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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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Wasitthankasem R, Vichaiwattana P, Siripon N, Posuwan N, Auphimai C, Klinfueng S, Thaneskongtong N, Vuthitanachot V, Saiyatha S, Thongmai C, Suwanpatoomlerd S, Sochoo S, Pongsuwan N, Poovorawan K, Tangkijvanich P, Vongpunsawad S, Poovorawan Y. Assessment of hepatitis C virus infection in two adjacent Thai provinces with drastically different seroprevalence. PLoS One 2017; 12:e0177022. [PMID: 28475637 PMCID: PMC5419576 DOI: 10.1371/journal.pone.0177022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/28/2017] [Indexed: 01/20/2023] Open
Abstract
Improved awareness of the hepatitis C virus (HCV) transmission has contributed to the overall decline in the HCV infection rate in some developing countries including Thailand. Chronic HCV infection in some rural Thai communities, however, presents a challenge in the efforts to treat and manage HCV-related diseases. Published and unpublished studies have suggested an unusually high incidence of HCV infection in a Thai province of Phetchabun compared to elsewhere in Thailand. To determine the magnitude of HCV infection and identify potential factors contributing to the higher rate of HCV infection in this province, we performed a population-based study in Phetchabun (n = 1667) and the neighboring Khon Kaen province (n = 1410) where HCV prevalence is much lower. Individuals between 30 and 64 years old completed detailed questionnaires designed to identify HCV risk factors and provided blood samples for anti-HCV antibody screening. The anti-HCV seropositive rates were 15.5% (259/1667) in Phetchabun and 3.6% (51/1410) in Khon Kaen. Positive samples were subsequently genotyped for HCV core gene sequence and assessed for the hepatitis B virus surface antigen (HBsAg) and human immunodeficiency virus antigen/antibody (HIV Ag/Ab). More individuals in Phetchabun possessed the combined presence of HBsAg (5.0%) and HIV Ag/Ab (0.4%) than those in Khon Kaen (3.9% HBsAg and 0.0% HIV Ag/Ab). While male gender, intravenous drug use (IVDU) and tattoos were significant HCV risk factors in both provinces (p <0.05), education less than high school and agriculture-related occupation were additionally associated with HCV in Phetchabun. HCV genotypes 6, 3, and 1 were identified in similar frequency in both provinces. We estimated that prevalence of HCV seropositivity and viremic carriers were higher in Phetchabun (143 and 111 per 1000) than in Khon Kaen (34 and 22 per 1000). Finally, we derived a simple risk factor-based scoring system as a useful preclinical tool to screen individuals at risk of chronic HCV infection prior to intervention. Knowledge gained from this study will assist in HCV screening and promote access to anti-viral treatment in high-risk groups.
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Affiliation(s)
- Rujipat Wasitthankasem
- 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
| | - Nipaporn Siripon
- 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
| | - Chompoonut Auphimai
- 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
| | | | | | - Supapith Saiyatha
- Phetchabun Provincial Public Health Office, Mueang Phetchabun, Phetchabun, Thailand
| | - Chaiwat Thongmai
- Phetchabun Provincial Public Health Office, Mueang Phetchabun, Phetchabun, Thailand
| | | | - Saowakon Sochoo
- Lomkao Crown Prince Hospital, Na-saeng, Lom Kao, Phetchabun, Thailand
| | - Natnada Pongsuwan
- Lomkao Crown Prince Hospital, Na-saeng, Lom Kao, Phetchabun, Thailand
| | - Kittiyod Poovorawan
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Research Unit of Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 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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3
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Yang L, Jiang C, Hu S, Diao Q, Li J, Si W, Chen M, Zhao RY. Evolving Diversity of Hepatitis C Viruses in Yunnan Honghe, China. Int J Mol Sci 2016; 17:403. [PMID: 26999127 PMCID: PMC4813258 DOI: 10.3390/ijms17030403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/26/2016] [Accepted: 03/09/2016] [Indexed: 12/23/2022] Open
Abstract
The Chinese Honghe Autonomous Prefecture (Honghe) in Yunnan Province is a unique ethnic area because it is inhabited by more than ten different minority ethnic groups. Geographically, Honghe directly shares a border with Vietnam. The objective of this study was to investigate genetic diversity and distribution of the Hepatitis C virus (HCV) in Honghe. Ninety nine subjects who were infected with HCV or HCV/HIV (Human Immunodeficiency Virus Type 1) were recruited into this study. HCV genotypes and subtypes were determined based on the sequences of the core/envelope 1 (C/E1) and the nonstructural protein 5B (NS5B) genomic regions. The viral diversity and origins of dissemination were examined by phylogenetic analyses. Three HCV genotypes (1, 3 and 6) with six subtypes (1b, 3b, 3a, 6a, 6n and 6v) were identified. The most predominant form was genotype 3 (54.6%) followed by 6 (34.3%), and 1 (9.1%). The HCV subtype 3b appeared to be the most frequent form (38.4%) followed by 6n (20.2%) and 3a (16.2%). Statistical analyses suggested a possible rise of the genotype 6a in Honghe among intravenous drug users with HCV/HIV co-infections. Further phylogenetic analyses suggested that similar HCV-6a viruses might have been circulating in the Honghe area for more than a decade, which likely originated from Vietnam or vice versa. Two HCV samples with single HCV infection (SC34 and SC45) were isolated that could represent new recombinant variants. Although the genetic prevalence of HCV in Honghe is in general agreement with that of Southwest China and Yunnan Province, the diversity of HCV genotypes and subtypes in Honghe is somewhat unique and evolving. Information presented here should provide useful information for future health surveillance and prevention of HCV infection in this area.
