Perspective on taxonomic classification of uncultivated viruses

Bas E Dutilh; Arvind Varsani; Yigang Tong; Peter Simmonds; Sead Sabanadzovic; Luisa Rubino; Simon Roux; Alejandro Reyes Muñoz; Cédric Lood; Elliot J Lefkowitz; Jens H Kuhn; Mart Krupovic; Robert A Edwards; J Rodney Brister; Evelien M Adriaenssens; Matthew B Sullivan

doi:10.1016/j.coviro.2021.10.011

Perspective on taxonomic classification of uncultivated viruses

Curr Opin Virol. 2021 Dec:51:207-215. doi: 10.1016/j.coviro.2021.10.011. Epub 2021 Nov 12.

Authors

Bas E Dutilh¹, Arvind Varsani², Yigang Tong³, Peter Simmonds⁴, Sead Sabanadzovic⁵, Luisa Rubino⁶, Simon Roux⁷, Alejandro Reyes Muñoz⁸, Cédric Lood⁹, Elliot J Lefkowitz¹⁰, Jens H Kuhn¹¹, Mart Krupovic¹², Robert A Edwards¹³, J Rodney Brister¹⁴, Evelien M Adriaenssens¹⁵, Matthew B Sullivan¹⁶

Affiliations

¹ Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Institute of Bioloversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany. Electronic address: [email protected].
² The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa.
³ Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
⁴ Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK.
⁵ Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS 39762, USA.
⁶ Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy.
⁷ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁸ Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
⁹ Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 23, 3001, Leuven, Belgium; Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
¹⁰ Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
¹¹ Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
¹² Institut Pasteur, Université de Paris, Archaeal Virology Unit, F-75015, Paris, France.
¹³ College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
¹⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA.
¹⁵ Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK.
¹⁶ Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA.

PMID: 34781105
DOI: 10.1016/j.coviro.2021.10.011

Abstract

Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Animals
Evolution, Molecular
Humans
Metagenomics
Phylogeny*
Viruses / classification*
Viruses / genetics
Viruses / growth & development

Abstract

Publication types

MeSH terms

Grants and funding