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

Abstract

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 Picornavirales; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus. Two additional genera of marine RNA viruses, Labyrnavirus (one species) and Bacillarnavirus (three species), were subsequently defined within the order Picornavirales but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family Marnaviridae. Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera Labyrnavirus and Bacillarnavirus to the family Marnaviridae and created four additional genera in the family: Locarnavirus (four species), Kusarnavirus (one species), Salisharnavirus (four species) and Sogarnavirus (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.

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

“…This clade contains the Marnaviridae and other protist-infecting viruses as well as viruses identified in holobionts of molluscs, annelids and other marine invertebrates whose diets include protists. The largest of the 323 broad RdRP clusters in the Yangshan virome-OV.1 (where OV indicates Ocean Viruses, an operational term for RdRP clusters), with 653 members (Supplementary Datasets 1 and 2)-fell entirely into the Marnaviridae, vastly expanding the diversity of this family and highlighting the need for a taxonomic upgrade 28 . Given that isolated Marnaviridae infect diatoms and other aquatic Stramenopile protists 21,22,26,39,45 , most OV.1 members are likely to infect related unicellular eukaryotes.…”

“…Although metaviromic analyses do not typically identify the virus hosts, some of the marine RNA virome components have been phylogenetically anchored through similarity to viruses with known hosts. Perhaps the best characterized group of such viruses is the family Marnaviridae, which combines picorna-like viruses of diatoms and other stramenopiles [21][22][23][24][25][26] with a growing number of species defined by metagenomics as probably infecting related aquatic unicellular eukaryotes 27,28 (hereafter referred to as 'protists').…”

ICTV Virus Taxonomy Profile: Marnaviridae 2021

“…Members possess monopartite positive-sense RNA genomes of 8.6–9.6 kb [2] containing one ( Locarnavirus , Marnavirus ) or two ORFs ( Locarnavirus , Kusarnavirus , Bacillarnavirus , Salisharnavirus , Sogarnavirus ); members of the genus Labyrnavirus have a third small overlapping open reading frame (ORF) at the 3′-end of the genome (). Virus genomes encode conserved helicase, RNA-directed RNA polymerase and structural protein domains.…”

Recognizing species as a new focus of virus research

“…This would represent a first but significant step forward in the effort to define a position for the virus entity in the natural world. Using species abundance as a census of virus diversity in different hosts (notably humans) [36] and biomes [37][38][39][40] would be another step in this direction. Importantly, these developments would also facilitate research into the full extent of viruses at the species level, as is common elsewhere in biology [41].…”