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Affiliation(s)
- Lanhui Yang
- Department of Clinical Laboratory, The First People's Hospital of Honghe, Mengzi 661100, China.
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, 21201 MD, USA.
| | - Chenyan Jiang
- Division of Life Science, College of Life Science and Technology, Honghe University, Mengzi 661100, China.
| | - Song Hu
- Department of Infectious Diseases, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Qiongni Diao
- Division of Life Science, College of Life Science and Technology, Honghe University, Mengzi 661100, China.
| | - Jia Li
- Department of Infectious Diseases, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Wei Si
- Department of Clinical Laboratory, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Mei Chen
- Department of Infectious Diseases, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Richard Y Zhao
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, 21201 MD, USA.
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4
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Analysis of HCV-6 isolates among Asian-born immigrants in North America reveals their high genetic diversity and a new subtype. Virology 2016; 492:25-31. [PMID: 26896932 DOI: 10.1016/j.virol.2016.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 12/28/2022]
Abstract
We characterized full-length genomes for 15 HCV-6 isolates, all from Asian immigrants living in North America. Among these isolates, nine were novel variants showing >15% nucleotide differences from their nearest relatives, representing lineages distinct from known subtypes. The other six were classified into subtypes 6c, 6h, 6q, 6r, and 6s. The partial sequences were also determined for five additional HCV-6 isolates, three from the US and two from Canada. The latter two were assigned to new subtype 6xf as they were found to classify with two other isolates for which we recently reported their full-length genomes. We further analyzed partial Core-E1 sequences of 100 HCV-6 isolates sampled in North America, seven from the US and 93 from Canada and all from Asian immigrants except for four from Caucasians. These 100 isolates belonged to 20 assigned subtypes and 16 unclassified lineages showing great genetic diversity and enhanced significance to public health.
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5
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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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6
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Li C, Pham VH, Abe K, Lu L. Nine additional complete genome sequences of HCV genotype 6 from Vietnam including new subtypes 6xb and 6xc. Virology 2014; 468-470:172-177. [PMID: 25173194 DOI: 10.1016/j.virol.2014.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 06/30/2014] [Accepted: 08/05/2014] [Indexed: 01/20/2023]
Abstract
We completely sequenced nine HCV-6 variants from Vietnam. They are grouped into six lineages beyond the 24 assigned subtypes, 6a-6xa, and 14 unclassified lineages that have been recently described with full-length genomes. Co-analysis with reference sequences in the NS5B region identified additional 22 such lineages, which made the total taxonomic number of HCV-6 increased to 66 that might be recognized at the subtype level. Because two of these six lineages revealed in this study each had >3 epidemiologically unlinked isolates identified, we proposed to assign them new subtypes 6xb and 6xc in following the eXtended format recently recommended in the expanded HCV nomenclature.
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Affiliation(s)
- Chunhua Li
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, MS 3046, 3901 Rainbow Boulevard, Kansas City, KS 66160, United States of America
| | - 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 Diagnostics Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam
| | - 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 Diagnostics Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam; Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Ling Lu
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, MS 3046, 3901 Rainbow Boulevard, Kansas City, KS 66160, United States of America.
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7
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An Y, Wu T, Wang M, Lu L, Li C, Zhou Y, Fu Y, Chen G. Conservation in China of a novel group of HCV variants dating to six centuries ago. Virology 2014; 464-465:21-25. [PMID: 25043585 DOI: 10.1016/j.virol.2014.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/15/2014] [Accepted: 06/10/2014] [Indexed: 12/18/2022]
Abstract
UNLABELLED We characterized a novel group of HCV variants that are genetically related but distinct from each other belonging to genotype 6 (HCV-6). From 26 infected Austronesian-descended aborigines on Hainan Island, China, HCV sequences were determined followed by genetic analyses. Six nearly full-length genomes and 20 E1 sequences of HCV were obtained, which differ from each other and from all known HCV lineages by nucleotides above the intra-subtype level of 13%. Together with subtypes 6g and 6w, they constitute a phylogenetic group sharing a common ancestor dating from the end of the 12th century. CONCLUSION Our data indicate the maintenance of an isolated HCV-6 indigenous circulation on Hainan Island at least for six centuries.
