1
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Vo-Quang E, Pawlotsky JM. 'Unusual' HCV genotype subtypes: origin, distribution, sensitivity to direct-acting antiviral drugs and behaviour on antiviral treatment and retreatment. Gut 2024; 73:1570-1582. [PMID: 38782565 PMCID: PMC11347264 DOI: 10.1136/gutjnl-2024-332177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
The high genetic diversity of hepatitis C virus (HCV) has led to the emergence of eight genotypes and a large number of subtypes in limited geographical areas. Currently approved pangenotypic DAA regimens have been designed and developed to be effective against the most common subtypes (1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a and 6a). However, large populations living in Africa and Asia, or who have migrated from these regions to industrialised countries, are infected with 'unusual', non-epidemic HCV subtypes, including some that are inherently resistant to currently available direct-acting antiviral (DAA) drugs due to the presence of natural polymorphisms at resistance-associated substitution positions. In this review article, we describe the origin and subsequent global spread of HCV genotypes and subtypes, the current global distribution of common and unusual HCV subtypes, the polymorphisms naturally present in the genome sequences of unusual HCV subtypes that may confer inherently reduced susceptibility to DAA drugs and the available data on the response of unusual HCV subtypes to first-line HCV therapy and retreatment. We conclude that the problem of unusual HCV subtypes that are inherently resistant to DAAs and its threat to the global efforts to eliminate viral hepatitis are largely underestimated and warrant vigorous action.
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Affiliation(s)
- Erwan Vo-Quang
- National Reference Centre for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale (INSERM U955), Créteil, France
- Department of Hepatology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Centre for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale (INSERM U955), Créteil, France
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2
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Guo L, Li B, Han P, Dong N, Zhu Y, Li F, Si H, Shi Z, Wang B, Yang X, Zhang Y. Identification of a Novel Hepacivirus in Southeast Asian Shrew ( Crocidura fuliginosa) from Yunnan Province, China. Pathogens 2023; 12:1400. [PMID: 38133285 PMCID: PMC10745850 DOI: 10.3390/pathogens12121400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/18/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
The genus Hepacivirus contains single-stranded positive-sense RNA viruses belonging to the family Flaviviridae, which comprises 14 species. These 14 hepaciviruses have been found in different mammals, such as primates, dogs, bats, and rodents. To date, Hepacivirus has not been reported in the shrew genus of Crocidura. To study the prevalence and genetic evolution of Hepacivirus in small mammals in Yunnan Province, China, molecular detection of Hepacivirus in small mammals from Yunnan Province during 2016 and 2017 was performed using reverse-transcription polymerase chain reaction (RT-PCR). Our results showed that the overall infection rate of Hepacivirus in small mammals was 0.12% (2/1602), and the host animal was the Southeast Asian shrew (Crocidura fuliginosa) (12.5%, 2/16). Quantitative real-time PCR showed that Hepacivirus had the highest viral RNA copy number in the liver. Phylogenetic analysis revealed that the hepaciviruses obtained in this study does not belong to any designated species of hepaciviruses and forms an independent clade. To conclude, a novel hepacivirus was identified for the first time in C. fuliginosa specimens from Yunnan Province, China. This study expands the host range and viral diversity of hepaciviruses.
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Affiliation(s)
- Ling Guo
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
- Chongqing Jiangbei District Center for Disease Control and Prevention, Chongqing 400020, China
| | - Bei Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Peiyu Han
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
| | - Na Dong
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
| | - Yan Zhu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Fuli Li
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
| | - Haorui Si
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Zhengli Shi
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650023, China
| | - Yunzhi Zhang
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
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3
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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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4
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Forni D, Cagliani R, Clerici M, Sironi M. Disease-causing human viruses: novelty and legacy. Trends Microbiol 2022; 30:1232-1242. [PMID: 35902319 DOI: 10.1016/j.tim.2022.07.002] [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: 01/26/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023]
Abstract
About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
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5
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Pacchiarotti G, Nardini R, Scicluna MT. Equine Hepacivirus: A Systematic Review and a Meta-Analysis of Serological and Biomolecular Prevalence and a Phylogenetic Update. Animals (Basel) 2022; 12:2486. [PMID: 36230228 PMCID: PMC9558973 DOI: 10.3390/ani12192486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Viral hepatitis has recently assumed relevance for equine veterinary medicine since a variety of new viruses have been discovered. Equine Hepacivirus (EqHV) is an RNA virus belonging to the Flaviviridae family that can cause subclinical hepatitis in horses, occasionally evolving into a chronic disease. EqHV, to date, is considered the closest known relative of human HCV. EqHV has been reported worldwide therefore assessing its features is relevant, considering both the wide use of blood products and transfusions in veterinary therapies and its similitude to HCV. The present review resumes the actual knowledge on EqHV epidemiology, risk factors and immunology, together with potential diagnostics and good practices for prevention. Moreover, adhering to PRISMA guidelines for systematic reviews a meta-analysis of serological and biomolecular prevalence and an updated phylogenetic description is presented as a benchmark for further studies.
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6
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Bezerra CDS, Limeira CH, Monteiro dos Anjos D, Nogueira DB, Morais DDA, Falcão BMR, Alves CJ, Santos CDSAB, Silva MLCR, de Azevedo SS. Global prevalence of RNA-positive horses for hepacivirus (EqHV): systematic review and meta-analysis. J Equine Vet Sci 2022; 114:104003. [DOI: 10.1016/j.jevs.2022.104003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
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7
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Meshram RJ, Kathwate GH, Gacche RN. Progress, evolving therapeutic/diagnostic approaches, and challenges in the management of hepatitis C virus infections. Arch Virol 2022; 167:717-736. [PMID: 35089390 PMCID: PMC8795940 DOI: 10.1007/s00705-022-05375-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) infections are emerging as one of the foremost challenges in healthcare owing to its chronicity and the virus's quasispecies nature. Worldwide, over 170 million people are chronically infected with HCV, with an annual mortality of over 500,000 people across the world. The emerging pathophysiological evidence links HCV infections to a risk of developing liver diseases such as cirrhosis and hepatocellular carcinoma. Despite the great strides that have been made towards understanding the pathophysiology of disease progression, the tailored treatments of HCV infection remain to be established. The present review provides an update of the literature pertaining to evolving therapeutic approaches and prophylactic measures for the effective management of HCV infections. An extensive discussion of established and experimental immune prophylactic measures also sheds light on current developments in the design of vaccination strategies against HCV infection. We have also attempted to address the application of nanotechnology in formulating effective therapeutic interventions against HCV. Pointing out the limitations of the existing diagnostic methods and therapeutic approaches against HCV might inspire the design and development of novel, efficient, reliable, and cost-effective diagnostic technologies as well as novel therapeutic and immune prophylactic interventions for the effective management of HCV.
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Affiliation(s)
| | | | - Rajesh Nivarti Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, MS, 411007, India.
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8
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Ghafari M, Simmonds P, Pybus OG, Katzourakis A. A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses. Curr Biol 2021; 31:4689-4696.e5. [PMID: 34478645 PMCID: PMC8585505 DOI: 10.1016/j.cub.2021.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/02/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023]
Abstract
Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.65. We show that standard substitution models fail to correctly estimate divergence times once the most rapidly evolving sites saturate, typically after hundreds of years in RNA viruses and thousands of years in DNA viruses. Our model successfully recreates the observed pattern of decay and explains the evolutionary processes behind the time-dependent rate phenomenon. We then apply our model to re-estimate the date of diversification of genotypes of hepatitis C virus to 423,000 (95% highest posterior density [HPD]: 394,000-454,000) years before present, a time preceding the dispersal of modern humans out of Africa, and show that the most recent common ancestor of sarbecoviruses dates back to 21,000 (95% HPD: 19,000-22,000) years ago, nearly thirty times older than previous estimates. This creates a new perspective for our understanding of the origins of these viruses and also suggests that a substantial revision of evolutionary timescales of other viruses can be similarly achieved.
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Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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9
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In Vitro Comparison of the Internal Ribosomal Entry Site Activity from Rodent Hepacivirus and Pegivirus and Construction of Pseudoparticles. Adv Virol 2021; 2021:5569844. [PMID: 34422054 PMCID: PMC8376455 DOI: 10.1155/2021/5569844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/20/2021] [Indexed: 01/17/2023] Open
Abstract
The 5′ untranslated region (5′ UTR) of rodent hepacivirus (RHV) and pegivirus (RPgV) contains sequence homology to the HCV type III internal ribosome entry sites (IRES). Utilizing a monocistronic expression vector with an RNA polymerase I promoter to drive transcription, we show cell-specific IRES translation and regions within the IRES required for full functionality. Focusing on RHV, we further pseudotyped lentivirus with RHV and showed cell surface expression of the envelope proteins and transduction of murine hepatocytes and we then constructed full-length RHV and RPgV replicons with reporter genes. Using the replicon system, we show that the RHV NS3-4A protease cleaves a mitochondrial antiviral signaling protein reporter. However, liver-derived cells did not readily support the complete viral life cycle.
