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Metagenomic sequencing and its impact on virus classification

ICTV Workshop on Classification of Viruses from Metagenomic Sequences

9th – 11th June, 2016
Simmons College, Harvard Campus, Boston, USA
Sponsored by the Wellcome Trust
Organized by members of the ICTV Executive Committee

A workshop funded by the Wellcome Trust (UK) to discuss frameworks for advancing viral taxonomy in the age of metagenomics was convened in Boston, MA, USA from 9-11 June 2016. It was organized and chaired by Peter Simmonds and administered locally by Max Nibert. Participants had wide-ranging expertise in viral genomics, metagenomic environmental studies, and virus classification (13 of the 26 participants were members of the International Committee on Taxonomy of Viruses (ICTV) Executive Committee) and based on data presentations and wide-ranging discussions set out to develop a series of expert proposals for future consideration by the ICTV Executive Committee.

The understanding in the workshop was that the term metagenomic applies to any viral sequence that lacks biological or other experimental characterization, although what a ‘lack’ means in practice has varied in the literature. Sequence data are already of paramount importance in viral taxonomy because they currently provide the only reliable means of representing evolutionary relationships at the required granularity; however, the workshop recognized that the data generated by high-throughput sequencing from environmental samples pose major challenges, particularly because increasingly powerful methods are generating overwhelming amounts of such data, which are linked to little or no biological information.

The workshop participants concluded that it is entirely valid to use metagenomic sequences in virus taxonomy in the absence of an isolate or direct biological data, such as visualization of viral particles or detection of signs or symptoms of disease. A set of proposals was developed and are discussed in the Consensus Statement article and meeting summary published in Nature Reviews Microbiology. These proposals were subsequently endorsed by the ICTV Executive Committee.