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1. Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014

Author

Jens H. Kuhn, Kristian G. Andersen, Sylvain Baize, Yīmíng Bào, Sina Bavari, Nicolas Berthet, Olga Blinkova, J. Rodney Brister, Anna N. Clawson, Joseph Fair, Martin Gabriel, Robert F. Garry, Stephen K. Gire, Augustine Goba, Jean-Paul Gonzalez, Stephan Günther, Christian T. Happi, Peter B. Jahrling, Jimmy Kapetshi, Gary Kobinger, Jeffrey R. Kugelman, Eric M. Leroy, Gael Darren Maganga, Placide K. Mbala, Lina M. Moses, Jean-Jacques Muyembe-Tamfum, Magassouba N'Faly, Stuart T. Nichol, Sunday A. Omilabu, Gustavo Palacios, Daniel J. Park, Janusz T. Paweska, Sheli R. Radoshitzky, Cynthia A. Rossi, Pardis C. Sabeti, John S. Schieffelin, Randal J. Schoepp, Rachel Sealfon, Robert Swanepoel, Jonathan S. Towner, Jiro Wada, Nadia Wauquier, Nathan L. Yozwiak, and Pierre Formenty

Subjects
Ebola, Ebola virus, ebolavirus, filovirid, Filoviridae, filovirus, genome annotation, Lomela, Lokolia, Makona, mononegavirad, Mononegavirales, mononegavirus, virus classification, virus isolate, virus nomenclature, virus strain, virus taxonomy, virus variant, Microbiology, QR1-502
Abstract

In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.

Published
2014
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2. Reorganization and expansion of the nidoviral family Arteriviridae

Author

Lark L. Coffey, B. A. Lapin, Nathan D. Wolfe, Elena Postnikova, Jean Michel Takuo, Joseph Le Doux Diffo, Jeffrey Rogers, Eric Delwart, Magdalena Dunowska, Tatyana V. Vishnevskaya, Zinaida V. Shevtsova, Ubald Tamoufe, Laura Bollinger, Matthew G. Lackemeyer, Bradley S. Schneider, Deriabin Pg, S. V. Alkhovsky, Michael Lauck, Matthew LeBreton, Peter B. Jahrling, Terry Fei Fan Ng, Amethyst Gillis, Nikola O. Kondov, Shchetinin Am, Anna N. Clawson, Adam L. Bailey, Yīmíng Bào, Jens H. Kuhn, David H. O’Connor, Jiro Wada, Tony L. Goldberg, Thomas C. Friedrich, Sheli R. Radoshitzky, and Gustavo Palacios

Subjects
0301 basic medicine, Simian hemorrhagic fever virus, 040301 veterinary sciences, viruses, Sequence Homology, Genome, Viral, Arteriviridae, Article, Virus, 0403 veterinary science, Arterivirus, Open Reading Frames, 03 medical and health sciences, RNA Virus Infections, Genus, Terminology as Topic, Virology, Cluster Analysis, Nomenclature, Phylogeny, Virus classification, biology, 04 agricultural and veterinary sciences, General Medicine, Porcine reproductive and respiratory syndrome virus, biology.organism_classification, 3. Good health, 030104 developmental biology, RNA, Viral, Taxonomy (biology)
Abstract

The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American “types” of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.

Published
2015
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3. Past, present, and future of arenavirus taxonomy

Author

Michael J. Buchmeier, Jean-Paul Gonzalez, Víctor Romanowski, Christopher S. Clegg, Anna N. Clawson, Rémi N. Charrel, Mark D. Stenglein, Joseph L. DeRisi, Maria S. Salvato, Jens H. Kuhn, Sébastien Emonet, Igor S. Lukashevich, Sheli R. Radoshitzky, Yīmíng Bào, Juan Carlos de la Torre, and Clarence J. Peters

Subjects
Otras Ciencias Biológicas, viruses, Arenaviridae, Biology, Viral hemorrhagic fever, Ciencias Biológicas, VIRAL HEMORRHAGIC FEVER, Phylogenetics, Virology, medicine, Clade, Nomenclature, Virus classification, Arenavirus, Species name, MAMMARENAVIRUS, virus diseases, General Medicine, VIRUS NOMENCLATURE, biology.organism_classification, medicine.disease, INTERNATIONAL COMMITTEE ON TAXONOMY OF VIRUSES, ARENAVIRUS, REPTARENAVIRUS, CIENCIAS NATURALES Y EXACTAS
Abstract

Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings. Fil: Radoshitzky, Sheli R.. United States Army Medical Research. Institute of Infectious Diseases; Estados Unidos Fil: Bào, Yīmíng. National Institutes of Health; Estados Unidos Fil: Buchmeier, Michael J.. University of California at Irvine; Estados Unidos Fil: Charrel, Rémi N.. École des Hautes Etudes en Santé Publique; Francia. Aix Marseille Université; Francia Fil: Clawson, Anna N.. National Institutes of Health; Estados Unidos Fil: Clegg, Christopher S.. Les Mandinaux; Francia Fil: DeRisi, Joseph L.. University of California; Estados Unidos Fil: Emonet, Sébastien. Echelon Recherche de Lyon. Institut de Recherche Biomedicale de Armees. Unité de Virologie; Francia Fil: Gonzalez, Jean Paul. Metabiota Inc.; Estados Unidos Fil: Kuhn, Jens H.. National Institutes of Health; Estados Unidos Fil: Lukashevich, Igor S.. University of Louisville; Estados Unidos Fil: Peters, Clarence J.. University of Texas; Estados Unidos Fil: Romanowski, Victor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina Fil: Salvato, Maria S.. University of Maryland; Estados Unidos Fil: Stenglein, Mark D.. State University of Colorado - Fort Collins; Estados Unidos Fil: de la Torre, Juan Carlos. La Jolla Institute for Allergy and Immunology; Estados Unidos

Published
2015
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4. Taxonomy of the order Mononegavirales: update 2016

Author

Ralf Dürrwald, Krisztián Bányai, Robert A. Lamb, Hideki Kondo, Alexander Bukreyev, Anna N. Clawson, Calogero Terregino, Robert B. Tesh, Andrew J. Easton, Andrea Maisner, Paul A. Rota, Gael Kurath, Kartik Chandran, Charles H. Calisher, Ralf G. Dietzgen, Janusz T. Paweska, Szilvia Marton, Dennis Rubbenstroth, Masayuki Horie, Juliana Freitas-Astúa, Bertus K. Rima, Jonathan S. Towner, Viktor E. Volchkov, Eric M. Leroy, David M. Stone, Susan Payne, Kwok-Yung Yuen, Hideki Ebihara, Lin-Fa Wang, Lìjiāng Liú, C. Li, Nikos Vasilakis, Olga Dolnik, Gaya K. Amarasinghe, Gary P. Kobinger, Jean L. Patterson, Sergio Lenardon, Xian Dan Lin, Leslie L. Domier, Mang Shi, Pierre Formenty, Ben Longdon, Anna E. Whitfield, Sina Bavari, Timothy H. Hyndman, Martin Verbeek, E. W. Kitajima, Elke Mühlberger, Peter J. Walker, Ayato Takada, Mark D. Stenglein, François Xavier Briand, David Wang, Elodie Ghedin, Jiāsēn Chéng, Keizo Tomonaga, Norbert Nowotny, Roger Hewson, Noël Tordo, Jun Hua Tian, Nicolás Bejerman, John M. Dye, Christopher F. Basler, Yong-Zhen Zhang, Kim R. Blasdell, Yanping Fu, Sophie J. Smither, Richard E. Randall, Jens H. Kuhn, Jiǎtāo Xiè, Victoria Wahl-Jensen, Thierry Wetzel, Martin Schwemmle, Michael M. Goodin, John A. Walsh, Thomas Briese, Yīmíng Bào, Peter L. Collins, Dàohóng Jiāng, Sergey V. Netesov, Ron A. M. Fouchier, Szilvia L. Farkas, Claudio L. Afonso, US Department of Agriculture, Washington University School of Medicine (WUSM), University of Washington [Seattle], Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA), National Center for Biotechnology Information (NCBI), Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de la Patagonia Austral (UNPA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Columbia Mailman School of Public Health, The University of Texas Medical Branch (UTMB), Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University System, Albert Einstein College of Medicine [New York], Huazhong Agricultural University, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation - Centre for Animal Science, University of Queensland [Brisbane], Philipps University of Marburg, University of Illinois [Chicago] (UIC), University of Illinois System, IDT Biologika, School of Life Sciences, Warwick University, Laboratory of Persistent Viral Diseases, LABOKLIN, Embrapa Cassava and Fruits, Brazilian Agricultural Research Corporation (Embrapa), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Department of Plant Pathology, University of Kentucky, University of Kentucky, Public Health England [Salisbury] (PHE), Kagoshima University, School of Veterinary and Life Sciences [Murdoch], Murdoch University, State Key Laboratory of Agricultural Microbiology, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Wēnzhōu Center for Disease Control and Prevention, Department of Genetics University of Cambridge, University of Cambridge [UK] (CAM), Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], College of Veterinary Medicine and Biomedical Sciences, National Institute for Communicable Diseases [Johannesburg] (NICD), Biomedical Sciences Research Complex [St Andrews, Scotland] (BSRC), University of St Andrews [Scotland], Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], Chinese Center for Disease Control and Prevention, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Colorado State University [Fort Collins] (CSU), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Wǔhàn Center for Disease Control and Prevention, Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur [Paris], Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Wageningen University and Research [Wageningen] (WUR), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Departments of Molecular Microbiology and Pathology & Immunology, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Kansas State University, State Key Laboratory of Emerging Infectious Diseases & Department of Microbiology, The University of Hong Kong (HKU)-Li Ka Shing Faculty of Medicine, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong (HKU), French Agency for Food, Environmental and Occupational Health & Safety (Anses) - Veterinary epidemiology, Albert Einstein College of Medicine, Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Hokkaido University, Istituto Zooprofilattico Sperimentale delle Venezie [Padova], Wageningen University and Research Centre [Wageningen] (WUR), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Duke NUS Medical School, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], Huazhong Agricultural University [Wuhan] (HZAU), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], University of Kentucky (UK), Universidade de São Paulo = University of São Paulo (USP), Kyoto University, Institut Pasteur [Paris] (IP), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Virology, and Biomedical Sciences Research Complex

