The basic reproduction number of COVID-19 across Africa

Abstract

The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) took the world by surprise. Following the first outbreak of COVID-19 in December 2019, several models have been developed to study and understand its transmission dynamics. Although the spread of COVID-19 is being slowed down by vaccination and other interventions, there is still a need to have a clear understanding of the evolution of the pandemic across countries, states and communities. To this end, there is a need to have a clearer picture of the initial spread of the disease in different regions. In this project, we used a simple SEIR model and a Bayesian inference framework to estimate the basic reproduction number of COVID-19 across Africa. Our estimates vary between 1.98 (Sudan) and 9.66 (Mauritius), with a median of 3.67 (90% CrI: 3.31-4.12). The estimates provided in this paper will help to inform COVID-19 modeling in the respective countries/regions.

Fig 1. Observed and estimated number of daily cases of COVID-19.

Top panel: West Africa (Nigeria, Ghana, Senegal and Mali), middle panel: Southern Africa (South Africa, Zambia, Namibia and Malawi), and bottom panel: North Africa (Egypt, Tunisia, Algeria and Morocco). The black dots are the daily reported cases of COVID-19, the solid lines are the median predicted cases, the narrower (darker) bands are the 50% CrI, while the wider (lighter) bands are the 90% CrI.

Fig 2

Same caption as Fig 1 but for East African countries: Ethiopia, Kenya, Rwanda and Sudan (top panel), Central African countries: Cameroon, Chad, Gabon and Congo (middle panel), and African Islands: Madagascar, Comoros, Mauritius, and Cape Verde (bottom panel).

Fig 3. Estimated basic reproduction numbers.

The estimated basic reproduction number for each country. The black dots are the median estimates of the reproduction numbers, while the thin bars are 90% credible intervals (CrI).