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10
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Sonon P, Brito Ferreira ML, Santos Almeida R, Saloum Deghaide NH, Henrique Willcox G, Guimarães EL, da Purificação Júnior AF, Cordeiro MT, Antunes de Brito CA, de Albuquerque MDFM, Lins RD, Donadi EA, Lucena-Silva N. Differential Frequencies of HLA-DRB1, DQA1, and DQB1 Alleles and Haplotypes Are Observed in the Arbovirus-Related Neurological Syndromes. J Infect Dis 2021; 224:517-525. [PMID: 33320259 DOI: 10.1093/infdis/jiaa764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/11/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND We took advantage of the 2015-2016 Brazilian arbovirus outbreak (Zika [ZIKV]/dengue/chikungunya viruses) associated with neurological complications to type HLA-DRB1/DQA1/DQB1 variants in patients exhibiting neurological complications and in bone marrow donors from the same endemic geographical region. METHODS DRB1/DQA1/DQB1 loci were typed using sequence-specific oligonucleotides. In silico studies were performed using X-ray resolved dimer constructions. RESULTS The DQA1*01, DQA1*05, DQB1*02, or DQB1*06 genotypes/haplotypes and DQA1/DQB1 haplotypes that encode the putative DQA1/DQB1 dimers were overrepresented in the whole group of patients and in patients exhibiting peripheral neurological spectrum disorders (PSD) or encephalitis spectrum disorders (ESD). The DRB1*04, DRB1*13, and DQA1*03 allele groups protected against arbovirus neurological manifestation, being underrepresented in whole group of patients and ESD and PSD groups. Genetic and in silico studies revealed that DQA1/DQB1 dimers (1) were primarily associated with susceptibility to arbovirus infections; (2) can bind to a broad range of ZIKV peptides (235 of 1878 peptides, primarily prM and NS2A); and (3) exhibited hydrophilic and highly positively charged grooves when compared to the DRA1/DRB1 cleft. The protective dimer (DRA1/DRB1*04) bound a limited number of ZIKV peptides (40 of 1878 peptides, primarily prM). CONCLUSION Protective haplotypes may recognize arbovirus peptides more specifically than susceptible haplotypes.
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Affiliation(s)
- Paulin Sonon
- Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | - Renata Santos Almeida
- Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | | | | | | | - Marli Tenório Cordeiro
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | | | - Roberto D Lins
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Eduardo A Donadi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Norma Lucena-Silva
- Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
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11
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Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses. Viruses 2021; 13:v13081509. [PMID: 34452374 PMCID: PMC8402684 DOI: 10.3390/v13081509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?
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12
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Leumi S, El Kassas M, Zhong J. Hepatitis C virus genotype 4: A poorly characterized endemic genotype. J Med Virol 2021; 93:6079-6088. [PMID: 34185316 DOI: 10.1002/jmv.27165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 12/16/2022]
Abstract
Globally, 13% of all hepatitis C virus (HCV) infections are caused by genotype 4 (GT4), which consists of 17 subtypes with various levels of susceptibility to anti-HCV therapy. This genotype is endemic in the Middle East and Africa and has considerably spread to Europe lately. The molecular features of HCV-GT4 infection, as well as its appropriate therapeutics, are poorly characterized as it has not been the subject of widespread basic research. As such, in this review, we aim to gather the current state of knowledge of this genotype with a particular emphasis on its heterogeneity, sequence signatures, resistance-associated substitutions, and available in vivo and in vitro models used for its study. We urge developing more cell-culture models based on different GT4 subtypes to better understand the virology and therapeutic response of this particular genotype. This review may raise more awareness about this genotype and trigger more basic research work to develop its research tools. This will be critical to design better therapeutics and help to provide adequate guidelines for physicians working with HCV-GT4 patients.
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Affiliation(s)
- Steve Leumi
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mohamed El Kassas
- Department of Endemic Medicine, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Jin Zhong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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Abbadi I, Lkhider M, Kitab B, Jabboua K, Zaidane I, Haddaji A, Nacer S, Matsuu A, Pineau P, Tsukiyama-Kohara K, Benjelloun S, Ezzikouri S. Non-primate hepacivirus transmission and prevalence: Novel findings of virus circulation in horses and dogs in Morocco. INFECTION GENETICS AND EVOLUTION 2021; 93:104975. [PMID: 34175479 DOI: 10.1016/j.meegid.2021.104975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
Non-primate hepacivirus (NPHV) is a homolog of hepatitis C virus and has been isolated from dogs and horses. Data on NPHV prevalence and distribution are not complete, and there is a particular lack of reports from the African continent. The present study represents the first investigation of NPHV prevalence in horses and dogs in North Africa. Blood was collected from 172 horses and 36 dogs at different locations in Morocco, and screened for NPHV RNA using nested PCR targeting 5'UTR and NS3 regions and analyzed for anti-NPHV NS3 antibody using a Gaussia luciferase immunoprecipitation system-to determine seroprevalence. Eight sequences of the NS3 region isolated from positive serum samples were targeted for phylogenetic analysis. Horses and dogs showed respective NPHV RNA positivity rates of 10.5% and 5.5%, and seroprevalences of 65.7% and 8.33%. Juvenile horses appeared more susceptible to infection, with a 23.5% NHPV RNA positivity rate. Seropositivity was more extensive in mares than stallions (77.14% vs. 46.27%, p < 0.0001). Phylogenetically, that NPHV NS3 genes isolated from horses and dog are clustered together. The NPHV strains we detected showed no correlation with geographic location within Morocco. In conclusion, Moroccan horses showed much evidence of previous and/or current NPHV infection, with young age and female sex as noted potential risk factors. Interestingly, NPHV is circulating in dogs as well as horses, suggesting that it has crossed species barriers and that horses and dogs are potential vectors by which an ancestor to hepatitis C virus was transmitted into human populations.
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Affiliation(s)
- Islam Abbadi
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco; Laboratory of Biosciences, School of Sciences and Technology, Mohammedia, Hassan II University of Casablanca, Morocco
| | - Mustapha Lkhider
- Laboratory of Biosciences, School of Sciences and Technology, Mohammedia, Hassan II University of Casablanca, Morocco
| | - Bouchra Kitab
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | | | - Imane Zaidane
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Asmaa Haddaji
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sabrine Nacer
- Laboratory of Biosciences, School of Sciences and Technology, Mohammedia, Hassan II University of Casablanca, Morocco
| | - Aya Matsuu
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Pascal Pineau
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
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14
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Cagliani R, Mozzi A, Pontremoli C, Sironi M. Evolution and Origin of Human Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Abstract
Laos is a landlocked country in South East Asia, ranking fifth for primary liver cancer incidence worldwide. Risk factors that might explain this worrying situation are poorly known. We conducted a review of the literature concerning the etiologies of terminal liver diseases in Laos. A double infectious burden with hepatitis B and C viruses and the liver fluke Opisthorchis viverrini seems to be the main cause of the high liver cancer incidence. Moreover, it was also suggested that mutagenic substances frequently found in tobacco, alcoholic beverages, fermented fish, and mold-contaminated cereals or nuts, which are all substances heavily consumed by Lao people, lead to the accumulation of DNA mutations in the liver cell genome causing tumor processes. However, the respective proportions of liver cancer cases attributable to each category of infections and substances consumed, as well as the histological nature of the neoplasia are still not precisely documented in Laos. The international medical and scientific communities as well as public health stakeholders should urgently consider the alarming situation of liver health in Laos to stimulate both research and subsequent implementation of prevention policies.
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16
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Bletsa M, Vrancken B, Gryseels S, Boonen I, Fikatas A, Li Y, Laudisoit A, Lequime S, Bryja J, Makundi R, Meheretu Y, Akaibe BD, Mbalitini SG, Van de Perre F, Van Houtte N, Těšíková J, Wollants E, Van Ranst M, Pybus OG, Drexler JF, Verheyen E, Leirs H, Gouy de Bellocq J, Lemey P. Molecular detection and genomic characterization of diverse hepaciviruses in African rodents. Virus Evol 2021; 7:veab036. [PMID: 34221451 PMCID: PMC8242229 DOI: 10.1093/ve/veab036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.
