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Mane A, Kasibhatla SM, Vidhate P, Saxena V, Patil S, Rao A, Nirmalkar A, Kulkarni-Kale U, Panda S. Phylogenetic Analysis of Spread of Hepatitis C Virus Identified during HIV Outbreak Investigation, Unnao, India. Emerg Infect Dis 2022; 28:725-733. [PMID: 35318918 PMCID: PMC8962895 DOI: 10.3201/eid2804.211845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
An HIV outbreak investigation during 2017–2018 in Unnao District, Uttar Pradesh, India, unearthed high prevalence of hepatitis C virus (HCV) antibodies among the study participants. We investigated these HCV infections by analyzing NS5B and core regions. We observed no correlation between HIV–HCV viral loads and clustering of HCV sequences, regardless of HIV serostatus. All HCV isolates belonged to genotype 3a. Monophyletic clustering of isolates in NS5B phylogeny indicates emergence of the outbreak from a single isolate or its closely related descendants. The nucleotide substitution rate for NS5B was 6 × 10−3 and for core was 2 × 10−3 substitutions/site/year. Estimated time to most recent common ancestor of these isolates was 2012, aligning with the timeline of this outbreak, which might be attributable to unsafe injection practices while seeking healthcare. HIV–HCV co-infection underlines the need for integrated testing, surveillance, strengthening of healthcare systems, community empowerment, and molecular analyses as pragmatic public health tools.
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Chuaypen N, Khlaiphuengsin A, Prasoppokakorn T, Susantitaphong P, Prasithsirikul W, Avihingsanon A, Tangkijvanich P, Praditpornsilpa K. Prevalence and genotype distribution of hepatitis C virus within hemodialysis units in Thailand: role of HCV core antigen in the assessment of viremia. BMC Infect Dis 2022; 22:79. [PMID: 35065604 PMCID: PMC8783655 DOI: 10.1186/s12879-022-07074-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/17/2022] [Indexed: 12/19/2022] Open
Abstract
Background Individuals with end-stage renal disease have a higher risk of hepatitis C virus (HCV) acquisition during long-term hemodialysis (HD). Our report was designed to investigate HCV prevalence and genotype, in addition to the clinical use of HCV core antigen (HCVcAg), within multiple HD facilities in Thailand. Methods This cross‐sectional report was investigated between January and June 2019. HCV infection was assessed by anti-HCV and confirmed active infection by measuring HCV RNA and HCVcAg. HCV genotype was determined by phylogenetic analysis using nucleotide sequences of NS5B region. Results Overall, 140 of 3,305 (4.2%) patients in 15 dialysis centers had anti-HCV positive. Among them, HCV RNA was further assessed in 93 patients and was detectable in 59 (63.4%) persons. Considering HCV viremia, HCVcAg measurement exhibited high accuracy (96.8%), sensitivity (94.9%) and specificity (100%) in comparison with HCV RNA testing. Moreover, individuals infected with HCV received a longer duration of dialysis vintage when compared to anti-HCV negative controls. The major sub-genotypes were 1a, 1b, 3a, 3b, 6f and 6n. Regarding phylogenetic analysis, there were 7 clusters of isolates with high sequence homology affecting 17 individuals, indicating possible HCV transmission within the same HD centers. Conclusions HCV frequency and common sub-genotypes in HD centers were different from those found in the Thai general population. HCVcAg might be an alternate testing for viremia within resource-limited countries. Enhanced preventive practices, dialyzer reuse policy and better access to antiviral therapy are crucial for HCV micro-elimination within HD facilities.
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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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4
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Roger S, Ducancelle A, Le Guillou-Guillemette H, Gaudy C, Lunel F. HCV virology and diagnosis. Clin Res Hepatol Gastroenterol 2021; 45:101626. [PMID: 33636428 DOI: 10.1016/j.clinre.2021.101626] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) infection is a major cause of severe liver disease including chronic hepatitis, cirrhosis and hepatocellular carcinoma. The HCV burden in public health is estimated at about 71 million people worldwide by World Health Organization (WHO) with at least 400,000 people that died every year from HCV disease [1]. New hepatitis C treatments with oral direct-acting antivirals (DAAs) showing high rates of response, with short treatment duration [2] have been available. HCV can now be eradicated with minimal side effects. Unfortunately, there is no vaccine yet available, but the development of a safe prophylactic vaccine remains a medical priority [3]. For this purpose, Hepatitis B-C subviral envelope particles can be produced by industrialized procedure. It seems to be very promising as this HBV-HCV vaccine candidate has been shown to elicit a broadly cross neutralizing activity against HCV [4]. Despite this revolution in the HCV-treatment, one of major challenge to achieve a global eradication of HCV remains to reduce the under diagnosis. The low rate of diagnosis is a major obstacle in resources limited countries and is mainly due to the cost of molecular tools, that are essential to diagnose and follow chronic HCV infection. In another hand, the mild clinical symptoms observed in HCV chronic disease, may explain that the majority of HCV infected individuals are unaware of their infection, because HCV testing is not generalized, like it is for HIV. HCV was discovered in 1989 after many years of work, by several researchers, who recently obtained the Nobel price [5-7]. This major discovery allowed the description of the HCV genome and later on of the virus replication and cell cycle, and also, importantly, the development of diagnostic tests for the detection of HCV antibodies (Ab) and RNA who were a priority in transfusion. In this review, we will try to get into the virology and cell biology of HCV. Thereafter, we will discuss the different categories of laboratory tests to diagnose/explore HCV infected subjects.
