Genomic Diversity and Phylogenetic Analysis of SARS-CoV-2 Circulating in Africa and Other Continents: Implications for Diagnosis, Transmission, and Prevention
Background: COVID-19 pandemic caused by SARS-CoV-2 remains a global health threat. Assessment of the genetic relatedness of the genome sequence is a prerequisite to understanding the dynamics, which is important to improve diagnosis and preventive measures. This study determined genomic diversity and SNP characteristic of genomes of SARS-CoV-2 from Africa and the rest of the world. The study involved molecular and phylogenetic analyses to understand the phylogeny and transmission dynamics of the virus. Methods: The SARS-CoV-2 genome sequence data were mined and retrieved from major databases for one year in two phases: Phase 1; December 2019 to May 2020 and Phase 2; June 2020 to December 2020. A maximum of the four sequences that fulfilled the following predetermined criteria from each country were randomly selected for inclusion in the study: (i) sequence length >29,700 nt, (ii) number of Ns in the sequence not >5%, (iii) inclusion of Poly-A tail in the sequence record to ensure completeness. Results: The similarity of SARS-Cov-2 genomes within and between countries was generally high with an average of 99.9%. Thus, SARS-CoV-2 vary between countries and continents by 0.1% as a result of SNPs in its genome. Phylogenetic data revealed multiple origin of SARS-CoV-2 in Africa and also suggested that the virus spreads by ‘founder’s effect’; whereby few viruses newly introduced into a population multiply rapidly and accumulate mutations as they spread quickly by community transfer to create population-based identity. Tree of continental consensus sequences retrieved in Phase 1 suggested that SARS-CoV-2 virus is of two major clusters: African cluster consisting of Africa, Europe, and North America and Asian cluster made up of Asia, South America, and Oceania. However, this clustering pattern vanished in phase 2. Thus, upholding the view that SARS-CoV-2 is constantly evolving. Conclusion: This dynamism and genetic diversity of SARS-CoV-2 have important implications in diagnosis, transmission, and prevention strategy.