The Hepatitis C Virus (HCV)
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Metagenomic Identification of Diverse Animal Hepaciviruses and Pegiviruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.16.100149; this version posted May 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Metagenomic identification of diverse animal hepaciviruses and 2 pegiviruses 3 4 5 Ashleigh F. Porter1, John H.-O. Pettersson1,2, Wei-Shan Chang1, Erin Harvey1, Karrie Rose3, 6 Mang Shi5, John-Sebastian Eden1,4, Jan Buchmann1, Craig Moritz6, Edward C. Holmes1 7 8 9 1. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 10 Environmental Sciences and School of Medical Sciences, The University of Sydney, 11 Sydney, Australia. 12 2. Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, 13 Uppsala University, Uppsala, Sweden. 14 3. Australian Registry of Wildlife Health, Taronga Conservation Society Australia, 15 Mosman, Australia. 16 4. Centre for Virus Research, Westmead Institute for Medical Research, Westmead, 17 Australia. 18 5. School of Medicine, Sun Yat-sen University, Guangzhou, China. 19 6. Research School of Biology, and Centre for Biodiversity Analysis, Australian National 20 University, Acton, ACT, Australia. 21 22 23 Address correspondence to: 24 Edward C. Holmes, 25 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 26 Environmental Sciences and School of Medical Sciences, The University of Sydney, 27 Sydney, Australia 28 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.16.100149; this version posted May 17, 2020. -
Origins and Evolution of the Global RNA Virome
bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Origins and Evolution of the Global RNA Virome 2 Yuri I. Wolfa, Darius Kazlauskasb,c, Jaime Iranzoa, Adriana Lucía-Sanza,d, Jens H. 3 Kuhne, Mart Krupovicc, Valerian V. Doljaf,#, Eugene V. Koonina 4 aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA 5 b Vilniaus universitetas biotechnologijos institutas, Vilnius, Lithuania 6 c Département de Microbiologie, Institut Pasteur, Paris, France 7 dCentro Nacional de Biotecnología, Madrid, Spain 8 eIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious 9 Diseases, National Institutes of Health, Frederick, Maryland, USA 10 fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA 11 12 #Address correspondence to Valerian V. Dolja, [email protected] 13 14 Running title: Global RNA Virome 15 16 KEYWORDS 17 virus evolution, RNA virome, RNA-dependent RNA polymerase, phylogenomics, horizontal 18 virus transfer, virus classification, virus taxonomy 1 bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 ABSTRACT 20 Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in 21 animals and plants. The recent advances of metaviromics prompted us to perform a detailed 22 phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. -
REVIEW Hepatitis C Virus
DOI:http://dx.doi.org/10.7314/APJCP.2012.13.12.5917 Hepatitis C Virus -Proteins, Diagnosis, Treatment and New Approaches for Vaccine Development REVIEW Hepatitis C Virus - Proteins, Diagnosis, Treatment and New Approaches for Vaccine Development Hossein Keyvani1, Mehdi Fazlalipour2*, Seyed Hamid Reza Monavari1, Hamid Reza Mollaie2 Abstract Background: Hepatitis C virus (HCV) causes acute and chronic human hepatitis infection and as such is an important global health problem. The virus was discovered in the USA in 1989 and it is now known that three to four million people are infected every year, WHO estimating that 3 percent of the 7 billion people worldwide being chronically infected. Humans are the natural hosts of HCV and this virus can eventually lead to permanent liver damage and carcinoma. HCV is a member of the Flaviviridae family and Hepacivirus genus. The diameter of the virus is about 50-60 nm and the virion contains a single-stranded positive