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Affiliation(s)
- Steven Roger
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France
| | - Alexandra Ducancelle
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France
| | - Hélène Le Guillou-Guillemette
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France
| | - Catherine Gaudy
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, 37000 Tours, France; INSERM U1259, Université de Tours, 37000 Tours, France
| | - Françoise Lunel
- Laboratoire de Virologie, CHU Angers et Université d'Angers, Laboratoire HIFIH UFR Santé Département Médecine, SFR 4208-UPRES EA3859, BAT IBS - 4 rue Larrey, 49000 Angers, France.
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5
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Posuwan N, Vuthitanachot V, Chinchai T, Wasitthankasem R, Wanlapakorn N, Poovorawan Y. Serological evidence of hepatitis A, B, and C virus infection in older adults in Khon Kaen, Thailand and the estimated rates of chronic hepatitis B and C virus infection in Thais, 2017. PeerJ 2019; 7:e7492. [PMID: 31489265 PMCID: PMC6705384 DOI: 10.7717/peerj.7492] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/16/2019] [Indexed: 01/02/2023] Open
Abstract
Hepatitis A (HAV), hepatitis B (HBV), and hepatitis C (HCV) viruses are hepatotropic viruses responsible for acute/chronic hepatitis associated with liver failure, cirrhosis, and hepatocellular carcinoma. Due to the limited data on the prevalence of hepatitis in the older population in Thailand, this study aimed to evaluate the seroprevalence of these viruses in elderly Thais. Using an automated immunoassay, serum samples from individuals older than 60 years of age in Chum Phae district of Khon Kaen province in northeast Thailand were analyzed for anti-HAV (n = 93), HBV markers (n = 460, HBsAg, anti-HBs, and anti-HBc), and anti-HCV (n = 460). Samples were classified into five age groups (61-65, 66-70, 71-75, 76-80, and >80 years). The overall seroprevalence of anti-HAV, HBsAg, anti-HBc, anti-HBs, and anti-HCV was 98.9%, 4.6%, 51.5%, 32.4%, and 1.3%, respectively. When samples were stratified into three groups representing three generations (children/young adults aged 6 months-30 years and middle-aged adults between 31-60 years old from a previous survey, and older adults aged >60 years from the current study), the highest levels of anti-HAV and anti-HBc were found in older adults. Children/young adults had the lowest levels of HBsAg and anti-HCV, and the highest level of anti-HBs. These findings are consistent with the integration of HBV vaccination into the Expanded Program on Immunization (EPI) in 1992 and coincide with increased awareness of blood-borne viral transmission in Thailand. Extrapolating from our data, the estimated numbers of cases of chronic HBV and HCV infection in Thailand in 2017 were 2.2 and 0.79 million, respectively. Thus, effective treatments for viral hepatitis B and C for middle-aged and elderly Thais are needed. This seroprevalence survey could be used to help formulate policies and possible guidelines for treatment and prevention in specific age groups, which is recommended to facilitate the elimination of viral hepatitis by 2030.
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Affiliation(s)
- Nawarat Posuwan
- Center of Excellence in Clinical Virology Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | | | - Teeraporn Chinchai
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Watthana, Bangkok, Thailand
| | - Rujipat Wasitthankasem
- Center of Excellence in Clinical Virology Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand.,National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, PathumThani, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand.,Division of Academic Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
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Martin M, Vanichseni S, Leelawiwat W, Anekvorapong R, Raengsakulrach B, Cherdtrakulkiat T, Sangkum U, Mock PA, Leethochawalit M, Chiamwongpaet S, McNicholl JM, Kittimunkong S, Curlin ME, Choopanya K. Hepatitis C virus infection among people who inject drugs in Bangkok, Thailand, 2005-2010. WHO South East Asia J Public Health 2019; 8:50-55. [PMID: 30950431 PMCID: PMC7954142 DOI: 10.4103/2224-3151.255350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
BACKGROUND Approximately 1% of adults in Thailand are infected with hepatitis C virus (HCV). New direct-acting antiviral agents achieve sustained virologic responses in >95% of HCV-infected patients and are becoming available in countries around the world. To prepare for new HCV treatment options in Thailand, this study characterized HCV infections among people who inject drugs (PWID) in Bangkok. METHODS The Bangkok Tenofovir Study (BTS) was a pre-exposure prophylaxis trial conducted among PWID, 2005-2013. Blood specimens were randomly selected from PWID screened for the BTS, to test for anti-HCV antibody and HCV RNA. The HVR1 region was amplified by polymerase chain reaction, using multiplex primer sets with unique identifier sequences; amplification products were pooled in sets of 25; and consensus sequencing was performed to characterize individual HCV genotypes. RESULTS The median age of 3679 participants tested for anti-HCV antibody was 31 years, 3016 (82.0%) were male and 447 (12.2%) were HIV infected. The prevalence of anti-HCV antibody was 44.3%. The adjusted odds of testing positive for anti-HCV antibody were higher in men (adjusted odds ratio [aOR] 3.2, 95% confidence interval [CI] 2.4-4.3), those aged 40 years or older (aOR 2.7, 95% CI 2.1-3.5), those who had more than a primary school education (aOR 1.7, 95% CI 1.4-2.1), and those who tested HIV positive (aOR 5.2, 95% CI 3.7-7.4). HCV RNA was detected in 644 (81.3%) of the 792 anti-HCV antibody-positive specimens, yielding an HCV RNA-positive prevalence of 36.0% (95% CI 33.8-38.2). Among a random sample of 249 of the 644 specimens, 218 could be characterized, and the most common HCV subtypes were 1a (30.3%), 1b (12.8%), 3a (35.8%), 3b (6.9%) and 6n (8.7%). CONCLUSION The prevalence of anti-HCV antibody among PWID was 44.3% and more than one third (36.0%) were HCV RNA positive. Genotypes 1, 3 and 6 accounted for all typable infections. As the government of Thailand considers introduction of direct-acting antiviral medications for people with hepatitis C, it will be important to ensure that the medications target these subtypes.