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Affiliation(s)
- Yuling An
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Tao Wu
- Department of Infectious Disease, Southern Medical University, Guangzhou, Guangdong 510515, China; Department of Infectious Disease, Hainan General Hospital, Haikou, Hainan 570311, China
| | - Min Wang
- Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Ling Lu
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China; Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yuanpin Zhou
- Department of Infectious Disease, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Guihua Chen
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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8
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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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9
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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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10
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Li C, Njouom R, Pépin J, Nakano T, Bennett P, Pybus OG, Lu L. Characterization of full-length hepatitis C virus sequences for subtypes 1e, 1h and 1l, and a novel variant revealed Cameroon as an area in origin for genotype 1. J Gen Virol 2013; 94:1780-1790. [PMID: 23677792 DOI: 10.1099/vir.0.048835-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this study, we characterized the full-length genome sequences of seven hepatitis C virus (HCV) isolates belonging to genotype 1. These represent the first complete genomes for HCV subtypes 1e, 1h, 1l, plus one novel variant that qualifies for a new but unassigned subtype. The genomes were characterized using 19-22 overlapping fragments. Each was 9400-9439 nt long and contained a single ORF encoding 3019-3020 amino acids. All viruses were isolated in the sera of seven patients residing in, or originating from, Cameroon. Predicted amino acid sequences were inspected and unique patterns of variation were noted. Phylogenetic analysis using full-length sequences provided evidence for nine genotype 1 subtypes, four of which are described for the first time here. Subsequent phylogenetic analysis of 141 partial NS5B sequences further differentiated 13 subtypes (1a-1m) and six additional unclassified lineages within genotype 1. As a result of this study, there are now seven HCV genotype 1 subtypes (1a-1c, 1e, 1g, 1h, 1l) and two unclassified genotype 1 lineages with full-length genomes characterized. Further analysis of 228 genotype 1 sequences from the HCV database with known countries is consistent with an African origin for genotype 1, and with the hypothesis of subsequent dissemination of some subtypes to Asia, Europe and the Americas.
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Affiliation(s)
- Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Richard Njouom
- Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur, Yaoundé, Cameroon
| | - Jacques Pépin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada
| | - Tatsunori Nakano
- Department of Internal Medicine, Fujita Health University Nanakuri Sanatorium Otoricho 424-1, Tsu, Mie 514-1295, Japan
| | - Phil Bennett
- Micropathology Ltd, University of Warwick Science Park, Coventry CV4 7EZ, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road OX1 3PS, UK
| | - Ling Lu
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
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11
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Genome sequence of the hepatitis C virus subtype 6n isolated from malaysia. GENOME ANNOUNCEMENTS 2013; 1:genomeA00168-12. [PMID: 23409272 PMCID: PMC3569350 DOI: 10.1128/genomea.00168-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 12/18/2012] [Indexed: 12/12/2022]
Abstract
We report the full genome sequence of hepatitis C virus (HCV) subtype 6n from Kuala Lumpur, Malaysia. Phylogenetic analysis of the isolate 10MYKJ032 suggests that Southeast Asia might be the origin for the HCV subtype 6n and highlights the possible spread of this lineage from Southeast Asia to other regions.
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12
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[Research activities in Kobe-Indonesia Collaborative Research Centers]. Uirusu 2013; 63:59-68. [PMID: 24769579 DOI: 10.2222/jsv.63.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Kobe-Indonesia Collaborative Research Center was established in Institute of Tropical Disease (ITD), Airlangga University, Surabaya, Indonesia in 2007 under the program of ''Founding Research Centers for Emerging and Reemerging Infectious Diseases'' supported by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and then it has been under the Japan Initiative for Global Research Network on Infectious Diseases (J-GRID) since 2010. Japanese researchers have been stationed at ITD, conducting joint researches on influenza, viral hepatitis, dengue and infectious diarrhea. Also, another Japanese researcher has been stationed at Faculty of Medicine, University of Indonesia, Jakarta, carrying out joint researches on'' Identification of anti-hepatitis C virus (HCV) substances and development of HCV and dengue vaccines'' in collaboration with University of Indonesia and Airlangga University through the Science and Technology Research Partnership for Sustainable Development (SATREPS) supported by the Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA) since 2009. In this article, we briefly introduce the background history of Kobe University Research Center in Indonesia, and discuss the research themes and outcomes of J-GRID and SATREPS activities.
