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Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences

Motayo, B. and Oluwasemowo, Olukunle Oluwapamilerin and Olusola, Babatunde Adebiyi and Akinduti, P. A. and Arege, Olamide T. and Obafemi, Yemisi Dorcas and Faneye, Adedayo Omotayo and Isibor, Patrick Omoregie and Aworunse, Oluwadurotimi S. and Oranusi, S. U. (2021) Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. International Journal of Infectious Diseases, 103. pp. 282-287.

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Background The ongoing SARS-CoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing a severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months, between 14th February to 24th April 2020, using whole genome sequences. Methods We performed recombination analysis against closely related CoV strains, Bayesian time scaled phylogeny, and investigation of spike protein amino acid mutations. Results Recombination signals were observed between the Afr-SARS-CoV-2 sequences and reference sequences within the RdRPs and S genes. The evolutionary rate of the Afr-SARS-CoV-2 was 4.133 × 10−4 Highest Posterior Density (HPD 4.132 × 10−4 to 4.134 × 10−4) substitutions/site/year. The time to most recent common ancestor (TMRCA) of the African strains was December 7th 2019, (95% HPD November 12th 2019-December 29th 2019). The Afr-SARCoV-2 sequences diversified into two lineages A and B, with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility (MCC) tree and PANGOLIN software. There was a high prevalence of the D614G spike protein amino acid mutation 59/69 (82.61%) among the African strains. Conclusion This study has revealed a rapidly diversifying viral population with the G614G spike protein variant dominatinge advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARS-CoV-2 in Africa.

Item Type: Article
Uncontrolled Keywords: SARSCoV-2Virus evolution Phylogeny Africa
Subjects: Q Science > Q Science (General)
Q Science > QH Natural history > QH301 Biology
Q Science > QR Microbiology
Divisions: Faculty of Medicine, Health and Life Sciences > School of Biological Sciences
Depositing User: Mrs Hannah Akinwumi
Date Deposited: 15 Jul 2022 12:09
Last Modified: 15 Jul 2022 12:09

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