RNA approximately 10,000 nucleotides in length and consisting of one ORF which is encapsulated by an external lipid envelope and icosahedral capsid. HCV is a heterogeneous virus, classified into 6 genotypes and more than 50 subtypes. Because of the genome variability, nucleotide sequences of genotypes differ by approximately 31-34%, and by 20-23% among subtypes. Quasi-species of mixed virus populations provide a survival advantage for the virus to create multiple variant genomes and a high rate of generation of variants to allow rapid selection of mutants for new environmental conditions. Direct contact with infected blood and blood products, sexual relationships and availability of injectable drugs have had remarkable effects on HCV epidemiology. -
Arenaviridae Astroviridae Filoviridae Flaviviridae Hantaviridae
Hantaviridae 0.7 Filoviridae 0.6 Picornaviridae 0.3 Wenling red spikefish hantavirus Rhinovirus C Ahab virus * Possum enterovirus * Aronnax virus * * Wenling minipizza batfish hantavirus Wenling filefish filovirus Norway rat hunnivirus * Wenling yellow goosefish hantavirus Starbuck virus * * Porcine teschovirus European mole nova virus Human Marburg marburgvirus Mosavirus Asturias virus * * * Tortoise picornavirus Egyptian fruit bat Marburg marburgvirus Banded bullfrog picornavirus * Spanish mole uluguru virus Human Sudan ebolavirus * Black spectacled toad picornavirus * Kilimanjaro virus * * * Crab-eating macaque reston ebolavirus Equine rhinitis A virus Imjin virus * Foot and mouth disease virus Dode virus * Angolan free-tailed bat bombali ebolavirus * * Human cosavirus E Seoul orthohantavirus Little free-tailed bat bombali ebolavirus * African bat icavirus A Tigray hantavirus Human Zaire ebolavirus * Saffold virus * Human choclo virus *Little collared fruit bat ebolavirus Peleg virus * Eastern red scorpionfish picornavirus * Reed vole hantavirus Human bundibugyo ebolavirus * * Isla vista hantavirus * Seal picornavirus Human Tai forest ebolavirus Chicken orivirus Paramyxoviridae 0.4 * Duck picornavirus Hepadnaviridae 0.4 Bildad virus Ned virus Tiger rockfish hepatitis B virus Western African lungfish picornavirus * Pacific spadenose shark paramyxovirus * European eel hepatitis B virus Bluegill picornavirus Nemo virus * Carp picornavirus * African cichlid hepatitis B virus Triplecross lizardfish paramyxovirus * * Fathead minnow picornavirus -
Hepatitis C Virus Vaccine Research: Time to Put up Or Shut Up
viruses Review Hepatitis C Virus Vaccine Research: Time to Put Up or Shut Up Alex S. Hartlage 1,2 and Amit Kapoor 1,3,* 1 Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA; [email protected] 2 Medical Scientist Training Program, College of Medicine and Public Health, The Ohio State University, Columbus, OH 43205, USA 3 Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH 43205, USA * Correspondence: [email protected] Abstract: Unless urgently needed to prevent a pandemic, the development of a viral vaccine should follow a rigorous scientific approach. Each vaccine candidate should be designed considering the in- depth knowledge of protective immunity, followed by preclinical studies to assess immunogenicity and safety, and lastly, the evaluation of selected vaccines in human clinical trials. The recently concluded first phase II clinical trial of a human hepatitis C virus (HCV) vaccine followed this approach. Still, despite promising preclinical results, it failed to protect against chronic infection, raising grave concerns about our understanding of protective immunity. This setback, combined with the lack of HCV animal models and availability of new highly effective antivirals, has fueled ongoing discussions of using a controlled human infection model (CHIM) to test new HCV vaccine candidates. Before taking on such an approach, however, we must carefully weigh all the ethical and health consequences of human infection in the absence of a complete understanding of HCV immunity and pathogenesis. We know that there are significant gaps in our knowledge of adaptive immunity necessary to prevent chronic HCV infection. -