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Affiliation(s)
- Michael Martin
- Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- US Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, United States of America
| | | | - Wanna Leelawiwat
- Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | | | - Boonyos Raengsakulrach
- Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Thitima Cherdtrakulkiat
- Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | | | - Philip A Mock
- Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | | | | | - Janet M McNicholl
- US Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, United States of America
| | | | - Marcel E Curlin
- Thailand Ministry of Public Health – US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Oregon Health and Science University, Portland, United States of America
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7
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Hoshino K, Sugiyama M, Date T, Maruwaka S, Arakaki S, Shibata D, Maeshiro T, Hokama A, Sakugawa H, Kanto T, Fujita J, Mizokami M. Phylogenetic and phylodynamic analyses of hepatitis C virus subtype 1a in Okinawa, Japan. J Viral Hepat 2018; 25:976-985. [PMID: 29577516 DOI: 10.1111/jvh.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 02/02/2018] [Indexed: 12/28/2022]
Abstract
Okinawa Island, located in Southern Japan, has a higher prevalence rate of hepatitis C virus subtype 1a (HCV-1a) infection than that in mainland Japan. Okinawa has a history of US military occupation after World War II. To elucidate the transmission history of HCV-1a in Okinawa, 26 whole-genome sequences were obtained from 29 patients during 2011-2016. Phylogenetic trees were reconstructed to identify the origin and characteristics of HCV-1a in Okinawa with epidemiological information. A phylogenetic tree based on whole-genome sequencing revealed that all of the samples were located below the US branches. Additionally, we identified one cluster comprised of 17 strains (Okinawa, n = 16; United States, n = 1). The majority of the patients in this cluster were people who inject drugs (PWID), indicating the presence of a people who inject drugs (PWID) cluster. Subsequently, Bayesian analyses were employed to reveal viral population dynamics. Intriguingly, a phylodynamic analysis uncovered a substantial increase in effective population size of HCV-1a from 1965 to 1980 and a slight increase in mid-2000, which were associated with an increase in illicit drug use in Okinawa. The estimated divergence time of the PWID cluster was 1967.6 (1964.2-1971.1). These findings suggest that HCV-1a was introduced into Okinawa from the United States in the late 1960s, coincident with the Vietnam War. Subsequently, HCV-1a might have spread among the Japanese population with the spread of injecting drug use. Our study provides an understanding of HCV transmission dynamics in Okinawa, as well as the key role of PWID in HCV transmission.
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Affiliation(s)
- K Hoshino
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan.,Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - M Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - T Date
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - S Maruwaka
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - S Arakaki
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - D Shibata
- Digestive Division, Heart Life Hospital, Okinawa, Japan
| | - T Maeshiro
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - A Hokama
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - H Sakugawa
- Digestive Division, Heart Life Hospital, Okinawa, Japan
| | - T Kanto
- Department of Liver Diseases, National Center for Global Health and Medicine, Chiba, Japan
| | - J Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - M Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
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8
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Molecular evolution of hepatitis C virus in China: A nationwide study. Virology 2018; 516:210-218. [PMID: 29407379 DOI: 10.1016/j.virol.2018.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 12/12/2022]
Abstract
The evolutionary and epidemic history and the regional differences of hepatitis C virus (HCV) are complex and remain unclear in the vast territory China. Here we recruited 1540 HCV-RNA positive patients sampled in 29 provinces across whole China, which is the largest sample capacity and the most comprehensive geographic coverage of China to our knowledge. 1b, 2a, 3b, 6a and 3a were the major subtypes in China. 1b was the most predominant subtype which presented in every province. The second most predominant subtype, 2a, appeared to concentrate in the north of China. Subtypes 3a and 3b were mainly found in the Southwest region, while 6a was restricted in the South region. We further estimated the origins of the dominating subtypes and discovered for the first time that a Chinese-specific transmission pattern for some strains of subtype 2a which was restricted in north China, and Chinese subtype 3b originated from Thailand.
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Tsukiyama-Kohara K, Kohara M. Hepatitis C Virus: Viral Quasispecies and Genotypes. Int J Mol Sci 2017; 19:ijms19010023. [PMID: 29271914 PMCID: PMC5795974 DOI: 10.3390/ijms19010023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 12/16/2017] [Accepted: 12/18/2017] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.
