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1. Four principles to establish a universal virus taxonomy

Author: Peter Simmonds, Evelien M. Adriaenssens, F. Murilo Zerbini, Nicola G. A. Abrescia, Pakorn Aiewsakun, Poliane Alfenas-Zerbini, Yiming Bao, Jakub Barylski, Christian Drosten, Siobain Duffy, W. Paul Duprex, Bas E. Dutilh, Santiago F. Elena, Maria Laura García, Sandra Junglen, Aris Katzourakis, Eugene V. Koonin, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Małgorzata Łobocka, Cédric Lood, Jennifer Mahony, Jan P. Meier-Kolthoff, Arcady R. Mushegian, Hanna M. Oksanen, Minna M. Poranen, Alejandro Reyes-Muñoz, David L. Robertson, Simon Roux, Luisa Rubino, Sead Sabanadzovic, Stuart Siddell, Tim Skern, Donald B. Smith, Matthew B. Sullivan, Nobuhiro Suzuki, Dann Turner, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, Nikos Vasilakis, University of Oxford, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Center for Cooperative Research in Biosciences [Derio, Spain], Mahidol University [Bangkok], University of Chinese Academy of Sciences [Beijing] (UCAS), Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), Utrecht University [Utrecht], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], National Institutes of Health [Bethesda] (NIH), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), MRC - University of Glasgow Centre for Virus Research, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Okayama University, University of the West of England [Bristol] (UWE Bristol), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), The University of Texas Medical Branch (UTMB), European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), TB, HIV and opportunistic diseases and pathogens (THOP), Faculty Common Matters (Faculty of Biology and Environmental Sciences), Molecular Principles of Viruses, Molecular and Integrative Biosciences Research Programme, and Molecular and Translational Virology
Subjects: Neuroscience(all), [SDV]Life Sciences [q-bio], principles, R Medicine, Medical and Health Sciences, General Biochemistry, Genetics and Molecular Biology, SDG 3 - Good Health and Well-being, Immunology and Microbiology(all), Humans, Bacteriophages, Phylogeny, Taxonomy, 11832 Microbiology and virology, Agricultural and Veterinary Sciences, General Immunology and Microbiology, Biochemistry, Genetics and Molecular Biology(all), General Neuroscience, universal virus taxonomy, Biodiversity, Biological Sciences, Medical Terminology, Infectious Diseases, 12D8623N#57012320, PDMT2/21/038#56345426, Viruses, 1181 Ecology, evolutionary biology, Metagenomics, Infection, General Agricultural and Biological Sciences, QR355 Virology, Developmental Biology
Abstract: 1759874.Y.B.wassupportedbythe ProfessionalAssociationoftheAllianceof Publisher Copyright: Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent. publishersversion published
Published: 2023

2. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author: Amadou A. Sall, Christopher F. Basler, Gary P. Kobinger, Amy J. Lambert, Rodrigo Jardim, John V. da Graça, Yong-Zhen Zhang, Víctor Romanowski, Massimo Turina, John W. McCauley, Lin-Fa Wang, Paul A. Rota, Olga Dolnik, Juan Carlos de la Torre, Gabriele Neumann, Natalie J. Thornburg, Tomohide Natsuaki, Jin Won Song, Kartik Chandran, Carol D. Blair, Michael A. Drebot, Guohui Zhou, Rémi N. Charrel, Heather L. Wells, Ralf G. Dietzgen, Bernadett Pályi, Arnfinn Lodden Økland, Ian Crozier, Gael Kurath, Gilda B. Jonson, Robert R. Martin, Xuejie Yu, Anthony R. Fooks, Renato O. Resende, Ali Mirazimi, Bernadette G. van den Hoogen, Scott Adkins, Colin R. Parrish, Alexander Bukreyev, Anthony Griffiths, Timothy H. Hyndman, Peter Simmonds, Rachel Breyta, Zhìqiáng Wú, Ralf Dürrwald, Jorlan Fernandes, Biao Chen, Udo Hetzel, Alexandro Guterres, Jessica R. Spengler, Michael J. Buchmeier, Rayapati A. Naidu, Janusz T. Paweska, Keizō Tomonaga, Kamil Sarpkaya, Ivan V. Kuzmin, Jens H. Kuhn, Piet Maes, Marco Marklewitz, Masayuki Horie, Arvind Varsani, Shin-Yi Lee Marzano, Ursula J. Buchholz, Jean-Paul Gonzalez, Angelantonio Minafra, Daniela Alioto, Simon J. Anthony, Florian Pfaff, Brian H. Bird, Peter J. Walker, Robert A. Lamb, Noël Tordo, Rainer G. Ulrich, Sergio H. Marshall, Eric M. Leroy, Ayato Takada, Kirsten Spann, Xavier de Lamballerie, John M. Dye, Inmaculada Casas, Manuela Sironi, J. Christopher S. Clegg, Paul Brown, Dennis Rubbenstroth, Yan Liu, Márcio Roberto Teixeira Nunes, Tatjana Avšič-Županc, Martin Verbeek, Andrew J. Easton, Beatriz Navarro, Hideki Ebihara, Benhur Lee, Pierre Formenty, Qi Jin, Hideki Kondō, Eric Bergeron, Sébastien Massart, Daniel R. Perez, S. V. Alkhovsky, Charles H. Calisher, Anna Papa, Xīnglóu Yáng, José A. Navarro, Xifeng Wang, Taiyun Wei, Kim R. Blasdell, Lucie Dufkova, Renata Carvalho de Oliveira, Elba Regina Sampaio de Lemos, Nikos Vasilakis, Pedro Luis Ramos-González, Tong Zhang, Holly R. Hughes, Leonie Forth, Serpil Karadağ, F. Murilo Zerbini, Xueping Zhou, María Laura García, Tomáš Bartonička, Sandra Junglen, Aziz ul Rahman, Petra Straková, Karen E. Keller, William G. Dundon, Jiří Salát, Dexin Li, Jussi Hepojoki, Maria S. Salvato, Hui Wang, Justin Bahl, Bernd Hoffmann, Alberto M. R. Dávila, Jonathan S. Towner, Wénwén Liú, Mifang Liang, Yuri I. Wolf, Gaya K. Amarasinghe, Jianwei Wang, Alex Pauvolid-Corrêa, Anna Maria Vaira, Roy A. Hall, William Marciel de Souza, Thomas Briese, Felicity J. Burt, Valerian V. Dolja, Boris Klempa, Satu Hepojoki, Mengji Cao, Selma Gago-Zachert, Il-Ryong Choi, Rik L. de Swart, Jan Felix Drexler, Gabriel Robles Luna, Igor S. Lukashevich, Maria Minutolo, Amara Jambai, Nihal Buzkan, Steven B. Bradfute, Are Nylund, Ioannis E. Tzanetakis, Xiǎohóng Shí, Stephan Günther, Aura R. Garrison, Takahide Sasaya, Mart Krupovic, Victoria Wahl, Seiji Hongo, Matthew J. Ballinger, María A. Ayllón, Jonas Klingström, David M. Stone, Sead Sabanadzovic, Tracey Goldstein, George Fú Gāo, Aiah Gbakima, Norbert Nowotny, Vicente Pallás, Carina Andrea Reyes, W. Paul Duprex, Roger Hewson, Muhammad Zubair Shabbir, Sophie J. Smither, John V. Williams, Hans Peter Mühlbach, John Chamberlain, Yukio Shirako, Elke Mühlberger, Lies Laenen, Martin Beer, Jiànróng Lǐ, Giovanni P. Martelli, Gustavo Palacios, Sina Bavari, Natalya Yutin, Elena Dal Bó, Michele Digiaro, Jonathan A. Runstadler, John Hammond, Martin Schwemmle, Robert B. Tesh, Dirk Höper, Martin H. Groschup, Francesco Di Serio, Teemu Smura, Sheli R. Radoshitzky, Juliana Freitas-Astúa, Susan Payne, Dennis A. Bente, Anne Balkema-Buschmann, Adolfo García-Sastre, Eugene V. Koonin, Nicholas Di Paola, Bertus K. Rima, Mark D. Stenglein, Mohamed Hassan, Michela Chiumenti, Koray Ergünay, Patrick L. Di Bello, Ron A. M. Fouchier, Anna E. Whitfield, Toufic Elbeaino, Xin Yang, Nicole Mielke-Ehret, Jana Širmarová, Daniel Ruzek, Dàohóng Jiāng, Stanley L. Langevin, Sergey V. Netesov, Zhengli Shi, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Centre collaborateur de l'OMS Arbovirus et Fièvres Hémorragiques virales - Stratégies antivirales (CC-OMS), Institut Pasteur de Guinée, Les Mandinaux, 16450 Le Grand Madieu, This work was supported in part through Laulima Government Solutions, LLC prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. This project has been funded in whole or in part with federal funds from the National Cancer Institute (NCI), National Institutes of Health (NIH), under Contract No. 75N91019D00024, Task Order No. 75N91019F00130 to I.C., who was supported by the Clinical Monitoring Research Program Directorate, Frederick National Lab for Cancer Research, sponsored by NCI. This work was also funded in part by Contract No. HSHQDC-15-C-00064 awarded by the US Department of Homeland Security (DHS) Science and Technology Directorate (S&T) for the management and operation of The National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center operated by the Battelle National Biodefense Institute (V.W.), and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges partial support from the Special Research Initiative of Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University, and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494., We thank W. Ian Lipkin and Rafal Tokarz (Columbia University Irving Medical Center, New York, New York, USA) for providing/approving new names for 'blacklegged tick phleboviruses 1 and 3' and Edward Holmes (University of Sydney, Australia) for providing/approving a new name for 'Norway phlebovirus'. Many authors are current members of 2017-2020 International Committee on Taxonomy of Viruses (ICTV) Study Groups: Arenaviridae (Jens H. Kuhn, Michael J. Buchmeier, Rémi N. Charrel, J. Christopher S. Clegg, Juan Carlos de la Torre, Jean-Paul J. Gonzalez, Stephan Günther, Mark D. Stenglein, Jussi Hepojoki, Manuela Sironi, Igor S. Lukashevich, Sheli R. Radoshitzky, Víctor Romanowski, Maria S. Salvato), Artoviridae (Jens H. Kuhn, Ralf G. Dietzgen, Dàohóng Jiāng, Nikos Vasilakis), Aspiviridae (John V. da Graça, Elena Dal Bó, Selma Gago-Zachert, María Laura García, John Hammond, Tomohide Natsuaki, José A. Navarro, Vicente Pallás, Carina A. Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis Tzanetakis, Anna Maria Vaira, Martin Verbeek), Bornaviridae (Jens H. Kuhn, Thomas Briese, Ralf Dürrwald, Masayuki Horie, Timothy H. Hyndman, Norbert Nowotny, Susan Payne, Dennis Rubbenstroth, Mark D. Stenglein, Keizō Tomonaga), Bunyavirales (Jens H. Kuhn, Scott Adkins, Juan Carlos de la Torre, Sandra Junglen, Amy J. Lambert, Piet Maes, Marco Marklewitz, Gustavo Palacios, Takahide Sasaya, Yong-Zhen Zhang), Filoviridae (Jens H. Kuhn, Gaya K. Amarasinghe, Christopher Basler, Sina Bavari, Alexander Bukreyev, Kartik Chandran, Ian Crozier, Olga Dolnik, John M. Dye, Pierre B. H. Formenty, Anthony Griffiths, Roger Hewson, Gary Kobinger, Eric M. Leroy, Elke Mühlberger, Sergey V. Netesov, Gustavo Palacios, Bernadett Pályi, Janusz T. Pawęska, Sophie Smither, Ayato Takada, Jonathan S. Towner, Victoria Wahl), Fimoviridae (Michele Digiaro, Toufic Elbeaino, Giovanni P. Martelli, Nicole Mielke-Ehret, Hans-Peter Mühlbach), Hantaviridae (Steven Bradfute, Charles H. Calisher, Boris Klempa, Jonas Klingström, Lies Laenen, Piet Maes, Jin-Won Song, Yong-Zhen Zhang), Jingchuvirales (Nicholas Di Paola), Monjiviricetes (Jens H. Kuhn, Ralf G. Dietzgen, W. Paul Duprex, Dàohóng Jiāng, Piet Maes, Janusz T. Pawęska, Bertus K. Rima, Dennis Rubbenstroth, Peter J. Walker, Yong-Zhen Zhang), Mymonaviridae (María A. Ayllón, Dàohóng Jiāng, Shin-Yi L. Marzano), Nairoviridae (Jens H. Kuhn, Sergey V. Alkhovsky, Tatjana Avšič-Županc, Dennis A. Bente, Éric Bergeron, Felicity Burt, Nicholas Di Paola, Koray Ergünay, Aura R. Garrison, Roger Hewson, Ali Mirazimi, Gustavo Palacios, Anna Papa, Amadou Alpha Sall, Jessica R. Spengler), Negarnaviricota (Jens H. Kuhn, Eugene V. Koonin, Mart Krupovic, Yuri I. Wolf), Nyamiviridae (Jens H. Kuhn, Ralf G. Dietzgen, Dàohóng Jiāng, Nikos Vasilakis), Orthomyxoviridae (Justin Bahl, Inmaculada Casas, Adolfo García-Sastre, Seiji Hongo, Sergio H. Marshall, John W. McCauley, Gabriele Neumann, Colin R. Parrish, Daniel R. Pérez, Jonathan A. Runstadler, Martin Schwemmle), Paramyxoviridae (Anne Balkema-Buschmann, William G. Dundon, W. Paul Duprex, Andrew J. Easton, Ron Fouchier, Gael Kurath, Benhur Lee, Bertus K. Rima, Paul Rota, Lin-Fa Wang, Robobert A. Lamb), Peribunyaviridae (Scott Adkins, Sergey V. Alkhovsky, Martin Beer, Carol D. Blair, Charles H. Calisher, Michael A. Drebot, Holly R. Hughes, Amy J. Lambert, William Marciel de Souza, Marco Marklewitz, Márcio R. T. Nunes, Xiǎohóng Shí), Phasmaviridae (Matthew J. Ballinger, Roy A. Hall, Sandra Junglen, Stanley L. Langevin, Alex Pauvolid-Corrêa), Phenuiviridae (Thomas Briese, Rémi N. Charrel, Xavier De Lamballerie, Hideki Ebihara, George Fú Gāo, Martin H. Groschup, Márcio R. T. Nunes, Gustavo Palacios, Takahide Sasaya, Jin-Won Song), Pneumoviridae (Paul A. Brown, Ursula J. Buchholz, Rik L. de Swart, Jan Felix Drexler, W. Paul Duprex, Andrew J. Easton, Jiànróng Lǐ, Kirsten Spann, Natalie J. Thornburg, Bernadette van den Hoogen, John V. Williams), Rhabdoviridae (Kim R. Blasdell, Rachel Breyta, Ralf G. Dietzgen, Anthony R. Fooks, Juliana Freitas-Astúa, Hideki Kondō, Gael Kurath, Ivan V. Kuzmin, David M. Stone, Robert B. Tesh, Noël Tordo, Nikos Vasilakis, Peter J. Walker, Anna E. Whitfield), Sunviridae (Timothy H. Hyndman, Gael Kurath), Tenuivirus (Il-Ryong Choi, Gilda B. Jonson, Takahide Sasaya, Yukio Shirako, Tàiyún Wèi, Xueping Zhou), and Tospoviridae (Scott Adkins, Amy J. Lambert, Rayapati Naidu, Renato O. Resende, Massimo Turina, Anna E. Whitfield), or are ICTV Executive Committee Members: the 2017–2020 ICTV Chair of the Fungal and Protist Viruses Subcommittee (Peter Simmonds), the 2018–2020 ICTV Proposal Secretary (Peter J. Walker), the 2017–2020 ICTV Chair of the Plant Viruses Subcommittee (F. Murilo Zerbini), the 2017–2020 ICTV Chair of the Animal dsRNA and ssRNA- Viruses Subcommittee (Jens H. Kuhn), and 2017–2020 Elected Members (Sead Sabanadzovic, Arvind Varsani). We would like to thank Anya Crane (NIH/NIAID/DCR/IRF-Frederick) for critically editing the manuscript., NIH - National Institute of Allergy and Infectious Diseases (NIAID) (Estados Unidos), NIH - National Cancer Institute (NCI) (Estados Unidos), United State Department of Homeland Security (Estados Unidos), National Biodefense Analysis and Countermeasures Center (NBACC) (Estados Unidos), Battelle National Biodefense Institute, Mississippi Agricultural and Forestry Experiment Station (MAFES) (Estados Unidos), Mississippi State University (Estados Unidos), United States Department of Agriculture. National Institute of Food and Agriculture, Institut Pasteur [Paris] (IP), Virology, H Kuhn, Jen, Adkins, Scott, Alioto, Daniela, V Alkhovsky, Sergey, K Amarasinghe, Gaya, J Anthony, Simon, Avšič-Županc, Tatjana, A Ayllón, María, Bahl, Justin, Balkema-Buschmann, Anne, J Ballinger, Matthew, Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, A Bente, Denni, Bergeron, Éric, H Bird, Brian, Blair, Carol, R Blasdell, Kim, B Bradfute, Steven, Breyta, Rachel, Briese, Thoma, A Brown, Paul, J Buchholz, Ursula, J Buchmeier, Michael, Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, H Calisher, Charle, Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, N Charrel, Rémi, Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, S Clegg, J Christopher, Crozier, Ian, V da Graça, John, Dal Bó, Elena, R Dávila, Alberto M, Carlos de la Torre, Juan, de Lamballerie, Xavier, L de Swart, Rik, L Di Bello, Patrick, Di Paola, Nichola, Di Serio, Francesco, G Dietzgen, Ralf, Digiaro, Michele, V Dolja, Valerian, Dolnik, Olga, A Drebot, Michael, Felix Drexler, Jan, Dürrwald, Ralf, Dufkova, Lucie, G Dundon, William, Paul Duprex, W, M Dye, John, J Easton, Andrew, Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, R Fooks, Anthony, H Formenty, Pierre B, F Forth, Leonie, M Fouchier, Ron A, Freitas-Astúa, Juliana, Gago-Zachert, Selma, Fú Gāo, George, Laura García, María, García-Sastre, Adolfo, R Garrison, Aura, Gbakima, Aiah, Goldstein, Tracey, J Gonzalez, Jean-Paul, Griffiths, Anthony, H Groschup, Martin, Günther, Stephan, Guterres, Alexandro, A Hall, Roy, Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, R Hughes, Holly, H Hyndman, Timothy, Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, B Jonson, Gilda, Junglen, Sandra, Karadağ, Serpil, E Keller, Karen, Klempa, Bori, Klingström, Jona, Kobinger, Gary, Kondō, Hideki, V Koonin, Eugene, Krupovic, Mart, Kurath, Gael, V Kuzmin, Ivan, Laenen, Lie, A Lamb, Robert, J Lambert, Amy, L Langevin, Stanley, Lee, Benhur, S Lemos, Elba R, M Leroy, Eric, Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, S Lukashevich, Igor, Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, H Marshall, Sergio, P Martelli, Giovanni, R Martin, Robert, L Marzano, Shin-Yi, Massart, Sébastien, W McCauley, John, Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, A Navarro, José, V Netesov, Sergey, Neumann, Gabriele, Nowotny, Norbert, T Nunes, Márcio R, Nylund, Are, L Økland, Arnfinn, C Oliveira, Renata, Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, R Parrish, Colin, Pauvolid-Corrêa, Alex, T Pawęska, Janusz, Payne, Susan, R Pérez, Daniel, Pfaff, Florian, R Radoshitzky, Sheli, Rahman, Aziz-Ul, L Ramos-González, Pedro, O Resende, Renato, A Reyes, Carina, K Rima, Bertu, Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Denni, A Runstadler, Jonathan, Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Alpha Sall, Amadou, S Salvato, Maria, Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Z Shabbir, Muhammad, Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin-Won, M Spann, Kirsten, R Spengler, Jessica, D Stenglein, Mark, M Stone, David, Straková, Petra, Takada, Ayato, B Tesh, Robert, J Thornburg, Natalie, Tomonaga, Keizō, Tordo, Noël, S Towner, Jonathan, Turina, Massimo, Tzanetakis, Ioanni, G Ulrich, Rainer, Maria Vaira, Anna, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Niko, Verbeek, Martin, Wahl, Victoria, J Walker, Peter, Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, E Whitfield, Anna, V Williams, John, I Wolf, Yuri, Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Murilo Zerbini, F, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou., Xueping
Subjects: Species complex, MESH: Terminology as Topic, Biología, VÍRUS DE RNA, Biology, Article, 03 medical and health sciences, Biointeractions and Plant Health, V?rus / classifica??o, MESH: Mononegavirales, Genus, Virology, Terminology as Topic, Life Science, Bunyavirales, Ciencias Exactas, Taxonomy, 030304 developmental biology, Order Mononegavirales, 0303 health sciences, 030306 microbiology, Phylum, General Medicine, 15. Life on land, Negarnaviricota, Filogenia, Taxon, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Mononegavirales
Abstract: In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Agrarias y Forestales, Centro de Investigaciones en Fitopatología, Facultad de Ciencias Exactas, Instituto de Biotecnologia y Biologia Molecular
Published: 2020

3. Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes

Author: Edward H. Egelman, Diana P. Baquero, Fengbin Wang, Eugene V. Koonin, Valerian V. Dolja, David Prangishvili, Jens H. Kuhn, Mart Krupovic, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Biochemistry and Molecular Genetics [Charlottesville], University of Virginia, Department of Botany and Plant Pathology, Oregon State University (OSU), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), M.K. was supported by l’Agence Nationale de la Recherche (grant ANR-20-CE20-0009-02) and Emergence(s) project MEMREMA from the Ville de Paris. E.V.K. is supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). E.H.E. was supported by NIH grant R35GM122510. This work was supported in part through a Laulima Government Solutions, LLC, prime contract with the U.S. NIAID under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), Institut Pasteur [Paris], and University of Virginia [Charlottesville]
Subjects: viruses, Immunology, Rudiviridae, virus taxonomy, Microbiology, Genome, Lipothrixviridae, 03 medical and health sciences, Monophyly, chemistry.chemical_compound, Virology, major capsid protein, virus classification, Virus classification, 030304 developmental biology, virus evolution, 0303 health sciences, International Committee on Taxonomy of Viruses (ICTV), Tokiviricetes, biology, 030306 microbiology, virus structure and assembly, Tristromaviridae, biology.organism_classification, Ligamenvirales, hyperthermophilic archaea, chemistry, Evolutionary biology, Insect Science, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Commentary, A-form DNA, DNA
Abstract: International audience; The International Committee on Taxonomy of Viruses (ICTV) has recently adopted a comprehensive, hierarchical system of virus taxa. The highest ranks in this hierarchy are realms, each of which is considered monophyletic but apparently originated independently of other realms. Here, we announce the creation of a new realm, Adnaviria, which unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses.
Published: 2021

4. Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes

Author: Eric Delwart, Mya Breitbart, F. Murilo Zerbini, Karyna Rosario, Yuri I. Wolf, Eugene V. Koonin, Mart Krupovic, Natalya Yutin, Valerian V. Dolja, Darius Kazlauskas, Jens H. Kuhn, Arvind Varsani, Balázs Harrach, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), Department of Integrative Biomedical Sciences [Cape Town], University of Cape Town, Life Science Center [Vilnius], Vilnius University [Vilnius], College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Vitalant Research Institute [San Francisco], Department of Laboratory Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Universidade Federal de Vicosa (UFV), Department of Botany and Plant Pathology, Oregon State University (OSU), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), M.K. was supported by l’Agence Nationale de la Recherche (project ENVIRA, no. ANR-17-CE15-0005-01). E.V.K., Y.I.W., and N.Y. are supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). B.H. was supported by the Hungarian National Research, Development, and Innovation Office (NN128309). This work was supported in part through the Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris] (IP), University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: Immunology, CRESS DNA viruses, Smacoviridae, Microbiology, Genome, Virus, 03 medical and health sciences, Virology, Geminiviridae, virus classification, Letter to the Editor, Virus classification, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, Redondoviridae, Circoviridae, virus evolution, 0303 health sciences, International Committee on Taxonomy of Viruses (ICTV), biology, 030306 microbiology, Phylum, Bacilladnaviridae, Genomoviridae, Nanoviridae, biology.organism_classification, Insect Science, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING
Abstract: International audience; Letter to the Editor
Published: 2020

