged to genotype D (n = 82, 97.6%), predominantly to the subgenotype D1/D2 cluster (n = 75/82, 91.5%). One sequence (74110) clustered as an outlier to this cluster, and six sequences belonged to subgenotype D3. Only two subgenotype A2 sequences were found. Cloning of six samples with ambiguous sequence chromatogram signals showed no mixed infections. Phylogenetic analysis of HCV sequences from 66 patients showed a predominance of subtype 1b (n = 63, 95.5%). Two sequences belonged to subtype 3a, and one to subtype 2a. HDV RNA belonging to genotype 1 was found in two sera (2/31, 6.5%). Thus, genotypes prevalent in Europe were detected for all three hepatitis viruses. For both HBV and HCV, one genotype was dominant, while occasional other variants seem to be restricted to certain cohorts and/or transmission routes.
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16
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Abstract
Hepatitis C virus (HCV) is a hepatotropic RNA virus that causes progressive liver damage, which might result in liver cirrhosis and hepatocellular carcinoma. Globally, between 64 and 103 million people are chronically infected. Major risk factors for this blood-borne virus infection are unsafe injection drug use and unsterile medical procedures (iatrogenic infections) in countries with high HCV prevalence. Diagnostic procedures include serum HCV antibody testing, HCV RNA measurement, viral genotype and subtype determination and, lately, assessment of resistance-associated substitutions. Various direct-acting antiviral agents (DAAs) have become available, which target three proteins involved in crucial steps of the HCV life cycle: the NS3/4A protease, the NS5A protein and the RNA-dependent RNA polymerase NS5B protein. Combination of two or three of these DAAs can cure (defined as a sustained virological response 12 weeks after treatment) HCV infection in >90% of patients, including populations that have been difficult to treat in the past. As long as a prophylactic vaccine is not available, the HCV pandemic has to be controlled by treatment-as-prevention strategies, effective screening programmes and global access to treatment.
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17
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Sistayanarain A, Chaiwong S. Molecular characterization of hepatitis C virus genotype 6 subtypes in Thai blood donors. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 50:26-31. [DOI: 10.1016/j.jmii.2015.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 01/02/2015] [Accepted: 01/19/2015] [Indexed: 02/08/2023]
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18
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Win NN, Kanda T, Nakamoto S, Yokosuka O, Shirasawa H. Hepatitis C virus genotypes in Myanmar. World J Gastroenterol 2016; 22:6095-6099. [PMID: 27468202 PMCID: PMC4945971 DOI: 10.3748/wjg.v22.i27.6095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/23/2016] [Accepted: 06/13/2016] [Indexed: 02/06/2023] Open
Abstract
Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.
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19
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Chen M, Ma Y, Chen H, Luo H, Dai J, Song L, Yang C, Mei J, Yang L, Dong L, Jia M, Lu L. Multiple Introduction and Naturally Occuring Drug Resistance of HCV among HIV-Infected Intravenous Drug Users in Yunnan: An Origin of China's HIV/HCV Epidemics. PLoS One 2015; 10:e0142543. [PMID: 26562015 PMCID: PMC4642981 DOI: 10.1371/journal.pone.0142543] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/25/2015] [Indexed: 02/07/2023] Open
Abstract
Background The human immunodeficiency virus 1 (HIV-1) epidemic in China historically stemmed from intravenous drug users (IDUs) in Yunnan. Due to a shared transmission route, hepatitis C virus (HCV)/HIV-1 co-infection is common. Here, we investigated HCV genetic characteristics and baseline drug resistance among HIV-infected IDUs in Yunnan. Methods Blood samples of 432 HIV-1/HCV co-infected IDUs were collected from January to June 2014 in six prefectures of Yunnan Province. Partial E1E2 and NS5B genes were sequenced. Phylogenetic, evolutionary and genotypic drug resistance analyses were performed. Results Among the 293 specimens successfully genotyped, seven subtypes were identified, including subtypes 3b (37.9%, 111/293), 3a (21.8%, 64/293), 6n (14.0%, 41/293), 1b (10.6%, 31/293), 1a (8.2%, 24/293), 6a (5.1%, 15/293) and 6u (2.4%, 7/293). The distribution of HCV subtypes was mostly related to geographic location. Subtypes 3b, 3a, and 6n were detected in all six prefectures, however, the other four subtypes were detected only in parts of the six prefectures. Phylogeographic analyses indicated that 6n, 1a and 6u originated in the western prefecture (Dehong) and spread eastward and showed genetic relatedness with those detected in Burmese. However, 6a originated in the southeast prefectures (Honghe and Wenshan) bordering Vietnam and was transmitted westward. These subtypes exhibited different evolutionary rates (between 4.35×10−4 and 2.38×10−3 substitutions site-1 year-1) and times of most recent common ancestor (tMRCA, between 1790.3 and 1994.6), suggesting that HCV was multiply introduced into Yunnan. Naturally occurring resistance-associated mutations (C316N, A421V, C445F, I482L, V494A, and V499A) to NS5B polymerase inhibitors were detected in direct-acting antivirals (DAAs)-naïve IDUs. Conclusion This work reveals the temporal-spatial distribution of HCV subtypes and baseline HCV drug resistance among HIV-infected IDUs in Yunnan. The findings enhance our understanding of the characteristics and evolution of HCV in IDUs and are valuable for developing HCV prevention and management strategies for this population.