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AMIN MOCHAMAD, JUNIASTUTI JUNIASTUTI, UTSUMI TAKAKO, YANO YOSHIHIKO, YUSUF MOCHAMAD, THAHA MOCHAMMAD, BUDI PURWONO PRIYO, HANDAJANI RETNO, SOETJIPTO SOETJIPTO, HOTTA HAK, HAYASHI YOSHITAKE, INGE LUSIDA MARIA. The Prevalence and Subtype Distribution of Hepatitis C Virus Infection among Hemodialysis Patients in a Private Hospital in Surabaya, Indonesia. MICROBIOLOGY INDONESIA 2012. [DOI: 10.5454/mi.6.4.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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14
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Lu L, Li C, Yuan J, Lu T, Okamoto H, Murphy DG. Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant. J Gen Virol 2012; 94:543-548. [PMID: 23152370 DOI: 10.1099/vir.0.049668-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.
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Affiliation(s)
- Ling Lu
- Cancer Research Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.,The Viral Oncology Center, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Chunhua Li
- Cancer Research Center, University of Kansas Medical Center, Kansas City, KS 66160, USA.,The Viral Oncology Center, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Jie Yuan
- Department of Biochemistry of Sun Yat-sen University, Guangzhou 510089, PR China
| | - Teng Lu
- University of Southern California, Los Angeles, CA 90089, USA
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Donald G Murphy
- Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
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15
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Wang H, Yuan Z, Barnes E, Yuan M, Li C, Fu Y, Xia X, Li G, Newton PN, Vongsouvath M, Klenerman P, Pybus OG, Murphy D, Abe K, Lu L. Eight novel hepatitis C virus genomes reveal the changing taxonomic structure of genotype 6. J Gen Virol 2012; 94:76-80. [PMID: 23015745 PMCID: PMC3542719 DOI: 10.1099/vir.0.047506-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Analysis of partial hepatitis C virus sequences has revealed many novel genotype 6 variants that cannot be unambiguously classified, which obscure the distinctiveness of pre-existing subtypes. To explore this uncertainty, we obtained genomes of 98.0–98.8 % full-length for eight such variants (KM35, QC273, TV257, TV476, TV533, L349, QC271 and DH027) and characterized them using phylogenetic analyses and per cent nucleotide similarities. The former four are closely related phylogenetically to subtype 6k, TV533 and L349 to subtype 6l, QC271 to subtypes 6i and 6j, and DH027 to subtypes 6m and 6n. The former six defined a high-level grouping that comprised subtypes 6k and 6l, plus related strains. The threshold between intra- and inter-subtype diversity in this group was indistinct. We propose that similar results would be seen elsewhere if more intermediate variants like QC271 and DH027 were sampled.
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Affiliation(s)
- Hongren Wang
- Vaccine Institute, 3rd Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Zhiguo Yuan
- Vaccine Institute, 3rd Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Eleanor Barnes
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, OX1 3SY, UK
| | - Manqiong Yuan
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Chunhua Li
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong, PR China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, PR China
| | - Gang Li
- Vaccine Institute, 3rd Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Paul N Newton
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.,Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK.,Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
| | - Manivanh Vongsouvath
- Wellcome Trust-Mahosot Hospital-Oxford Tropical Medicine Research Collaboration, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Paul Klenerman
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, OX1 3SY, UK
| | - Oliver G Pybus
- Institut National de Santé Publique du Québec, Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Donald Murphy
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Kenji Abe
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ling Lu
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
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16
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Pan S, Rao Y, Li J, Yang H, Tang J, Zhong R, Zhai J, Liu J, Wang H, Liu W, Xie Y. Hepatitis C virus genotype diversity in Shanghai, China. Arch Virol 2012; 158:187-91. [PMID: 22941570 DOI: 10.1007/s00705-012-1457-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 07/10/2012] [Indexed: 01/06/2023]
Abstract
We studied 67 hepatitis C virus (HCV) isolates from 64 hospitalized patients in Shanghai, China. Genotype 1 was prevalent, and genotypes 2, 3, 6 were found for the first time in Shanghai. A rare mixed infection with three subtypes (1a, 1b, 2a) was found. The complete genome sequence of a subtype 3b isolate was determined and analyzed.
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Affiliation(s)
- Shaokun Pan
- Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
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17
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Li C, Cao H, Lu L, Murphy D. Full-length sequences of 11 hepatitis C virus genotype 2 isolates representing five subtypes and six unclassified lineages with unique geographical distributions and genetic variation patterns. J Gen Virol 2012; 93:1173-1184. [PMID: 22357752 DOI: 10.1099/vir.0.038315-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this study, we characterized full-length hepatitis C virus (HCV) genome sequences for 11 genotype 2 isolates. They were isolated from the sera of 11 patients residing in Canada, of whom four had an African origin. Full-length genomes, each with 18-25 overlapping fragments, were obtained by PCR amplification. Five isolates represent the first complete genomes of subtypes 2d, 2e, 2j, 2m and 2r, while the other six correspond to variants that do not group within any assigned subtypes. These sequences had lengths of 9508-9825 nt and each contained a single ORF encoding 3012-3106 aa. Predicted amino acids were carefully inspected and unique variation patterns were recognized, especially for a 2e isolate, QC64. Phylogenetic analysis of complete genome sequences provides evidence that there are a total of 16 subtypes, of which 11 have been described here. Co-analysis with 68 partial NS5B sequences also differentiated 18 assigned subtypes, 2a-2r, and eight additional lineages within genotype 2, which is consistent with the analysis of complete genome sequences. The data from this study will now allow 10 assigned subtypes and six additional lineages of HCV genotype 2 to have their full-length genomes defined. Further analysis with 2021 genotype 2 sequences available in the HCV database indicated that the geographical distribution of these subtypes is consistent with an African origin, with particular subtypes having spread to Asia and the Americas.