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Affiliation(s)
- Kyoko Tsukiyama-Kohara
- Joint Faculty of Veterinary Meedicine, Kagoshima University, 1-21-24 Korimoto Kagoshima-city, Kgoshima 890-0065, Japan.
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute, 2-1-6 Kamikitazawa, Setagaya-Ku 156-8506, Japan.
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10
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Welzel TM, Bhardwaj N, Hedskog C, Chodavarapu K, Camus G, McNally J, Brainard D, Miller MD, Mo H, Svarovskaia E, Jacobson I, Zeuzem S, Agarwal K. Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses. J Hepatol 2017; 67:224-236. [PMID: 28343981 DOI: 10.1016/j.jhep.2017.03.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/10/2017] [Accepted: 03/06/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND & AIMS HCV genotype, subtype, and presence of resistance-associated substitutions (RASs) are key determinants for the selection of direct-acting antiviral (DAA) treatment regimens. However, current HCV genotyping assays have limitations in differentiating between HCV subtypes, and RAS prevalence is largely undefined. The aim of this study was to investigate HCV epidemiology in 12,615 patient samples from 28 different countries across five geographic regions. METHODS We compared HCV genotype and subtypes using INNO-LiPA 2.0 vs. amplicon sequencing among 8,945 patients from phase II/III clinical trials of DAAs. Global HCV molecular epidemiology in 12,615 patients was investigated. Subtype RAS prevalence was determined by population or deep sequencing, and phylogenetic analyses investigating subtype diversity were performed. RESULTS Although there was high concordance between INNO-LiPA and sequencing for genotype determination, INNO-LiPA was insufficient for subtype determination for genotype 2, 3, 4, and 6. Sequencing provided subtype refinement for 42%, 10%, 81%, and 78% of genotype 2, 3, 4, and six patients, respectively. Genotype discordance (genotype 2-genotype 1) was observed in 28 of 950 (3%) genotype 2 patients, consistent with inter-genotype recombinants. Sequencing-based analyses demonstrated variations in regional subtype prevalence, notably within genotype 2, 4 and 6. RAS prevalence varied by subtype, with the clinically relevant NS3 RAS Q80K found in genotype 1a, 5a and 6a and the NS5A RAS Y93H in genotype 1b, 3a, 4b, 4r and 7. CONCLUSIONS Together, these analyses provide an understanding of subtyping accuracy and RAS distribution that are crucial for the implementation of global HCV treatment strategies. LAY SUMMARY Hepatitis C virus (HCV) is highly variable, with seven genotypes and 67 subtypes characterized to date. The aim of this study was to i) compare two different methods of discriminating between genotypes; ii) investigate the prevalence of HCV subtypes for each genotype around the world; iii) find the prevalence of resistance-associated substitutions (RASs) in different subtypes. We found that both methods showed high concordance in genotype discrimination, but specific subtypes were not always identified accurately. Sequencing-based analyses demonstrated variations in regional subtype prevalence for some genotypes, notably within GT2, 4 and 6. RAS prevalence also varied by subtype. These variations could determine how successful different drugs are for treating HCV.
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Affiliation(s)
- Tania M Welzel
- Johann Wolfgang Goethe University Medical Center, Frankfurt am Main, Germany
| | | | | | | | | | | | | | | | | | | | - Ira Jacobson
- Mount Sinai Beth Israel Medical Center, New York, USA
| | - Stefan Zeuzem
- Johann Wolfgang Goethe University Medical Center, Frankfurt am Main, Germany
| | - Kosh Agarwal
- King's College Hospital Foundation Trust, London, UK
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11
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Durier N, Yunihastuti E, Ruxrungtham K, Van Kinh N, Kamarulzaman A, Boettiger D, Widhani A, Avihingsanon A, Huy BV, Omar SFBS, Sanityoso A, Chittmittrapap S, Dung NTH, Pillai V, Suwan-Ampai T, Law M, Sohn AH, Matthews G. Chronic hepatitis C infection and liver disease in HIV-coinfected patients in Asia. J Viral Hepat 2017; 24:187-196. [PMID: 27917597 PMCID: PMC5272750 DOI: 10.1111/jvh.12630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 10/05/2016] [Indexed: 12/14/2022]
Abstract
Data on markers of hepatitis C virus (HCV) disease in HIV-HCV-coinfected patients in resource-limited settings are scarce. We assessed HCV RNA, HCV genotype (GT), IL28B GT and liver fibrosis (FibroScan® ) in 480 HIV-infected patients with positive HCV antibody in four HIV treatment centres in South-East Asia. We enrolled 165 (34.4%) patients in Jakarta, 158 (32.9%) in Bangkok, 110 (22.9%) in Hanoi and 47 (9.8%) in Kuala Lumpur. Overall, 426 (88.8%) were male, the median (IQR) age was 38.1 (34.7-42.5) years, 365 (76.0%) reported HCV exposure through injecting drug use, and 453 (94.4%) were on combination antiretroviral therapy. The median (IQR) CD4 count was 446 (325-614) cells/mm3 and 208 (94.1%) of 221 patients tested had HIV-1 RNA <400 copies/mL. A total of 412 (85.8%) had detectable HCV RNA, at a median (IQR) of 6.2 (5.4-6.6) log10 IU/mL. Among 380 patients with HCV GT, 223 (58.7%) had GT1, 97 (25.5%) had GT3, 43 (11.3%) had GT6, eight (2.1%) had GT4, two (0.5%) had GT2, and seven (1.8%) had indeterminate GT. Of 222 patients with IL28B testing, 189 (85.1%) had rs12979860 CC genotype, and 199 (89.6%) had rs8099917 TT genotype. Of 380 patients with FibroScan® , 143 (37.6%) had no/mild liver fibrosis (F0-F1), 83 (21.8%) had moderate fibrosis (F2), 74 (19.5%) had severe fibrosis (F3), and 79 (20.8%) had cirrhosis (F4). One patient (0.3%) had FibroScan® failure. In conclusion, a high proportion of HIV-HCV-coinfected patients had chronic HCV infection. HCV GT1 was predominant, and 62% of patients had liver disease warranting prompt treatment (≥F2).
