High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

Original languageEnglish
Pages (from-to)4023-4037.e18
Issue number21
StatePublished - 13 Oct 2022


FundersFunder number
Edmond J. Safra Center for Bioinformatics
U.S. Department of Energy Joint Genome Institute
National Institutes of Health
U.S. Department of EnergyDE-AC02-05CH11231
U.S. National Library of Medicine
National Aeronautics and Space AdministrationDE-FG02-94ER20137
Office of Science
Basic Energy Sciences
Chemical Sciences, Geosciences, and Biosciences Division
European Research CouncilERC-AdG 787514
Agence Nationale de la RechercheANR-20-CE20-009-02, ANR-21-CE11-0001-01
Tel Aviv University
European Social FundNNX16SJ62G, 09.3.3- LMT-K-712-14-0027


    • Bactriophage
    • Functional protein annotation
    • Metatranscriptomics
    • RNA Virus
    • RNA dependent RNA polymerase
    • Viral Ecology
    • Virus
    • Virus - Host prediction
    • viral phylogeny


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