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Affiliation(s)
- Min Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Yanling Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Huichao Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Hongbing Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Jie Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Lijun Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Chaojun Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Jingyuan Mei
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Li Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Lijuan Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
| | - Manhong Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
- * E-mail: (MJ); (LL)
| | - Lin Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, 650022, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, 650500, China
- * E-mail: (MJ); (LL)
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20
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Cheng CH, Chen HL, Lin IT, Wu CH, Lee YK, Wong MW, Bair MJ. The genotype distribution of hepatitis C in southeastern Taiwan: Clinical characteristics, racial difference, and therapeutic response. Kaohsiung J Med Sci 2015; 31:597-602. [PMID: 26678941 DOI: 10.1016/j.kjms.2015.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/04/2015] [Accepted: 09/14/2015] [Indexed: 02/07/2023] Open
Abstract
The genotypes of hepatitis C virus (HCV) are associated with the therapeutic response. The racial diversity of Taitung, Taiwan is heterogeneous and a distinguishing feature; how such racial differences influence the genotype distribution and treatment outcome has not been well studied. The objective of this study is to elucidate the HCV genotype distribution in southeastern Taiwan and to analyze the racial differences influencing genotypes and clinical implications. In this retrospective cohort study, we included 343 patients who had been treated with peginterferon-alpha plus ribavirin. The predominant HCV genotype in the southeastern area was type 1 (43.7%), followed by type 2 (37.0%). The proportion of patients mixed with genotype 1 was lower in indigenous vis-à-vis nonindigenous groups (46.1% and 60.2%, p = 0.02). The prevalence of genotype 6 (5.2%) seems higher than in the general population of Taiwan and showed no difference between indigenous and nonindigenous people. The sustained virological response rate was higher in patients without genotype 1, low baseline HCV RNA (≤ 400,000 IU/mL), and in patients who achieved rapid virological response. Racial differences did not influence the therapeutic response. In this retrospective study, the proportion of HCV genotype 6 appeared slightly higher in southeastern areas than in the general population in Taiwan. The prevalence of genotype 1 in indigenous people was statistically lower than in nonindigenous people. Sustained virological response rate did not show any significant difference between indigenous and nonindigenous people in the current study.
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Affiliation(s)
- Chun-Han Cheng
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan
| | - Huan-Lin Chen
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan
| | - I-Tsung Lin
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan
| | - Chia-Hsien Wu
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan
| | - Yuan-Kai Lee
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan
| | - Ming-Wun Wong
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan
| | - Ming-Jong Bair
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taitung, Taiwan; Department of Medicine, Mackay Medical College, New Taipei, Taiwan.
