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Population genomics insights into the recent evolution of SARS-CoV-2

Maria Vasilarou, View ORCID ProfileNikolaos Alachiotis, Joanna Garefalaki, View ORCID ProfileApostolos Beloukas, View ORCID ProfilePavlos Pavlidis
doi: https://doi.org/10.1101/2020.04.21.054122
Maria Vasilarou
1Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology Hellas (FORTH)
2Department of Biology, University of Crete, Crete, Greece
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Nikolaos Alachiotis
3Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH)
4Technical University of Crete, Crete, Greece
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Joanna Garefalaki
3Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH)
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Apostolos Beloukas
5Department of Biomedical Sciences, University of West Attica, Athens, Greece
6Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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  • For correspondence: abeloukas@uniwa.gr beloukas@liverpool.ac.uk pavlidis@ics.forth.gr pavlidisp@gmail.com
Pavlos Pavlidis
3Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH)
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  • ORCID record for Pavlos Pavlidis
  • For correspondence: abeloukas@uniwa.gr beloukas@liverpool.ac.uk pavlidis@ics.forth.gr pavlidisp@gmail.com
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Abstract

The current coronavirus disease 2019 (COVID-19) pandemic is caused by the SARS-CoV-2 virus and is still spreading rapidly worldwide. Full-genome-sequence computational analysis of the SARS-CoV-2 genome will allow us to understand the recent evolutionary events and adaptability mechanisms more accurately, as there is still neither effective therapeutic nor prophylactic strategy. In this study, we used population genetics analysis to infer the mutation rate and plausible recombination events that may have contributed to the evolution of the SARS-CoV-2 virus. Furthermore, we localized targets of recent and strong positive selection. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from non-human hosts appeared to have taken place in the past. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., Hedgehog and Sparrow. Even though recombination events within human hosts cannot be directly assessed, due to the high similarity of SARS-CoV-2 genomes, we infer that recombinations may have recently occurred within human hosts using a linkage disequilibrium analysis. In addition, we employed an Approximate Bayesian Computation approach to estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian and Northern American cohorts, and we demonstrated that a rapid exponential growth in population size can support the observed polymorphism patterns in SARS-CoV-2 genomes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵# AB and PP shared last authorship and correspondence to this work

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 4.0 International license.
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Posted April 23, 2020.
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Population genomics insights into the recent evolution of SARS-CoV-2
Maria Vasilarou, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, Pavlos Pavlidis
bioRxiv 2020.04.21.054122; doi: https://doi.org/10.1101/2020.04.21.054122
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Population genomics insights into the recent evolution of SARS-CoV-2
Maria Vasilarou, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, Pavlos Pavlidis
bioRxiv 2020.04.21.054122; doi: https://doi.org/10.1101/2020.04.21.054122

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