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Petabase-scale sequence alignment catalyses viral discovery

Author

Listed:
  • Robert C. Edgar

    (Independent researcher)

  • Brie Taylor

    (Independent researcher)

  • Victor Lin

    (Independent researcher)

  • Tomer Altman

    (Altman Analytics)

  • Pierre Barbera

    (Heidelberg Institute for Theoretical Studies)

  • Dmitry Meleshko

    (St Petersburg State University
    Weill Cornell Medical College)

  • Dan Lohr

    (Unaffiliated)

  • Gherman Novakovsky

    (University of British Columbia)

  • Benjamin Buchfink

    (Max Planck Institute for Biology)

  • Basem Al-Shayeb

    (University of California, Berkeley)

  • Jillian F. Banfield

    (University of California, Berkeley)

  • Marcos Peña

    (Universidad Politécnica de Valencia–CSIC)

  • Anton Korobeynikov

    (St Petersburg State University
    St Petersburg State University)

  • Rayan Chikhi

    (G5 Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur)

  • Artem Babaian

    (Independent researcher)

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, which (at the time of writing) exceeds 20 petabases and is growing exponentially1. 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 105 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.

Suggested Citation

  • Robert C. Edgar & Brie Taylor & Victor Lin & Tomer Altman & Pierre Barbera & Dmitry Meleshko & Dan Lohr & Gherman Novakovsky & Benjamin Buchfink & Basem Al-Shayeb & Jillian F. Banfield & Marcos Peña &, 2022. "Petabase-scale sequence alignment catalyses viral discovery," Nature, Nature, vol. 602(7895), pages 142-147, February.
  • Handle: RePEc:nat:nature:v:602:y:2022:i:7895:d:10.1038_s41586-021-04332-2
    DOI: 10.1038/s41586-021-04332-2
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    Cited by:

    1. Natalia Quinones-Olvera & Siân V. Owen & Lucy M. McCully & Maximillian G. Marin & Eleanor A. Rand & Alice C. Fan & Oluremi J. Martins Dosumu & Kay Paul & Cleotilde E. Sanchez Castaño & Rachel Petherbr, 2024. "Diverse and abundant phages exploit conjugative plasmids," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. David Hueting & Karen Schriever & Rui Sun & Stelios Vlachiotis & Fanglei Zuo & Likun Du & Helena Persson & Camilla Hofström & Mats Ohlin & Karin Walldén & Marcus Buggert & Lennart Hammarström & Harold, 2023. "Design, structure and plasma binding of ancestral β-CoV scaffold antigens," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Eric Ros-Moner & Tamara Jiménez-Góngora & Luis Villar-Martín & Lana Vogrinec & Víctor M. González-Miguel & Denis Kutnjak & Ignacio Rubio-Somoza, 2024. "Conservation of molecular responses upon viral infection in the non-vascular plant Marchantia polymorpha," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Marco Forgia & Beatriz Navarro & Stefania Daghino & Amelia Cervera & Andreas Gisel & Silvia Perotto & Dilzara N. Aghayeva & Mary F. Akinyuwa & Emanuela Gobbi & Ivan N. Zheludev & Robert C. Edgar & Ray, 2023. "Hybrids of RNA viruses and viroid-like elements replicate in fungi," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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