Ribavirin Inhibits West Nile Virus Replication and Cytopathic Effect in Neural Cells
1214 CONCISE COMMUNICATION Ribavirin Inhibits West Nile Virus Replication and Cytopathic Effect in Neural Cells Ingo Jordan,1 Thomas Briese,1 Nicole Fischer,1 1Emerging Diseases Laboratory, Departments of Microbiology Johnson Yiu-Nam Lau,2 and W. Ian Lipkin1 and Molecular Genetics, Neurology, and Anatomy and Neurobiology, University of California, Irvine, and 2ICN Pharmaceuticals, Costa Mesa, California West Nile virus (WNV) is an emerging mosquito-borne pathogen that was reported for the ®rst time in the Western hemisphere in August 1999, when an encephalitis outbreak in New York City resulted in 62 clinical cases and 7 deaths. WNV, for which no antiviral therapy has been described, was recently recovered from a pool of mosquitoes collected in New York City. In anticipation of the recurrence of WNV during the summer of 2000, an analysis was made of the ef®cacy of the nucleoside analogue ribavirin, a broad-spectrum antiviral compound with activity against several RNA viruses, for treatment of WNV infection. High doses of ribavirin were found to inhibit WNV replication and cytopathogenicity in human neural cells in vitro. The Flaviviridae, a family of enveloped positive-strand RNA substantial [3]. Genetic analysis of the envelope protein se- viruses, include West Nile virus (WNV), as well as other sig- quence indicated that the viral strain most closely resembled ni®cant human pathogens, such as hepatitis C, yellow fever, an isolate from a goose in Israel in 1998, demonstrating the dengue, Japanese encephalitis, and St. Louis encephalitis vi- wide geographic distribution of this emerging pathogen [4, 5]. ruses [1]. Whereas hepatitis C virus (genus Hepacivirus) may Antiviral therapy for hepatitis C has been described [6]; how- be transmitted by blood products or sexual activity, most mem- ever, no speci®c treatment has been reported for WNV or other bers of the Flavivirus genus, including WNV, are transmitted ¯avivirus infections. -
Conventional and Unconventional Mechanisms for Capping Viral Mrna
REVIEWS Conventional and unconventional mechanisms for capping viral mRNA Etienne Decroly1, François Ferron1, Julien Lescar1,2 and Bruno Canard1 Abstract | In the eukaryotic cell, capping of mRNA 5′ ends is an essential structural modification that allows efficient mRNA translation, directs pre-mRNA splicing and mRNA export from the nucleus, limits mRNA degradation by cellular 5′–3′ exonucleases and allows recognition of foreign RNAs (including viral transcripts) as ‘non-self’. However, viruses have evolved mechanisms to protect their RNA 5′ ends with either a covalently attached peptide or a cap moiety (7‑methyl-Gppp, in which p is a phosphate group) that is indistinguishable from cellular mRNA cap structures. Viral RNA caps can be stolen from cellular mRNAs or synthesized using either a host- or virus-encoded capping apparatus, and these capping assemblies exhibit a wide diversity in organization, structure and mechanism. Here, we review the strategies used by viruses of eukaryotic cells to produce functional mRNA 5′-caps and escape innate immunity. Pre-mRNA splicing The cap structure found at the 5′ end of eukaryotic reactions involved in the viral RNA-capping process, A post-transcriptional mRNAs consists of a 7‑methylguanosine (m7G) moi‑ and the specific cellular factors that trigger a response modification of pre-mRNA, in ety linked to the first nucleotide of the transcript via a from the innate immune system. which introns are excised and 5′–5′ triphosphate bridge1 (FIG. 1a). The cap has several exons are joined in order to form a translationally important biological roles, such as protecting mRNA Capping, decapping and turnover of host RNA functional, mature mRNA. -
