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Ongoing recombination in SARS-CoV-2 revealed through genealogical reconstruction
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Ignatieva, Anastasia, Hein, Jotun and Jenkins, Paul A. (2022) Ongoing recombination in SARS-CoV-2 revealed through genealogical reconstruction. Molecular Biology and Evolution, 39 (2). msac028. doi:10.1093/molbev/msac028 ISSN 0737-4038.
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Official URL: http://dx.doi.org/10.1093/molbev/msac028
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 us to pinpoint specific recombination events that could have generated the data. We propose a statistical 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 South Africa and find evidence of ongoing recombination.
Item Type: | Journal Article | ||||||||||||
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Subjects: | Q Science > QH Natural history R Medicine > RA Public aspects of medicine |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science Faculty of Science, Engineering and Medicine > Science > Statistics |
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Library of Congress Subject Headings (LCSH): | COVID-19 (Disease) , COVID-19 (Disease) -- Epidemiology, Genetic recombination , COVID-19 (Disease) -- Genetic aspects | ||||||||||||
Journal or Publication Title: | Molecular Biology and Evolution | ||||||||||||
Publisher: | Oxford University Press | ||||||||||||
ISSN: | 0737-4038 | ||||||||||||
Official Date: | 2 February 2022 | ||||||||||||
Dates: |
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Volume: | 39 | ||||||||||||
Number: | 2 | ||||||||||||
Number of Pages: | 11 | ||||||||||||
Article Number: | msac028 | ||||||||||||
DOI: | 10.1093/molbev/msac028 | ||||||||||||
Status: | Peer Reviewed | ||||||||||||
Publication Status: | Published | ||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
Date of first compliant deposit: | 3 March 2022 | ||||||||||||
Date of first compliant Open Access: | 7 March 2022 | ||||||||||||
RIOXX Funder/Project Grant: |
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