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Affiliation(s)
- Chunhua Li
- Cancer Research Center, University of Kansas Medical Center, Kansas City, KS, USA.,The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Hong Cao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Ling Lu
- Cancer Research Center, University of Kansas Medical Center, Kansas City, KS, USA.,The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Donald Murphy
- Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
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18
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Nakano T, Lau GMG, Lau GML, Sugiyama M, Mizokami M. An updated analysis of hepatitis C virus genotypes and subtypes based on the complete coding region. Liver Int 2012; 32:339-45. [PMID: 22142261 DOI: 10.1111/j.1478-3231.2011.02684.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 10/09/2011] [Indexed: 12/23/2022]
Abstract
BACKGROUND The hepatitis C virus (HCV) genomic database is expanding rapidly. AIMS There is a need to provide an updated phylogenetic tree analysis based on the complete coding region of HCV. METHODS All available HCV complete genome sequences in the HCV databases available through October 2010 were analyzed. RESULTS The assignment of all known complete sequences up-to-date confirmed the previous six major genotypes and one new sequence, which have been provisionally assigned as subtype 7a. New recombinant forms of HCV, although uncommon, have been detected and were found to have different crossover points. CONCLUSION This updated analysis based on the complete region of HCV confirmed the validity of the previously assigned genotypes/subtypes and provided an up-to-date reference for future basic research and clinical studies.
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Affiliation(s)
- Tatsunori Nakano
- Department of Internal Medicine, Fujita Health University Nanakuri Sanatorium, Mie, Japan
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19
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Fu Y, Wang Y, Xia W, Pybus OG, Qin W, Lu L, Nelson K. New trends of HCV infection in China revealed by genetic analysis of viral sequences determined from first-time volunteer blood donors. J Viral Hepat 2011; 18:42-52. [PMID: 20196805 PMCID: PMC3020328 DOI: 10.1111/j.1365-2893.2010.01280.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recently, we studied hepatitis C virus (HCV) sera-prevalence among 559 890 first-time volunteer blood donors in China. From randomly selected 450 anti-HCV positive donors, we detected HCV RNA in 270 donors. In this study, we amplified HCV E1 and/or NS5B sequences from 236 of these donors followed by DNA sequencing and phylogenetic analysis. The results indicate new trends of HCV infection in China. The HCV genotype distribution differed according to the donors' region of origin. Among donors from Guangdong province, we detected subtypes 6a, 1b, 3a, 3b, 2a, and 1a at frequencies of 49.7%, 31.0%, 7.6%, 5.5%, 4.1%, and 2.1%, respectively. Among donors from outside Guangdong, we detected 1b, 2a, 6a, 3b, 3a, 6e, and 6n at frequencies 57.1%, 13.2%, 11.0%, 9.9%, 4.4%, 2.2%, and 2.2%, respectively. Although we found no significant differences among regions in age or gender, subtype 6a was more common (P < 0.001) in donors from Guangdong than those from elsewhere, whilst subtypes 1b (P < 0.02) and 2a (P < 0.001) were more frequent outside Guangdong. Disregarding origins, the male/female ratio was higher for subtype 6a-infected donors (P < 0.05) than for subtype 1b donors, whilst the mean age of subtype 2a donors was 8-10 years older (P < 0.05) than that for all other subtypes. Detailed phylogenetic analysis of our sequence data provides further insight into the transmission of HCV within China, and between China and other countries. The predominance of HCV 6a among blood donors in Guangdong is striking and mandates studies into risk factors for its acquisition.
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Affiliation(s)
- Y Fu
- Guangzhou Blood Center, Guangzhou, China.
