Robert C. Edgar, Jeff Taylor, Victor Lin, Tomer Altman, Pierre Barbera, Dmitry Meleshko, Dan Lohr, Gherman Novakovsky, Benjamin Buchfink, Basem Al-Shayeb, Jillian F. Banfield, Marcos de la Peña, Anton Korobeynikov, Rayan Chikhi, Artem Babaian, Sans affiliation, Altman Analytics LLC, Heidelberg Institute for Theoretical Studies (HITS ), St Petersburg State University (SPbU), Weill Medical College of Cornell University [New York], University of British Columbia (UBC), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, University of California [Berkeley] (UC Berkeley), University of California (UC), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Algorithmes pour les séquences biologiques - Sequence Bioinformatics, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), PB was financially supported by the Klaus Tschira Foundation, RC by ANR Transipedia, Inception and PRAIRIE grants (PIA/ANR-16-CONV-0005, ANR-18-CE45-0020, ANR-19-P3IA-0001), MdlP by Ministerio de Econom ́ıa y Competitividad of Spain and FEDER grant (BFU2017-87370-P), AK and DM were supported by the Russian Science Foundation (grant 19-14-00172) and computation was carried out in part by Resource Centre 'Computer Centre of SPbU'., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-18-CE45-0020,Transipedia,Signatures transcriptionnelles pour une analyse RNA-seq globale(2018), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), sans affiliation, University of California [Berkeley], University of California, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, Serratus, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community. Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones.