Population Genomics Insights into the First Wave of COVID-19
1
Foundation for Research and Technology Hellas (FORTH) and Department of Biology, Institute of Molecular Biology and Biotechnology (IMBB), University of Crete, 70013 Crete, Greece
2
Faculty of EEMCS, University of Twente, 7522NB Enschede, The Netherlands
3
Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece
4
Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece
5
Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
*
Authors to whom correspondence should be addressed.
†
M.V. and N.A. contributed equally, thus sharing first authorship to this work.
Academic Editor: Alexey V. Polonikov
Life 2021, 11(2), 129; https://doi.org/10.3390/life11020129
Received: 23 December 2020
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Revised: 30 January 2021
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Accepted: 4 February 2021
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Published: 7 February 2021
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. 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., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we 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 demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.
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Keywords:
SARS-CoV-2; population genetics; recombination; mutation rate; selective sweeps; demographic inference
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MDPI and ACS Style
Vasilarou, M.; Alachiotis, N.; Garefalaki, J.; Beloukas, A.; Pavlidis, P. Population Genomics Insights into the First Wave of COVID-19. Life 2021, 11, 129. https://doi.org/10.3390/life11020129
AMA Style
Vasilarou M, Alachiotis N, Garefalaki J, Beloukas A, Pavlidis P. Population Genomics Insights into the First Wave of COVID-19. Life. 2021; 11(2):129. https://doi.org/10.3390/life11020129
Chicago/Turabian StyleVasilarou, Maria, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, and Pavlos Pavlidis. 2021. "Population Genomics Insights into the First Wave of COVID-19" Life 11, no. 2: 129. https://doi.org/10.3390/life11020129
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