Pan-African evolution of within- and between-country COVID-19 dynamics

May 25, 2021

Paddy Ssentongo, Claudio Fronterre, Andrew Geronimo, Steven J. Greybush, Pamela K. Mbabazi, Joseph Muvawala, Sarah B. Nahalamba, Phillip O. Omadi, Bernard T. Opar, Shamim A. Sinnar, Yan Wangg, Andrew J. Whalen, Leonhard Held, Christopher Jewell, Abraham J. B. Muwanguzi, Helen greatrex, Michael M. Norton, Peter J. Diggle, and Steven J. Schiff.


The pan-African COVID-19 surveillance and modelling framework was used to understand and predict the spread of COVID-19 throughout Africa. The tool assessed the burden of COVID-19 cases, factors associated with its spread, and made short-term predictions for new cases. In August 2020, over one million cases and 20,000 deaths were reported in the African Union. Over half of the cases occurred in the southern region while North Africa had a 4% case fatality rate. South Africa and Djibouti had case rates significantly higher than the continental average, and the Republic of Congo had a rate significantly lower than the continental average. High variability in geographic distribution and epidemiologic curves were noted across countries. Within-country spread was found to be reduced with increased availability of COVID-19 testing and better testing policy. Interestingly, these factors increased transmission from neighbouring countries. Landlocked countries had high between-country transmission due to challenges in implementing and enforcing strict border closures. Temperature and humidity also had small but significant associations with spread. When forecasting case counts in the short-term, the predictions were well-aligned with observations for most countries. The pan-African surveillance tool is useful for predicting COVID-19 cases as well as providing insight into other factors that contribute to transmission.

Ssentongo P, Fronterre C, Geronimo A, et al. Pan-African evolution of within- and between-country COVID-19 dynamics. Proc Natl Acad Sci 2021; 118: e2026664118.

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