Petabase-scale sequence alignment catalyses viral discovery
| Title: | Petabase-scale sequence alignment catalyses viral discovery |
|---|---|
| Authors: | Edgar, Robert C.; Taylor, Brie; Lin, Victor; Tomer, Alma; Barbera, Pierre; Meleshko, Dmitry; Lohr, Dan; Novakovsky, G.; Buchfink, B.; Al-Shayeb, B.; Banfield, Jillian F.; Korobeynikov, A.; Chikhi, R.; Babaian, Artem; La Peña Del Rivero, Marcos de |
| Contributors: | Max Planck Society; Klaus Tschira Stiftung; Russian Science Foundation; University of British Columbia; Agencia Estatal de Investigación; Agence Nationale de la Recherche, Francia |
| Publisher Information: | Nature Publishing Group |
| Publication Year: | 2022 |
| Collection: | Universitat Politécnica de Valencia: RiuNet / Politechnical University of Valencia |
| Subject Terms: | Structural basis; Search; Hepatitis; Viruses |
| Description: | [EN] Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by a lack of efficient methods for searching this corpus, which (at the time of writing) exceeds 20 petabases and is growing exponentially(1). Here we developed a cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at the petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) for the hallmark gene RNA-dependent RNA polymerase and identified well over 10(5) novel RNA viruses, thereby expanding the number of known species by roughly an order of magnitude. We characterized novel viruses related to coronaviruses, hepatitis delta virus and huge phages, respectively, and analysed their environmental reservoirs. To catalyse the ongoing revolution of viral discovery, we established a free and comprehensive database of these data and tools. Expanding the known sequence diversity of viruses can reveal the evolutionary origins of emerging pathogens and improve pathogen surveillance for the anticipation and mitigation of future pandemics. ; The Serratus project is an initiative of the hackseqRNA genomics hackathon (https://www.hackseq.com).We thank the many contributors for code snippets and bioinformatic discussion (E. Erhan, J. Chu, S. Jackman, I. Birol, K. Wellman, O. Fornes, C. Xu, M. Huss, K. Ha, M. Krzywinski, E. Nawrocki, R. McLaughlin, C. Morgan-Lang, C. Blumberg and the J. Brister laboratory); A. Rodrigues, S. McMillan, V. Wu, C. Kennett, K. Chao, and N. Pereyaslavsky for AWS support; the J. Joy laboratory, G. Mordecai, J. Taylor, S. Roux, N. Kyrpides, E. Jan, T. Reddy, L. Bergner, R. Orton and D. Streicker for virology discussions; and H.-G. Drost and D. Weigel for supporting the adoption of DIAMOND v2 for Serratus protein alignments as part of an extended feature request. We are grateful to the entire team managing the NCBI SRA and the biology community for data sharing, with particular thanks to the E. Brodie, ... |
| Document Type: | article in journal/newspaper |
| File Description: | application/pdf |
| Language: | English |
| ISSN: | 35082445 |
| Relation: | Nature; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2017-87370-P/ES/PAPEL DE LOS RNAS AUTOCATALITICOS Y CIRCULARES EN EL MECANISMO DE RETROTRANSPOSICION DEL DNA EUCARIOTICO/; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-116008GB-I00/ES/CARACTERIZACION DE NUEVOS RIBOZIMAS DE AUTOCORTE Y RNAS CIRCULARES EN EUCARIOTAS: MECANISMOS, FUNCIONES Y POTENCIAL APLICACION BIOTECNOLOGICA/; info:eu-repo/grantAgreement/ANR//ANR-16-CONV-0005/FR/Institut Convergences pour l¿étude de l¿Emergence des Pathologies au Travers des Individus et des populatiONs/; info:eu-repo/grantAgreement/ANR//ANR-19-P3IA-0001/FR/PaRis Artificial Intelligence Research InstitutE/; info:eu-repo/grantAgreement/RSF//19-14-00172/; info:eu-repo/grantAgreement/ANR//18CE45-0020/; https://doi.org/10.1038/s41586-021-04332-2; https://riunet.upv.es/handle/10251/227805 |
| DOI: | 10.1038/s41586-021-04332-2 |
| Availability: | https://riunet.upv.es/handle/10251/227805; https://doi.org/10.1038/s41586-021-04332-2 |
| Rights: | http://rightsstatements.org/vocab/InC/1.0/ ; info:eu-repo/semantics/closedAccess |
| Accession Number: | edsbas.BD9154CE |
| Database: | BASE |