5. Global Organization and Proposed Megataxonomy of the Virus World

Author: Yuri I. Wolf, Eugene V. Koonin, Mart Krupovic, Valerian V. Dolja, Natalya Yutin, F. Murilo Zerbini, Arvind Varsani, Jens H. Kuhn, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Department of Botany and Plant Pathology, Oregon State University (OSU), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), University of Cape Town, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), E.V.K., Y.I.W., and N.Y. are supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). M.K. was supported by l’Agence Nationale de la Recherche (project ENVIRA, no. ANR-17-CE15-0005-01). J.H.K. is supported through Battelle Memorial Institute’s prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272200700016I., We thank Jiro Wada (Integrated Research Facility at Fort Detrick) for help with figure preparation., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris], and Universidade Federal de Vicosa (UFV)
Subjects: DNA Replication, realm, Genes, Viral, viruses, megataxonomy, virus nomenclature, Genome, Viral, Review, Biology, phylogeny, virus taxonomy, Microbiology, Genome, Virus, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, ICTV, RNA polymerase, evolution, RNA Viruses, virus classification, Molecular Biology, Gene, Virus classification, 030304 developmental biology, virosphere, 0303 health sciences, 030306 microbiology, DNA Viruses, RNA, phylogenomics, Reverse transcriptase, Infectious Diseases, chemistry, Viral replication, Evolutionary biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Virus Physiological Phenomena
Abstract: International audience; SUMMARY : Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
Published: 2020

6. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

Author: Dennis Rubbenstroth, Thomas Briese, Victoria Wahl, Timothy H. Hyndman, Andrew D. Haddow, Sead Sabanadzovic, Arvind Varsani, Rémi N. Charrel, J. Rodney Brister, Mart Krupovic, Scott C. Weaver, Márcio Roberto Teixeira Nunes, Boris Klempa, A. Desiree LaBeaud, Takahide Sasaya, Jonas Klingström, Norbert Nowotny, Sandra Junglen, Sheli R. Radoshitzky, Susan Payne, Martin H. Groschup, Piet Maes, Ralf Dürrwald, Charles F. Fulhorst, Hideki Ebihara, Francisco Murilo Zerbini, Jens H. Kuhn, Mark D. Stenglein, Charles H. Calisher, Nikos Vasilakis, Andrew M. Kropinski, George Fú Gāo, Colorado State University [Fort Collins] (CSU), Columbia University [New York], National Institutes of Health [Bethesda] (NIH), Unité des Virus Emergents (UVE), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Robert Koch Institute [Berlin] (RKI), Mayo Clinic, The University of Texas Medical Branch (UTMB), Chinese Center for Disease Control and Prevention, Friedrich-Loeffler-Institut (FLI), United States Army (U.S. Army), Murdoch University, Humboldt State University (HSU), Slovak Academy of Science [Bratislava] (SAS), Karolinska Institutet [Stockholm], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), University of Veterinary Medicine [Vienna] (Vetmeduni), Ministry of Health [Brasília, Brazil], Texas A&M University [College Station], Mississippi State University [Mississippi], National Agriculture and Food Research Organization (NARO), Arizona State University [Tempe] (ASU), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Universidade Federal de Vicosa (UFV), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), This work was supported by Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.), by US National Institutes of Health (NIH) grant R24 AI120942 (S.C.W and N.V.), and by the Intramural Research Program of the NIH, National Library of Medicine (J.R.B.). S.S. acknowledges support from Mississippi State University (MSU)—Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. This work was also funded in part under ContractNo. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center (V.W.), The authors thank Laura Bollinger, Integrated Research Facility, for critically editing the manuscript. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Defense or the US Army, of the US Department of Health and Human Services, the Department of Homeland Security (DHS) Science and Technology Directorate (S&T), of the International Committee on Taxonomy of Viruses, or of the institutions and companies affiliated with the authors. In no event shall any of these entities have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The US departments do not endorse any products or commercial services mentioned in this publication, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, Classifica??o / m?todos, International Cooperation, viruses, [SDV]Life Sciences [q-bio], 030106 microbiology, species, virus, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, International Committee on Taxonomy of Viruses, Virus, Points of View, 03 medical and health sciences, taxonomy, Unclassified Viruses, (ICTV), Virology, Genetics, Nomenclature, Ecology, Evolution, Behavior and Systematics, Virus classification, Taxonomy, 2. Zero hunger, Species, Arbovirus, Phylum, Arbovirus / classifica??o, Classification, humanities, 3. Good health, 030104 developmental biology, Taxon, classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mandate, Taxonomy (biology), nomenclature, Terminologia como Assunto
Abstract: This work was supported by Battelle Memorial Institute?s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.), by US National Institutes of Health (NIH) grant R24 AI120942 (S.C.W and N.V.), and by the Intramural Research Program of the NIH, National Library of Medicine (J.R.B.). S.S. acknowledges support from Mississippi State University (MSU)?Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants. This work was also funded in part under ContractNo. HSHQDC-15-C-00064 awarded by DHS S&T for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a federally funded research and development center (V.W.) Colorado State University. College of Veterinary Medicine and Biomedical Sciences. Department of Microbiology, Immunology and Pathology. Arthropod-borne and Infectious Diseases Laboratory. Fort Collins, CO, USA. Columbia University. Mailman School of Public Health. Center for Infection and Immunity. Department of Epidemiology. New York, NY, USA. National Institutes of Health. National Library of Medicine. National Center for Biotechnology. Bethesda, MD, USA. Universit? Aix-Marseille. Facult? de M?decine. HU M?diterran?e Infection. Unit? des Virus Emergents. Marseille, France. Robert Koch-Institut. Department of Infectious Diseases. Berlin, Germany. Guggenheim Building. Mayo Clinic. Department of Molecular Medicine. Rochester, MN USA. University of Texas Medical Branch. Department of Pathology. Galveston, TX, USA. Chinese Center for Disease Control and Prevention. National Institute for Viral Disease Control and Prevention. Beijing, China. Friedrich-Loeffler-Institut, S?dufer. Institut f?r Virusdiagnostik. Greifswald-Insel Riems, Germany. United States Army Medical Research Institute of Infectious Diseases. Department of Virology. Frederick, MD, USA. Murdoch University. School of Veterinary and Life Sciences. College of Veterinary Medicine. Australia Australia. Humboldt-University Berlin. Berlin Institute of Health. Charit? Universit?tsmedizin Berlin. Institute of Virology. Berlin, Germany / Inhoffenstra?e 7. Deutsches Zentrum f?r Infektionsforschung. Braunschweig, Germany. Slovensk? Akad?mia Vied. Biomedic?nske centrum. Virologick? ?stav. D?bravsk?, Bratislava, Slovakia. Robert Koch-Institut. Department of Infectious Diseases. Berlin, Germany. University of Guelph. Department of Food Sciencen. Guelph, Ontario, Canada / University of Guelph. Department of Pathobiology. Guelph, Ontario, Canada. Institut Pasteur. Departement of Microbiology. Paris, France. Stanford University School of Medicine. Department of Pediatrics. Division of Infectious Diseases. Stanford, CA, USA. KU Leuven. Department of Microbiology, Immunology and Transplantation. Rega Institute. Zoonotic Infectious Diseases unit. Leuven, Belgium. University of Veterinary Medicine Vienna. Department of Pathobiology. Institute of Virology. Veterin?rplatz, Vienna, Austria / Mohammed Bin Rashid University of Medicine and Health Sciences. Department of Basic Medical Sciences. College of Medicine. Dubai, United Arab Emirates. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Texas A&M University. Veterinary Medical Sciences Building. College of Veterinary Medicine and Biomedical Sciences. Department of Veterinary Pathobiology. TX, USA. United States Army Medical Research Institute of Infectious Diseases. Molecular and Translational Sciences. Frederick, MD, USA. Friedrich-Loeffler-Institut, S?dufer. Institut f?r Virusdiagnostik. Greifswald-Insel Riems, Germany / Universit?tsklinikum Freiburg. Institut f?r Virologie. Freiburg, Germany. Mississippi State University. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology. Mississippi State, MS, USA. National Agriculture and Food Research Organization. Department of Planning and Coordination. Ibaraki, Japan. Colorado State University. Department of Microbiology, Immunology and Pathology. Fort Collins, CO, USA. Arizona State University. School of Life Sciences, Center for Evolution and Medicine. The Biodesign Center for Fundamental and Applied Microbiomics. Tempe, AZ, USA. National Biodefense Analysis and Countermeasures Center. Frederick, MD, USA. University of Texas Medical Branch. Institute for Human Infections and Immunity. Department of Microbiology and Immunology. Galveston, TX, USA. Universidade Federal de Vi?osa. Departamento de Fitopatologia/BIOAGRO and National Institute of Science and Technology for Plant-Pest Interactions. Vi?osa, MG, Brazil. University of Texas Medical Branch. Institute for Human Infection and Immunity. Center for Tropical Diseases. Department of Pathology, Center for Biodefense and Emerging Infectious Diseases. Galveston, TX, USA. Integrated Research Facility at Fort Detrick. Frederick, MD, USA. The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.
Published: 2019

