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Petabase-scale sequence alignment catalyses viral discovery

View ORCID ProfileRobert C. Edgar, Jeff Taylor, View ORCID ProfileVictor Lin, View ORCID ProfileTomer Altman, View ORCID ProfilePierre Barbera, View ORCID ProfileDmitry Meleshko, Dan Lohr, Gherman Novakovsky, View ORCID ProfileBenjamin Buchfink, View ORCID ProfileBasem Al-Shayeb, View ORCID ProfileJillian F. Banfield, View ORCID ProfileMarcos de la Peña, View ORCID ProfileAnton Korobeynikov, View ORCID ProfileRayan Chikhi, View ORCID ProfileArtem Babaian
doi: https://doi.org/10.1101/2020.08.07.241729
Robert C. Edgar
1Unaffiliated
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Jeff Taylor
1Unaffiliated
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Victor Lin
1Unaffiliated
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Tomer Altman
2Altman Analytics LLC, San Francisco, California, USA
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Pierre Barbera
3Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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Dmitry Meleshko
4Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
5Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, USA
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Dan Lohr
1Unaffiliated
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Gherman Novakovsky
6Department of Medical Genetics, University of British Columbia. Vancouver, BC, Canada
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Benjamin Buchfink
7Computational Biology Group, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Basem Al-Shayeb
8Department of Plant and Microbial Biology, University of California, Berkeley, USA
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Jillian F. Banfield
9Department of Earth and Planetary Science, University of California, Berkeley, USA
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Marcos de la Peña
10Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
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Anton Korobeynikov
4Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
11Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia
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Rayan Chikhi
12Institut Pasteur, CNRS, Paris, France
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Artem Babaian
1Unaffiliated
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  • For correspondence: ababaian@bccrc.ca
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Abstract

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, now exceeding multiple petabases and growing exponentially [1, 2]. 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, identifying well over 105 novel RNA viruses and thereby expanding the number of known species by roughly an order of magnitude. We characterised novel viruses related to coronaviruses and to hepatitis δ virus, respectively and explored their environmental reservoirs. To catalyse a new era 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Added a search of 5.7 million libraries for viral RdRP.

  • https://github.com/ababaian/serratus

  • 1 https://bitbucket.org/tomeraltman/darth/

  • 2 https://gitlab.pasteur.fr/rchikhi_pasteur/serratus-batch-assembly/-/blob/master/template/template.yaml

  • 3 https://gitlab.pasteur.fr/rchikhi_pasteur/serratus-batch-assembly/-/blob/master/stats/bgc_parse_and_extract.py

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 14, 2021.
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Petabase-scale sequence alignment catalyses viral discovery
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
bioRxiv 2020.08.07.241729; doi: https://doi.org/10.1101/2020.08.07.241729
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Petabase-scale sequence alignment catalyses viral discovery
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
bioRxiv 2020.08.07.241729; doi: https://doi.org/10.1101/2020.08.07.241729

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