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Affiliation(s)
- Nicolas Durier
- TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
| | - Evy Yunihastuti
- Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Kiat Ruxrungtham
- HIVNAT, the Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - David Boettiger
- The Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia
| | - Alvina Widhani
- Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Anchalee Avihingsanon
- HIVNAT, the Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Bui Vu Huy
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | | | - Andri Sanityoso
- Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | | | | | - Veena Pillai
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Matthew Law
- The Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia
| | - Annette H. Sohn
- TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
| | - Gail Matthews
- The Kirby Institute, UNSW Australia, Sydney NSW 2052, Australia
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12
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Rodrigo C, Eltahla AA, Bull RA, Luciani F, Grebely J, Dore GJ, Applegate T, Page K, Bruneau J, Morris MD, Cox AL, Osburn W, Kim AY, Shoukry NH, Lauer GM, Maher L, Schinkel J, Prins M, Hellard M, Lloyd AR. Phylogenetic analysis of full-length, early infection, hepatitis C virus genomes among people with intravenous drug use: the InC 3 Study. J Viral Hepat 2017; 24:43-52. [PMID: 27808453 PMCID: PMC5191976 DOI: 10.1111/jvh.12616] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/16/2016] [Indexed: 12/11/2022]
Abstract
Cross-continental phylogenetic analysis is important to understand subtle molecular differences of currently circulating hepatitis C virus (HCV) subtypes. Existence of such differences can be crucial in pursuing a universal hepatitis C vaccine. We characterized molecular epidemiology of early HCV infections identified across nine cohorts [North America (n=4), Australia (n=4) and Europe (n=1)] in the International Collaborative of Incident HIV and Hepatitis C in Injecting Cohorts (InC3 ). One hundred and ninety-two full-length HCV genomes were amplified from plasma of incident infections and subjected to next generation sequencing to establish the largest cross-continental, full-length acute HCV genomic data set available to date. Genomes from the most common subtypes (1a: n=94, 2b: n=15 and 3a: n=68) were used in phylogenetic analysis. Using full genome trees, 78 sequences (44%) were found to lie within 29 phylogenetic clusters/pairs defined on the basis of molecular similarity of consensus sequences. Of these, 26 each had exclusively Australian or North American sequences indicating a strong geographical bias for molecular similarity. On further analysis of behavioural and demographic associations, binary logistic regression analysis showed that older age and non-Caucasian ethnicity were significantly associated with clustering. HCV probably evolves in micro-epidemics within geographically isolated communities.
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Affiliation(s)
| | | | | | | | | | | | | | - Kimberly Page
- University of New Mexico, Albuquerque, New Mexico, USA, CRCHUM
| | | | | | - Andrea L. Cox
- Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | | | | | | | - Lisa Maher
- The Kirby Institute, UNSW, NSW, Australia
| | - Janke Schinkel
- Academic Medical Center, Amsterdam, The Netherlands,GGD Public Health Service of Amsterdam
| | - Maria Prins
- Academic Medical Center, Amsterdam, The Netherlands,GGD Public Health Service of Amsterdam
| | - Margaret Hellard
- Burnet Institute, Melbourne, VIC, Australia,Monash University, Australia,Alfred Hospital, Melbourne, Australia
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13
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Ghori NUH, Shafique A, Hayat MQ, Anjum S. The Phylogeographic and Spatiotemporal Spread of HCV in Pakistani Population. PLoS One 2016; 11:e0164265. [PMID: 27764129 PMCID: PMC5072696 DOI: 10.1371/journal.pone.0164265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/22/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C Virus (HCV) is the most prevalent human pathogen in Pakistan and is the major cause of liver cirrhosis and hepatocellular carcinoma in infected patients. It has shifted from being hypo-endemic to being hyper-endemic. There was no information about the origin and evolution of the local variants. Here we use newly developed phyloinformatic methods of sequence analysis to conduct the first comprehensive investigation of the evolutionary and biogeographic history in unprecedented detail and breadth. Considering evolutionary rate and molecular-clock hypothesis in context, we reconstructed the spatiotemporal spread of HCV in the whole territory of its circulation using a combination of Bayesian MCMC methods utilizing all sequences available in GenBank. Comparative analysis were performed and were addressed. Whole genome and individual gene analysis have shown that sub-types 1a, 1b and 3a are recognized as epidemic strains and are distributed globally. Here we confirm that the origin of HCV 3a genotypes is in South Asia and HCV has evolved in the region to become stably adapted to the host environment.
