Expansion of the global RNA virome reveals diverse clades of bacteriophages

Cell. 2022 Oct 13;185(21):4023-4037.e18. doi: 10.1016/j.cell.2022.08.023. Epub 2022 Sep 28.

Abstract

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.

Keywords: Bactriophage; Functional protein annotation; Metatranscriptomics; RNA Virus; RNA dependent RNA polymerase; Viral Ecology; Virus; Virus - Host prediction; viral phylogeny.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Bacteriophages* / genetics
  • DNA-Directed RNA Polymerases / genetics
  • Genome, Viral
  • Phylogeny
  • RNA
  • RNA Viruses* / genetics
  • RNA-Dependent RNA Polymerase / genetics
  • Virome

Substances

  • RNA
  • RNA-Dependent RNA Polymerase
  • DNA-Directed RNA Polymerases