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Affiliation(s)
- Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Antonios Fikatas
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Sebastian Lequime
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Rhodes Makundi
- Pest Management Center -Sokoine University of Agriculture, Morogoro, Tanzania
| | - Yonas Meheretu
- Department of Biology and Institute of Mountain Research & Development, Mekelle University, Mekelle, Ethiopia
| | - Benjamin Dudu Akaibe
- Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Sylvestre Gambalemoke Mbalitini
- Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Frederik Van de Perre
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Natalie Van Houtte
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Elke Wollants
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Jan Felix Drexler
- Charite-Universitatsmedizin Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Erik Verheyen
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- OD Taxonomy and Phylogeny-Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Herwig Leirs
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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17
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Porter AF, Pettersson JHO, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC. Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evol 2020; 6:veaa064. [PMID: 33240526 PMCID: PMC7673076 DOI: 10.1093/ve/veaa064] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.
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Affiliation(s)
- Ashleigh F Porter
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - John H-O Pettersson
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Wei-Shan Chang
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Erin Harvey
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman 2088, Australia
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - John-Sebastian Eden
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Jan Buchmann
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Craig Moritz
- Research School of Biology, Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
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18
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SARS-CoV-2 will constantly sweep its tracks: a vaccine containing CpG motifs in 'lasso' for the multi-faced virus. Inflamm Res 2020; 69:801-812. [PMID: 32656668 PMCID: PMC7354743 DOI: 10.1007/s00011-020-01377-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022] Open
Abstract
During the current COVID-19 pandemic, the global ratio between the dead and the survivors is approximately 1 to 10, which has put humanity on high alert and provided strong motivation for the intensive search for vaccines and drugs. It is already clear that if we follow the most likely scenario, which is similar to that used to create seasonal influenza vaccines, then we will need to develop improved vaccine formulas every year to control the spread of the new, highly mutable coronavirus SARS-CoV-2. In this article, using well-known RNA viruses (HIV, influenza viruses, HCV) as examples, we consider the main successes and failures in creating primarily highly effective vaccines. The experience accumulated dealing with the biology of zoonotic RNA viruses suggests that the fight against COVID-19 will be difficult and lengthy. The most effective vaccines against SARS-CoV-2 will be those able to form highly effective memory cells for both humoral (memory B cells) and cellular (cross-reactive antiviral memory T cells) immunity. Unfortunately, RNA viruses constantly sweep their tracks and perhaps one of the most promising solutions in the fight against the COVID-19 pandemic is the creation of 'universal' vaccines based on conservative SARS-CoV-2 genome sequences (antigen-presenting) and unmethylated CpG dinucleotides (adjuvant) in the composition of the phosphorothioate backbone of single-stranded DNA oligonucleotides (ODN), which can be effective for long periods of use. Here, we propose a SARS-CoV-2 vaccine based on a lasso-like phosphorothioate oligonucleotide construction containing CpG motifs and the antigen-presenting unique ACG-containing genome sequence of SARS-CoV-2. We found that CpG dinucleotides are the most rare dinucleotides in the genomes of SARS-CoV-2 and other known human coronaviruses, and hypothesized that their higher frequency could be responsible for the unwanted increased lethality to the host, causing a ‘cytokine storm’ in people who overexpress cytokines through the activation of specific Toll-like receptors in a manner similar to TLR9-CpG ODN interactions. Interestingly, the virus strains sequenced in China (Wuhan) in February 2020 contained on average one CpG dinucleotide more in their genome than the later strains from the USA (New York) sequenced in May 2020. Obviously, during the first steps of the microevolution of SARS-CoV-2 in the human population, natural selection tends to select viral genomes containing fewer CpG motifs that do not trigger a strong innate immune response, so the infected person has moderate symptoms and spreads SARS-CoV-2 more readily. However, in our opinion, unmethylated CpG dinucleotides are also capable of preparing the host immune system for the coronavirus infection and should be present in SARS-CoV-2 vaccines as strong adjuvants.
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19
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Novel HCV-Like Virus Detected in Avian Livers in Southern China and Its Implications for Natural Recombination Events. Virol Sin 2020; 36:149-151. [PMID: 32617899 DOI: 10.1007/s12250-020-00256-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/26/2020] [Indexed: 10/23/2022] Open
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20
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Elia G, Caringella F, Lanave G, Martella V, Losurdo M, Tittarelli M, Colitti B, Decaro N, Buonavoglia C. Genetic heterogeneity of bovine hepacivirus in Italy. Transbound Emerg Dis 2020; 67:2731-2740. [PMID: 32426936 DOI: 10.1111/tbed.13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022]
Abstract
Viruses similar to human hepatitis C virus (HCV) in the Hepacivirus genus have been identified in several animal hosts, including cattle. Since its first discovery in Germany, bovine hepacivirus (BovHepV) has been described in several countries globally. However, limited data are available on BovHepV epidemiology and genetic variability. The aim of this study was to investigate the prevalence and genetic diversity of BovHepV in Italy. Viral RNA was identified in 37 (0.15%) of 24,820 bovine sera, with titres ranging from 1.09 × 103 to 8.27 × 106 RNA copies/ml. Upon sequencing and phylogenetic analysis of the 5'UTR and NS3 genomic portions, the Italian BovHepV strains segregated into at least four distinct subtypes (A, B, C and F) that are also co-circulating globally.
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Affiliation(s)
- Gabriella Elia
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | | | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Michele Losurdo
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Manuela Tittarelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Teramo, Italy
| | - Barbara Colitti
- Department of Veterinary Science, University of Torino, Grugliasco (Torino), Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Canio Buonavoglia
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
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21
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Ploss A, Kapoor A. Animal Models of Hepatitis C Virus Infection. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036970. [PMID: 31843875 DOI: 10.1101/cshperspect.a036970] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is an important and underreported infectious disease, causing chronic infection in ∼71 million people worldwide. The limited host range of HCV, which robustly infects only humans and chimpanzees, has made studying this virus in vivo challenging and hampered the development of a desperately needed vaccine. The restrictions and ethical concerns surrounding biomedical research in chimpanzees has made the search for an animal model all the more important. In this review, we discuss different approaches that are being pursued toward creating small animal models for HCV infection. Although efforts to use a nonhuman primate species besides chimpanzees have proven challenging, important advances have been achieved in a variety of humanized mouse models. However, such models still fall short of the overarching goal to have an immunocompetent, inheritably susceptible in vivo platform in which the immunopathology of HCV could be studied and putative vaccines development. Alternatives to overcome this include virus adaptation, such as murine-tropic HCV strains, or the use of related hepaciviruses, of which many have been recently identified. Of the latter, the rodent/rat hepacivirus from Rattus norvegicus species-1 (RHV-rn1) holds promise as a surrogate virus in fully immunocompetent rats that can inform our understanding of the interaction between the immune response and viral outcomes (i.e., clearance vs. persistence). However, further characterization of these animal models is necessary before their use for gaining new insights into the immunopathogenesis of HCV and for conceptualizing HCV vaccines.
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Affiliation(s)
- Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Amit Kapoor
- Nationwide Children's Hospital, Columbus, Ohio 43205, USA
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22
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Date T, Sugiyama M, Lkhagvasuren D, Wakita T, Oyunsuren T, Mizokami M. Prevalence of equine hepacivirus infection in Mongolia. Virus Res 2020; 282:197940. [PMID: 32259615 DOI: 10.1016/j.virusres.2020.197940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 01/05/2020] [Accepted: 03/15/2020] [Indexed: 01/17/2023]
Abstract
Equine hepacivirus (EHV) belongs to the hepacivirus A and is related to hepatitis C virus (HCV). This virus shows hepatic tropism and is known to chronically infect horses. EHV has been reported from various countries, but the prevalence in Mongolia, where large horse populations are pastured, remains unknown. This study collected serum samples from horses in six areas across Mongolia, in order to investigate the status of infection. The possibility of human infection was also examined. The results showed an infection rate among horses of about 40 % in all regions. However, no evidence of EHV viremia was found in human serum. A mutation characteristic of Mongolian EHV was found in the 5'-untranslated region of the viral sequence. Molecular phylogenetic trees for core, NS3, and NS5B sequences showed the formation of two clusters depending on the area from which samples were taken. The same results were obtained from molecular phylogenetic analyses using the full genome. From detailed calculations of genetic diversity calculated using the full genome, EHV appears divisible into two subgenotypes. Blood samples were collected again after a 7-month interval to examine infection persistence. Seventeen of 19 horses retested showed positive results for EHV after 7 months, suggesting a high rate of persistent infection. These results indicate a relatively higher frequency of EHV infection in Mongolia than in Europe or North America, with virus strains divided into at least two subgenotypes.
