The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate

JH Tay; AF Porter; W Wirth; S Duchene

Journal article

The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate

JH Tay, AF Porter, W Wirth, S Duchene

Molecular Biology and Evolution | Published : 2022

DOI: 10.1093/molbev/msac013

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Abstract

The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the substitution rate of SARS-CoV-2 suggest that its genome accrues around two mutations per month. However, VOCs can have 15 or more defining mutations and it is hypothesized that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analyzed genome..

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University of Melbourne Researchers

Wytamma Wirth Author

Sebastian Duchene Garzon Author

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Funding Acknowledgements

This work was supported by the Australian Research Council (DE190100805) and the Australian Medical Research Future Fund (MRF9200006). This research was underaken using the LIEF HPC GPGPU facilty hosted at the University of Melbourne. This Facility was established with the assistance of LIEF Grant LE170100200. We acknowledge efforts by originating and submitting laboratories for the sequence data in GISAID EpiCoV on which our analyses are based. We are grateful to Prof. Edward Holmes for useful suggestions and comments on ideas developed in this study. We also thank two anonymous reviewers for useful suggestion and comments of earlier versions of this manuscript.