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20
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Li C, Lu L, Zhang X, Murphy D. Entire genome sequences of two new HCV subtypes, 6r and 6s, and characterization of unique HVR1 variation patterns within genotype 6. J Viral Hepat 2009; 16:406-17. [PMID: 19281488 DOI: 10.1111/j.1365-2893.2009.01086.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hepatitis C virus genotype 6 currently contains 21 recognized subtypes, 6a-6u, for which 6r and 6s lack complete genome sequences. In this study, we entirely sequenced variants QC245 and QC66 from Cambodian immigrants in Canada representing subtypes 6r and 6s, respectively. The two genomes shared 75.3% nucleotide similarities to each other and 72.0-82.9% to 21 reference sequences representing subtypes 6a-6q, 6t-6u and variants km41 and gz52557. QC66 and QC245 displayed genome lengths of 9473 and 9450 nt and each contained a single open reading frame of 9051 nt. In 10 protein encoding regions QC245 and QC66 shared common sizes with TV249/6t and 537796/6l isolates, respectively. Phylogenetic analyses demonstrated that QC245 was more closely related to subtype 6f, but both QC66 and QC245 were subtypically different from all other genotype 6 subtypes. Our full-length sequence data confirmed the status of subtype 6r and 6s within genotype 6. Analysis of partial sequences revealed seven 6t and two 6s isolates that were all isolated from Cambodian immigrants. Analysis of the hypervariable region 1 sequences of 81 genotype 6 variants revealed two unique patterns of variation. First, most variants showed an amino acid deletion at the 4th position and second, many contained a basic residue at the 7th position. Possible roles of these two variation patterns are further discussed.
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Affiliation(s)
- C Li
- Division of Gastroenterology-Hepatology, and Nutrition, Department of Medicine, University of Utah, Salt Lake City, UT 84132, USA
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21
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Kasai D, Adachi T, Deng L, Nagano-Fujii M, Sada K, Ikeda M, Kato N, Ide YH, Shoji I, Hotta H. HCV replication suppresses cellular glucose uptake through down-regulation of cell surface expression of glucose transporters. J Hepatol 2009; 50:883-94. [PMID: 19303158 DOI: 10.1016/j.jhep.2008.12.029] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Revised: 11/19/2008] [Accepted: 12/11/2008] [Indexed: 01/06/2023]
Abstract
BACKGROUND/AIMS Persistent infection with hepatitis C virus (HCV) causes extrahepatic diseases, including diabetes. We investigated the possible effect(s) of HCV replication on cellular glucose uptake and expression of the facilitative glucose transporter (GLUT) 2 and 1. METHODS We used Huh-7.5 cells harboring either an HCV subgenomic RNA replicon (SGR) or an HCV full-genomic RNA replicon (FGR), HCV-infected cells, and the respective cells treated with interferon (IFN). We also used liver tissue samples obtained from patients with or without HCV infection. RESULTS Glucose uptake and surface expression of GLUT2 and GLUT1 were suppressed in SGR, FGR and HCV-infected cells compared to the control cells. Expression levels of GLUT2 mRNA, but not GLUT1 mRNA, were lower in SGR, FGR and HCV-infected cells than in the control. Luciferase reporter assay demonstrated decreased GLUT2 promoter activities in SGR, FGR and HCV-infected cells. IFN treatment restored glucose uptake, GLUT2 surface expression, GLUT2 mRNA expression and GLUT2 promoter activities. Also, GLUT2 expression was reduced in hepatocytes of liver tissues obtained from HCV-infected patients. CONCLUSIONS HCV replication down-regulates cell surface expression of GLUT2 partly at the transcriptional level, and possibly at the intracellular trafficking level as suggested for GLUT1, thereby lowering glucose uptake by hepatocytes.
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Affiliation(s)
- Daisuke Kasai
- Division of Microbiology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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22
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A new HCV genotype 6 subtype designated 6v was confirmed with three complete genome sequences. J Clin Virol 2009; 44:195-9. [PMID: 19179105 DOI: 10.1016/j.jcv.2008.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 12/12/2008] [Accepted: 12/17/2008] [Indexed: 02/05/2023]
Abstract
BACKGROUND Although hepatitis C virus (HCV) genotype 6 is classified into 21 subtypes, 6a-6u, new variants continue to be identified. OBJECTIVE To characterize the full-length genomes of three novel HCV genotype 6 variants: KMN02, KM046 and KM181. STUDY DESIGN From sera of patients with HCV infection, the entire HCV genome was amplified by RT-PCR followed by direct DNA sequencing and phylogenetic analysis. RESULTS The sera contained HCV genomes of 9461, 9429, and 9461nt in length, and each harboured a single ORF of 9051nt. The genomes showed 95.3-98.1% nucleotide similarity to each other and 72.2-75.4% similarity to 23 genotype 6 reference sequences, which represent subtypes 6a-6u and unassigned variants km41 and gz52557. Phylogenetic analyses demonstrated that they were genotype 6, but were subtypically distinct. Based on the current criteria of HCV classification, they were designed to represent a new subtype, 6v. Analysis of E1 and NS5B region partial sequences revealed two additional related variants, CMBD-14 and CMBD-86 that had been previously reported in northern Thailand and sequences dropped into Genbank. CONCLUSION Three novel HCV genotype 6 variants were entirely sequenced and designated subtype 6v.