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Affiliation(s)
- Tomoko Date
- Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba, 272-8516, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba, 272-8516, Japan.
| | - Damdindorj Lkhagvasuren
- Laboratory of Molecular Biology, Institute of Biology, Mongolian Academy of Sciences, Peace av.54b, Bayanzurkh 3, Ulaanbaatar, 13330, Mongolia
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Tsendsuren Oyunsuren
- Laboratory of Molecular Biology, Institute of Biology, Mongolian Academy of Sciences, Peace av.54b, Bayanzurkh 3, Ulaanbaatar, 13330, Mongolia
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba, 272-8516, Japan
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23
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Further Evidence for in Utero Transmission of Equine Hepacivirus to Foals. Viruses 2019; 11:v11121124. [PMID: 31817371 PMCID: PMC6950541 DOI: 10.3390/v11121124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
(1) Background: Equine hepacivirus (EqHV), also referred to as non-primate hepacivirus (NPHV), infects horses—and dogs in some instances—and is closely related to hepatitis C virus (HCV) that has infected up to 3% of the world’s human population, causing an epidemic of liver cirrhosis and cancer. EqHV also chronically infects the liver of horses, but does not appear to cause serious liver damages. Previous studies have been looking to identify route(s) of EqHV transmission to and between horses. (2) Methods: In this retrospective study, we sought to evaluate the prevalence of vertical transmission taking place in utero with measuring by quantitative RT-PCR the amounts of EqHV genome in samples from 394 dead foals or fetuses, paired with the allantochorion whenever available. (3) Results: Detection of EqHV in three foals most likely resulted from a vertical transmission from the mares to the fetuses, consistent with the in utero transmission hypothesis. In support of this observation, the presence of EqHV genome was found for the first time in two of the allantochorions. (4) Conclusions: As seemingly benign viruses could turn deadly (e.g., Zika flavivirus) and EqHV happens to have infected a significant proportion of the world’s horse herds, EqHV infectious cycle should be further clarified.
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24
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Cagliani R, Forni D, Sironi M. Mode and tempo of human hepatitis virus evolution. Comput Struct Biotechnol J 2019; 17:1384-1395. [PMID: 31768229 PMCID: PMC6872792 DOI: 10.1016/j.csbj.2019.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023] Open
Abstract
Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
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25
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Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China. Arch Virol 2019; 164:2401-2410. [PMID: 31243554 DOI: 10.1007/s00705-019-04303-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
Rodent populations are known to be reservoirs of viruses with the potential to infect humans. However, a large number of such viruses remain undiscovered. In this study, we investigated the shedding of unknown viruses in long-tailed ground squirrel (Spermophilus undulatus) feces by high-throughput sequencing. A novel and highly divergent virus related to members of the genus Hepacivirus was identified in ground squirrel liver. This virus, tentatively named RHV-GS2015, was found to have a genome organization that is typical of hepaciviruses, including a long open reading frame encoding a polyprotein of 2763 aa. Sequence alignment of RHV-GS2015 with the most closely related hepaciviruses yielded p-distances of the NS3 and NS5B regions of 0.546 and 0.476, respectively, supporting the conclusion that RHV-GS2015 is a member of a new hepacivirus species, which we propose to be named "Hepacivirus P". Phylogenetic analysis of the NS3 and NS5B regions indicated that RHV-GS2015 shares common ancestry with other rodent hepaciviruses (species Hepacivirus E, and species Hepacivirus F), Norway rat hepacivirus 1 (species Hepacivirus G), and Norway rat hepacivirus 2 (species Hepacivirus H). A phylogenetic tree including the seven previously identified rodent hepaciviruses revealed extreme genetic heterogeneity among these viruses. RHV-GS2015 was detected in 7 out of 12 ground squirrel pools and was present in liver, lung, and spleen tissues. Furthermore, livers showed extremely high viral loads of RHV-GS2015, ranging from 2.5 × 106 to 2.0 × 108 copies/g. It is reasonable to assume that this novel virus is hepatotropic, like hepatitis C virus. The discovery of RHV-GS2015 extends our knowledge of the genetic diversity and host range of hepaciviruses, helping to elucidate their origins and evolution.
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Lu G, Ou J, Sun Y, Wu L, Xu H, Zhang G, Li S. Natural recombination of equine hepacivirus subtype 1 within the NS5A and NS5B genes. Virology 2019; 533:93-98. [PMID: 31136896 DOI: 10.1016/j.virol.2019.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/20/2022]
Abstract
Equine hepacivirus (EqHV) was first reported in 2012 and is the closest known homolog of hepatitis C virus (HCV). A number of studies have reported HCV recombination events. The aim of this study was to determine whether recombination events occur in EqHV strains. Considering that no information on the Chinese EqHV genome sequence is available, we first sequenced the near-complete genomes of three field EqHV strains. Through systemic analysis, we obtained strong evidence supporting a recombination event within the NS5A and NS5B genes in the American EqHV strains, but not in the strains from China or other countries. Finally, using cut-off values for determination of HCV genotypes and subtypes, we classified the EqHV strains from around the world into one unique genotype and three subtypes. The recombination event occurred in subtype 1 EqHV strains. This study provides critical insights into the genetic variability and evolution of EqHV.
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Affiliation(s)
- Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Technological Engineering Research Center for Pet, Guangzhou, Guangdong Province, People's Republic of China
| | - Jiajun Ou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Technological Engineering Research Center for Pet, Guangzhou, Guangdong Province, People's Republic of China
| | - Yankuo Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China
| | - Liyan Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Technological Engineering Research Center for Pet, Guangzhou, Guangdong Province, People's Republic of China
| | - Haibin Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Technological Engineering Research Center for Pet, Guangzhou, Guangdong Province, People's Republic of China
| | - Guihong Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China.
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People's Republic of China; Guangdong Technological Engineering Research Center for Pet, Guangzhou, Guangdong Province, People's Republic of China.
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Bamford CGG, McLauchlan J. Comparative host genomics: how has human evolution affected our immune defence against hepatitis C virus? Future Virol 2019. [DOI: 10.2217/fvl-2019-0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Connor GG Bamford
- MRC – University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - John McLauchlan
- MRC – University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
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Rasche A, Sander AL, Corman VM, Drexler JF. Evolutionary biology of human hepatitis viruses. J Hepatol 2019; 70:501-520. [PMID: 30472320 PMCID: PMC7114834 DOI: 10.1016/j.jhep.2018.11.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis viruses are major threats to human health. During the last decade, highly diverse viruses related to human hepatitis viruses were found in animals other than primates. Herein, we describe both surprising conservation and striking differences of the unique biological properties and infection patterns of human hepatitis viruses and their animal homologues, including transmission routes, liver tropism, oncogenesis, chronicity, pathogenesis and envelopment. We discuss the potential for translation of newly discovered hepatitis viruses into preclinical animal models for drug testing, studies on pathogenesis and vaccine development. Finally, we re-evaluate the evolutionary origins of human hepatitis viruses and discuss the past and present zoonotic potential of their animal homologues.
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Affiliation(s)
- Andrea Rasche
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany,German Center for Infection Research (DZIF), Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany,German Center for Infection Research (DZIF), Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany; German Center for Infection Research (DZIF), Germany.
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Guo H, Cai C, Wang B, Zhuo F, Jiang R, Wang N, Li B, Zhang W, Zhu Y, Fan Y, Chen W, Chen W, Yang X, Shi Z. Novel hepacivirus in Asian house shrew, China. SCIENCE CHINA-LIFE SCIENCES 2019; 62:701-704. [PMID: 30701456 PMCID: PMC7088713 DOI: 10.1007/s11427-018-9435-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022]
Affiliation(s)
- Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Chunlin Cai
- Luohu Center for Disease Control and Prevention, Shenzhen, 518020, China
| | - Bo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Fei Zhuo
- Luohu Center for Disease Control and Prevention, Shenzhen, 518020, China
| | - Rendi Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Ning Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wei Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yi Fan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wushen Chen
- Luohu Center for Disease Control and Prevention, Shenzhen, 518020, China
| | - Weihong Chen
- Luohu Center for Disease Control and Prevention, Shenzhen, 518020, China
| | - Xinglou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs. Arch Virol 2018; 164:509-522. [PMID: 30460488 DOI: 10.1007/s00705-018-4099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022]
Abstract
Lemurs are highly endangered mammals inhabiting the forests of Madagascar. In this study, we performed virus discovery on serum samples collected from 84 wild lemurs and identified viral sequence fragments from 4 novel viruses within the family Flaviviridae, including members of the genera Hepacivirus and Pegivirus. The sifaka hepacivirus (SifHV, two genotypes) and pegivirus (SifPgV, two genotypes) were discovered in the diademed sifaka (Propithecus diadema), while other pegiviral fragments were detected in samples from the indri (Indri indri, IndPgV) and the weasel sportive lemur (Lepilemur mustelinus, LepPgV). Although data are preliminary, each viral species appeared host species-specific and frequent infection was detected (18 of 84 individuals were positive for at least one virus). The complete coding sequence and partial 5' and 3' untranslated regions (UTRs) were obtained for SifHV and its genomic organization was consistent with that of other hepaciviruses, with one unique polyprotein and highly structured UTRs. Phylogenetic analyses showed the SifHV belonged to a clade that includes several viral species identified in rodents from Asia and North America, while SifPgV and IndPgV were more closely related to pegiviral species A and C, that include viruses found in humans as well as New- and Old-World monkeys. Our results support the current proposed model of virus-host co-divergence with frequent occurrence of cross-species transmission for these genera and highlight how the discovery of more members of the Flaviviridae can help clarify the ecology and evolutionary history of these viruses. Furthermore, this knowledge is important for conservation and captive management of lemurs.
