A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

Abstract

High-throughput RNA sequencing offers unprecedented opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology.

Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris

“…Lastly, we used our results to search on two recently released large RNA viral databases ( Edgar et al. 2022 ; Neri et al. 2022 ) where authors used an iterated homology approach to investigate a broad collection of metatranscriptomic samples and identified over 100k and 300k new viral RdRP, respectively.…”

“…3 shows some conservation among the ormycoviruses we detected through similarity searches that allowed to perform the phylogenetic analysis. Ormycovirus-like sequences identified from the RVMT ( Neri et al. 2022 ; Supplementary Table S3 ) were included in the analysis and named with the reference of the metatranscriptomic sample of origin.…”

“…2020 ). Specific bioinformatic approaches have allowed to include in recent versions of the tree also viruses with a permutated palm domain order, which have originated at different points in virus evolution ( Neri et al. 2022 ).…”

“…We also searched for ormycovirus presence in the RNA virus databases resulting from a very large metatrascriptomes (RVMT) database that was recently made public ( Neri et al. 2022 ) through DIAMOND software.…”

“…Finally, two distinct efforts to mine public databases (particularly metatranscriptomes) for RNA viruses resulted in order of magnitude increases in viral taxa corresponding to the genus/species level, with much-expanded knowledge of virus diversity ( Edgar et al. 2022 ; Neri et al. 2022 ).…”