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

Abstract

Highlights We established the introduction of diverse sub-Lineages of Lineage B into Africa within the first few months of the SARSCoV-2 outbreak. The evolutionary rate of SARSCoV-2 sequences in Africa is consistent with previous reports indicating congruence with global viral evolution. The G614 spike protein mutant was the most prevalent in this study.

Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective

“…Our study presents that the highest substitution rate of the ORF10 protein appeared in Europe, followed by Africa ( Figure 2 B). Previous studies have reported the import of SARS-CoV-2 from Europe to Africa [ 47 , 48 ], which explains some similar patterns between Europe and Africa. To support surveillance, a paucity of SARS-CoV-2 sequence data from Africa requires further sequencing efforts on the African continent [ 47 ].…”

“…Previous studies have reported the import of SARS-CoV-2 from Europe to Africa [ 47 , 48 ], which explains some similar patterns between Europe and Africa. To support surveillance, a paucity of SARS-CoV-2 sequence data from Africa requires further sequencing efforts on the African continent [ 47 ]. Additionally, other viral proteins are also known to interact with many host proteins that participate in multiple biological processes such as protein trafficking, translation, and transcription [ 49 ].…”

Coding-Complete Genome Sequence and Phylogenetic Relatedness of a SARS-CoV-2 Strain Detected in March 2020 in Cameroon

“…Phylogenetic analysis showed that these viruses diversified during the duration of the pandemic into two major lineages, A and B, with several sublineage diversifications ( 4 ). A recent study indicated that the African SARS-CoV-2 sequences also diversified into two lineages, A and B, with B being more diverse with multiple sublineages ( 5 ). Here, we report the coding-complete genome sequence of a SARS-CoV-2 strain obtained from a sample taken on 5 March 2020 in Cameroon from a 58-year-old French patient who arrived from France on 24 February 2020.…”

Efficacy and safety of tocilizumab in COVID-19 patients: a living systematic review and meta-analysis – Author’s reply

“…Third, similar to other RNA viruses, SARS-CoV-2 has been shown to have a high mutational rate. Emerging data report world-wide evolutionary changes of the SARS-CoV-2 virus [ [7] , [8] , [9] ]. In one study, the rate of SARS-CoV-2 mutation was estimated to be 4.133 x 10 -4 substitutions/site/year [ 8 ], which is similar to the mutation rate of other coronaviruses [ 10 ].…”

“…Emerging data report world-wide evolutionary changes of the SARS-CoV-2 virus [ [7] , [8] , [9] ]. In one study, the rate of SARS-CoV-2 mutation was estimated to be 4.133 x 10 -4 substitutions/site/year [ 8 ], which is similar to the mutation rate of other coronaviruses [ 10 ]. Interestingly, the majority of documented SARS-CoV-2 mutations involve G-U and C-U substitutions with nearly 50% of all mutations involving C-U substitutions [ 10 , 11 ].…”