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Schlottau K, Fereidouni S, Beer M, Hoffmann B. Molecular identification and characterization of nonprimate hepaciviruses in equines. Arch Virol 2018; 164:391-400. [PMID: 30361815 DOI: 10.1007/s00705-018-4077-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/01/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is a positive-sense RNA virus belonging to the genus Hepacivirus, family Flaviviridae. Its genome has a length of 9.6 kb and encodes a single polyprotein flanked by two untranslated regions. HCV can cause liver cirrhosis and hepatocellular carcinoma, and approximately 2% of the world's population is chronically infected. The investigation of pathogenesis is complicated due to the lack of an animal model. The origin of this virus remains unclear, but in the last few years, relatives of HCV were initially identified in dogs and later in horses, rodents, bats and Old World monkeys. Non-primate hepacivirus (NPHV), which infects dogs and horses, is the closest relative to HCV. We established a pan-reactive "panHepaci"-RT-qPCR assay, which is able to detect human HCV as well as equine NPHV, and additionally, an equine-specific "equHepaci"-RT-qPCR for confirmation of positive results. Serum samples from 1158 clinically inconspicuous horses from Germany and several samples from other mammalian species were screened. We found 2.4% of the horses positive for hepacivirus RNA, and furthermore, the "panHepaci"-RT-qPCR assay also detected a hepacivirus in a donkey from Egypt. This virus had only 78% sequence identity in the E2 gene when compared to other known NPHVs. The established method could be useful for screening purposes, since it is likely that related hepaciviruses also occur in other species.
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Affiliation(s)
- Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
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Palladino C, Ezeonwumelu IJ, Marcelino R, Briz V, Moranguinho I, Serejo F, Velosa JF, Marinho RT, Borrego P, Taveira N. Epidemic history of hepatitis C virus genotypes and subtypes in Portugal. Sci Rep 2018; 8:12266. [PMID: 30116054 PMCID: PMC6095915 DOI: 10.1038/s41598-018-30528-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Any successful strategy to prevent and control HCV infection requires an understanding of the epidemic behaviour among the different genotypes. Here, we performed the first characterization of the epidemic history and transmission dynamics of HCV subtypes in Portugal. Direct sequencing of NS5B was performed on 230 direct-acting antiviral drugs (DAA)-treatment naïve patients in Lisbon. Phylogenetic analysis was used for subtyping and transmission cluster identification. Bayesian methods were used to reconstruct the epidemic history of HCV subtypes. Sequences were analysed for resistance-associated substitutions (RAS). The majority of strains were HCV-GT1 (62.6%), GT3 (18.3%, all subtype 3a) and GT4 (16.1%). Among GT1, the most frequent were subtypes 1a (75.5%) and 1b (24.5%). Polyphyletic patterns were found in all but 12 lineages suggesting multiple introductions of the different subtypes in this population. Five distinct epidemics were identified. The first significant HCV epidemic in Portugal occurred between 1930s and 1960s, was caused almost exclusively by GT1b and was likely associated with blood transfusions. Rapid expansion of GT3a occurred in the 1960s and GT1a in the 1980s, associated with intravenous drug use. The most recent epidemics were caused by GT4a and GT4d and seem to be associated with the resurgence of opioid use. The C316N substitution was found in 31.4% of GT1b-patients. Close surveillance of patients bearing this mutation and undergoing dasabuvir-based regimens will be important to determine its impact on treatment outcome.
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Affiliation(s)
- Claudia Palladino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - Ifeanyi Jude Ezeonwumelu
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rute Marcelino
- Global Health and Tropical Medicine (GHTM), Unit of Medical Microbiology, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, Lisbon, Portugal
| | - Verónica Briz
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Inês Moranguinho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Fátima Serejo
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - José Fernando Velosa
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Tato Marinho
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Borrego
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Centro de Administração e Políticas Públicas (CAPP), Instituto Superior de Ciências Sociais e Políticas, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Taveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal.
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da Silva MS, Junqueira DM, Baumbach LF, Cibulski SP, Mósena ACS, Weber MN, Silveira S, de Moraes GM, Maia RD, Coimbra VCS, Canal CW. Comprehensive evolutionary and phylogenetic analysis of Hepacivirus N (HNV). J Gen Virol 2018; 99:890-896. [DOI: 10.1099/jgv.0.001082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- M. S. da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - D. M. Junqueira
- Centro Universitário Ritter dos Reis – UniRitter, Rua Orfanotrófio, 555 - Santa Tereza, Porto Alegre – RS, CEP 90840-440. Porto Alegre, Rio Grande do Sul, Brazil
| | - L. F. Baumbach
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - S. P. Cibulski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - A. C. S. Mósena
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - M. N. Weber
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - S. Silveira
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - G. M. de Moraes
- Ministério da Agricultura, Pecuária e Abastecimento, Brasília, Distrito Federal, Brazil
| | - R. D. Maia
- Instituto de Defesa e Inspeção Agropecuária do Rio Grande do Norte (IDIARN), Natal, Rio Grande do Norte, Brazil
| | - V. C. S. Coimbra
- Agência Estadual de Defesa Agropecuária do Maranhão (AGED-MA), São Luís, Maranhão, Brazil
| | - C. W. Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9090 - Agronomia, CEP 91540-000, Porto Alegre, Rio Grande do Sul, Brazil
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Ecological drivers of Hepacivirus infection in a neotropical rodent inhabiting landscapes with various degrees of human environmental change. Oecologia 2018; 188:289-302. [PMID: 29936542 DOI: 10.1007/s00442-018-4210-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
Abstract
Anthropogenic environmental change can impact community and population traits such as species diversity and population densities, which have been shown to influence the prevalence of viruses in wildlife reservoirs. In particular, host species resilient to changes in their natural habitat may increase in numbers, which in turn can affect the prevalence of directly transmitted viruses. We have carried out a survey of small mammal communities in three tropical landscapes differing in their degree of environmental change in Central Panama and investigated the effects of community changes on Hepacivirus prevalence. The modification of continuous habitat into partly connected or isolated habitat patches during the past century was linked to changes in species diversity and species assemblages, which was further associated with shifts in the abundance of generalist marsupial (Didelphis marsupialis, Philander opossum) and rodent (Proechimys semispinosus) species. The latter has become dominant in isolated habitat patches and was the only identified Hepacivirus host in our study system. Our analyses suggest that, in addition to the effects of host age and sex, host population density in interaction with sex ratio is a crucial predictor of infection probability. Although we found no significant relationships between species diversity per se and infection probability, the lowest prevalence detected in the landscape with the highest species diversity indicates that shifts in species assemblages (e.g. changes in the presence and abundance of marsupial predators) impact the host's intraspecific contact rates, the probability of virus transmission and, thus, the virus prevalence. Our study additionally provides important data on the influence of human-induced landscape changes on infection probability and, therefore, on virus prevalence in wildlife and emphasizes the importance of a landscape-scale approach with concomitant consideration of the complex interactions between ecological factors.
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Forni D, Cagliani R, Pontremoli C, Pozzoli U, Vertemara J, De Gioia L, Clerici M, Sironi M. Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV. Front Microbiol 2018; 9:854. [PMID: 29765366 PMCID: PMC5938362 DOI: 10.3389/fmicb.2018.00854] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) belongs to the Hepacivirus genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle. Using a selection-informed evolutionary model, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago (CI: 3192–5221 years ago), with the oldest genotypes being endemic to Asia. EHV originated around 1100 CE (CI: 291–1640 CE). These time estimates exclude that EHV transmission was mainly sustained by widespread veterinary practices and suggest that HCV originated from a single zoonotic event with subsequent diversification in human populations. We also describe a number of biologically important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance-associated variants are significantly enriched at positively selected sites. HCV exploits several cell-surface molecules for cell entry, but only two of these (CD81 and OCLN) determine the species-specificity of infection. Herein evolutionary analyses do not support a long-standing association between primates and hepaciviruses, and signals of positive selection at CD81 were only observed in Chiroptera. No evidence of selection was detected for OCLN in any mammalian order. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity.