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21
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Cai Q, Zhang X, Lin C, Shao X, Guan Y, Deng H, Wei M, Huang M, Ren Z, Lu L, Mei Y, Xu M, Zhu J, Shi H, Lin G, Liu Y, Hu F, Luo Q, Lan Y, Guo F, Zhao Z, Gao Z. 24 versus 48 Weeks of Peginterferon Plus Ribavirin in Hepatitis C Virus Genotype 6 Chronically Infected Patients with a Rapid Virological Response: A Non-Inferiority Randomized Controlled Trial. PLoS One 2015; 10:e0140853. [PMID: 26509605 PMCID: PMC4624894 DOI: 10.1371/journal.pone.0140853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/29/2015] [Indexed: 12/27/2022] Open
Abstract
Objectives The optimal treatment of hepatitis C virus (HCV) genotype 6 is unclear owing to its limited geographic distribution. Because of a high predictive value of rapid virological response (RVR) for sustained virological response (SVR), we conducted an open-label randomized controlled trial to compare 24- and 48-week peginterferon/ribavirin combination therapy for patients with HCV genotype 6 in Southern China who achieved an RVR. Methods and Findings Treatment-naive, non-cirrhotic patients with chronic hepatitis C genotype 6 were treated with pegylated interferon α-2a (180 μg/week) and ribavirin (800–1,200 mg, according to weight) for 4 weeks. Patients who achieved an RVR, which was defined as HCV RNA negativity at week 4 (<50 IU), were randomized to receive either an additional 20 or 44 weeks of treatment (24- and 48-week treatment groups, respectively). The primary outcome measure was SVR. From January 2011 to June 2014, 152(152/210, 72.4%) patients with HCV genotype 6a and RVR were randomized 1:1 to the 24- or 48-week treatment group. The SVR rates in the 24- and 48-week groups in the intention-to-treat analysis were 90.8% (69/76) and 88.2% (67/76), respectively; those in the per-protocol analysis were 95.7% (67/70) and 97.0% (64/66), respectively. More patients in the 48-week group had anemia (46.1% vs. 28.9%, P = 0.03), but other adverse events were comparable between the groups. The limitation of the present study was that only patients from Southern China were enrolled which may inhibit the extensive application of the findings. Conclusion Twenty-four weeks of peginterferon/ribavirin combination therapy was non-inferior to 48 weeks in patients with HCV genotype 6a in Southern China who achieved an RVR. Trial Registration ClinicalTrials.gov NCT01263860
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Affiliation(s)
- Qingxian Cai
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaohong Zhang
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chaoshuang Lin
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaoqiong Shao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yujuan Guan
- Eighth People’s Hospital of Guangzhou, Guangzhou, Guangdong, China
| | - Hong Deng
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Min Wei
- Zhongshan Second People’s Hospital, Zhongshan, Guangdong, China
| | | | - Zefang Ren
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Ling Lu
- Laboratory for Hepatology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yongyu Mei
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Min Xu
- Eighth People’s Hospital of Guangzhou, Guangzhou, Guangdong, China
| | - Jianyun Zhu
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Haiyan Shi
- Eighth People’s Hospital of Guangzhou, Guangzhou, Guangdong, China
| | - Guoli Lin
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ying Liu
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Fengyu Hu
- Eighth People’s Hospital of Guangzhou, Guangzhou, Guangdong, China
| | - Qiumin Luo
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yun Lan
- Eighth People’s Hospital of Guangzhou, Guangzhou, Guangdong, China
| | - Fengxia Guo
- Eighth People’s Hospital of Guangzhou, Guangzhou, Guangdong, China
| | - Zhixin Zhao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- * E-mail:
| | - Zhiliang Gao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
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22
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Wasitthankasem R, Vongpunsawad S, Siripon N, Suya C, Chulothok P, Chaiear K, Rujirojindakul P, Kanjana S, Theamboonlers A, Tangkijvanich P, Poovorawan Y. Genotypic distribution of hepatitis C virus in Thailand and Southeast Asia. PLoS One 2015; 10:e0126764. [PMID: 25962112 PMCID: PMC4427325 DOI: 10.1371/journal.pone.0126764] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/07/2015] [Indexed: 02/06/2023] Open
Abstract
The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world’s population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5’ untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27–36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread.
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Affiliation(s)
- Rujipat Wasitthankasem
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nipaporn Siripon
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chutima Suya
- Chiangrai Prachanukroh Hospital, Chiang Rai, Thailand
| | | | | | - Pairaya Rujirojindakul
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sawan Kanjana
- Regional Blood Center XI Nakhorn Si Thammarat, Thai Red Cross Society, Thung Song District, Nakhon Si Thammarat, Thailand
| | - Apiradee Theamboonlers
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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23
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Li C, Barnes E, Newton PN, Fu Y, Vongsouvath M, Klenerman P, Okamoto H, Abe K, Pybus OG, Lu L. An expanded taxonomy of hepatitis C virus genotype 6: Characterization of 22 new full-length viral genomes. Virology 2015; 476:355-363. [PMID: 25589238 PMCID: PMC4376965 DOI: 10.1016/j.virol.2014.12.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/06/2014] [Accepted: 12/16/2014] [Indexed: 12/25/2022]
Abstract
We characterized the full-length genomes of 22 hepatitis C virus genotype 6 (HCV-6) isolates: 10 from Vietnam (classified into subtypes 6e, 6h, 6p, 6r, 6s, and 6u), one from China (confirmed as a new subtype 6xd), and 11 from the Lao PDR (representing a new subtype 6xe plus eight novel variants). With these 22 new genomes, HCV-6 now has a diverse and extended taxonomic structure, comprised of 28 assigned subtypes (denoted 6a-6xe) and 27 unassigned lineages, all of which have been represented by full-length genomes. Our phylogenetic analyses also included many partially-sequenced novel variants of HCV-6 from Lao PDR. This revealed that Lao HCV isolates are genetically very diverse and are phylogenetically distributed in multiple lineages within genotype 6. Our results suggest that HCV-6 has been maintained in Laos, a landlocked country, since the common ancestor of genotype 6 and indicates historical dispersal of HCV-6 across Southeast Asia. We characterized 22 full-length genomes of HCV-6. They confirmed two new subtypes 6xd and 6xe plus eight novel variants. We also reanalyzed many partially-sequenced novel HCV-6 variants from Lao PDR. They are phylogenetically distributed across the whole of genotype 6. They indicate historical dispersal of HCV-6 across Southeast Asia.
