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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Published in:PLoS biology Vol. 21; no. 2; p. e3001922
Main Authors: Simmonds, Peter, Adriaenssens, Evelien M., Zerbini, F. Murilo, Abrescia, Nicola G. A., Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W. Paul, Dutilh, Bas E., Elena, Santiago F., García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V., Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Lefkowitz, Elliot J., Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P., Mushegian, Arcady R., Oksanen, Hanna M., Poranen, Minna M., Reyes-Muñoz, Alejandro, Robertson, David L., Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B., Sullivan, Matthew B., Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos
Format: Journal Article
Language:English
Published: United States Public Library of Science 13.02.2023
Public Library of Science (PLoS)
Subjects:
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
United States
ISSN:1545-7885, 1544-9173, 1545-7885
Online Access:Get full text
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Summary: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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PMCID: PMC9925010
USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)
USDOE
AC02-05CH11231
The authors have declared that no competing interests exist.
ISSN:1545-7885
1544-9173
1545-7885
DOI:10.1371/journal.pbio.3001922