Subjects
0301 basic medicine, 030106 microbiology, Zoology, Genome, Viral, Article, 03 medical and health sciences, Genus, Phylogenetics, Virology, Crustavirus, Life Science, Viral, Mononegavirales, Phylogeny, Order Mononegavirales, QR355, Genome, biology, Entomology & Disease Management, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Pneumoviridae, Subfamily Pneumovirinae, MONONEGAVIRALES, 030104 developmental biology, Evolutionary biology, Wildlife Ecology and Conservation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), RA, RC
Abstract

International audience; In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Published
2016
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5. Nomenclature- and Database-Compatible Names for the Two Ebola Virus Variants that Emerged in Guinea and the Democratic Republic of the Congo in 2014

Author

Gael Darren Maganga, Magassouba N’Faly, Martin Gabriel, Augustine Goba, Sunday Omilabu, Eric M. Leroy, J. Rodney Brister, Stephen K. Gire, Jens H. Kuhn, Nathan L. Yozwiak, Placide Mbala, Rachel Sealfon, Lina M. Moses, Jeffrey R. Kugelman, Kristian G. Andersen, Olga Blinkova, Christian T. Happi, Jimmy Kapetshi, Peter B. Jahrling, P. Formenty, Nicolas Berthet, Cynthia A. Rossi, Yīmíng Bào, Joseph N. Fair, John S. Schieffelin, Jonathan S. Towner, Gustavo Palacios, Robert Swanepoel, Robert F. Garry, Daniel Park, Janusz T. Paweska, Jiro Wada, Anna N. Clawson, Gary Kobinger, Sylvain Baize, Nadia Wauquier, Jean-Paul Gonzalez, Sina Bavari, Stuart T. Nichol, Randal J. Schoepp, Sheli R. Radoshitzky, Stephan Günther, Jean-Jacques Muyembe-Tamfum, Pardis C. Sabeti, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), FAS Center for Systems Biology, Harvard University, Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP), National Center for Biotechnology Information (NCBI), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Centre International de Recherches Médicales de Franceville (CIRMF), Fondation Mérieux, Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), German Center for Infection Research, Partnersite Munich (DZIF), Tulane University, Harvard FAS Center for Systems Biologyy, Kenema Government Hospital, Metabiota Inc. [San Francisco], Redeemer's University [Lagos, Nigeria], Institut National de Recherche Biomédicale [Kinshasa] (INRB), Special Pathogens Programme, National Microbiology Laboratory, Public Health Agency of Canada, Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Donka National Hospital, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos, Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), National Institute for Communicable Diseases [Johannesburg] (NICD), Computer Science and Artificial Intelligence Laboratory [Cambridge] (CSAIL), Massachusetts Institute of Technology (MIT), University of Pretoria [South Africa], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Harvard University [Cambridge], Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], U.S. Army Medical Research Institute of Infectious Diseases, and Massachusetts Institute of Technology (MIT)-Harvard University [Cambridge]

