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

Motayo, Babatunde Olarenwaju; Oluwasemowo, Olukunle Oluwapamilerin; Olusola, Babatunde Adebiyi; Akinduti, Paul Akiniyi; Arege, Olamide T; Obafemi, Yemisi Dorcas; Faneye, Adedayo Omotayo; Isibor, Patrick Omoregbe; Aworunse, Oluwadurotimi Samuel; Oranusi, Solomon Uche

BACKGROUND: The ongoing SARSCoV-2 pandemic was introduced into Africa on 14(th) February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months between 14(th) February to 24(th) April 2020, using whole genome sequences. METHODS: We performed recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. RESULTS: recombination signals were observed between the AfrSARSCoV-2 sequences and reference sequences within the RdRPs and S genes. The evolutionary rate of the AfrSARSCoV-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 7(th) 2019, (95% HPD November 12(th) 2019-December 29(th) 2019). The AfrSARCoV-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 D614-G 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 G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.