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Affiliation(s)
- Noor-Ul-Huda Ghori
- School of Earth and Environment, The University of Western Australia, Perth, Australia
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- * E-mail:
| | - Atif Shafique
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sadia Anjum
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Department of Biology, College of Sciences, University Of Hail, PO Box 2440, Hail, Kingdom of Saudi Arabia
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14
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Wasitthankasem R, Posuwan N, Vichaiwattana P, Theamboonlers A, Klinfueng S, Vuthitanachot V, Thanetkongtong N, Saelao S, Foonoi M, Fakthongyoo A, Makaroon J, Srisingh K, Asawarachun D, Owatanapanich S, Wutthiratkowit N, Tohtubtiang K, Yoocharoen P, Vongpunsawad S, Poovorawan Y. Decreasing Hepatitis C Virus Infection in Thailand in the Past Decade: Evidence from the 2014 National Survey. PLoS One 2016; 11:e0149362. [PMID: 26871561 PMCID: PMC4752320 DOI: 10.1371/journal.pone.0149362] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/29/2016] [Indexed: 12/23/2022] Open
Abstract
Hepatitis C virus (HCV) infection affects ≥ 180 million individuals worldwide especially those living in developing countries. Recent advances in direct-acting therapeutics promise effective treatments for chronic HCV carriers, but only if the affected individuals are identified. Good treatment coverage therefore requires accurate epidemiological data on HCV infection. In 2014, we determined the current prevalence of HCV in Thailand to assess whether over the past decade the significant number of chronic carriers had changed. In total, 5964 serum samples from Thai residents between 6 months and 71 years of age were obtained from 7 provinces representing all 4 geographical regions of Thailand and screened for the anti-HCV antibody. Positive samples were further analyzed using RT-PCR, sequencing, and phylogenetic analysis to identify the prevailing HCV genotypes. We found that 56 (0.94%) samples tested positive for anti-HCV antibody (mean age = 36.6±17.6 years), while HCV RNA of the core and NS5B subgenomic regions was detected in 23 (41%) and 19 (34%) of the samples, respectively. The seropositive rates appeared to increase with age and peaked in individuals 41–50 years old. These results suggested that approximately 759,000 individuals are currently anti-HCV-positive and that 357,000 individuals have viremic HCV infection. These numbers represent a significant decline in the prevalence of HCV infection. Interestingly, the frequency of genotype 6 variants increased from 8.9% to 34.8%, while the prevalence of genotype 1b declined from 27% to 13%. These most recent comprehensive estimates of HCV burden in Thailand are valuable towards evidence-based treatment coverage for specific population groups, appropriate allocation of resources, and improvement in the national public health policy.
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Affiliation(s)
- Rujipat Wasitthankasem
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 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
| | - Apiradee Theamboonlers
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | | | | | | | | | | | | | | | | | | | - Pornsak Yoocharoen
- Bureau of General Communicable Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, 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
- * E-mail:
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15
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Ederth J, Jern C, Norder H, Magnius L, Alm E, Rognsvåg BK, Sundin CG, Brytting M, Esbjörnsson J, Mild M. Molecular characterization of HCV in a Swedish county over 8 years (2002-2009) reveals distinct transmission patterns. Infect Ecol Epidemiol 2016; 6:30670. [PMID: 26854010 PMCID: PMC4744866 DOI: 10.3402/iee.v6.30670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 02/06/2023] Open
Abstract
Background Hepatitis C virus (HCV) is a major public health concern and data on its molecular epidemiology in Sweden is scarce. We carried out an 8-year population-based study of newly diagnosed HCV cases in one of Sweden's centrally situated counties, Södermanland (D-county). The aim was to characterize the HCV strains circulating, analyze their genetic relatedness to detect networks, and in combination with demographic data learn more about transmission. Methods Molecular analyses of serum samples from 91% (N=557) of all newly notified cases in D-county, 2002–2009, were performed. Phylogenetic analysis (NS5B gene, 300 bp) was linked to demographic data from the national surveillance database, SmiNet, to characterize D-county transmission clusters. The linear-by-linear association test (LBL) was used to analyze trends over time. Results The most prevalent subtypes were 1a (38%) and 3a (34%). Subtype 1a was most prevalent among cases transmitted via sexual contact, via contaminated blood, or blood products, while subtype 3a was most prevalent among people who inject drugs (PWIDs). Phylogenetic analysis revealed that the subtype 3a sequences formed more and larger transmission clusters (50% of the sequences clustered), while the 1a sequences formed smaller clusters (19% of the sequences clustered), possibly suggesting different epidemics. Conclusion We found different transmission patterns in D-county which may, from a public health perspective, have implications for how to control virus infections by targeted interventions.
