Four principles to establish a universal virus taxonomy
5
Issued Date
2023-02-01
Resource Type
ISSN
15449173
eISSN
15457885
Scopus ID
2-s2.0-85147927122
Pubmed ID
36780432
Journal Title
PLoS Biology
Volume
21
Issue
2
Rights Holder(s)
SCOPUS
Bibliographic Citation
PLoS Biology Vol.21 No.2 (2023)
Suggested Citation
Simmonds P. Four principles to establish a universal virus taxonomy. PLoS Biology Vol.21 No.2 (2023). doi:10.1371/journal.pbio.3001922 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/81661
Title
Four principles to establish a universal virus taxonomy
Author(s)
Author's Affiliation
Norwich Research Park
MRC-University of Glasgow Centre for Virus Research
College of Agriculture and Life Sciences
Berliner Institut für Gesundheitsforschung
Université Paris Cité
Departement Microbiologie, Immunologie en Transplantatie
Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
Instituto de Biotecnología y Biología Molecular (CONICET- Universidad Nacional de La Plata)
CIC BioGUNE
Ikerbasque, Basque Foundation for Science
National Center for Biotechnology Information (NCBI)
National Center for Emerging and Zoonotic Infectious Diseases
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Instituto de Higiene e Medicina Tropical
Universidad de Los Andes, Colombia
Santa Fe Institute
Friedrich-Schiller-Universität Jena
School of Environmental and Biological Sciences
University of Chinese Academy of Sciences
The University of Alabama at Birmingham
University of Oxford
Charité – Universitätsmedizin Berlin
School of Life Sciences
KU Leuven
Okayama University
University of Bristol
University of Arizona Cancer Center
University of the West of England
Chinese Academy of Sciences
University of Texas Medical Branch, School of Medicine
National Institute of Allergy and Infectious Diseases (NIAID)
U.S. Department of Energy Joint Genome Institute
Uniwersytet im. Adama Mickiewicza w Poznaniu
Universidade Federal de Vicosa
National Science Foundation
Mahidol University
Medizinische Universität Wien
Nuffield Department of Medicine
Universiteit Utrecht
APC Microbiome Ireland
The Ohio State University
Helsingin Yliopisto
Universitat de València
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences
University of Pittsburgh School of Medicine
MRC-University of Glasgow Centre for Virus Research
College of Agriculture and Life Sciences
Berliner Institut für Gesundheitsforschung
Université Paris Cité
Departement Microbiologie, Immunologie en Transplantatie
Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
Instituto de Biotecnología y Biología Molecular (CONICET- Universidad Nacional de La Plata)
CIC BioGUNE
Ikerbasque, Basque Foundation for Science
National Center for Biotechnology Information (NCBI)
National Center for Emerging and Zoonotic Infectious Diseases
Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Instituto de Higiene e Medicina Tropical
Universidad de Los Andes, Colombia
Santa Fe Institute
Friedrich-Schiller-Universität Jena
School of Environmental and Biological Sciences
University of Chinese Academy of Sciences
The University of Alabama at Birmingham
University of Oxford
Charité – Universitätsmedizin Berlin
School of Life Sciences
KU Leuven
Okayama University
University of Bristol
University of Arizona Cancer Center
University of the West of England
Chinese Academy of Sciences
University of Texas Medical Branch, School of Medicine
National Institute of Allergy and Infectious Diseases (NIAID)
U.S. Department of Energy Joint Genome Institute
Uniwersytet im. Adama Mickiewicza w Poznaniu
Universidade Federal de Vicosa
National Science Foundation
Mahidol University
Medizinische Universität Wien
Nuffield Department of Medicine
Universiteit Utrecht
APC Microbiome Ireland
The Ohio State University
Helsingin Yliopisto
Universitat de València
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences
University of Pittsburgh School of Medicine
Other Contributor(s)
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.