Consensus statement: Virus taxonomy in the age of metagenomics

By Peter Simmonds, Michael J. Adams, M. Benkő, Mya Breitbart, J. R. Brister, E. Carstens, Andrew J. Davison, E. Delwart, Alexander E. Gorbalenya, B. Harrach and 16 more. Nature Reviews Microbiology, 2017

625 citations recorded by the source corpus.

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

Subfields: Animal Science and Zoology, Ecology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a0202269fcc42b29b17513caffe18bd37a18405d

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Citations in the corpus

VICTOR: genome-based phylogeny and classification of prokaryotic viruses (2017, background): “A stronger role of genome sequences in phage classification was recommended though (Krupovic et al. 2016; Simmonds et al. 2017).”
A review of methods and databases for metagenomic classification and assembly (2019, background): “Faced with this rapid growth in the variety of viral species, a scientific consortium recently proposed a new framework for incorporating viruses discovered through metagenomic sequencing into the official taxonomy of the International Committee on Taxonomy of Viruses [151].”
The human gut virome is highly diverse, stable and individual-specific (2019, background): “3 metagenomic studies is currently not possible, although frameworks are under discussion 64 (Simmonds et al., 2017).”
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses (2020, background): “Uncultivated Virus Genomes or UViGs, has now become undeniable (14,20).”
Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV) (2017, methodology): “…approach to virus taxonomy through, for example, moving to sequence-based characters as the primary source of information needed for classification (30); developing and utilizing automated computational methods to facilitate the grouping of viruses into taxa (existing and new) based on a…”