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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
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    Cited by:

    1. 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.
    2. 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.

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