Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

What is it about?

There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARSCoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures.

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Photo by Jordan McDonald on Unsplash

Photo by Jordan McDonald on Unsplash

Why is it important?

This work describes the molecular epidemiology, analyzes the genetic variability of SARSCoV- 2 in Africa, and highlights the need for continuous genomic and epidemiological surveillance, which is imperative for tracing the emergence of genetic variants that can have significant effects on antigenicity, immunity, transmissibility, and potential vaccine escape. This information will also allow investigation of the transmission dynamics and resurgence of waves of infection, as well as optimize public health measures, such as the deployment of vaccine formulations across the continent.

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