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Affiliation(s)
- Chunhua Li
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Eleanor Barnes
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road and Oxford NIHR Biomedical Research Centre, OX1 3SY, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine and Global Health, Churchill Hospital, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou 510095, China
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic
| | - Paul Klenerman
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road and Oxford NIHR Biomedical Research Centre, OX1 3SY, UK
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi Tochigi 329-0498, Japan
| | - Kenji Abe
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
| | - Ling Lu
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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24
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Li C, Yuan M, Lu L, Lu T, Xia W, Pham VH, Vo AXD, Nguyen MH, Abe K. The genetic diversity and evolutionary history of hepatitis C virus in Vietnam. Virology 2014; 468-470:197-206. [PMID: 25193655 DOI: 10.1016/j.virol.2014.07.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 12/21/2022]
Abstract
Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6 e, 6h, 6k, 6l, 6 o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6 e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955 to 1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2.
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Affiliation(s)
- Chunhua Li
- Department of pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Manqiong Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen, Fujian, 361102, PR China
| | - Ling Lu
- Department of pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, KS, United States of America.
| | - Teng Lu
- Department of pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, KS, United States of America; University of Southern California, Los Angeles, CA, United States of America
| | - Wenjie Xia
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Van H Pham
- Center for Molecular Biomedicine, School of Medicine, University of Medicine and Pharmacy in Ho Chi Minh City, Ho Chi Minh City, Vietnam; Molecular Diagnostic Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam
| | - An X D Vo
- Molecular Diagnostic Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam
| | - Mindie H Nguyen
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Palo Alto, CA, United States of America
| | - Kenji Abe
- Center for Molecular Biomedicine, School of Medicine, University of Medicine and Pharmacy in Ho Chi Minh City, Ho Chi Minh City, Vietnam; Molecular Diagnostic Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam; Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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25
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Thong VD, Akkarathamrongsin S, Poovorawan K, Tangkijvanich P, Poovorawan Y. Hepatitis C virus genotype 6: virology, epidemiology, genetic variation and clinical implication. World J Gastroenterol 2014; 20:2927-40. [PMID: 24659883 PMCID: PMC3961978 DOI: 10.3748/wjg.v20.i11.2927] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/06/2014] [Accepted: 01/19/2014] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is a serious public health problem affecting 170 million carriers worldwide. It is a leading cause of chronic hepatitis, cirrhosis, and liver cancer and is the primary cause for liver transplantation worldwide. HCV genotype 6 (HCV-6) is restricted to South China, South-East Asia, and it is also occasionally found in migrant patients from endemic countries. HCV-6 has considerable genetic diversity with 23 subtypes (a to w). Although direct sequencing followed by phylogenetic analysis is the gold standard for HCV-6 genotyping and subtyping, there are also now rapid genotyping tests available such as the reverse hybridization line probe assay (INNO-LiPA II; Innogenetics, Zwijnaarde, Belgium). HCV-6 patients present with similar clinical manifestations as patients infected with other genotypes. Based on current evidence, the optimal treatment duration of HCV-6 with pegylated interferon/ribavirin should be 48 wk, although a shortened treatment duration of 24 wk could be sufficient in patients with low pretreatment viral load who achieve rapid virological response. In addition, the development of direct-acting antiviral agents is ongoing, and they give high response rate when combined with standard therapy. Herein, we review the epidemiology, classification, diagnosis and treatment as it pertain to HCV-6.
