Population Genomics Insights into the First Wave of COVID-19



Vasilarou, Maria, Alachiotis, Nikolaos, Garefalaki, Joanna, Beloukas, Apostolos ORCID: 0000-0001-5639-0528 and Pavlidis, Pavlos
(2021) Population Genomics Insights into the First Wave of COVID-19. LIFE-BASEL, 11 (2). 129-.

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Abstract

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.

Item Type: Article
Uncontrolled Keywords: SARS-CoV-2, population genetics, recombination, mutation rate, selective sweeps, demographic inference
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 08 Jun 2021 07:39
Last Modified: 18 Jan 2023 22:35
DOI: 10.3390/life11020129
Open Access URL: https://doi.org/10.3390/life11020129
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3125567