Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales .

Metagenomics has altered our understanding of microbial diversity and ecology. This includes its applications to viruses in marine environments that have demonstrated their enormous diversity. Within these are RNA viruses, many of which share genetic features with members of the order ; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the , which was founded based on discovery and characterization of the species . Two additional genera of marine RNA viruses, (one species) and (three species), were subsequently defined within the order but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family . Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera and to the family and created four additional genera in the family: (four species), (one species), (four species) and (six species). We used pairwise capsid protein comparisons to delineate species within families, with 75 per cent identity as the species demarcation threshold. The family displays high sequence diversities and Jukes-Cantor distances for both the RdRp and capsid genes, suggesting that the classified viruses are not representative of all of the virus diversity within the family and that there are many more extant taxa. Our proposed taxonomic framework provides a sound classification system for this group of viruses that will have broadly applicable principles for other viral groups. It is based on sequence data alone and provides a robust taxonomic framework to include viruses discovered via metagenomic studies, thereby greatly expanding the realm of viruses subject to taxonomic classification.