Four principles to establish a universal virus taxonomy

Simmonds, P. et al. (2023) Four principles to establish a universal virus taxonomy. PLoS Biology, 21(2), e3001922. (doi: 10.1371/journal.pbio.3001922) (PMID:36780432) (PMCID:PMC9925010)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Robertson, Professor David

Creator Roles

Robertson, D. L.: Conceptualization, Investigation, Writing – review and editing

• Authors: Simmonds, P., Adriaenssens, E. M., Zerbini, F. M., Abrescia, N. G. A., Aiewsakun, P., Alfenas-Zerbini, P., Bao, Y., Barylski, J., Drosten, C., Duffy, S., Duprex, W. P., Dutilh, B. E., Elena, S. F., García, M. L., Junglen, S., Katzourakis, A., Koonin, E. V., Krupovic, M., Kuhn, J. H., Lambert, A. J., Lefkowitz, E. J., Łobocka, M., Lood, C., Mahony, J., Meier-Kolthoff, J. P., Mushegian, A. R., Oksanen, H. M., Poranen, M. M., Reyes-Muñoz, A., Robertson, D. L., Roux, S., Rubino, L., Sabanadzovic, S., Siddell, S., Skern, T., Smith, D. B., Sullivan, M. B., Suzuki, N., Turner, D., Van Doorslaer, K., Vandamme, A.-M., Varsani, A., and Vasilakis, N.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: PLoS Biology
• Publisher: Public Library of Science
• ISSN: 1544-9173
• ISSN (Online): 1545-7885
• Published Online: 13 February 2023
• Copyright Holders: 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
• First Published: First published in PLoS Biology 21(2): e3001922
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
172630014		Cross-Cutting Programme – Viral Genomics and Bioinformatics (Programme 9)	David Robertson	Medical Research Council (MRC)	MC_UU_12014/12	III - Centre for Virus Research