TY - JOUR
T1 - Four principles to establish a universal virus taxonomy
AU - Simmonds, Peter
AU - Adriaenssens, Evelien M.
AU - Murilo Zerbini, F.
AU - Abrescia, Nicola G.A.
AU - Aiewsakun, Pakorn
AU - Alfenas-Zerbini, Poliane
AU - Bao, Yiming
AU - Barylski, Jakub
AU - Drosten, Christian
AU - Duffy, Siobain
AU - Paul Duprex, W.
AU - Dutilh, Bas E.
AU - Elena, Santiago F.
AU - García, Maria Laura
AU - Junglen, Sandra
AU - Katzourakis, Aris
AU - Koonin, Eugene V.
AU - Krupovic, Mart
AU - Kuhn, Jens H.
AU - Lambert, Amy J.
AU - Lefkowitz, Elliot J.
AU - Łobocka, Małgorzata
AU - Lood, Cédric
AU - Mahony, Jennifer
AU - Meier-Kolthoff, Jan P.
AU - Mushegian, Arcady R.
AU - Oksanen, Hanna M.
AU - Poranen, Minna M.
AU - Reyes-Muñoz, Alejandro
AU - Robertson, David L.
AU - Roux, Simon
AU - Rubino, Luisa
AU - Sabanadzovic, Sead
AU - Siddell, Stuart
AU - Skern, Tim
AU - Smith, Donald B.
AU - Sullivan, Matthew B.
AU - Suzuki, Nobuhiro
AU - Turner, Dann
AU - Van Doorslaer, Koenraad
AU - Vandamme, Anne Mieke
AU - Varsani, Arvind
AU - Vasilakis, Nikos
N1 - 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.
PY - 2023/2
Y1 - 2023/2
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/85147927122
U2 - 10.1371/journal.pbio.3001922
DO - 10.1371/journal.pbio.3001922
M3 - Article
C2 - 36780432
AN - SCOPUS:85147927122
SN - 1544-9173
VL - 21
JO - PLOS Biology
JF - PLOS Biology
IS - 2
M1 - e3001922
ER -
SDG 3 Good Health and Well-being