Expansion of the global RNA virome reveals diverse clades of bacteriophages

Uri Neri (1) , Yuri I Wolf (2) , Simon Roux (3) , Antonio Pedro Camargo (3) , Benjamin Lee (2, 4) , Darius Kazlauskas (5) , I. Min Chen (3) , Natalia Ivanova (3) , Lisa Zeigler Allen (6) , David Paez-Espino (3) , Donald A Bryant (7) , Devaki Bhaya (8) , Adrienne B Narrowe , Alexander J Probst , Alexander Sczyrba , Annegret Kohler , Armand Séguin , Ashley Shade , Barbara J Campbell , Björn D Lindahl , Brandi Kiel Reese , Breanna M Roque , Chris Derito , Colin Averill , Daniel Cullen , David A.C. Beck , David A Walsh , David M Ward , Dongying Wu , Emiley Eloe-Fadrosh , Eoin L Brodie , Erica B Young , Erik A Lilleskov , Federico J Castillo , Francis M Martin , Gary R Lecleir , Graeme T Attwood , Hinsby Cadillo-Quiroz , Holly M Simon , Ian Hewson , Igor V Grigoriev , James M Tiedje , Janet K Jansson , Janey Lee , Jean S Vandergheynst , Jeff Dangl , Jeff S Bowman , Jeffrey L Blanchard , Jennifer L Bowen , Jiangbing Xu , Jillian F Banfield , Jody W Deming , Joel E Kostka , John M Gladden , Josephine Z Rapp , Joshua Sharpe , Katherine D Mcmahon , Kathleen K Treseder , Kay D Bidle , Kelly C Wrighton , Kimberlee Thamatrakoln , Klaus Nusslein , Laura K Meredith , Lucia Ramirez , Marc Buee , Marcel Huntemann , Marina G Kalyuzhnaya , Mark P Waldrop , Matthew B Sullivan , Matthew O Schrenk , Matthias Hess , Michael A Vega , Michelle A O’malley , Monica Medina , Naomi E Gilbert , Nathalie Delherbe , Olivia U Mason , Paul Dijkstra , Peter F Chuckran , Petr Baldrian , Philippe Constant , Ramunas Stepanauskas , Rebecca A Daly , Regina Lamendella , Robert J Gruninger , Robert M Mckay , Samuel Hylander , Sarah L Lebeis , Sarah P Esser , Silvia G Acinas , Steven S Wilhelm , Steven W Singer , Susannah S Tringe , Tanja Woyke , T.B.K. Reddy , Terrence H Bell , Thomas Mock , Tim Mcallister , Vera Thiel , Vincent J Denef , Wen-Tso Liu , Willm Martens-Habbena , Xiao-Jun Allen Liu , Zachary S Cooper , Zhong Wang , Mart Krupovic (9) , Valerian V Dolja (2, 10) , Nikos C Kyrpides (3) , Eugene V Koonin (2) , Uri Gophna (1)

1 TAU - Tel Aviv University
2 NCBI - National Center for Biotechnology Information
3 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
4 University of Oxford
5 Vilnius University [Vilnius]
6 JCVI - J. Craig Venter Institute [La Jolla, USA]
7 Penn State - Pennsylvania State University
8 Carnegie Institution for Science
9 Virologie des archées - Archaeal Virology
10 OSU - Oregon State University

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

Domains: Life Sciences [q-bio]; Microbiology and Parasitology; Virology

Uri Neri, Yuri I Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin Lee, et al.. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 2022, 185 (21), pp.4023-4037.e18. ⟨10.1016/j.cell.2022.08.023⟩. ⟨pasteur-03816108⟩