The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

An extensive network of African scientists analyzed the first 100,000 SARS CoV-2 genomic sequences from the continent, characterizing the pandemic’s progression and highlighting the dispersal patterns of Variants of Concern, including Delta and Omicron. The work has been published in the esteemed journal Science (Impact Factor 47.73)

UFS researchers, Prof. Martin Nyaga (Next Generation Sequencing Unit and Division of Virology), Mr. Philip Armand Bester (National Health Laboratory Services – NHLS and Division of Virology), Prof. Dominique Goedhals (NHLS and Division of Virology, currently at PathCare), were part of this continental collaborative study.

The study demonstrates the utility of NGS technologies in understanding the genomics of SARS-CoV-2 disease. Genomic studies provide deeper insights regarding diseases and provide timely solutions, such as accelerating vaccine development, to solving diseases affecting the African continent.

Fig. 1. Epidemiological progression of the COVID-19 pandemic on the African continent.
(A) Total reported new case counts per million inhabitants in Africa (Data Source: Our World in Data; OWID; log-transformed) along with the distribution of VOCs, the Eta VOI and other lineages through time (size of circles proportional to the number of genomes sampled per month for each category). (B to F) Breakdown of reported new cases per million (Data Source: Our World in Data; OWID; log-transformed) and monthly sampling of VOCs, regional variant or lineage of interest and other lineages for three selected countries for North, Southern, West, Central and East Africa respectively. For each region, a different variant or lineage of interest is shown, relevant to that region (C.36, C.1.2, Eta, B.1.620 and A.23.1, respectively).