Four principles to establish a universal virus taxonomy
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 virolog...
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| Vydané v: | PLoS biology Ročník 21; číslo 2; s. e3001922 |
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| Hlavní autori: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
United States
Public Library of Science
13.02.2023
Public Library of Science (PLoS) |
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| ISSN: | 1545-7885, 1544-9173, 1545-7885 |
| On-line prístup: | Získať plný text |
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| Abstract | 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. |
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| AbstractList | 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.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. 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. 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. Transforming an existing phenotypic classification of viruses into one based on evolutionary relationships that can accommodate the vast number of viruses characterized in metagenomics and environmental studies is an ongoing challenge. This Consensus View explains how such a taxonomy can be expanded to encapsulate viral diversity and to recognize independent biological origins of different virus groups. |
| Audience | Academic |
| Author | Aiewsakun, Pakorn Elena, Santiago F. Zerbini, F. Murilo Skern, Tim Adriaenssens, Evelien M. Reyes-Muñoz, Alejandro Siddell, Stuart Meier-Kolthoff, Jan P. Łobocka, Małgorzata Dutilh, Bas E. Lefkowitz, Elliot J. Simmonds, Peter Lood, Cédric Krupovic, Mart Poranen, Minna M. Turner, Dann Robertson, David L. Duprex, W. Paul Rubino, Luisa Sullivan, Matthew B. Bao, Yiming Koonin, Eugene V. Abrescia, Nicola G. A. Drosten, Christian Barylski, Jakub Mushegian, Arcady R. Smith, Donald B. Alfenas-Zerbini, Poliane Oksanen, Hanna M. Junglen, Sandra Suzuki, Nobuhiro Lambert, Amy J. Van Doorslaer, Koenraad Varsani, Arvind Duffy, Siobain Vandamme, Anne-Mieke Vasilakis, Nikos García, Maria Laura Mahony, Jennifer Katzourakis, Aris Kuhn, Jens H. Sabanadzovic, Sead Roux, Simon |
| AuthorAffiliation | 22 Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France 38 Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria 7 Departamento de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil 20 Department of Biology, University of Oxford, Oxford, United Kingdom 33 MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom 14 The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America 41 School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom 19 Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina 26 Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland 1 Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom 9 University of Chinese Acad |
| AuthorAffiliation_xml | – name: 14 The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America – name: 8 National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China – name: 12 Berlin Institute of Health, Berlin, Germany – name: 37 School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom – name: 7 Departamento de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil – name: 36 Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America – name: 39 Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America – name: 43 KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium – name: 31 Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland – name: 22 Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France – name: 42 School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America – name: 29 Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany – name: 32 Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia – name: 15 Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany – name: 16 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands – name: 18 Santa Fe Institute, Santa Fe, New Mexico, United States of America – name: 38 Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria – name: 24 Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America – name: 23 Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America – name: 5 Basque Foundation for Science, IKERBASQUE, Bilbao, Spain – name: 1 Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom – name: 4 Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain – name: 3 Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil – name: 35 Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy – name: 19 Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina – name: 25 Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America – name: 45 The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America – name: 13 Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America – name: 26 Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland – name: 40 Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan – name: 2 Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom – name: 11 Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany – name: 30 Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America – name: 17 Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain – name: 46 Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America – name: 33 MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom – name: 44 Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal – name: 27 Department of Biosystems, KU Leuven, Leuven, Belgium – name: 20 Department of Biology, University of Oxford, Oxford, United Kingdom – name: 41 School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom – name: 21 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America – name: 28 School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland – name: 9 University of Chinese Academy of Sciences, Beijing, China – name: 10 Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland – name: 34 Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America – name: 6 Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36780432$$D View this record in MEDLINE/PubMed https://pasteur.hal.science/pasteur-03988048$$DView record in HAL https://www.osti.gov/biblio/1924363$$D View this record in Osti.gov |
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| SubjectTerms | Analysis Bacteriophages BASIC BIOLOGICAL SCIENCES Biology Biology and Life Sciences Classification Communication Computer and Information Sciences Consensus View Debates Epidemiology Evolution evolutionary genetics evolutionary systematics Genetic aspects Genomes Humans Identification and classification Immunodeficiency Life Sciences Metagenomics Nomenclature Pathogenicity Pathogens Phages Phenetics phylogenetics Phylogeny Principles Quality control RNA viruses Taxonomy viral evolution viral genomics viral taxonomy Viruses Viruses - genetics |
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| Title | Four principles to establish a universal virus taxonomy |
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