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Affiliation(s)
- Diego Forni
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
| | - Jacopo Vertemara
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation Onlus, IRCCS, Milan, Italy
| | - Manuela Sironi
- Bioinformatics Laboratory, Scientific Institute IRCCS E.Medea, Bosisio Parini, Italy
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Van Nguyen D, Van Nguyen C, Bonsall D, Ngo TT, Carrique-Mas J, Pham AH, Bryant JE, Thwaites G, Baker S, Woolhouse M, Simmonds P. Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam. Viruses 2018; 10:v10030102. [PMID: 29495551 PMCID: PMC5869495 DOI: 10.3390/v10030102] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Rodents and bats are now widely recognised as important sources of zoonotic virus infections in other mammals, including humans. Numerous surveys have expanded our knowledge of diverse viruses in a range of rodent and bat species, including their origins, evolution, and range of hosts. In this study of pegivirus and human hepatitis-related viruses, liver and serum samples from Vietnamese rodents and bats were examined by PCR and sequencing. Nucleic acids homologous to human hepatitis B, C, E viruses were detected in liver samples of 2 (1.3%) of 157 bats, 38 (8.1%), and 14 (3%) of 470 rodents, respectively. Hepacivirus-like viruses were frequently detected (42.7%) in the bamboo rat, Rhizomys pruinosus, while pegivirus RNA was only evident in 2 (0.3%) of 638 rodent serum samples. Complete or near-complete genome sequences of HBV, HEV and pegivirus homologues closely resembled those previously reported from rodents and bats. However, complete coding region sequences of the rodent hepacivirus-like viruses substantially diverged from all of the currently classified variants and potentially represent a new species in the Hepacivirus genus. Of the viruses identified, their routes of transmission and potential to establish zoonoses remain to be determined.
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MESH Headings
- Animals
- Chiroptera/virology
- Genome, Viral
- Hepatitis Viruses/classification
- Hepatitis Viruses/genetics
- Hepatitis, Viral, Animal/diagnosis
- Hepatitis, Viral, Animal/epidemiology
- Hepatitis, Viral, Animal/virology
- Hepatitis, Viral, Human/diagnosis
- Hepatitis, Viral, Human/epidemiology
- Hepatitis, Viral, Human/virology
- Humans
- Phylogeny
- Public Health Surveillance
- RNA, Viral
- Rodentia/virology
- Vietnam/epidemiology
- Zoonoses/epidemiology
- Zoonoses/virology
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Affiliation(s)
- Dung Van Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Cuong Van Nguyen
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Tue Tri Ngo
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
| | - Juan Carrique-Mas
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
| | - Anh Hong Pham
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
| | - Juliet E Bryant
- Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), 69365 Lyon CEDEX 07, France.
| | - Guy Thwaites
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford OX3 7FZ, UK.
- The London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK.
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
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37
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Kaufman J. Generalists and Specialists: A New View of How MHC Class I Molecules Fight Infectious Pathogens. Trends Immunol 2018; 39:367-379. [PMID: 29396014 PMCID: PMC5929564 DOI: 10.1016/j.it.2018.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/24/2022]
Abstract
In comparison with the major histocompatibility complexes (MHCs) of typical mammals, the chicken MHC is simple and compact with a single dominantly expressed class I molecule that can determine the immune response. In addition to providing useful information for the poultry industry and allowing insights into the evolution of the adaptive immune system, the simplicity of the chicken MHC has allowed the discovery of phenomena that are more difficult to discern in the more complicated mammalian systems. This review discusses the new concept that poorly expressed promiscuous class I alleles act as generalists to protect against a wide variety of infectious pathogens, while highly expressed fastidious class I alleles can act as specialists to protect against new and dangerous pathogens. A broad overview of classical MHC I expression and bound peptides reveals an inverse correlation between repertoire breadth and cell-surface expression in some chicken and human alleles. Several chicken class I alleles with wide peptide-binding repertoires (promiscuity) are associated with resistance to a variety of common diseases. Conversely, a narrow peptide-binding repertoire (fastidiousness) in some human HLA-B alleles is associated with resistance to HIV progression. Cell-surface expression of some classical class I alleles depends on the regulation of translocation to the cell surface rather than of transcription or translation. MHC translocation is influenced by peptide translocation in chickens and by tapasin interaction in humans.
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Affiliation(s)
- Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK.
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38
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Abstract
Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus.
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Affiliation(s)
- Alex S Hartlage
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205;
| | - John M Cullen
- North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina 27606
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205; .,Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, Ohio 43210
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39
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Affiliation(s)
- Paul Klenerman
- Translational Gastroenterology Unit and Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK.
| | - Eleanor J Barnes
- Translational Gastroenterology Unit and Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK
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40
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Elia G, Lanave G, Lorusso E, Parisi A, Cavaliere N, Patruno G, Terregino C, Decaro N, Martella V, Buonavoglia C. Identification and genetic characterization of equine hepaciviruses in Italy. Vet Microbiol 2017; 207:239-247. [PMID: 28757030 DOI: 10.1016/j.vetmic.2017.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/04/2017] [Accepted: 07/04/2017] [Indexed: 01/26/2023]
Abstract
Viruses similar to human hepatitis C virus, hepaciviruses, have been identified in various animal species. Equine hepacivirus (EqHV) is the closest relative of human hepaciviruses. Although detected worldwide, information on EqHV epidemiology, genetic diversity and pathogenicity is still limited. In this study we investigated the prevalence and genetic diversity of EqHV in Italian equids. The RNA of EqHV was detected in 91/1932 sera (4.7%) whilst it was not detectable in 134 donkey sera screened by a TaqMan-based quantitative assay. Upon sequencing and phylogenetic analysis of genomic portions located in the NS5B, 5'UTR and NS3 genes, the Italian EqHV strains segregated into two distinct clades that are also co-circulating globally, without apparent geographic restrictions.
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Affiliation(s)
- Gabriella Elia
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy.
| | - Gianvito Lanave
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Eleonora Lorusso
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Foggia, Italy
| | - Nicola Cavaliere
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Foggia, Italy
| | | | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Nicola Decaro
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Canio Buonavoglia
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
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41
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Fukuhara T, Yamamoto S, Ono C, Nakamura S, Motooka D, Mori H, Kurihara T, Sato A, Tamura T, Motomura T, Okamoto T, Imamura M, Ikegami T, Yoshizumi T, Soejima Y, Maehara Y, Chayama K, Matsuura Y. Quasispecies of Hepatitis C Virus Participate in Cell-Specific Infectivity. Sci Rep 2017; 7:45228. [PMID: 28327559 PMCID: PMC5361118 DOI: 10.1038/srep45228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/21/2017] [Indexed: 02/08/2023] Open
Abstract
It is well documented that a variety of viral quasispecies are found in the patients with chronic infection of hepatitis C virus (HCV). However, the significance of quasispecies in the specific infectivity to individual cell types remains unknown. In the present study, we analyzed the role of quasispecies of the genotype 2a clone, JFH1 (HCVcc), in specific infectivity to the hepatic cell lines, Huh7.5.1 and Hep3B. HCV RNA was electroporated into Huh7.5.1 cells and Hep3B/miR-122 cells expressing miR-122 at a high level. Then, we adapted the viruses to Huh7 and Hep3B/miR-122 cells by serial passages and termed the resulting viruses HCVcc/Huh7 and HCVcc/Hep3B, respectively. Interestingly, a higher viral load was obtained in the homologous combination of HCVcc/Huh7 in Huh7.5.1 cells or HCVcc/Hep3B in Hep3B/miR-122 cells compared with the heterologous combination. By using a reverse genetics system and deep sequence analysis, we identified several adaptive mutations involved in the high affinity for each cell line, suggesting that quasispecies of HCV participate in cell-specific infectivity.
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Affiliation(s)
- Takasuke Fukuhara
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Satomi Yamamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Veterinary Microbiology, School of Veterinary Medicine, Kitasato University, Aomori, Japan
| | - Chikako Ono
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takeshi Kurihara
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Asuka Sato
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tomokazu Tamura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takashi Motomura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toru Okamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical &Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Toru Ikegami
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuji Soejima
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical &Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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42
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Kim HS, Moon HW, Sung HW, Kwon HM. First identification and phylogenetic analysis of equine hepacivirus in Korea. INFECTION GENETICS AND EVOLUTION 2017; 49:268-272. [PMID: 28161473 DOI: 10.1016/j.meegid.2017.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/25/2017] [Accepted: 01/28/2017] [Indexed: 12/11/2022]
Abstract
Non-primate hepacivirus (NPHV) corresponds a group of isolates recently characterized in horses and dogs that present similar genomic organization and are closely related to hepatitis C virus. Since canine hapacivirus, NPHV identified in dogs, was first discovered in dogs in the United States, equine hepacivirus (EqHV, NPHV identified in horses) has been identified in horses in several countries. However, no epidemiological studies have investigated EqHV in horses in Korea. In this study, a total of 74 (n=74) serum samples collected from horses in four regions of Korea were tested for EqHV RNA using nested RT-PCR. Overall, 14 samples were identified as positive (18.9%) and further analyzed according to gender, age, breed, and region. There were high positive rates in males, young horses, and Thoroughbreds; however, these rates differed regionally. Sequencing of the partial NS3 region of 12 samples and the polyprotein encoding regions of two samples positive for EqHV RNA revealed that the Korean EqHV isolates shared approximately 85.3-99.6% and 97.7-100% homology at the nucleotide and deduced amino acid level, respectively. Phylogenetic analysis revealed that the partial NS3 genes clustered with sequences previously reported as NPHV. Notably, sequences of EqHV detected in horses in the same region showed sequence divergence. The sequences of the polyprotein encoding region of two representative EqHVs shared 83.9% and 95.7% homology with each other at the nucleotide and deduced amino acid level, respectively. Comparison of the sequences of polyprotein encoding regions of Korean EqHV isolates and hepaciviruses from different hosts revealed that the NS3 and NS5B regions were most conserved among hepaciviruses. The results of the present study demonstrate that there is a high positive rate of EqHV in Korea and provide significant information regarding the geographical distribution and genetic variability of Korean EqHV isolates that will help improve global epidemiology of EqHV.