Subjects
virus strain, MESH: Sequence Analysis, DNA, Letter, genome annotation, lcsh:QR1-502, Filoviridae, virus nomenclature, medicine.disease_cause, lcsh:Microbiology, Disease Outbreaks, West africa, virus variant, Ebola virus, Makona, Lokolia, MESH: Disease Outbreaks, Mononegavirales, virus classification, MESH: Phylogeny, Nomenclature, Phylogeny, MESH: Guinea, biology, 3. Good health, Lomela, Infectious Diseases, MESH: RNA, Viral, Ebola, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Democratic Republic of the Congo, RNA, Viral, filovirus, MESH: Terminology as Topic, filovirid, virus taxonomy, Terminology as Topic, Virology, medicine, Humans, virus isolate, MESH: Ebolavirus, Virus classification, ebolavirus, Ebolavirus, mononegavirus, MESH: Humans, mononegavirad, Outbreak, Sequence Analysis, DNA, MESH: Democratic Republic of the Congo, Hemorrhagic Fever, Ebola, biology.organism_classification, MESH: Hemorrhagic Fever, Ebola, Guinea
Abstract

International audience; In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: "Makona", Middle Africa: "Lomela") and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures.

Published
2014
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6. Taxonomic reorganization of the family Bornaviridae

Author

Kathryn M. Carbone, Dennis Rubbenstroth, Martin Schwemmle, Wolfgang Garten, Norbert Nowotny, Yīmíng Bào, Thomas Briese, Jolanta Kolodziejek, Ralf Dürrwald, Peter B. Jahrling, Mark D. Stenglein, Keizo Tomonaga, Anna N. Clawson, Joseph L. DeRisi, Jens H. Kuhn, and Herbert Weissenböck

Subjects
Borna disease, Disease reservoir, Phylogenetic tree, Zoology, General Medicine, Genome, Viral, Biology, Genome, Virology, Virus, Article, Proventricular dilatation disease, Phylogenetics, Evolutionary biology, Borna Disease, Bornaviridae, Animals, Taxonomy (biology), Amino Acid Sequence, Sequence Alignment, Phylogeny, Disease Reservoirs
Abstract

Knowledge of bornaviruses has expanded considerably during the last decade. A possible reservoir of mammalian Borna disease virus has been identified, divergent bornaviruses have been detected in birds and reptiles, and endogenous bornavirus-like elements have been discovered in the genomes of vertebrates of several species. Previous sequence comparisons and alignments have indicated that the members of the current family Bornaviridae are phylogenetically diverse and are not adequately classified in the existing bornavirus taxonomy supported by the International Committee on Taxonomy of Viruses (ICTV). We provide an update of these analyses and describe their implications for taxonomy. We propose retaining the family name Bornaviridae and the genus Bornavirus but reorganizing species classification. PAirwise Sequence Comparison (PASC) of bornavirus genomes and Basic Local Alignment Search Tool (BLAST) comparison of genomic and protein sequences, in combination with other already published phylogenetic analyses and known biological characteristics of bornaviruses, indicate that this genus should include at least five species: Mammalian 1 bornavirus (classical Borna disease virus and divergent Borna disease virus isolate No/98), Psittaciform 1 bornavirus (avian/psittacine bornaviruses 1, 2, 3, 4, 7), Passeriform 1 bornavirus (avian/canary bornaviruses C1, C2, C3, LS), Passeriform 2 bornavirus (estrildid finch bornavirus EF), and Waterbird 1 bornavirus (avian bornavirus 062CG). This classification is also in line with biological characteristics of these viruses and their vertebrate hosts. A snake bornavirus, proposed to be named Loveridge’s garter snake virus 1, should be classified as a member of an additional species (Elapid 1 bornavirus), unassigned to a genus, in the family Bornaviridae. Avian bornaviruses 5, 6, MALL, and another “reptile bornavirus” (“Gaboon viper virus”) should stay unclassified until further information becomes available. Finally, we propose new virus names and abbreviations when necessary to achieve clear differentiation and unique identification.

