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No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

Author

Listed:
  • Lucy Dorp

    (University College London)

  • Damien Richard

    (Cirad, UMR PVBMT
    Université de la Réunion, UMR PVBMT)

  • Cedric C. S. Tan

    (University College London)

  • Liam P. Shaw

    (University of Oxford)

  • Mislav Acman

    (University College London)

  • François Balloux

    (University College London)

Abstract

COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.

Suggested Citation

  • Lucy Dorp & Damien Richard & Cedric C. S. Tan & Liam P. Shaw & Mislav Acman & François Balloux, 2020. "No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19818-2
    DOI: 10.1038/s41467-020-19818-2
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    Cited by:

    1. Emily E. Bendall & Amy P. Callear & Amy Getz & Kendra Goforth & Drew Edwards & Arnold S. Monto & Emily T. Martin & Adam S. Lauring, 2023. "Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    2. Christiaan H. van Dorp & Emma E. Goldberg & Nick Hengartner & Ruian Ke & Ethan O. Romero-Severson, 2021. "Estimating the strength of selection for new SARS-CoV-2 variants," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    3. Gianni Barcaccia & Vincenzo D’Agostino & Alessandro Zotti & Bruno Cozzi, 2020. "Impact of the SARS-CoV-2 on the Italian Agri-Food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart," Sustainability, MDPI, vol. 12(14), pages 1-28, July.
    4. Cedric C. S. Tan & Su Datt Lam & Damien Richard & Christopher J. Owen & Dorothea Berchtold & Christine Orengo & Meera Surendran Nair & Suresh V. Kuchipudi & Vivek Kapur & Lucy van Dorp & François Ball, 2022. "Transmission of SARS-CoV-2 from humans to animals and potential host adaptation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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