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Affiliation(s)
- Ho-Seong Kim
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyun-Woo Moon
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Haan Woo Sung
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyuk Moo Kwon
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea.
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43
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Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys. J Virol 2016; 91:JVI.01711-16. [PMID: 27795428 DOI: 10.1128/jvi.01711-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/13/2016] [Indexed: 12/13/2022] Open
Abstract
The hepatitis C virus (HCV) is a major human pathogen. Genetically related viruses in animals suggest a zoonotic origin of HCV. The closest relative of HCV is found in horses (termed equine hepacivirus [EqHV]). However, low EqHV genetic diversity implies relatively recent acquisition of EqHV by horses, making a derivation of HCV from EqHV unlikely. To unravel the EqHV evolutionary history within equid sister species, we analyzed 829 donkeys and 53 mules sampled in nine European, Asian, African, and American countries by molecular and serologic tools for EqHV infection. Antibodies were found in 278 animals (31.5%), and viral RNA was found in 3 animals (0.3%), all of which were simultaneously seropositive. A low RNA prevalence in spite of high seroprevalence suggests a predominance of acute infection, a possible difference from the mostly chronic hepacivirus infection pattern seen in horses and humans. Limitation of transmission due to short courses of infection may explain the existence of entirely seronegative groups of animals. Donkey and horse EqHV strains were paraphyletic and 97.5 to 98.2% identical in their translated polyprotein sequences, making virus/host cospeciation unlikely. Evolutionary reconstructions supported host switches of EqHV between horses and donkeys without the involvement of adaptive evolution. Global admixture of donkey and horse hepaciviruses was compatible with anthropogenic alterations of EqHV ecology. In summary, our findings do not support EqHV as the origin of the significantly more diversified HCV. Identification of a host system with predominantly acute hepacivirus infection may enable new insights into the chronic infection pattern associated with HCV. IMPORTANCE The evolutionary origins of the human hepatitis C virus (HCV) are unclear. The closest animal-associated relative of HCV occurs in horses (equine hepacivirus [EqHV]). The low EqHV genetic diversity implies a relatively recent acquisition of EqHV by horses, limiting the time span for potential horse-to-human infections in the past. Horses are genetically related to donkeys, and EqHV may have cospeciated with these host species. Here, we investigated a large panel of donkeys from various countries using serologic and molecular tools. We found EqHV to be globally widespread in donkeys and identify potential differences in EqHV infection patterns, with donkeys potentially showing enhanced EqHV clearance compared to horses. We provide strong evidence against EqHV cospeciation and for its capability to switch hosts among equines. Differential hepacivirus infection patterns in horses and donkeys may enable new insights into the chronic infection pattern associated with HCV.
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44
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Pronost S, Hue E, Fortier C, Foursin M, Fortier G, Desbrosse F, Rey FA, Pitel PH, Richard E, Saunier B. Prevalence of Equine Hepacivirus Infections in France and Evidence for Two Viral Subtypes Circulating Worldwide. Transbound Emerg Dis 2016; 64:1884-1897. [PMID: 27882682 DOI: 10.1111/tbed.12587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 12/20/2022]
Abstract
Like hepatitis C virus (HCV) in humans, the newly identified equine hepacivirus (NPHV) displays a predominating liver tropism that may evolve into chronic infections. The genomes of the two viruses share several organizational and functional features and are phylogenetically closest amongst the Hepacivirus genus. A limited amount of data is available regarding the spread of hepacivirus infections in horses. In this study, we asked whether in a more representative sample the prevalence and distribution of NPHV infections in France would resemble that reported so far in other countries. A total of 1033 horses sera from stud farms throughout France were analysed by qRT-PCR to determine the prevalence of ongoing NPHV infections and viral loads; in positive samples, partial sequences of NPHV's genome (5'UTR, NS3 and NS5B genes) were determined. Serum concentrations of biliary acids, glutamate dehydrogenase (GLDH) and L-gamma-glutamyl transferase (γ-GT) were measured for most horses. We detected NPHV infections in 6.2% of the horses, a prevalence that reached 8.3% in thoroughbreds and was significantly higher than in other breeds. The presence of circulating virus was neither significantly associated with biological disturbances nor with clinical hepatic impairment. Our phylogenetic analysis was based on both neighbour-joining and maximum-likelihood approaches. Its result shows that, like almost everywhere else in the world so far, two major groups of NPHV strains infect French domestic horses. Based on genetic distances, we propose a classification into two separate NPHV subtypes. Viral loads in the serum of horses infected by the main subtype were, in average, four times higher than in those infected by the second subtype. We hypothesize that amino acid substitutions in the palm domain of NS5B between NPHV subtypes could underlie viral phenotypes that explain this result.
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Affiliation(s)
- S Pronost
- Unité de Recherche Risques Microbiens (U2RM), EA 4655, Université de Caen Basse-Normandie, Caen, France.,LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - E Hue
- Unité de Recherche Risques Microbiens (U2RM), EA 4655, Université de Caen Basse-Normandie, Caen, France.,LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - C Fortier
- LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - M Foursin
- Clinique Equine de la Boisrie, Chailloué, France
| | - G Fortier
- Unité de Recherche Risques Microbiens (U2RM), EA 4655, Université de Caen Basse-Normandie, Caen, France.,LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - F Desbrosse
- Clinique Equine Desbrosse, Saint Lambert, France
| | - F A Rey
- Structural Virology Unit - CNRS UMR 3569, Institut Pasteur, Paris, France
| | - P-H Pitel
- LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - E Richard
- LABÉO Frank Duncombe, Caen, France.,Hippolia Fondation, Caen, France
| | - B Saunier
- Structural Virology Unit - CNRS UMR 3569, Institut Pasteur, Paris, France
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45
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Hepacivirus NS3/4A Proteases Interfere with MAVS Signaling in both Their Cognate Animal Hosts and Humans: Implications for Zoonotic Transmission. J Virol 2016; 90:10670-10681. [PMID: 27654291 DOI: 10.1128/jvi.01634-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
Multiple novel members of the genus Hepacivirus have recently been discovered in diverse mammalian species. However, to date, their replication mechanisms and zoonotic potential have not been explored in detail. The NS3/4A serine protease of hepatitis C virus (HCV) is critical for cleavage of the viral polyprotein. It also cleaves the cellular innate immune adaptor MAVS, thus decreasing interferon (IFN) production and contributing to HCV persistence in the human host. To investigate the conservation of fundamental aspects of the hepaciviral life cycle, we explored if MAVS cleavage and suppression of innate immune signaling represent a common mechanism employed across different clades of the genus Hepacivirus to enhance viral replication. To estimate the zoonotic potential of these nonhuman hepaciviruses, we assessed if their NS3/4A proteases were capable of cleaving human MAVS. NS3/4A proteases of viruses infecting colobus monkeys, rodents, horses, and cows cleaved the MAVS proteins of their cognate hosts and interfered with the ability of MAVS to induce the IFN-β promoter. All NS3/4A proteases from nonhuman viruses readily cleaved human MAVS. Thus, NS3/4A-dependent cleavage of MAVS is a conserved replication strategy across multiple clades within the genus Hepacivirus Human MAVS is susceptible to cleavage by these nonhuman viral proteases, indicating that it does not pose a barrier for zoonotic transmission of these viruses to humans. IMPORTANCE Virus infection is recognized by cellular sensor proteins triggering innate immune signaling and antiviral defenses. While viruses have evolved strategies to thwart these antiviral programs in their cognate host species, these evasion mechanisms are often ineffective in a novel host, thus limiting viral transmission across species. HCV, the best-characterized member of the genus Hepacivirus within the family Flaviviridae, uses its NS3/4A protease to disrupt innate immune signaling by cleaving the cellular adaptor protein MAVS. Recently, a large number of HCV-related viruses have been discovered in various animal species, including wild, livestock, and companion animals. We show that the NS3/4A proteases of these hepaciviruses from different animals and representing various clades of the genus cleave their cognate host MAVS proteins in addition to human MAVS. Therefore, cleavage of MAVS is a common strategy of hepaciviruses, and human MAVS is likely unable to limit replication of these nonhuman viruses upon zoonotic exposure.