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26
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Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 2014; 59:318-27. [PMID: 24115039 PMCID: PMC4063340 DOI: 10.1002/hep.26744] [Citation(s) in RCA: 924] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/29/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED The 2005 consensus proposal for the classification of hepatitis C virus (HCV) presented an agreed and uniform nomenclature for HCV variants and the criteria for their assignment into genotypes and subtypes. Since its publication, the available dataset of HCV sequences has vastly expanded through advancement in nucleotide sequencing technologies and an increasing focus on the role of HCV genetic variation in disease and treatment outcomes. The current study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near-)complete genome sequences of HCV available on public databases in May 2013. Analysis resolved several nomenclature conflicts between genotype designations and using consensus criteria created a classification of HCV into seven confirmed genotypes and 67 subtypes. There are 21 additional complete coding region sequences of unassigned subtype. The study additionally describes the development of a Web resource hosted by the International Committee for Taxonomy of Viruses (ICTV) that maintains and regularly updates tables of reference isolates, accession numbers, and annotated alignments (http://talk.ictvonline.org/links/hcv/hcv-classification.htm). The Flaviviridae Study Group urges those who need to check or propose new genotypes or subtypes of HCV to contact the Study Group in advance of publication to avoid nomenclature conflicts appearing in the literature. While the criteria for assigning genotypes and subtypes remain unchanged from previous consensus proposals, changes are proposed in the assignment of provisional subtypes, subtype numbering beyond "w," and the nomenclature of intergenotypic recombinant. CONCLUSION This study represents an important reference point for the consensus classification of HCV variants that will be of value to researchers working in clinical and basic science fields.
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Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenDenmark
| | - Carla Kuiken
- Theoretical Biology and Biophysics group, Los Alamos National LaboratoryLos Alamos, NM, USA
| | | | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller UniversityNew York, NY, USA
| | - Jack T Stapleton
- Medical Service, Iowa City Veterans Affairs Medical Center, Departments of Internal Medicine and Microbiology, University of IowaIowa City, IA, USA
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
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27
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Bunchorntavakul C, Chavalitdhamrong D, Tanwandee T. Hepatitis C genotype 6: A concise review and response-guided therapy proposal. World J Hepatol 2013; 5:496-504. [PMID: 24073301 PMCID: PMC3782687 DOI: 10.4254/wjh.v5.i9.496] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/05/2013] [Accepted: 08/13/2013] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C genotype 6 is endemic in Southeast Asia [prevalence varies between 10%-60% among all hepatitis C virus (HCV) infection], as well as also sporadically reported outside the area among immigrations. The diagnosis of HCV genotype can be inaccurate with earlier methods of genotyping due to identical 5’-UTR between genotype 6 and 1b, hence the newer genotyping methods with core sequencing are preferred. Risk factors and clinical course of HCV genotype 6 do not differ considerably from other genotypes. Treatment outcome of HCV genotype 6 with a combination of pegylated interferon and ribavirin is superior to genotype 1, and nearly comparable to genotype 3, with expected sustained virological response (SVR) rates of 60%-90%. Emerging data suggests that a shorter course 24-wk treatment is equally effective as a standard 48-wk treatment, particularly for those patients who attained undetectable HCV RNA at week 4 (RVR). In addition, baseline and on-treatment predictors of response used for other HCV genotypes appear effective with genotype 6. Although some pan-genotypic direct-acting antivirals have completed phase II/III studies (sofosbuvir and simeprevir) with clinical benefit demonstrated in small number of patients with genotype 6, broad availability of these agents in Southeast Asia may not be expected in the near future. While awaiting the newer therapy, response-guided therapy seems appropriate for patients with HCV genotype 6. Patients with RVR (representing > 70% of patients) are suitable for 24-wk treatment with expected SVR rates > 80%. Patients without RVR and/or those with poor response predictors may benefit from 48 wk of therapy, and a detectable HCV RNA at week 12 (with no early virological response) serves as a stopping rule. This treatment scheme is likely to have a major economic impact on HCV therapy, particularly in Southeast Asia, wherein treatment can be truncated securely in the majority of patients with HCV genotype 6.
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28
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Akkarathamrongsin S, Hacharoen P, Tangkijvanich P, Theamboonlers A, Tanaka Y, Mizokami M, Poovorawan Y. Molecular epidemiology and genetic history of hepatitis C virus subtype 3a infection in Thailand. Intervirology 2013; 56:284-294. [PMID: 23838334 DOI: 10.1159/000351621] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 04/22/2013] [Indexed: 10/10/2023] Open
Abstract
OBJECTIVE Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. METHODS Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. RESULTS Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. CONCLUSION The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.