Published
2014

7. Dichorhavirus: a proposed new genus for Brevipalpus mite-transmitted, nuclear, bacilliform, bipartite, negative-strand RNA plant viruses

Author

Michael M. Goodin, Jens H. Kuhn, Anna N. Clawson, Ralf G. Dietzgen, Anna E. Whitfield, Hideki Kondo, Juliana Freitas-Astúa, E. W. Kitajima, and Thierry Wetzel

Subjects
Brevipalpus, Molecular Sequence Data, Nucleic acid sequence, RNA, General Medicine, Genome, Viral, Sequence Analysis, DNA, Biology, biology.organism_classification, Genome, Virology, Plant Viruses, RHABDOVIRIDAE, Genus, Plant virus, Animals, Cluster Analysis, RNA Viruses, RNA, Viral, Orchid fleck virus, Gene, Acari, Phylogeny
Abstract

Orchid fleck virus (OFV) is an unassigned negative-sense, single-stranded (-)ssRNA plant virus that was previously suggested to be included in the family Rhabdoviridae, order Mononegavirales. Although OFV shares some biological characteristics, including nuclear cytopathological effects, gene order, and sequence similarities, with nucleorhabdoviruses, its taxonomic status is unclear because unlike all mononegaviruses, OFV has a segmented genome and its particles are not enveloped. This article analyses the available biological, physico-chemical, and nucleotide sequence evidence that seems to indicate that OFV and several other Brevipalpus mite-transmitted short bacilliform (-)ssRNA viruses are likely related and may be classified taxonomically in novel species in a new free-floating genus Dichorhavirus.

Published
2013

8. Viral Hemorrhagic Fevers

Author

Anna N. Clawson, Victoria Wahl-Jensen, Peter B. Jahrling, Sina Bavari, Jens H. Kuhn, and Sheli R. Radoshitzky

Subjects
Hemorrhagic Fevers, business.industry, Immunology, Medicine, business
Published
2013
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9. Nyamiviridae: Proposal for a new family in the order Mononegavirales

Author

Anna N. Clawson, Marieke Herrel, Yíngyún Caì, Nobuhiro Suzuki, Kris N. Lambert, Peter Staeheli, Sadia Bekal, Hideki Kondo, Urs Schneider, Lin-Fa Wang, Ralf G. Dietzgen, Jens H. Kuhn, Leslie L. Domier, David Wang, Kathie A. Mihindukulasuriya, Robert B. Tesh, Peter B. Jahrling, Norbert Nowotny, and Sheli R. Radoshitzky

Subjects
Virus Cultivation, biology, Nematoda, Bird Diseases, viruses, Soybean cyst nematode, General Medicine, Nyamiviridae, biology.organism_classification, Virus Replication, Virology, Virus, Article, Birds, Tissue Culture Techniques, Viral replication, Phylogenetics, Plant virus, Veterinary virology, Animals, RNA Viruses, Phylogeny
Abstract

Nyamanini virus (NYMV) and Midway virus (MIDWV) are unclassified tick-borne agents that infect land birds and seabirds, respectively. The recent molecular characterization of both viruses confirmed their already known close serological relationship and revealed them to be nonsegmented, single- and negative-stranded RNA viruses that are clearly related to, but quite distinct from, members of the order Mononegavirales (bornaviruses, filoviruses, paramyxoviruses, and rhabdoviruses). A third agent, soybean cyst nematode virus 1 (SbCNV-1, previously named soybean cyst nematode nyavirus), was recently found to be an additional member of this new virus group. Here, we review the current knowledge about all three viruses and propose classifying them as members of a new mononegaviral family, Nyamiviridae.

