PT  - JOURNAL ARTICLE
AU  - Lucy van Dorp
AU  - Damien Richard
AU  - Cedric CS. Tan
AU  - Liam P. Shaw
AU  - Mislav Acman
AU  - François Balloux
TI  - No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
AID  - 10.1101/2020.05.21.108506
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.21.108506
4099  - http://biorxiv.org/content/early/2020/08/19/2020.05.21.108506.short
4100  - http://biorxiv.org/content/early/2020/08/19/2020.05.21.108506.full
AB  - The COVID-19 pandemic 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 extremely recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that some lineages of SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible candidate mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any of the recurrent mutations that have been observed in SARS-CoV-2 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 carefully 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 SARS-CoV-2 mutations currently in circulation appear to be evolutionary neutral. Recurrent mutations also seem primarily induced by the human immune system via host RNA editing, rather than being signatures of adaptation to the novel human host. In conclusion, we find no evidence at this stage for the emergence of significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.Competing Interest StatementThe authors have declared no competing interest.