7. ICTV Virus Taxonomy Profile: Arenaviridae

Author: Stephan Günther, Michael J. Buchmeier, Jean-Paul Gonzalez, J. Christopher S. Clegg, Sheli R. Radoshitzky, Jens H. Kuhn, Juan Carlos de la Torre, Víctor Romanowski, Rémi N. Charrel, Mark D. Stenglein, Manuela Sironi, Igor S. Lukashevich, Jussi Hepojoki, Maria S. Salvato, U.S. Army Medical Research Institute of Infectious Diseases, University of California, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Les Mandinaux, 16450 Le Grand Madieu, Conditions et territoires d'émergence des maladies : dynamiques spatio-temporelles de l'émergence, évolution, diffusion/réduction des maladies, résistance et prémunition des hôtes (CTEM), Department of Virology, Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), University of Helsinki, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland, Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), University of Louisville, Departamento de Ciencia y Tecnología [Buenos Aires], Universidad Nacional de Quilmes (UNQ), University of Maryland School of Medicine, University of Maryland System, Centro San Giovanni di Dio, Fatebenefratelli, Brescia (IRCCS), Università degli Studi di Brescia [Brescia], Colorado State University [Fort Collins] (CSU), The Scripps Research Institute [La Jolla], University of California [San Diego] (UC San Diego), University of California-University of California, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), University of California (UC), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Università degli Studi di Brescia = University of Brescia (UniBs), The Scripps Research Institute [La Jolla, San Diego], and HAL AMU, Administrateur
Subjects: 0301 basic medicine, viruses, Arenaviridae, [SDV]Life Sciences [q-bio], 030106 microbiology, Family Arenaviridae, Genome, Viral, Genome, 03 medical and health sciences, Viral Proteins, Viral genetics, Phylogenetics, Virology, Animals, Arenaviridae Infections, Humans, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Virus classification, Phylogeny, ComputingMilieux_MISCELLANEOUS, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Arenavirus, biology, Fishes, Reptiles, biology.organism_classification, [SDV] Life Sciences [q-bio], 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, Mammarenavirus
Abstract: Members of the family Arenaviridae produce enveloped virions containing genomes consisting of two or three single-stranded RNA segments totalling about 10.5 kb. Arenaviruses can infect mammals, including humans and other primates, snakes, and fish. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Arenaviridae, which is available at www.ictv.global/report/arenaviridae.
Published: 2019

8. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment

Author: Aaron Aruna, Ousmane Faye, Martine Peeters, Stomy Karhemere, Jean Jacques Muyembe-Tamfum, Amadou A. Sall, Ibrahima Socé Fall, Audrey Lacroix, Katie Caviness, Daniel Mukadi, Mariano Sanchez-Lockhart, Moussa Moïse Diagne, Bathe Ndjoloko, Christian Julian Villabona-Arenas, Elisabeth Pukuta, Jeffrey R. Kugelman, Felix Mulangu, Karla Prieto, Nicholas Di Paola, Joseph A. Chitty, Sheila Makiala-Mandanda, Anastasie Mulumba, Nicole Vidal, Steve Ahuka-Mundeke, Brett Beitzel, Gary P. Schroth, Patrick Mukadi, Eric Delaporte, Maggie L. Bartlett, Jason T. Ladner, Junhua J. Zhao, Boubacar Diallo, Mathias Mossoko, Catherine B. Pratt, Jens H. Kuhn, Amuri Aziza, Michael R. Wiley, Peter A. Larson, John Kombe, Martin Faye, Michel Yao, Jeanette Gonzalez, Roger Tim, Placide Mbala-Kingebeni, Ahidjo Ayouba, Gustavo Palacios, Shanmuga Sozhamannan, Justus Nsio, Mamadou Diop, Stephen M. Gross, Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM), Institut National de Recherche Biomédicale [Kinshasa] (INRB), Institut National de la Santé et de la Recherche Médicale (INSERM), University of Nebraska Medical Center, University of Nebraska System, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), This work was supported by the Defense Biological Product Assurance Office through a task order award to the National Strategic Research Institute (FA4600-12-D-9000). We thank Laura Bollinger (National Institute of Allergy and Infectious Diseases, Frederick, MD, USA) for critically editing this manuscript. This work was funded in part through Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases under contract number HHSN272200700016I., Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), and Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)
Subjects: 0301 basic medicine, viruses, [SDV]Life Sciences [q-bio], Genomics, Biology, ZMapp, medicine.disease_cause, Antiviral Agents, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Humans, 030212 general & internal medicine, Ebola Vaccines, Pathogen, Retrospective Studies, Ebola virus, GeneXpert MTB/RIF, Transmission (medicine), Antibodies, Monoclonal, Outbreak, Hemorrhagic Fever, Ebola, Biological product, Ebolavirus, Virology, 3. Good health, 030104 developmental biology, Infectious Diseases, Medical Countermeasures, Democratic Republic of the Congo, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, medicine.drug
Abstract: Summary Background The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of genomic information at the start of the 2018 Ebola virus disease (EVD) outbreak in North Kivu Province. Methods We used targeted-enrichment sequencing to produce two coding-complete Ebola virus genomes 5 days after declaration of the EVD outbreak in North Kivu. Subsequent sequencing efforts yielded an additional 46 genomes. Genomic information was used to assess early transmission, medical countermeasures, and evolution of Ebola virus. Findings The genomic information demonstrated that the EVD outbreak in the North Kivu and Ituri Provinces was distinct from the 2018 EVD outbreak in Equateur Province of the Democratic Republic of the Congo. Primer and probe mismatches to Ebola virus were identified in silico for all deployed diagnostic PCR assays, with the exception of the Cepheid GeneXpert GP assay. Interpretation The first two coding-complete genomes provided actionable information in real-time for the deployment of the rVSVΔG-ZEBOV-GP Ebola virus envelope glycoprotein vaccine, available therapeutics, and sequence-based diagnostic assays. Based on the mutations identified in the Ebola virus surface glycoprotein (GP12) observed in all 48 genomes, deployed monoclonal antibody therapeutics (mAb114 and ZMapp) should be efficacious against the circulating Ebola virus variant. Rapid Ebola virus genomic characterisation should be included in routine EVD outbreak response procedures to ascertain efficacy of medical countermeasures. Funding Defense Biological Product Assurance Office.
Published: 2019

9. Reply to Holmes and Duchêne, 'Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?': Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless

Author: Yuri I. Wolf, Valerian V. Dolja, Darius Kazlauskas, Adriana Lucía-Sanz, Jens H. Kuhn, Eugene V. Koonin, Mart Krupovic, Jaime Iranzo, National Center for Biotechnology Information (NCBI), Vilnius University [Vilnius], Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Centro de Astrobiologia [Madrid] (CAB), Instituto Nacional de Técnica Aeroespacial (INTA)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Oregon State University (OSU), and Institut Pasteur [Paris]
Subjects: Computer science, Sequence analysis, [SDV]Life Sciences [q-bio], Ecological and Evolutionary Science, RNA-dependent RNA polymerase, Microbiology, Evolution, Molecular, Viral Proteins, 03 medical and health sciences, Phylogenetics, Virology, Phylogenomics, Animals, Cluster Analysis, RNA Viruses, Human virome, virus classification, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Sequence (medicine), Author Reply, virus evolution, Virus classification, 0303 health sciences, Biological data, Sequence Homology, Amino Acid, Phylogenetic tree, 030306 microbiology, RNA virome, Computational Biology, phylogenomics, Plants, Virus evolution, QR1-502, Evolutionary biology, Viral evolution, RNA-dependent rna polymerase, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (-) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas -RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.
Published: 2019