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Affiliation(s)
- S Akkarathamrongsin
- Inter-Department of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
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29
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Nguyen LH, Nguyen MH. Systematic review: Asian patients with chronic hepatitis C infection. Aliment Pharmacol Ther 2013; 37:921-36. [PMID: 23557103 DOI: 10.1111/apt.12300] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 10/16/2012] [Accepted: 03/12/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND Chronic hepatitis C (CHC) infection is a risk factor for both the development of end-stage liver disease and hepatocellular carcinoma (HCC). Globally, approximately 170 million people are chronically infected with the hepatitis C virus (HCV), and the majority of these individuals come from the western Pacific and Southeast Asia regions (94.6 million persons combined). CHC is an understudied and underappreciated health problem in many Asian countries and in the US, where Asians represent one of the fastest growing groups of new Americans. AIM To perform a systematic review of the current literature on the epidemiology, diagnosis and screening, clinical characteristics and response to anti-viral therapy of Asians with CHC. METHODS Using a PubMed search of 'hepatitis C' and 'Asia,' 341 original manuscripts published in peer-reviewed journals were identified, and 99 were selected based on their relevance. RESULTS Many Asian CHC patients do not have easily identifiable risk factors and may be underdiagnosed. Rates of HCV infection in Asians on community screening in the US are unexpectedly high, and there is a high prevalence of HCV genotype 6 in Southeast Asia and Southern China. HCV-infected Asians tend to present at older age and may have higher risk of HCC; however, they respond better to anti-viral therapy than non-Asians across all HCV genotypes. CONCLUSIONS Given the high HCV endemicity in Asia, lack of identifiable risk factors and favourable treatment response rates in Asians, we advocate the screening for HCV infection of all Asians who come from areas where HCV prevalence is ≥2%.
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Affiliation(s)
- L H Nguyen
- Stanford University School of Medicine, Stanford, CA, USA
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30
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Rong X, Lu L, Wang J, Xiong H, Huang J, Chen J, Huang K, Xu R, Wang M, Zhang X, Guo T, Liu Y, Gao G, Fu Y, Nelson KE. Correlation of viral loads with HCV genotypes: higher levels of virus were revealed among blood donors infected with 6a strains. PLoS One 2012; 7:e52467. [PMID: 23285053 PMCID: PMC3524124 DOI: 10.1371/journal.pone.0052467] [Citation(s) in RCA: 19] [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: 09/10/2012] [Accepted: 11/13/2012] [Indexed: 12/18/2022] Open
Abstract
Background Both HCV genotypes and viral loads are predictors of therapeutic outcomes among patients treated with α-interferon plus ribavirin; however, such correlation has only been studied for genotypes 1, 2, and 3 but not for genotype 6. Methodology/Findings 299 voluntary blood donors were recruited who were HCV viremic. Their mean age was 31.8; the male/female ratio was 3.82 (225/59). The viral loads of HCV were measured using the COBAS AmpliPrep/COBAS TaqMan test (CAP/CTM) while HCV genotypes were determined by direct sequencing the partial NS5B region. HCV genotypes 1, 2, 3, and 6 were determined in 48.9%, 8.7%, 12.3%, and 30.1% of the donors, respectively, and the levels of mean viral loads in genotype 1 and 6 significantly higher than that of 2 and 3 (P<0.001). As a whole, the viral loads in male donors were higher than in female (P = 0.006). Moreover, the donors' gender and HCV genotypes are independently correlated with the measured viral loads. Conclusion HCV genotype 1 and 6 had significantly higher viral loads than genotype 2 and 3.
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Affiliation(s)
- Xia Rong
- Department of Biochemistry, Medical College of Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Ling Lu
- Center for Viral Oncology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Junzhi Wang
- National Institutes for Food and Drug Control, Beijing, China
| | | | | | - Jinyan Chen
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Ke Huang
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Ru Xu
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Min Wang
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Xuemei Zhang
- Department of Biochemistry, Medical College of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tai Guo
- National Institutes for Food and Drug Control, Beijing, China
| | - Yueyue Liu
- National Institutes for Food and Drug Control, Beijing, China
| | - Guoquan Gao
- Department of Biochemistry, Medical College of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong, China
- * E-mail:
| | - Kenrad E. Nelson
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| |
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