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

•We establish the introduction of diverse sub-Lineages of Lineage B into Africa within the first few months of the SARS-CoV-2 outbreak.•The evolutionary rate of SARS-CoV-2 sequences in Africa is in congruence with global viral evolution.•The D614G spike protein mutant was the most prevalent in this study. 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. We performed recombination analysis against closely related CoV strains, Bayesian time scaled phylogeny, and investigation of spike protein amino acid mutations. 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. 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.