Genetic diversity and transmission dynamics of SARS-CoV-2 in East Africa

COVID-19 is a respiratory disease caused by the SARS-CoV-2 virus, which put the entire world on hold for two years from 2020 to March 2022 before the rapid roll-out of vaccines. This virus claimed many lives, 6,331,727 deaths globally, and 172,390 people in Africa died from the disease, while Uganda lost 3,620 people in the same period. The study aimed to analyse the spread patterns of SARS-CoV-2 in Uganda and neighbouring countries and understand the community transmission within Uganda. The study utilised genomic sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) repository. Bayesian Phylogeography methods were used via the BEAST software. The first case of COVID-19 in Uganda likely originated from Kenya. The virus spread from Kenya to other East African countries. Cross-border movements, especially by truck drivers and refugees, played a significant role in the spread. The study highlights the importance of cross-border collaborations to control infectious disease spread. The spread pattern was influenced by trade routes and the movement of people, emphasising the need for robust border control measures during pandemics. Understanding the origin and spread of SARS-CoV-2 can inform better public health strategies and preparedness for future pandemics.