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

Introduction

The first case of COVID-19 in Africa was reported in Egypt on Feb 14, 2020, just 14 days after WHO had declared the outbreak a public health emergency of international concern.1, 2 In an act of continental solidarity and leadership, the African Union (AU) Commission, through the Africa Centres for Disease Control and Prevention (Africa CDC), convened an emergency meeting of all ministers of health on Feb 22, 2020, to develop and endorse a Joint Continental Strategy for COVID-19 Outbreak.³ Since February, 2020, Africa CDC has rolled out six additional pandemic response initiatives across the continent targeting surveillance and testing; medical supply availability; public health and social measures (PHSMs); safe travel, livelihoods, and economies; pathogen genomics; and vaccine development and supply.4, 5, 6

To successfully and equitably inform the implementation of the continental strategy and all of the associated initiatives across the continent, it was important to understand the regional and AU Member State-specific infection rates, mortality rates, testing capacity, ability to implement mitigation measures, and overall pandemic effect. Africa CDC has monitored the evolution of the pandemic across the globe since early January, 2020, through routine event-based surveillance. Within Africa, this information provided situational awareness and informed continental response efforts.

Despite the spread of COVID-19 to almost all countries in Africa within 3 months, country-reported case counts suggest that the pandemic has spread much slower on the continent than in the rest of the world.7, 8, 9 To date, a comprehensive analysis of the heterogeneity of the pandemic across all five AU regions and 55 Member States has not been done.9, 10, 11, 12, 13, 14, 15, 16 Further, many of the initial modelling projections, response recommendations, and pandemic evolution discussions about COVID-19 in Africa have come wholly or partly from entities outside of the continent trying to fit other global experiences to Africa, not fully appreciating the diversity and differences across the continent.17, 18, 19, 20, 21, 22, 23, 24

Africa is characterised by the heterogeneity in its demography, geography, economy, culture, politics, language, social equity, and disease patterns.²⁵ These differences are seen at the regional, country, and subnational levels and extend into areas of social services, health systems, and attainment of International Health Regulation capacity; these elements affect each country's response to the COVID-19 pandemic.26, 27 The differences across Africa show the importance of evaluations that go beyond an aggregated case number for the continent, which can misrepresent the true situation within. We aimed to analyse epidemiology, testing, and PHSM-related data reported from the five AU regions and all 55 AU Member States to further understand the COVID-19 situation across the continent.

Methods

Results

As of Dec 31, 2020, 2 763 421 cases of COVID-19 were reported from the 55 AU Member States (table 1 ), representing 3·4% of the 82 312 150 cases reported globally.⁸ 31 (56%) of 55 countries detected their first cases between March 8–21, 2020. Sahrawi Arab Democratic Republic was the last country to report its first case on July 24, 2020 (appendix p 1). The proportion of cumulative cases and deaths varied across the five geographical AU regions: 43% of cases and 46% of deaths in the Southern region, 12% of cases and 9% of deaths in the Eastern region, 34% of cases and 37% of deaths in the Northern region, 3% of cases and 2% of deaths in the Central region, and 9% of cases and 5% of deaths in the Western region. The Southern region reported more cases than the other regions (table 1). Nine countries accounted for 2 283 613 cases, 82·6% of the COVID-19 cases reported in Africa: South Africa (38·3%), Morocco (15·9%), Tunisia (5·1%), Egypt (5·0%), Ethiopia (4·5%), Libya (3·6%), Algeria (3·6%), Kenya (3·5%), and Nigeria (3·2%). The remaining 46 countries reported between 34 and 55 000 cases each (table 1, figure 1 ). Cabo Verde (1973·3), South Africa (1819·6), Libya (1526·4), Morocco (1200·0), and Tunisia (1191·2) reported the highest cumulative incidence of cases per 100 000 population. By region, the Southern region had the highest incidence (640·5) per 100 000 population, primarily driven by the high incidence in South Africa (table 1).

