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bioRxiv · 10.1101/2020.12.15.422866

No detectable signal for ongoing genetic recombination in SARS-CoV-2

Richard, D.·Owen, C. J.·van Dorp, L.·Balloux, F.
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Abstract

The COVID-19 pandemic has led to an unprecedented global sequencing effort of its viral agent SARS-CoV-2. The first whole genome assembly of SARS-CoV-2 was published on January 5 2020. Since then, over 150,000 high-quality SARS-CoV-2 genomes have been made available. This large genomic resource has allowed tracing of the emergence and spread of mutations and phylogenetic reconstruction of SARS-CoV-2 lineages in near real time. Though, whether SARS-CoV-2 undergoes genetic recombination has been largely overlooked to date. Recombination-mediated rearrangement of variants that arose independently can be of major evolutionary importance. Moreover, the absence of recombination is a key assumption behind the application of phylogenetic inference methods. Here, we analyse the extant genomic diversity of SARS-CoV-2 and show that, to date, there is no detectable hallmark of recombination. We assess our detection power using simulations and validate our method on the related MERS-CoV for which we report evidence for widespread genetic recombination.

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Richard, D., Owen, C. J., van Dorp, L., Balloux, F.. 2020-12-15. No detectable signal for ongoing genetic recombination in SARS-CoV-2. https://doi.org/10.1101/2020.12.15.422866

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