Estimation of exponential growth rate and basic reproduction number of the coronavirus disease 2019 (COVID-19) in Africa

Abstract

Background: Since the first case of coronavirus disease 2019 (COVID-19) in Africa was detected on February 14, 2020, the cumulative confirmations reached 15 207 including 831 deaths by April 13, 2020. Africa has been described as one of the most vulnerable region with the COVID-19 infection during the initial phase of the outbreak, due to the fact that Africa is a great commercial partner of China and some other EU and American countries. Which result in large volume of travels by traders to the region more frequently and causing African countries face even bigger health threat during the COVID-19 pandemic. Furthermore, the fact that the control and management of COVID-19 pandemic rely heavily on a country's health care system, and on average Africa has poor health care system which make it more vulnerable indicating a need for timely intervention to curtail the spread. In this paper, we estimate the exponential growth rate and basic reproduction number (R₀) of COVID-19 in Africa to show the potential of the virus to spread, and reveal the importance of sustaining stringent health measures to control the disease in Africa.

Methods: We analyzed the initial phase of the epidemic of COVID-19 in Africa between 1 March and 13 April 2020, by using the simple exponential growth model. We examined the publicly available materials published by the WHO situation report to show the potential of COVID-19 to spread without sustaining strict health measures. The Poisson likelihood framework is adopted for data fitting and parameter estimation. We modelled the distribution of COVID-19 generation interval (GI) as Gamma distributions with a mean of 4.7 days and standard deviation of 2.9 days estimated from previous work, and compute the basic reproduction number.

Results: We estimated the exponential growth rate as 0.22 per day (95% CI: 0.20-0.24), and the basic reproduction number, R₀, as 2.37 (95% CI: 2.22-2.51) based on the assumption that the exponential growth starting from 1 March 2020. With an R₀ at 2.37, we quantified the instantaneous transmissibility of the outbreak by the time-varying effective reproductive number to show the potential of COVID-19 to spread across African region.

Conclusions: The initial growth of COVID-19 cases in Africa was rapid and showed large variations across countries. Our estimates should be useful in preparedness planning against further spread of the COVID-19 epidemic in Africa.

Keywords: COVID-19; Pandemic; Reproduction number; Statistical modelling.

Fig. 1

The observed (dots) and fitted (curves) daily number of COVID-19 cases time series in Africa. The blue dots are observations, and the curves are fitting results. The red bold curve represents the mean fitting result, and the red dashed curves are the 95% confidence intervals. Multiple R-squared is 0.76

Fig. 2

The reported cumulative death confirmations of COVID-19 in top 12 African countries. The horizontal axis is the days since the cumulative exceeded 20 in a country

Fig. 3

The reported cases (blue cicle line) and the time-varying reproductive number (the three solid lines are the median and 95% CI) for the 12 African countries with top number of COVID-19 deaths. CI: Confidence interval