10. Classify viruses — the gain is worth the pain

Author: Yong-Zhen Zhang, Valerian V. Dolja, Eugene V. Koonin, Yuri I. Wolf, Piet Maes, Jens H. Kuhn, Mart Krupovic, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Département de Microbiologie - Department of Microbiology, Fudan University [Shanghai], Chinese Center for Disease Control and Prevention, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Oregon State University (OSU), and Institut Pasteur [Paris] (IP)
Subjects: 0303 health sciences, Multidisciplinary, 030306 microbiology, viruses, [SDV]Life Sciences [q-bio], MEDLINE, Biodiversity, Classification, 3. Good health, Epistemology, ComputingMilieux_MANAGEMENTOFCOMPUTINGANDINFORMATIONSYSTEMS, 03 medical and health sciences, Virology, ComputerApplications_GENERAL, Viruses, Animals, Humans, Phage Therapy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Psychology, ComputingMilieux_MISCELLANEOUS, Phylogeny, 030304 developmental biology
Abstract: International audience; Earth probably harbours a million times more virus particles than there are stars in the observable Universe. These viruses could hold solutions to many of humanity’s current problems.Phage therapy could someday be used to treat diseases caused by multidrug-resistant bacteria, for instance. Enzymes encoded by new viruses could help researchers to develop pharmaceuticals. Or viruses that kill algal cells could be used to control harmful blooms.Tapping into the benefits — and threats — requires describing and cataloguing viruses and mapping their evolutionary relationships.But, so far, just 4,958 virus species have been formally described.
Published: 2019

11. Origins and Evolution of the Global RNA Virome

Author: Adriana Lucía-Sanz, Eugene V. Koonin, Jens H. Kuhn, Yuri I. Wolf, Valerian V. Dolja, Darius Kazlauskas, Mart Krupovic, Jaime Iranzo, National Center for Biotechnology Information (NCBI), Vilnius University [Vilnius], Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris], Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Biocomputing Unit [Madrid], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Oregon State University (OSU), Y.I.W. and E.V.K. are supported through the intramural program of the U.S. National Institutes of Health. D.K. was partly supported by a Short Term Fellowship from the Federation of European Biochemical Societies (FEBS). M.K. was supported by l’Agence Nationale de la Recherche (ANR) (France) project ENVIRA. This work was funded in part through Battelle Memorial Institute’s prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272200700016I (J.H.K.)., V.V.D. is grateful to Barbara and Simon Gvakharia for their support and inspiration. We thank Jiro Wada (Integrated Research Facility [IRF]—Frederick) for help with figure creation., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris] (IP), and Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)
Subjects: 0301 basic medicine, RNA virus, viruses, [SDV]Life Sciences [q-bio], RNA-dependent RNA polymerase, Computational biology, Ecological and Evolutionary Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Virus, 03 medical and health sciences, chemistry.chemical_compound, Virology, RNA polymerase, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], evolution, Human virome, Gene, Capsid protein, Evolution, Virome, 030304 developmental biology, 0303 health sciences, virome, Phylogenetic tree, biology, 030306 microbiology, RNA, biology.organism_classification, QR1-502, capsid protein, RNA silencing, 030104 developmental biology, chemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Research Article
Abstract: The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses., Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.
Published: 2018

12. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

Author: Peter Simmonds, Arcady Mushegian, Jens H. Kuhn, Luisa Rubino, Francisco Murilo Zerbini, Hélène Sanfaçon, Stuart G. Siddell, Michael J. Adams, Sead Sabanadzovic, Alexander E. Gorbalenya, Max L. Nibert, Andrew M. Q. King, Balázs Harrach, Nick J. Knowles, Mart Krupovic, Robert L. Harrison, Arvind Varsani, Bas E. Dutilh, Andrew J. Davison, Andrew M. Kropinski, Elliot J. Lefkowitz, Sandra Junglen, Institute for Animal Health, the Pirbright Institute, University of Alabama at Birmingham [ Birmingham] (UAB), National Science Foundation [Arlington] (NSF), Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], Leiden University Medical Center (LUMC), Lomonosov Moscow State University (MSU), Hungarian Academy of Sciences (MTA), USDA Agricultural Research Service [Maricopa, AZ] (USDA), United States Department of Agriculture (USDA), Humboldt State University (HSU), German Centre for Infection Research (DZIF), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Mississippi State University [Mississippi], Agriculture and Agri-Food [Ottawa] (AAFC), University of Bristol [Bristol], University of Oxford [Oxford], Arizona State University [Tempe] (ASU), Universidade Federal de Vicosa (UFV), University of Glasgow, A.J.D. is supported by the Medical Research Council (MC_UU_12014/3). B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi Grant 864.14.004. A.E.G. is partially supported by EU project EVAg 653316 and the Leids Universiteits Fonds. N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. 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 (J.H.K). A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), his work on this project was supported in part by the NSF Independent Research and Development program, but the statements and opinions expressed herein are made in a personal capacity and do not imply endorsement by NSF or the government of the United States. S.S. acknowledges financial support from Mississippi State University (MSU)—Mississippi Agricultural and Forestry Experiment Station (MAFES) Strategic Research Initiative grants., The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Universiteit Leiden, Institut Pasteur [Paris] (IP), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Agriculture and Agri-Food (AAFC), University of Oxford, Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
Subjects: 0301 basic medicine, International Code of Virus Classification, viruses, [SDV]Life Sciences [q-bio], education, 030106 microbiology, Coronacrisis-Taverne, Library science, Committee Membership, virus, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, International Committee on Taxonomy of Viruses, Executive committee, taxonomy, ICTV, 03 medical and health sciences, Viral genetics, Terminology as Topic, Virology, skin and connective tissue diseases, Nomenclature, health care economics and organizations, Virus classification, Taxonomy, General Medicine, 3. Good health, International code, 030104 developmental biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Classification methods, Taxonomy (biology), sense organs
Abstract: International audience; This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).
Published: 2018

13. Taxonomy of the order Mononegavirales: update 2018

Author: Kang Seuk Choi, Nikos Vasilakis, Claudio Verdugo, Janusz T. Paweska, Thomas Briese, Víctor Manuel Neira Ramírez, Andrew J. Bennett, Masayuki Horie, Charles H. Calisher, Robert Kityo, Anthony R. Fooks, Martin Schwemmle, Sunil K. Mor, Nidia G. Aréchiga Ceballos, Timothy H. Hyndman, Ayato Takada, Yíngyún Caì, Robert A. Lamb, Alexander Bukreyev, Paul A. Rota, Tony L. Goldberg, Lin-Fa Wang, Benhur Lee, Kartik Chandran, Hideki Ebihara, Michael R. Wiley, Ralf G. Dietzgen, Anna E. Whitfield, Mark D. Stenglein, Piet Maes, Andrew J. Easton, Jean L. Patterson, Valerian V. Dolja, Olga Dolnik, Eugene V. Koonin, James F. X. Wellehan, Ralf Dürrwald, Peter L. Collins, Qisheng Song, Susan Payne, Jonathan S. Towner, Sina Bavari, Sonia Vázquez-Morón, Pierre Formenty, Sophie J. Smither, Keizō Tomonaga, Leslie L. Domier, Dàohóng Jiāng, Gael Kurath, Robert B. Tesh, Sergey V. Netesov, Elodie Ghedin, Andrea Maisner, Denise A. Marston, Cristine Campos Lawson, Elke Mühlberger, Christopher F. Basler, Conrad M. Freuling, Yǒng Zhèn Zhāng, Dennis Rubbenstroth, Peter J. Walker, Gōngyín Yè, David Wang, Ron A. M. Fouchier, Gustavo Palacios, Gary P. Kobinger, Yuri I. Wolf, Timothy Song, Hideki Kondō, Mart Krupovic, Karla Prieto, David M. Stone, Luciano M. Thomazelli, Colin A. Chapman, Ashley C. Banyard, Jens H. Kuhn, Stuart G. Siddell, Noël Tordo, John M. Dye, Terry Fei Fan Ng, Charles Y. Chiu, Kim R. Blasdell, Bertus K. Rima, Victoria Wahl, Eric M. Leroy, Gaya K. Amarasinghe, Juan Emilio Echevarría, Norbert Nowotny, Roger Hewson, Thomas Müller, Viktor E. Volchkov, Washington University School of Medicine (WUSM), University of Washington [Seattle], Laboratorio de Rabia, Instituto de Diagnóstico y Referencias Epidemiológicos, Animal and Plant Health Agency [Weybridge] (APHA), Georgia State University, University System of Georgia (USG), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison-Influenza Research Institute, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, Columbia University [New York], The University of Texas Medical Branch (UTMB), Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Department of Anthropology [Montréal], McGill University = Université McGill [Montréal, Canada], Wildlife Conservation Society (WCS), Primate Research Institute, Kyoto University, University of California [San Francisco] (UC San Francisco), University of California (UC), Avian Disease Research Division, Animal and Plant Quarantine Agency, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Department of Botany and Plant Pathology, Oregon State University (OSU), Center for Genome Research and Biocomputing, Philipps Universität Marburg = Philipps University of Marburg, University of Chicago, IDT Biologika, School of Life Sciences, University of Warwick [Coventry], Department of Biochemistry and Molecular Biology, University of Rochester [USA], Institute of Health Carlos III, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, 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), Public Health England [Salisbury] (PHE), Kagoshima University, Murdoch University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University [Wuhan] (HZAU), Makerere University [Kampala, Ouganda] (MAK), 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, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Centre International de Recherches Médicales de Franceville (CIRMF), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Neuromuscular Diagnostic Laboratory, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Universidad de Chile = University of Chile [Santiago] (UCHILE), Novosibirsk State University (NSU), Department of Medicine [San Francisco], University of California (UC)-University of California (UC), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], University of Bristol [Bristol], Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), University of Missouri [Columbia] (Mizzou), University of Missouri System, Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Universidade de São Paulo - USP (BRAZIL), Institute for Virus Research, 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, Facultad de Ciencias Veterinarias [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), 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), 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], University of Florida [Gainesville] (UF), University of Nebraska Medical Center, University of Nebraska System, Kansas State University, State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Albert Einstein College of Medicine, McGill University, Kyoto University [Kyoto], University of California [San Francisco] (UCSF), University of California, Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Philipps University of Marburg, Warwick University, Public Health England [Porton Down, Salisbury], Huazhong Agricultural University, Makerere University (MAK), Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Institut Pasteur [Paris], Centre International de Recherches Médicales de Franceville, University of Minnesota [Twin Cities], Universidad de Chile, University of California-University of California, Texas Biomedical Research Institute [San Antonio, Texas], National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], University of Bristol (School of Cellular and Molecular Medicine), University of Missouri [Columbia], Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, 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), Duke NUS Medical School, University of Florida [Gainesville], and Virology
Subjects: 0301 basic medicine, Order Mononegavirales, 040301 veterinary sciences, Mononegavirales Infections, 04 agricultural and veterinary sciences, General Medicine, Biology, Data science, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Article, 0403 veterinary science, 03 medical and health sciences, 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Animals, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), Mononegavirales, Phylogeny
Abstract: International audience; In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
Published: 2018

14. Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

Author: Katja R. Richert-Pöggeler, Emmanuelle Muller, Neil E. Olszewski, Michael Tristem, Pierre-Yves Teycheney, Benham E Lockhart, Balázs Harrach, Hanu R. Pappu, Jens Mayer, Andrew D. W. Geering, Jan Kreuze, John M. Coffin, Robert J. Gifford, Jonathan P. Stoye, James E. Schoelz, Hung Fan, Mikhail M. Pooggin, Livia Stavolone, Susan Seal, Hélène Sanfaçon, Sead Sabanadzovic, Jens H. Kuhn, Carlos Llorens, Welkin E. Johnson, Eugene V. Koonin, Dirk Lindemann, Indranil Dasgupta, Mart Krupovic, Jonas Blomberg, Roger Hull, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Uppsala University, Tufts University School of Medicine [Boston], University of Delhi, University of California [Irvine] (UCI), University of California, University of Queensland [Brisbane], University of Glasgow, Hungarian Academy of Sciences (MTA), John Innes Centre [Norwich], Boston College (BC), International Potato Center [Lima] (CIP), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institute of Virology [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Universitat de València (UV), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Saarland University [Saarbrücken], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Washington State University (WSU), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Mississippi State University [Mississippi], Agriculture and Agri-Food [Ottawa] (AAFC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of Greenwich, International Institute of Tropical Agriculture, Imperial College London, National Institutes of Health [Bethesda] (NIH), This work was supported in part through Battelle Memorial Institute's prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID, contract no. HHSN272200700016I, J.H.K.). E.V.K. is supported by intramural funds from the U.S. Department of Health and Human Services (to the National Library of Medicine). S.S. acknowledges support from SRI Funds from Mississippi Agriculture and the Forestry Experiment Station of Mississippi State University. J.F.K. is supported by the CGIAR Research Program on Roots, Tubers and Bananas (RTB) and supported by CGIAR Fund Donors (http://www.cgiar.org/aboutus/our-funders/). M.K. is supported by l’Agence Nationale de la Recherche (France) project ENVIRA., M. Krupovic, B. Harrach, S. Sabanadzovic, H. Sanfaçon, and J. H. Kuhn were members of the 2014–2017 International Committee on Taxonomy of Viruses (ICTV) Executive Committee. J. Blomberg, J. M. Coffin, H. Fan, R. Gifford, W. Johnson, D. Lindemann, J. Mayer, J. P. Stoye, and M. Tristem were members of the 2014–2017 ICTV Retroviridae Study Group. I. Dasgupta, A. D. Geering, R. Hull, J. F. Kreuze, B. Lockhart, E. Muller, N. Olszewski, H. R. Pappu, M. Pooggin, K. R. Richert-Pöggeler, J. E. Schoelz, S. Seal, L. Stavolone, and P.-Y. Teycheney were members of the 2014–2017 ICTV Caulimoviridae Study Group. R. Hull is retired from the John Innes Centre, Norwich, Norfolk, United Kingdom, ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), International Potato Center, Technische Universität Dresden (TUD), University of Minnesota [Twin Cities], Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Julius Kühn Institute (JKI), University of Missouri [Columbia], Institut Pasteur [Paris] (IP), University of California [Irvine] (UC Irvine), University of California (UC), Biotechnology and Biological Sciences Research Council (BBSRC), Agriculture and Agri-Food (AAFC), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: 0301 basic medicine, S1, retroviruses, viruses, [SDV]Life Sciences [q-bio], Immunology, retroviridae, MESH: Reverse Transcription, L73 - Maladies des animaux, Virus Replication, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Virus, belpaoviridae, MESH: Viruses, 03 medical and health sciences, Virology, international committee on taxonomy of viruses (ICTV), Metaviridae, virus classification, Letter to the Editor, Virus classification, Genetics, Ty3/Gypsy and Ty1/Copia LTR retrotransposons, caulimoviridae, virus evolution, biology, fungi, MESH: Virus Replication, RNA, Pseudoviridae, Reverse Transcription, biology.organism_classification, MESH: Caulimoviridae, genomic DNA, 030104 developmental biology, MESH: Retroviridae, MESH: Hepadnaviridae, Insect Science, Viral evolution, hepadnaviridae, Belpaoviridae, Caulimoviridae, Hepadnaviridae, International Committee on Taxonomy of Viruses (ICTV), Retroviridae, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, metaviridae, pseudoviridae
Abstract: International audience; Reverse-transcribing viruses, which synthesize a copy of genomic DNA from an RNA template, are widespread in animals, plants, algae, and fungi (1, 2). This broad distribution suggests the ancient origin(s) of these viruses, possibly [...]
Published: 2018

15. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

Author: Janusz T. Paweska, Elke Mühlberger, Jonathan S. Towner, Sina Bavari, Kartik Chandran, Eric M. Leroy, Gary P. Kobinger, Ayato Takada, Olga Dolnik, Gaya K. Amarasinghe, Roger Hewson, Victoria Wahl-Jensen, Sophie J. Smither, Christopher F. Basler, Jean L. Patterson, Viktor E. Volchkov, Jens H. Kuhn, Pierre Formenty, Hideki Ebihara, Sergey V. Netesov, John M. Dye, Alexander Bukreyev, Yīmíng Bào, Beijing Institute of Genomics, Chinese Academy of Sciences [Beijing] (CAS)-China Graduate University of the Chinese Academy of Sciences, Department of Pathology and Immunology, Washington University School of Medicine, Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), The University of Texas Medical Branch (UTMB), Albert Einstein College of Medicine, Philipps University of Marburg, Department of Biochemistry and Molecular Biology, University of Rochester [USA], Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Public Health England [Porton Down, Salisbury], Département de Biochimie et Microbiologie, Université Laval, Centre International de Recherches Médicales de Franceville (CIRMF), Centre International de Recherches Médicales de Franceville, National Emerging Infectious Diseases Laboratories (NEIDL), Boston University [Boston] (BU), Novosibirsk State University (NSU), Texas Biomedical Research Institute [San Antonio, Texas], National Institute for Communicable Diseases (NICD), Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Hokkaido University, 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, 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, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Beijing Genomics Institute [Shenzhen] (BGI), Albert Einstein College of Medicine [New York], Public Health England [Salisbury] (PHE), Université Laval [Québec] (ULaval), Texas Biomedical Research Institute [San Antonio, TX], National Institute for Communicable Diseases [Johannesburg] (NICD), Hokkaido University [Sapporo, Japan], Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), 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), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Philipps Universität Marburg = Philipps University of Marburg, 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), and 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)
Subjects: 0301 basic medicine, Letter, marburgvirus, lcsh:QR1-502, lcsh:Microbiology, ICTV, Genus, Software Design, RefSeq, Viral, virus classification, Phylogeny, Genome, Ebolavirus, Cuevavirus, Infectious Diseases, GenBank, Ebola, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Databases, Nucleic Acid, cuevavirus, Sequence Analysis, Algorithms, filovirus, 030106 microbiology, Genome, Viral, Biology, virus taxonomy, 03 medical and health sciences, Databases, Type (biology), Species Specificity, Virology, ebolavirus, Virus classification, Whole genome sequencing, Base Sequence, Nucleic Acid, Whole Genome Sequencing, Genetic Variation, Sequence Analysis, DNA, DNA, biology.organism_classification, Filoviridae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Taxon, Marburgvirus, Evolutionary biology, Mononegavirales
Abstract: The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (approximate to 50% for genera, approximate to 30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel "filovirus." Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.
Published: 2017

16. Phylogenetic analysis of avian infectious bronchitis virus isolates from Morocco: a retrospective study (1983 to 2014)

Author: My Mustapha Ennaji, Jens H. Kuhn, Slimane Khayi, Jean-Luc Guérin, Mohammed El Houadfi, Mariette F. Ducatez, Siham Fellahi, Mehdi El Harrak, Unité de Pathologie Aviaire, Département de Pathologie et Santé Publique Vétérinaire, Institut Agronomique et Vétérinaire Hassan II - IAV (MOROCCO) (IAV), Société de Produits Biologiques et Pharmaceutiques Vétérinaires, Biotechnology Research Unit, Institut National de la Recherche Agronomique du Maroc (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Laboratoire de Virologie Microbiologie & Qualité/ Eco-toxicologie & Biodiversité [Casablanca], Faculte des sciences et Techniques Mohammedia [Casablanca] (FSTM), and Université Hassan II [Casablanca] (UH2MC)-Université Hassan II [Casablanca] (UH2MC)
Subjects: 0301 basic medicine, medicine.medical_specialty, Letter, animal structures, Genotype, 040301 veterinary sciences, Infectious bronchitis virus, Immunology, Sequence Homology, Biology, Poultry, 0403 veterinary science, 03 medical and health sciences, Medical microbiology, Phylogenetics, Virology, Epidemiology, Genetic variation, medicine, Animals, Cluster Analysis, Phylogeny, Poultry Diseases, Retrospective Studies, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Phylogenetic tree, Reverse Transcriptase Polymerase Chain Reaction, [SDV.BA]Life Sciences [q-bio]/Animal biology, Genetic Variation, Sequence Analysis, DNA, 04 agricultural and veterinary sciences, biology.organism_classification, humanities, 3. Good health, body regions, Morocco, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Spike Glycoprotein, Coronavirus, embryonic structures, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, Molecular Medicine, Flock, Avian infectious bronchitis virus, Coronavirus Infections
Abstract: In Morocco, molecular and genetic characterization of IBV strain diversity have been very limited. A long-term retrospective study on Moroccan isolates is required to improve understanding of IBV evolution and IB epidemiology. The objective of this report is to perform a retrospective analysis of the origin and evolution of 62 Moroccan IBV isolates obtained from unvaccinated (21%) and vaccinated (70%) poultry flocks showing clinical signs of IB between 1983 and 2014.
Published: 2017

17. 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

18. A classification system for virophages and satellite viruses

Author: Jens H. Kuhn, Matthias G. Fischer, Mart Krupovic, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Institutes of Health [Bethesda] (NIH), Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Virophages, viruses, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Genome, Viral, Biology, MESH: Base Sequence, Genome, Virus, Animal Diseases, 03 medical and health sciences, MESH: Plant Diseases, Virology, Hepatitis Delta, Virus Giant, Animals, MESH: Animals, MESH: Phylogeny, Gene, Necrosis Virus, Phylogeny, Plant Diseases, Genetics, MESH: Molecular Sequence Data, Base Sequence, Virophage, RNA, General Medicine, Classification, Virus Helper, Capsid Protein, MESH: Satellite Viruses, MESH: Animal Diseases, Satellite virus, MESH: Classification, 030104 developmental biology, Satellite Viruses, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Satellite, Virus Tobacco, MESH: Genome, Viral, MESH: RNA, Satellite
Abstract: International audience; Satellite viruses encode structural proteins required for the formation of infectious particles but depend on helper viruses for completing their replication cycles. Because of this unique property, satellite viruses that infect plants, arthropods, or mammals, as well as the more recently discovered satellite-like viruses that infect protists (virophages), have been grouped with other, so-called "sub-viral agents." For the most part, satellite viruses are therefore not classified. We argue that possession of a coat-protein-encoding gene and the ability to form virions are the defining features of a bona fide virus. Accordingly, all satellite viruses and virophages should be consistently classified within appropriate taxa. We propose to create four new genera - Albetovirus, Aumaivirus, Papanivirus, and Virtovirus - for positive-sense single-stranded (+) RNA satellite viruses that infect plants and the family Sarthroviridae, including the genus Macronovirus, for (+)RNA satellite viruses that infect arthopods. For double-stranded DNA virophages, we propose to establish the family Lavidaviridae, including two genera, Sputnikvirus and Mavirus.
Published: 2016

19. 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

20. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Author: John M. Dye, Sergey V. Netesov, Janusz T. Paweska, Mark S. Lever, Travis K. Warren, Peter B. Jahrling, Jean L. Patterson, Stephan Becker, Alexander Bukreyev, Jens H. Kuhn, Lisa E. Hensley, Kartik Chandran, Eric M. Leroy, Sophie J. Smither, J. Rodney Brister, Erica Ollmann Saphire, Victoria Wahl-Jensen, Yiming Bao, Steven B. Bradfute, Manfred Weidmann, Robert Swanepoel, Karl M. Johnson, Jonathan S. Towner, Gene G. Olinger, Viktor E. Volchkov, Olga Dolnik, Anna N. Honko, Louise Pitt, Sina Bavari, Gary P. Kobinger, Guido van der Groen, Sheli R. Radoshitzky, Gustavo Palacios, Robert A. Davey, Sven Enterlein, Elke Mühlberger, Stuart T. Nichol, Institut für Virologie, Philipps University, Centre International de Recherches Médicales de Franceville (CIRMF), National Institute for Communicable Diseases [Johannesburg] (NICD), University of Göttingen - Georg-August-Universität Göttingen, Centers for Disease Control and Prevention [Atlanta] (CDC), and Centers for Disease Control and Prevention
Subjects: MESH: Terminology as Topic, [SDV]Life Sciences [q-bio], Filoviridae, Computational biology, medicine.disease_cause, Article, 03 medical and health sciences, Virology, MESH: Filoviridae Infections, medicine, MESH: Animals, Nomenclature, Virus classification, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Ebola virus, MESH: Humans, biology, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, 3. Good health, Gene nomenclature, MESH: Classification, MESH: Filoviridae, Homo sapiens, Taxonomy (biology)
Abstract: The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Published: 2013

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20 results on '"Jens H. Kuhn"'

1. Four principles to establish a universal virus taxonomy

2. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

3. Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes

4. Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes

5. Global Organization and Proposed Megataxonomy of the Virus World

6. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species

7. ICTV Virus Taxonomy Profile: Arenaviridae

8. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment

9. Reply to Holmes and Duchêne, 'Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?': Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless

10. Classify viruses — the gain is worth the pain

11. Origins and Evolution of the Global RNA Virome

12. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

13. Taxonomy of the order Mononegavirales: update 2018

14. Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses

15. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

16. Phylogenetic analysis of avian infectious bronchitis virus isolates from Morocco: a retrospective study (1983 to 2014)

17. Taxonomy of the order Mononegavirales: update 2016

18. A classification system for virophages and satellite viruses

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

20. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

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