Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations

Abstract

The dynamics of COVID- 19 disease have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 6139 complete nucleotide genomes from 51 African nations were obtained and analyzed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of SARS-CoV-2 lineages circulating in Africa. We investigated their diversity using several clade and lineage nomenclature systems, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 193 of the 2050 Pango lineages discovered worldwide circulated in Africa after two years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations because they had the most SARS-CoV-2 genomes sampled and sequenced. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa. Genomic surveillance is one of the important techniques in the pandemic preparedness toolbox and to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa, genomic surveillance activities across the continent must be expanded. The effectiveness of molecular surveillance as a method for tracking pandemics strongly depends on continuous and reliable sampling, speedy virus genome sequencing, and prompt reporting and we have to improve in all these aspects in Africa. Additionally, the pandemic breakout revealed that current land-border regulations aimed at limiting virus's international transmission are ineffective and a lot needs to be done to implement and improve our African land-borders as far as epidemiology is concerned in order to contain such outbreaks in the future.