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23
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Li C, Lu L, Wu X, Wang C, Bennett P, Lu T, Murphy D. Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t. J Gen Virol 2009; 90:1820-1826. [PMID: 19357224 DOI: 10.1099/vir.0.010330-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In this study, we characterized the full-length genomic sequences of 13 distinct hepatitis C virus (HCV) genotype 4 isolates/subtypes: QC264/4b, QC381/4c, QC382/4d, QC193/4g, QC383/4k, QC274/4l, QC249/4m, QC97/4n, QC93/4o, QC139/4p, QC262/4q, QC384/4r and QC155/4t. These were amplified, using RT-PCR, from the sera of patients now residing in Canada, 11 of which were African immigrants. The resulting genomes varied between 9421 and 9475 nt in length and each contains a single ORF of 9018-9069 nt. The sequences showed nucleotide similarities of 77.3-84.3 % in comparison with subtypes 4a (GenBank accession no. Y11604) and 4f (EF589160) and 70.6-72.8 % in comparison with genotype 1 (M62321/1a, M58335/1b, D14853/1c, and 1?/AJ851228) reference sequences. These similarities were often higher than those currently defined by HCV classification criteria for subtype (75.0-80.0 %) and genotype (67.0-70.0 %) division, respectively. Further analyses of the complete and partial E1 and partial NS5B sequences confirmed these 13 'provisionally assigned subtypes'.
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Affiliation(s)
- Chunhua Li
- Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Ling Lu
- Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Xianghong Wu
- Department of Biology, Kunming Teacher's College, Kunming, Yunnan, PR China
| | - Chuanxi Wang
- Guangzhou Blood Center, Guangzhou, Guangdong, PR China.,Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Phil Bennett
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Teng Lu
- University of Georgia, Athens, GA, USA
| | - Donald Murphy
- Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
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24
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Reply. Transfusion 2008. [DOI: 10.1111/j.1537-2995.2008.01963.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Lu L, Tatsunori N, Li C, Waheed S, Gao F, Robertson BH. HCV selection and HVR1 evolution in a chimpanzee chronically infected with HCV-1 over 12 years. Hepatol Res 2008; 38:704-16. [PMID: 18328069 DOI: 10.1111/j.1872-034x.2008.00320.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
AIM To study hepatitis C virus (HCV) selection and hypervariable region-1 (HVR1) evolution in a chimpanzee chronically infected with HCV-1 over 12 years after inoculation with a human factor VIII concentrate contaminated with HCV. METHODS From the inoculum, the earliest chimpanzee plasma and 12 annual plasma samples, HCV fragments including HVR1 were amplified followed by cloning and sequencing. RESULTS Five HCV subtypes - 1a, 1b, 2a, 2b, 3a - and multiple 1a strains were identified in the inoculum. Two 1a strains were found in the earliest chimpanzee sample, while a single HCV-1 strain was detected in the 12 annual samples. None of the chimpanzee sequences were identical to those found in the inoculum. Over 12 years, HVR1 patterns changed irregularly, but a few patterns showed identical nucleotide or amino acid sequences. In the last three years, the variety of HVR1 patterns decreased, while the proportion of major patterns increased. These corresponded to a higher virus load and a lower number of amino acid substitutions. Simultaneously, the HVR1 sequences became more similar to the consensus sequence of the 1a subtype. CONCLUSION HCV selection was observed from the inoculum to the inoculated chimpanzee and from the early acute hepatitis to the persistent chronic infection. The selection occurred at three levels: among subtypes after transmission, among isolates during acute hepatitis and among quasispecies in chronic infection.
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Affiliation(s)
- Ling Lu
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Utah, Utah, USA
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26
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Bracho MA, Saludes V, Martró E, Bargalló A, González-Candelas F, Ausina V. Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses. Virol J 2008; 5:72. [PMID: 18533988 PMCID: PMC2438343 DOI: 10.1186/1743-422x-5-72] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 06/05/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. RESULTS We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. CONCLUSION In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.
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Affiliation(s)
- Maria A Bracho
- Institut "Cavanilles" de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna (València), Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Verónica Saludes
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Elisa Martró
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Ana Bargalló
- Servei d'Aparell Digestiu, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Fernando González-Candelas
- Institut "Cavanilles" de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna (València), Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Vicent Ausina
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
- CIBER en Enfermedades Respiratorias (CIBERES), Spain
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Noppornpanth S, Poovorawan Y, Lien TX, Smits SL, Osterhaus ADME, Haagmans BL. Complete genome analysis of hepatitis C virus subtypes 6t and 6u. J Gen Virol 2008; 89:1276-1281. [PMID: 18420806 DOI: 10.1099/vir.0.83593-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) genomes exhibit high nucleotide sequence diversity. In this study, we performed complete genome sequence analysis of 11 HCV genotype 6 samples from Vietnam and Thailand. We identified nine HCV complete genomes belonging to subtypes 6a (D9), 6e (D42 and D88), 6f (TH52), 6i (TH24), 6l (D33), 6n (TH22 and TH31) and 6o (D85). Phylogenetic analysis of the core/E1 and NS5B regions from unclassified genotype 6 isolates from Asian immigrants in Canada revealed that two other viruses (D49 and D83) could be classified as novel candidates of HCV subtypes 6t and 6u.