65 602 deaths were reported from 54 (96%) AU Member States, with most (77%) coming from five countries: South Africa, Egypt, Morocco, Tunisia, and Algeria (table 1). The continent has maintained a CFR of 2·4% since Aug 25, 2020. Of 53 (96%) countries actively reporting and reporting more than 100 COVID-19 cases, 17 reported CFRs higher than the continental and global CFR of 2·2%: Sudan (6·1%), Egypt (5·5%), Chad (4·9%), Liberia (4·6%), Mali (3·8), Tunisia (3·4%), DR Congo (3·3%), The Gambia (3·3%), Niger (3·1%), Malawi (2·9%), Sierra Leone (2·9%), Algeria (2·8%), Somalia (2·8%), South Africa (2·7%), Zimbabwe (2·6%), Mauritania (2·3%), and Angola (2·3%). The Southern region reported the most deaths (30 453 [46·4%]) and both the Northern and Southern regions reported the highest regional CFRs (both 2·6%).

Regarding laboratory testing and testing ratios, as of Dec 31, 2020, more than 26 million COVID-19 tests (19 956 tests per million population) were done by the 55 AU Member States (table 1). Six countries (South Africa, Morocco, Ethiopia, Kenya, Egypt, and Nigeria), representing four regions, accounted for more than 62% of all tests performed. By the end of March, 2020, most countries (n=49; 89%) had the ability to test for SARS-CoV-2 by PCR; expanding to all 55 AU Member States by July, 2020 (appendix p 1). Since mid-March, 2020, the continent has maintained a crude ratio of tests per case reported between nine and 18. In December, 2020, the Northern region had the highest proportion of countries (five [71%] of seven) that reported less than ten tests per case (figure 1). For the 40 countries where testing data were available at the start of their first peak, 28 (70%) had adequate testing capacity (test per case ratios >10, range 10·2–381·9). This figure decreased to 26% (14 of 53 countries) during the peak of the first wave and 36% (four of 11 countries for which data were available) during the peak of the second wave, and increased to 85% (40 of 47) during the trough periods after the first wave and 75% (three of four countries for which data were available) during the trough period after the second wave. Four (8%) of 53 countries (Algeria, Sahrawi Arab Democratic Republic, Somalia, and Sudan) reported test per case ratios less than ten and CFRs greater than 2·2 during both the first wave peak and trough (appendix p 2).

For active cases and recoveries, of the 2 763 421 reported cases as of Dec 31, 2020, 2 219 663 (80·3%) were reported as having recovered from COVID-19. Six countries (Central African Republic, Cabo Verde, Côte d'Ivoire, Djibouti, Gabon, and Ghana) were all reporting COVID-19 recovery rates equal to or greater than 98% (table 1). As of Dec 31, 2020, 478 156 people with confirmed COVID-19 were considered actively infected. Most (54·2%) of the active cases were reported from South Africa (n=161 095) and Libya (n=98 418). The highest numbers of active cases per 100 000 population were reported in Libya (n=1491), South Africa (n=277), Tunisia (n=257), Eswatini (n=150), and Namibia (n=141).

Between Feb 14 and Dec 31, 2020, PHSM reports were monitored using the Partnership for Evidence-Based Response to COVID-19 dashboard⁴ and Oxford COVID-19 Government Response Tracker.²⁸ For the 50 Member States for which PHSM data were available, 36 (72%) reported implementing their first stringent PHSM a mean of 15 days (range 1–68) before reporting their first COVID-19 case, whereas the remaining 14 Member States reported implementing their first stringent PHSM a mean of 9 days (1–30) after their first case. By April 15, 2020, 48 (96%) Member States reported having five or more stringent PHSMs in place, with the most common being international travel controls (50 Member States [100%]), school closures (49 Member States [98%]), cancelled public events (49 Member States [98%]), and restrictions on gatherings (48 Member States [96%]). By Dec 31, 2020, the number of Member States with five or more stringent PHSMs in place had decreased to 36 (72%).

