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Evidence of ongoing recombination in SARS-CoV-2 through genealogical reconstruction

Anastasia Ignatieva, Jotun Hein, Paul A. Jenkins
doi: https://doi.org/10.1101/2021.01.21.427579
Anastasia Ignatieva
1Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
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Jotun Hein
2Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, UK
4The Alan Turing Institute, British Library, London NW1 2DB, UK
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Paul A. Jenkins
1Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
3Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK
4The Alan Turing Institute, British Library, London NW1 2DB, UK
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  • For correspondence: p.jenkins@warwick.ac.uk
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Abstract

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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 21, 2021.
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Evidence of ongoing recombination in SARS-CoV-2 through genealogical reconstruction
Anastasia Ignatieva, Jotun Hein, Paul A. Jenkins
bioRxiv 2021.01.21.427579; doi: https://doi.org/10.1101/2021.01.21.427579
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Evidence of ongoing recombination in SARS-CoV-2 through genealogical reconstruction
Anastasia Ignatieva, Jotun Hein, Paul A. Jenkins
bioRxiv 2021.01.21.427579; doi: https://doi.org/10.1101/2021.01.21.427579

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