Structure Unveils Relationships Between RNA Virus Polymerases
viruses Article Structure Unveils Relationships between RNA Virus Polymerases Heli A. M. Mönttinen † , Janne J. Ravantti * and Minna M. Poranen * Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland; heli.monttinen@helsinki.fi * Correspondence: janne.ravantti@helsinki.fi (J.J.R.); minna.poranen@helsinki.fi (M.M.P.); Tel.: +358-2941-59110 (M.M.P.) † Present address: Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), 00014 Helsinki, Finland. Abstract: RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure- based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. -
Metagenomic Snapshots of Viral Components in Guinean Bats
microorganisms Communication Metagenomic Snapshots of Viral Components in Guinean Bats Roberto J. Hermida Lorenzo 1,†,Dániel Cadar 2,† , Fara Raymond Koundouno 3, Javier Juste 4,5 , Alexandra Bialonski 2, Heike Baum 2, Juan Luis García-Mudarra 4, Henry Hakamaki 2, András Bencsik 2, Emily V. Nelson 2, Miles W. Carroll 6,7, N’Faly Magassouba 3, Stephan Günther 2,8, Jonas Schmidt-Chanasit 2,9 , César Muñoz Fontela 2,8 and Beatriz Escudero-Pérez 2,8,* 1 Morcegos de Galicia, Magdalena G-2, 2o izq, 15320 As Pontes de García Rodríguez (A Coruña), Spain; [email protected] 2 WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; [email protected] (D.C.); [email protected] (A.B.); [email protected] (H.B.); [email protected] (H.H.); [email protected] (A.B.); [email protected] (E.V.N.); [email protected] (S.G.); [email protected] (J.S.-C.); [email protected] (C.M.F.) 3 Laboratoire des Fièvres Hémorragiques en Guinée, Université Gamal Abdel Nasser de Conakry, Commune de Matoto, Conakry, Guinea; [email protected] (F.R.K.); [email protected] (N.M.) 4 Estación Biológica de Doñana, CSIC, 41092 Seville, Spain; [email protected] (J.J.); [email protected] (J.L.G.-M.) 5 CIBER Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain 6 Public Health England, Porton Down, Wiltshire SP4 0JG, UK; [email protected] 7 Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford OX3 7BN, UK Citation: Hermida Lorenzo, R.J.; 8 German Centre for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel, Cadar, D.; Koundouno, F.R.; Juste, J.; 38124 Braunschweig, Germany Bialonski, A.; Baum, H.; 9 Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20148 Hamburg, Germany García-Mudarra, J.L.; Hakamaki, H.; * Correspondence: [email protected] Bencsik, A.; Nelson, E.V.; et al. -
Characterization of Nonprimate Hepacivirus and Construction of a Functional Molecular Clone
Characterization of nonprimate hepacivirus and construction of a functional molecular clone Troels K. H. Scheela,b,c, Amit Kapoord, Eiko Nishiuchia, Kenny V. Brocke, Yingpu Yua, Linda Andrusa, Meigang Gua, Randall W. Renshawf, Edward J. Dubovif, Sean P. McDonoughg, Gerlinde R. Van de Walleh, W. Ian Lipkind, Thomas J. Diversi, Bud C. Tennanti, and Charles M. Ricea,1 aLaboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065; bCopenhagen Hepatitis C Program, Department of Infectious Disease and Clinical Research Centre, Copenhagen University Hospital, DK-2650 Hvidovre, Denmark; cDepartment of International Health, Immunology, and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; dCenter for Infection and Immunity, Columbia University, New York, NY 10032; eDepartment of Biomedical Sciences, Edward Via College of Osteopathic Medicine, Auburn, AL 36866; and fVirology Laboratory, Animal Health Diagnostic Center, gDepartment of Biomedical Sciences, hBaker Institute for Animal Health, and