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Affiliation(s)
- Suwanna Noppornpanth
- Department of Virology, Erasmus Medical Center, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Yong Poovorawan
- Center of Excellence in Viral Hepatitis Research, Department of Pediatrics, Chulalongkorn Hospital, Bangkok, Thailand
| | - Truong Xuan Lien
- Department of Biological Analysis, Pasteur Institute Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Saskia L Smits
- Department of Virology, Erasmus Medical Center, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Department of Virology, Erasmus Medical Center, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Virology, Erasmus Medical Center, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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Lu L, Murphy D, Li C, Liu S, Xia X, Pham PH, Jin Y, Hagedorn CH, Abe K. Complete genomes of three subtype 6t isolates and analysis of many novel hepatitis C virus variants within genotype 6. J Gen Virol 2008; 89:444-452. [PMID: 18198375 DOI: 10.1099/vir.0.83460-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study, the complete genomic sequence was determined for three hepatitis C virus variants (VT21, TV241 and TV249) of genotype 6 that do not classify within the established subtypes. All three genomes were isolated from patients in Vietnam and sequenced using 100 microl of serum. They showed 91.4-93.6% nucleotide similarities to each other but only 71.7-79.4% similarities to 17 reference sequences representing subtypes 6a-6q and to isolates km41 and gz52557. VT21, TV241 and TV249 displayed genome lengths of 9407, 9460 and 9445 nt, respectively. All three isolates contained a single open reading frame of 9051 nt while the 5'UTRs and 3'UTRs were 324-338 nt and 32-71 nt, respectively. They shared common sizes with QC227/6o and QC216/6p isolates in all ten protein regions. Phylogenetic analyses demonstrated that VT21, TV241 and TV249 clustered independently and were assigned subtype 6t, following the recent designations of 6r and 6s. Analysis of partial genomic sequences available for genotype 6 variants revealed five additional subtype 6t isolates, all originating from Vietnam. This analysis revealed two additional groups of isolates, and at least seven novel variants analogous to km41 and gz52557 that group independently and do not classify within the subtypes 6a-6t. This suggests the existence of at least 11 additional subtypes for genotype 6. In addition, the existence of isolates showing genetic distances greater than those within subtypes, but lesser than those between subtypes, raises interesting questions regarding the classification of HCV.
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Affiliation(s)
- Ling Lu
- Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Donald Murphy
- Institut National de Santé Publique du Québec, Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Chunhua Li
- The First People's Hospital of Yunnan Province, Kunming, PR China.,Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Shuanghu Liu
- Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, PR China
| | - Phiet Hoang Pham
- Department of Immunology and Physiopathology, University of Medicine and Pharmacy in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Yuhuai Jin
- Department of Microbiology, Hebei Medical University, Shijiazhuang, PR China
| | - Curt H Hagedorn
- Division of Gastroenterology-Hepatology and Nutrition, Department of Medicine, University of Utah, 30N 1900E, Salt Lake City, UT 84132, USA
| | - Kenji Abe
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
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Lu L, Li C, Fu Y, Gao F, Pybus OG, Abe K, Okamoto H, Hagedorn CH, Murphy D. Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6. J Gen Virol 2007; 88:1519-1525. [PMID: 17412981 DOI: 10.1099/vir.0.82820-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Five hepatitis C virus (HCV) complete genome sequences (Th846, 537796, QC227, QC216 and QC99) from a blood donor in Thailand and three Asian immigrants and one Caucasian in North America were determined. Phylogenetically, they represent the first complete genomes for subtypes 6c, 6l, 6o, 6p and 6q, respectively. Similarity analysis showed no evidence of inter- or intrasubtype recombination. Further analysis in conjunction with partial sequences from the Los Alamos HCV database led to the identification of other closely related isolates from south-eastern Asia or immigrants from that region. However, Th846 did not cluster with any reference sequence and is the sole isolate of subtype 6c reported so far. This study completes the full genome sequencing of all 17 assigned HCV genotype 6 subtypes (6a-6q). The utility of this panel of complete sequences for accurate detection and classification of infection, and for estimating the origin of this genotype of HCV, is discussed.
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Affiliation(s)
- Ling Lu
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
| | - Chunhua Li
- The First People's Hospital of Yunnan Province, Kunming, China
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
| | - Yongshui Fu
- Gunagzhou Blood Center, Guangzhou City, Guangdong Province, China
| | - Fengxiang Gao
- Public Health Laboratories, New Hampshire Department of Health and Human Services, Concord, NH, USA
| | | | - Kenji Abe
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken, Japan
| | - Curt H Hagedorn
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
| | - Donald Murphy
- Institut National de Santé Publique du Quebec, Laboratoire de Santé Publique du Quebec, Sainte-Anne-de-Bellevue, Quebec, Canada
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