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Affiliation(s)
- Josefine Ederth
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden;
| | - Camilla Jern
- Stockholm South General Hospital, Stockholm, Sweden
| | - Helené Norder
- Department of Infectious Medicine, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Magnius
- Department of Infectious Medicine, Institute of Biomedicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Alm
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | | | | | - Mia Brytting
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.,Nuffield Department Medicine, University of Oxford, Oxford, United Kingdom
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
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16
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Gondeau C, Pageaux GP, Larrey D. Hepatitis C virus infection: Are there still specific problems with genotype 3? World J Gastroenterol 2015; 21:12101-13. [PMID: 26576095 PMCID: PMC4641128 DOI: 10.3748/wjg.v21.i42.12101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/07/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection is one of the most common causes of chronic liver disease and the main indication for liver transplantation worldwide. As promising specific treatments have been introduced for genotype 1, clinicians and researchers are now focusing on patients infected by non-genotype 1 HCV, particularly genotype 3. Indeed, in the golden era of direct-acting antiviral drugs, genotype 3 infections are no longer considered as easy to treat and are associated with higher risk of developing severe liver injuries, such as cirrhosis and hepatocellular carcinoma. Moreover, HCV genotype 3 accounts for 40% of all HCV infections in Asia and is the most frequent genotype among HCV-positive injecting drug users in several countries. Here, we review recent data on HCV genotype 3 infection/treatment, including clinical aspects and the underlying genotype-specific molecular mechanisms.
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17
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Ho SH, Ng KP, Kaur H, Goh KL. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia. Hepatobiliary Pancreat Dis Int 2015; 14:281-6. [PMID: 26063029 DOI: 10.1016/s1499-3872(15)60363-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. METHODS This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. RESULTS Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. CONCLUSIONS In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.
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Affiliation(s)
- Shiaw-Hooi Ho
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
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18
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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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19
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Caliskan A, Kirisci O, Ozkaya E, Ozden S, Tumer S, Caglar S, Guler SA, Senol H. Distribution and predominance of genotype 3 in hepatitis C virus carriers in the province of kahramanmaras, Turkey. HEPATITIS MONTHLY 2015; 15:e25142. [PMID: 25972903 PMCID: PMC4426333 DOI: 10.5812/hepatmon.15(4)2015.25142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/02/2015] [Accepted: 04/02/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND The hepatitis C virus (HCV) has six major genotypes and more than 100 subtypes, and the determination of the responsible genotype, collection of epidemiological data, tailoring antiviral therapy, and prediction of prognosis have an important place in disease management. OBJECTIVES The aim of the present study was to determine the distribution of HCV genotypes across geographic regions and compare these data with those obtained from other geographic locations. PATIENTS AND METHODS The HCV genotypes were identified in HCV RNA positive blood samples, obtained from different centers. The HCV genotype was determined using molecular methods [Real-Time Polymerase Chain Reaction (RT-PCR)] in 313 patients, who were found to be positive for HCV RNA. The presence of HCV RNA was investigated using the RT-PCR method in serum samples delivered to the Microbiology Laboratory at Kahramanmaras Necip Fazıl City Hospital, Kahramanmaras, Turkey, from the centers located in Kahramanmaras City center and peripheral districts of the province, between March 2010 and August 2014. The HCV genotype analysis was performed in HCV RNA positive samples, using RT-PCR reagents kit. Urine samples from the patients were tested for amphetamine with an Amphetamines II (AMPS2) kit, cocaine was tested with a Cocaine II (COC2) kit, opiates were tested with an Opiates II (OPI2) kit, and cannabinoids were tested with a Cannabinoids II (THC2) kit in Roche/Hitachi Cobas c501 device. RESULTS The blood samples collected from 313 patients were included in the study. Of these patients, 212 (67.7%) were male and 101 (32.3%) were female. The mean age of the patients was 41.29 ± 20.32 years. In terms of HCV genotype distribution, 162 patients (51.7%) had genotype 1, 144 patients (46%) had genotype 3, four patients (1.3%) had genotype 2, and three patients (1%) had genotype 4. The results of urine drug tests were available in only 65 patients (20.2%). Of these, 61 (93.8%) patients had HCV genotype 3. CONCLUSIONS In conclusion, the prevalence of HCV genotype 1 was 51.7%, which was lower than the rates reported in other studies in Turkey, while the prevalence of HCV genotype 3 was 46%, which was remarkably higher than the reported Turkish data. In addition, the prevalence rate for genotype 3 reported in the present study is the highest that has ever been reported in the literature.
