PT  - JOURNAL ARTICLE
AU  - Anastasia Ignatieva
AU  - Jotun Hein
AU  - Paul A. Jenkins
TI  - Evidence of ongoing recombination in SARS-CoV-2 through genealogical reconstruction
AID  - 10.1101/2021.01.21.427579
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.21.427579
4099  - http://biorxiv.org/content/early/2021/01/21/2021.01.21.427579.short
4100  - http://biorxiv.org/content/early/2021/01/21/2021.01.21.427579.full
AB  - The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem, and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables the analysis of recombination events that could have generated the data. We propose a framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and in South Africa, and find compelling evidence of ongoing recombination.Competing Interest StatementThe authors have declared no competing interest.