iDepartment of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 Contributed by Charles M. Rice, January 8, 2015 (sent for review November 17, 2014; reviewed by Harvey Alter and Volker Lohmann) Nonprimate hepacivirus (NPHV) is the closest known relative of associated virus, TDAV) (13, 14) pegiviruses were discovered. In- hepatitis C virus (HCV) and its study could enrich our understanding terestingly, strong epidemiological evidence links serum hepatitis of HCV evolution, immunity, and pathogenesis. High seropositivity of horses (Theiler’s disease) to infection with TDAV (13). is found in horses worldwide with ∼3% viremic. NPHV natural his- The NPHV genome resembles that of HCV, with a long ORF tory and molecular virology remain largely unexplored, however. -
Emerging Encephalitis ESCMID Online Lecture Library © by Author
Emerging encephalitis Nipah, Enterovirus 71, West Nile, and others … © by author O. Epaulard Department of Infectious Diseases ESCMID OnlineGrenoble Lecture University HospitalLibrary Unit of Virus - host cell interactions UMI 3265 UJF-EMBL-CNRS Declaration of interest • No contradictory interest © by author ESCMID Online Lecture Library Menu • General considerations • Flaviviruses West Nile virus • Henipaviruses © by author • Enterovirus 71 • ESCMIDHEV Online Lecture Library DNA viruses RNA viruses © by author ESCMID Online Lecture Library Hepeviridae Rubivirus Alphavirus Caliciviridae Flavivirus (HEV) (Rubella) (Chikungunya, O Nyong- (Norwalk) (YF, Dengue, JE, Nyong, Am. Eq. Enc.) WNV, TBE) Togaviridae Hepacivirus Enterovirus (HCV) (Coxsackie, echovirus, …) Flaviviridae Hepatovirus (HAV) picornaviridae Rabies Rhinovirus Rhabdoviridae Parechovirus RNA viruses Coronaviridae Morbillivirus Filoviridae (measles) (Marburg, Ebola) Paramyxoviridae© by author Orthomyxoviridae RubulavirusESCMIDPneumovirus OnlineBunyaviridae Lecture Library (mumps) (RSV) Henipavirus Retroviridae (Nipah, Hendra) Hantaviruses influenza Hepeviridae Rubivirus Alphavirus Flavivirus Caliciviridae (HEV) (Rubella) (Chikungunya, O Nyong- (Y (Norwalk) F, Dengue, JE, Nyong, Am. Eq. Enc.) TBE, WNV) Enterovirus Togaviridae Hepacivirus (Coxsackie, echovirus, …) (HCV) Hepatovirus Flaviviridae (HAV) picornaviridae Rhinovirus Rabies Rhabdoviridae Parechovirus RNA viruses Coronaviridae Morbillivirus Filoviridae (measles) (Marburg, Ebola) Paramyxoviridae© by author Orthomyxoviridae -
Origins and Evolution of the Global RNA Virome Yuri Wolf, Darius Kazlauskas, Jaime Iranzo, Adriana Lucía-Sanz, Jens Kuhn, Mart Krupovic, Valerian Dolja, Eugene Koonin
Origins and Evolution of the Global RNA Virome Yuri Wolf, Darius Kazlauskas, Jaime Iranzo, Adriana Lucía-Sanz, Jens Kuhn, Mart Krupovic, Valerian Dolja, Eugene Koonin To cite this version: Yuri Wolf, Darius Kazlauskas, Jaime Iranzo, Adriana Lucía-Sanz, Jens Kuhn, et al.. Origins and Evo- lution of the Global RNA Virome. mBio, American Society for Microbiology, 2018, 9 (6), pp.e02329-18. 10.1128/mBio.02329-18. pasteur-01977324 HAL Id: pasteur-01977324 https://hal-pasteur.archives-ouvertes.fr/pasteur-01977324 Submitted on 10 Jan 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright RESEARCH ARTICLE Ecological and Evolutionary Science crossm Origins and Evolution of the Global RNA Virome Yuri I. Wolf,a Darius Kazlauskas,b,c Jaime Iranzo,a Adriana Lucía-Sanz,a,d Jens H. Kuhn,e Mart Krupovic,c Valerian V. Dolja,f Eugene V. Koonina aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Downloaded from Bethesda, Maryland, USA bInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania cDépartement de Microbiologie, Institut Pasteur, Paris, France dCentro Nacional de Biotecnología, Madrid, Spain eIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA http://mbio.asm.org/ ABSTRACT Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants.