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The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study

Our take —

This study sought to examine COVID-19 incidence, case fatality, and testing capacity and positivity across the continent of Africa, with both by-country and by-region analyses. They found 2,763,421 cases across 55 countries between February 14 and December 31, 2020 and a case fatality of 2.4%. South Africa was particularly hard hit, with the highest percentage of cases (38.3%) and highest number of deaths (43.3%). The test per case ratio across the continent ranged from 9 to 12% throughout the pandemic suggesting insufficient testing capacity. The study was limited by what data were reported to the Africa CDC, and therefore countries that used rapid antigen tests or symptomatic-only testing regimens may had false negatives or reduced cases compared to those actually with the disease in the country. This study is the first to offer a high-level overview of COVID-19 with data from 55 countries in Africa.

Study design


Study population and setting

The study sought to describe COVID-19 infections and mortality across Africa between February 14 and December 31, 2020. The study used data from the Africa CDC’s event-based surveillance data and publicly available public health data from 55 African Union member states and 5 regions. The outcomes of interest were country-specific and region-specific cumulative incidence per 100,000 people, weekly incidence per 100,000 people, case fatality ratio, testing ratio (defined as number of tests per 1 million population), and tests per case (defined as 3-week positive yield in tests conducted). Population estimates were taken from the UN Population Fund 2019 data. Active COVID-19 cases were estimated by subtracting reported deaths and recoveries from cumulative total cases reported.

Summary of Main Findings

The study identified 2,763,421 cases across 55 African Union member states. The majority (56%, N=31) of countries identified their first case between March 8 and 21, and 43% of cases were reported in the Southern region, followed by 34% in the Northern region, 12% in the Eastern region, 9% in the Western, and 3% in the Central region. Overall, 9 countries made up 82.6% of cases, with South Africa having the plurality of 38.3%, followed by Morocco (15.9%) and Tunisia (5.1%). Per 100,000 people, Cabo Verde had the highest incidence rate (1973.3/100,000), followed by South Africa (1819.6 per 100,000) and Libya (1526.4 per 100,000). 65,602 deaths were reported, with South Africa also having the most (43.3%, N=28,469). Across the continent the case fatality ratio was estimated at 2.4% and held steady since August 25. More than 26 million COVID-19 tests were conducted (19,956 tests per 1 million), with South Africa conducting the most. From March onwards, the tests per case ratio (3-week yield in positive tests) was between 9% and 12%, with heterogeneity between countries ranging from Algeria as 2.3% to Burundi with 94.1%.

Study Strengths

The study used data across all African Union member countries to examine by-country and by-region differences. Given there was initial concern of expected high rates of COVID-19 in Africa, the study was able to examine heterogeneity between countries across different epidemiological metrics in order to provide a nuanced picture of the continent. The study had temporal data across the weeks, which allowed them to compare trends from early in the pandemic to later in the pandemic when restrictions and non-pharmaceutical intervention mandates had shifted or lifted. Additionally, by also recording changes in testing capacity and tests conducted, they were able to examine whether changes in incidence rates reflect the number of tests or actual spread of disease.


The study used passive ascertainment which is subject to any limitations in the way data were collected in each country. For instance, if countries did not report testing data daily, there may be bias towards underestimating calculations of growth rate, case fatality ratio, active cases, and tests per case ratios. Different countries also may use different testing approaches, such as only symptomatic testing or asymptomatic testing as well. Other countries used rapid antigen tests which may have higher false negative results. There was also no way for the study to discern duplicate tests reported, and therefore the number of tests conducted may not reflect the number of people who received tests, and would deflate the test per case ratios. Finally, some of their numbers may be driven by specific countries, such as South Africa in the Southern region had the highest number of cases, while other countries in the region had much lower testing capacity as well as lower cases; therefore the region as a whole is reflective more of South Africa’s experience with COVID-19 than other countries.

Value added

This is the first continent-wide study of COVID-19 in Africa.

This review was posted on: 3 May 2021