IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v609y2022i7929d10.1038_s41586-022-05189-9.html
   My bibliography  Save this article

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

Author

Listed:
  • Yatish Turakhia

    (University of California, Santa Cruz
    University of California, Santa Cruz
    University of California, San Diego)

  • Bryan Thornlow

    (University of California, Santa Cruz
    University of California, Santa Cruz)

  • Angie Hinrichs

    (University of California, Santa Cruz)

  • Jakob McBroome

    (University of California, Santa Cruz
    University of California, Santa Cruz)

  • Nicolas Ayala

    (University of California, Santa Cruz
    University of California, Santa Cruz)

  • Cheng Ye

    (University of California, San Diego)

  • Kyle Smith

    (University of California, San Diego)

  • Nicola De Maio

    (Wellcome Genome Campus)

  • David Haussler

    (University of California, Santa Cruz
    University of California, Santa Cruz
    University of California, Santa Cruz)

  • Robert Lanfear

    (Australian National University)

  • Russell Corbett-Detig

    (University of California, Santa Cruz
    University of California, Santa Cruz)

Abstract

Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses1–4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution5. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.

Suggested Citation

  • Yatish Turakhia & Bryan Thornlow & Angie Hinrichs & Jakob McBroome & Nicolas Ayala & Cheng Ye & Kyle Smith & Nicola De Maio & David Haussler & Robert Lanfear & Russell Corbett-Detig, 2022. "Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape," Nature, Nature, vol. 609(7929), pages 994-997, September.
    • Handle: RePEc:nat:nature:v:609:y:2022:i:7929:d:10.1038_s41586-022-05189-9
    DOI: 10.1038/s41586-022-05189-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41586-022-05189-9
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/s41586-022-05189-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Ana S. Gonzalez-Reiche & Hala Alshammary & Sarah Schaefer & Gopi Patel & Jose Polanco & Juan Manuel Carreño & Angela A. Amoako & Aria Rooker & Christian Cognigni & Daniel Floda & Adriana Guchte & Zain, 2023. "Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Orsolya Anna Pipek & Anna Medgyes-Horváth & József Stéger & Krisztián Papp & Dávid Visontai & Marion Koopmans & David Nieuwenhuijse & Bas B. Oude Munnink & István Csabai, 2024. "Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:609:y:2022:i:7929:d:10.1038_s41586-022-05189-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.