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46
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Smith DB, Becher P, Bukh J, Gould EA, Meyers G, Monath T, Muerhoff AS, Pletnev A, Rico-Hesse R, Stapleton JT, Simmonds P. Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family. J Gen Virol 2016; 97:2894-2907. [PMID: 27692039 PMCID: PMC5770844 DOI: 10.1099/jgv.0.000612] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Proposals are described for the assignment of recently reported viruses, infecting rodents, bats and other mammalian species, to new species within the Hepacivirus and Pegivirus genera (family Flaviviridae). Assignments into 14 Hepacivirus species (Hepacivirus A–N) and 11 Pegivirus species (Pegivirus A–K) are based on phylogenetic relationships and sequence distances between conserved regions extracted from complete coding sequences for members of each proposed taxon. We propose that the species Hepatitis C virus is renamed Hepacivirus C in order to acknowledge its unique historical position and so as to minimize confusion. Despite the newly documented genetic diversity of hepaciviruses and pegiviruses, members of these genera remain phylogenetically distinct, and differ in hepatotropism and the possession of a basic core protein; pegiviruses in general lack these features. However, other characteristics that were originally used to support their division into separate genera are no longer definitive; there is overlap between the two genera in the type of internal ribosomal entry site and the presence of miR-122 sites in the 5′ UTR, the predicted number of N-linked glycosylation sites in the envelope E1 and E2 proteins, the presence of poly U tracts in the 3′ UTR and the propensity of viruses to establish a persistent infection. While all classified hepaciviruses and pegiviruses have mammalian hosts, the recent description of a hepaci-/pegi-like virus from a shark and the likely existence of further homologues in other non-mammalian species indicate that further species or genera remain to be defined in the future.
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Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Scotland, UK
| | - Paul Becher
- Institute of Virology, University of Veterinary Medicine, Hannover, Germany
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark.,Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ernest A Gould
- EHESP French School of Public Health, French Institute of Research for Development (IRD), Aix Marseille Université, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France
| | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Thomas Monath
- Hookipa Biotech AG, Vienna, Austria.,PaxVax Inc., Menlo Park and Redwood City, CA, USA
| | - A Scott Muerhoff
- Abbott Diagnostics Research and Development, Abbott Park, IL, USA
| | - Alexander Pletnev
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rebecca Rico-Hesse
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jack T Stapleton
- Medical Service, Iowa City Veterans Affairs Medical Center, Iowa City, IA, USA.,Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.,Department of Microbiology, University of Iowa, Iowa City, IA, USA
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Scotland, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
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47
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Vandegrift KJ, Critchlow JT, Kapoor A, Friedman DA, Hudson PJ. Peromyscus as a model system for human hepatitis C: An opportunity to advance our understanding of a complex host parasite system. Semin Cell Dev Biol 2016; 61:123-130. [PMID: 27498234 DOI: 10.1016/j.semcdb.2016.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023]
Abstract
Worldwide, there are 185 million people infected with hepatitis C virus and approximately 350,000 people die each year from hepatitis C associated liver diseases. Human hepatitis C research has been hampered by the lack of an appropriate in vivo model system. Most of the in vivo research has been conducted on chimpanzees, which is complicated by ethical concerns, small sample sizes, high costs, and genetic heterogeneity. The house mouse system has led to greater understanding of a wide variety of human pathogens, but it is unreasonable to expect Mus musculus to be a good model system for every human pathogen. Alternative animal models can be developed in these cases. Ferrets (influenza), cotton rats (human respiratory virus), and woodchucks (hepatitis B) are all alternative models that have led to a greater understanding of human pathogens. Rodent models are tractable, genetically amenable and inbred and outbred strains can provide homogeneity in results. Recently, a rodent homolog of hepatitis C was discovered and isolated from the liver of a Peromyscus maniculatus. This represents the first small mammal (mouse) model system for human hepatitis C and it offers great potential to contribute to our understanding and ultimately aid in our efforts to combat this serious public health concern. Peromyscus are available commercially and can be used to inform questions about the origin, transmission, persistence, pathology, and rational treatment of hepatitis C. Here, we provide a disease ecologist's overview of this new virus and some suggestions for useful future experiments.
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Affiliation(s)
- Kurt J Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Justin T Critchlow
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States
| | - Amit Kapoor
- Center for Vaccines and Immunity, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, United States
| | - David A Friedman
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States
| | - Peter J Hudson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, United States
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Gather T, Walter S, Todt D, Pfaender S, Brown RJP, Postel A, Becher P, Moritz A, Hansmann F, Baumgaertner W, Feige K, Steinmann E, Cavalleri JMV. Vertical transmission of hepatitis C virus-like non-primate hepacivirus in horses. J Gen Virol 2016; 97:2540-2551. [PMID: 27461949 DOI: 10.1099/jgv.0.000561] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Non-primate hepacivirus (NPHV), a recently discovered hepatotropic virus infecting horses, is phylogenetically the closest known homologue of hepatitis C virus (HCV). The main route for acquiring HCV infection in childhood is vertical transmission. However, nothing is known about the natural mode of transmission for NPHV. To investigate the possibility of vertically transmitted NPHV infection in horses, 20 Thoroughbred broodmares and their foals were monitored during foaling season 2015 until 6 months post-partum. Prepartal serum was taken from the mares, and during foaling umbilical cord blood and colostrum samples were collected. Postnatal serum samples were taken from the foals after delivery. In addition, serum was taken at 3 and 6 months after foaling from all mares and foals. Samples were analysed for the presence of NPHV RNA by quantitative real-time PCR and for the presence of anti-NPHV NS3 antibodies by luciferase immunoprecipitation system. Identified NPHV isolates were sequenced and phylogenetic analysis of the viral glycoproteins was used to track the course of naturally occurring infections and the circulation of distinct isolates within the herd. At parturition, 16 mares were seropositive, including four viraemic mares. Vertical transmission occurred in one of these four mare-foal pairs. Interestingly, NPHV isolates of newly infected foals and mares after 3 and 6 months cluster in their respective pasture herds suggesting another horizontal route of transmission.
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Affiliation(s)
- Theresa Gather
- Clinic for Horses, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hannover, Germany
| | - Stephanie Walter
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Daniel Todt
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Stephanie Pfaender
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Richard J P Brown
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Alexander Postel
- Department of Infectious Diseases, Institute for Virology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Paul Becher
- Department of Infectious Diseases, Institute for Virology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Andreas Moritz
- Small Animal Clinic, Department of Veterinary Clinical Sciences, Justus-Liebig-University, Frankfurter Straße 108, 35392 Giessen, Germany
| | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Wolfgang Baumgaertner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Karsten Feige
- Clinic for Horses, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hannover, Germany
| | - Eike Steinmann
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Str. 7, 30625 Hannover, Germany
| | - Jessika-M V Cavalleri
- Clinic for Horses, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hannover, Germany
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49
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First Description of Hepacivirus and Pegivirus Infection in Domestic Horses in China: A Study in Guangdong Province, Heilongjiang Province and Hong Kong District. PLoS One 2016; 11:e0155662. [PMID: 27182887 PMCID: PMC4868292 DOI: 10.1371/journal.pone.0155662] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/02/2016] [Indexed: 02/06/2023] Open
Abstract
Since 2012, three viruses, known as equine hepacivirus (EqHV), equine pegivirus (EPgV) and Theiler’s disease-associated virus (TDAV), have been discovered in equines. Given that these viruses are the newest members of the Flaviviridae family, genomic information concerning circulating EqHV, EPgV and TDAV strains around the world is limited. To date, no genetic surveillance studies have been performed on these three viruses in the equine population of China. Here, a total of 177 serum samples were collected from equines across China between 2014 and 2015. Using PCR, we detected viral RNA in the serum samples, six of which were EqHV positive and two of which were EPgV positive. Co-infection with the two viruses was not observed among the Chinese equines studied, and TDAV RNA was not detected in the equine serum samples collected for this study. Phylogenetic analysis of partial NS5B open reading frame (ORF), NS3 ORF, and 5’ untranslated region nucleotide sequences from EqHV as well as partial NS3 ORF sequence from EPgV indicated that EqHV and EPgV have evolved into two main clades by themselves, both of which are circulating in China. Based on the partial NS5B and NS3 ORF sequences of EqHV, the sequences of one clade were also split into two subclades. This study enriches our knowledge of the geographic distribution of these three equine viruses.
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