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Affiliation(s)
- Ahmet Caliskan
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Ozlem Kirisci
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Esra Ozkaya
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Sevinc Ozden
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Seray Tumer
- Department of Medical Microbiology, Necip Fazil City Hospital, Kahramanmaras, Turkey
| | - Serkan Caglar
- Department of Medical Biohemistry, Necip Fazıl City Hospital, Kahramanmaras, Turkey
| | - Selma Ates Guler
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sutcu Imam University, Kahramanmaras, Turkey
| | - Hande Senol
- Department of Biostatistics, Faculty of Medicine, Pamukkale University, Denizli, Turkey
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20
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Chusri P, Kumthip K, Pantip C, Thongsawat S, O'Brien A, Maneekarn N. Influence of amino acid variations in the NS3, NS4A and NS4B of HCV genotypes 1a, 1b, 3a, 3b and 6f on the response to pegylated interferon and ribavirin combination therapy. Virus Res 2014; 196:37-43. [PMID: 25445343 DOI: 10.1016/j.virusres.2014.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/21/2014] [Accepted: 11/04/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND It has been suggested that HCV proteins, core, NS3/4A, NS4B, and NS5A, contribute to the resistance of HCV to IFN and ribavirin (RBV) treatments. AIM To assess the effects of HCV amino acid variations in NS3, NS4A and NS4B of HCV subtypes 1a, 1b, 3a, 3b and 6f on the response to pegylated interferon (Peg-IFN) and RBV therapy. METHODS One hundred and thirty four HCV isolates of genotypes 1a, 1b, 3a, 3b and 6f obtained from HCV patients both before and at week 4 of treatments were evaluated. Amino acid sequences of NS3, NS4A and NS4B were analyzed and in compared to reference sequences of corresponding genotypes. RESULTS The data revealed that amino acid variations within the full-length NS3, protease and helicase domains of NS3 of HCV 1a from responders were significantly higher than those from treatment failure groups as compared to reference sequences of each corresponding genotype. Similar results were observed in the full-length and helicase domain but not in the protease domain of HCV 1b. However, the number of amino acid variations in NS3 of HCV 3a, 3b and 6f as well as in NS4A and NS4B showed no difference between the viruses from responders and treatment failure group. Analysis of amino acid variations both before and at week 4 of treatment revealed that the mean number of amino acid variation in the full-length NS3 of HCV 3a and 3b from responders were also significantly higher than those from the treatment failure group. CONCLUSION Our study suggests that the increase of amino acid variations within the NS3 protein of HCV 1a, 1b, 3a and 3b were associated with the response to Peg-IFN and RBV treatment in Thai patients.
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Affiliation(s)
- Pattranuch Chusri
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chansom Pantip
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Satawat Thongsawat
- Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Amornrat O'Brien
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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Kumthip K, Chusri P, Pantip C, Thongsawat S, O'Brien A, Nelson KE, Maneekarn N. Hepatitis C virus genotypes circulating in patients with chronic hepatitis C in Thailand and their responses to combined PEG-IFN and RBV therapy. J Med Virol 2014; 86:1360-5. [PMID: 24777626 DOI: 10.1002/jmv.23962] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 01/06/2023]
Abstract
Different genotypes of hepatitis C virus (HCV) are circulating in different areas of the world. In Thailand, distribution of HCV genotypes has been investigated mostly in the central area while the information in other regions is limited. This study aimed to determine the HCV genotypes circulating in chronic hepatitis C patients in Chiang Mai, Thailand and to investigate the response of different HCV genotypes to pegylated interferon (PEG-IFN) and ribavirin (RBV) treatment. Patients infected chronically with HCV were treated with PEG-IFN/RBV based on the standard regimens for each HCV genotype and followed up the patients until the end of treatment and 6 months afterward. Out of 158 patients, three major HCV genotypes and eight subtypes were identified. Genotype 3 was the most predominant at 54.5%, followed by genotypes 1 (31%) and 6 (14.5%). Among subtypes, 3a was the most prevalent subtype (45%), followed by 1b (18.4%), 1a and 6f (each at 12.6%), 3b (9.5%), and 6a, 6i, 6n (each at 0.63%). Patients with genotype 3 showed higher rate of responding to the treatment at 80.2% compared to genotypes 1 (73.5%) and 6f (65%). Additionally, patients with genotype 6f showed higher rate of relapsing (25%) compared to genotypes 1 and 3 (14.3% and 16.3%, respectively). In conclusion, this study reported multiple HCV genotypes circulated in Thai patients and the response of different HCV genotypes to PEG-IFN/RBV treatment.
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Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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Ampuero J, Romero-Gómez M, Reddy KR. Review article: HCV genotype 3 – the new treatment challenge. Aliment Pharmacol Ther 2014; 39:686-98. [PMID: 24612116 DOI: 10.1111/apt.12646] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/27/2013] [Accepted: 01/13/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Over the past several years, hepatitis C therapy has been pegylated interferon and ribavirin based. Although protease inhibitor-based therapy has enhanced response rates in genotype 1, the recent advances in therapy have demonstrated a challenge in genotype 3, a highly prevalent infection globally. AIM To provide a comprehensive summary of the literature evaluating the unique characteristics and evolving therapies in genotype 3. METHODS A structured search in PubMed, the Cochrane Library and EMBASE was performed using defined key words, including only full text papers and abstracts in English. RESULTS HCV genotype 3 is more prevalent in Asia and among intra-venous drug users. Furthermore, it interferes with lipid and glucose metabolism, and the natural history involves a more rapid progression of liver disease and a higher incidence of hepatocellular carcinoma (HCC). New therapies with protease inhibitors have focused on genotype 1 largely and have demonstrated enhanced responses, but have limited activity against genotype 3. Thus far, in clinical trials, NS5B and NS5A inhibitors have performed more poorly in genotype 3, while a cyclophilin inhibitor, alisporivir, has shown promise. CONCLUSIONS As treatments for HCV have evolved, genotype 3 has become the most difficult to treat. Furthermore, genotype 3 has special characteristics, such as insulin resistance and alterations in lipid metabolism, which may partly explain the lower treatment responses. A great deal of emphasis on advancing therapy is needed in this population that appears to have a more rapid progression of liver disease and a higher incidence of HCC.
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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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