Published
2013

10. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

Author

Sbina Bavari, Susan Payne, Alexander Bukreyev, Arvind Varsani, Víctor Romanowski, Kartik Chandran, Ralf G. Dietzgen, Mark D. Stenglein, Anna N. Clawson, Sead Sabanadzovic, Gael Kurath, Andrea Maisner, Peter J. Walker, Ralf Dürrwald, Juan Carlos de la Torre, Eric M. Leroy, Mária Benko, Keizo Tomonaga, Gary P. Kobinger, Robert A. Lamb, Hideki Kondo, F. Murilo Zerbini, Martin Schwemmle, Robert B. Tesh, Gaya K. Amarasinghe, Andrew J. Easton, Michael J. Buchmeier, Jean-Paul Gonzalez, Anna E. Whitfield, Nikos Vasilakis, Jonathan S. Towner, Pierre Formenty, Jens H. Kuhn, Norbert Nowotny, Roger Hewson, Ayato Takada, Mart Krupovic, Igor S. Lukashevich, David M. Stone, Clarence J. Peters, Sheli R. Radoshitzky, Bertus K. Rima, Janusz T. Paweska, Masayuki Horie, Christopher S. Clegg, Victoria Wahl-Jensen, Christopher F. Basler, Sébastian Emonet, Charles H. Calisher, Lin-Fa Wang, Rémi N. Charrel, Jean L. Patterson, Elodie Ghedin, Dennis Rubbenstroth, Dàohóng Jiāng, Sergey V. Netesov, Hélène Sanfaçon, Thomas S. Postler, Ron A. M. Fouchier, Peter L. Collins, Noël Tordo, Maria S. Salvato, John M. Dye, Arcady Mushegian, Sophie J. Smither, Joseph L. DeRisi, Olga Dolnik, Kim R. Blasdell, Balázs Harrach, Viktor E. Volchkov, Thomas Briese, Andrew M. Kropinski, Columbia University College of Physicians and Surgeons, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Washington University School of Medicine (WUSM), University of Washington [Seattle], Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute for Soil Sciences and Agricultural Chemistry (ATK TAKI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, University of California [Irvine] (UCI), University of California, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Les Mandinaux, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Immunology and Microbial Science, Scripps Research Institute, Department of Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Unité de Virologie, Institut de Recherche Biomédicale des Armées (IRBA), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Health for Development, Public Health England [Salisbury] (PHE), Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), Department of Pharmacology and Toxicology, University of Louisville, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas at Austin [Austin], Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), University of Freiburg [Freiburg], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Summerland Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), University of Maryland School of Medicine, University of Maryland System, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Center for Fundamental and Applied Microbiomics, Arizona State University [Tempe] (ASU)-Biodesign Institute, Kansas State University, Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Vicosa (UFV), This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This work was also funded in part under National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and R24AI120942 (N.V., R.B.T.), and the National Science Foundation (NSF) Individual Research and Development (IR/D) program (A.R.M.)., We thank Laura Bollinger (NIH/NIAID Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for critically editing the manuscript, Andrew J. Davison (MRC – University of Glasgow Centre for Virus Research, Glasgow, UK) and Michael J. Adams (Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Herts, UK) of the ICTV Executive Committee for suggestions on manuscript improvement, and Arya Ariël Kuhn for sustained vocal support and (dia)critical remarks, Albert Einstein College of Medicine, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, Departamento de Fitopatologia/BIOAGRO, Virology, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], University of California [Irvine] (UC Irvine), University of California (UC), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Scripps Research Institute [La Jolla, San Diego], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Huazhong Agricultural University [Wuhan] (HZAU), Institut Pasteur [Paris] (IP), Agriculture and Agri-Food (AAFC), Kyoto University, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)

Subjects
0301 basic medicine, MESH: Terminology as Topic, media_common.quotation_subject, Biología, 030106 microbiology, Binomials, Zoology, Biology, Points of View, 03 medical and health sciences, Genus, Terminology as Topic, Genetics, MESH: Classification, Epithet, Arenaviridae, Ecology, Evolution, Behavior and Systematics, Virus classification, media_common, Order Mononegavirales, Evolutionary Biology, Virus taxonomy, Classification, MESH: Viruses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virus nomenclature, Genealogy, Ictv, International committee on taxonomy of viruses, 030104 developmental biology, Homo sapiens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Mononegavirales
Abstract

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted toconvert all currently official names ofspecies included in the viru sfamily Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment., La lista completa de autores que integran el documento puede consultarse en el archivo, Instituto de Biotecnologia y Biologia Molecular

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