For the most populous countries in each region (DR Congo in the Central region, Ethiopia in the Eastern region, Egypt in the Northern region, South Africa in the Southern region, and Nigeria in the Western region), three had at least one or more stringent PHSMs in place between 5 days and 12 days before their first case or cases were reported. All seven stringent PHSMs were reported to be in place between March 24–30, 2020, for all five countries. The weekly growth rate for the most populous country in each region 1 day before implementing all seven stringent PHSMs was 366% (range 30 to 1000). The weekly growth rate after implementing all seven stringent PHSMs for 14 days was 17% (−17 to 78). All countries reported maintaining these seven stringent PHSMs through the peak of their first wave of cases; however, three countries (Egypt, Nigeria, and South Africa) loosened two or more PHSMs before the peak of their first wave (figure 2 ). The first PHSMs were loosened a mean of 108 days (range 36 to 194) after they were put in place. Restrictions on public transportation were the most commonly loosened PHSMs (three [60%] of five countries; table 2 ). For these five countries, the weekly growth rate 14 days after easing of the first PHSM was 10% (range −17 to 57).

For wave analysis, at the continental level, the peak weekly incidence (97) of the first wave occurred in mid-July, 2020, with a mean of 18 273 new cases being reported per day for epidemiological week 29. By the end of December, 2020, the African continent had not yet declared the peak of its second wave; however, the weekly incidence reported for epidemiological week 53 was 129 and mean number of new daily cases was 23 790. As of Dec 31, 2020, 14 (25%) of 55 countries had only experienced or were still experiencing their first wave of cases, 40 (73%) had experienced or were still experiencing a second wave of cases, and four (7%) had experienced or were still experiencing their third wave of cases. No information was available to assess the pandemic progression for Tanzania. Of the 40 countries who had experienced or were starting to experience a second wave of cases, 24 (60%) reported a mean increase of 403% (range 10–4602) in the mean number of new cases per day being reported from wave start to peak when comparing the first and the second waves. Of the 38 countries that previously experienced or were experiencing a second wave and reporting on PHSM implementation, 17 (45%) had a mean of two (range 1–6) less PHSMs in place during the second wave than the first (appendix p 1).

Discussion

By the end of 2020, most of the African continent was experiencing a fast evolving second wave of the COVID-19 pandemic, reporting a 30% increase in both the weekly incidence and the mean daily new cases when comparing the peak of the first wave to epidemiological week 53. Progression, response, and effect have varied greatly among the AU regions and Member States reporting COVID-19 cases. Compared with other continents, it appears that Africa has not experienced the pandemic at the same magnitude with respect to the overall COVID-19 case and death counts.7, 34 However, when the situation is examined for a few African countries like Cabo Verde, South Africa, Libya, and Morocco, whose cumulative incidence rates have been particularly high in comparison to other African countries, we observed stark similarities to what other countries across the world are reporting.7, 8

The late importation of cases and early implementation of PHSMs⁴ compared with other continents bought time for some African countries to boost their detection and response capacity.⁷ The continent went from three countries having COVID-19 diagnostic capacity at the beginning of February, 2020, to 49 countries representing all five regions by the end of March, 2020, and to all 55 AU Member States by July, 2020. Although the high availability of diagnostic testing and a continental push to increase testing volumes in June, 2020,³⁵ has resulted in nearly achieving the WHO recommended tests per case ratio for the continent as a whole, as of Dec 31, 2020, a third of countries (including most of the countries in the Northern region) had reported less than ten tests per reported COVID-19 case identified, suggesting a less than adequate distribution or use of tests within communities. Further, it is noted that although most countries are able to maintain adequate testing capacity beyond the peak infection, many struggle to maintain adequate testing volumes during the peak outbreak periods. This finding supports the need to continue promoting laboratory capacity building initiatives like the Partnership to Accelerate COVID-19 Testing³⁵ and the use of rapid antigen tests³⁶ in specific countries and regions, while still ensuring the continent has enough capacity in the face of the global shortage of testing reagents and extraction kits.

The initial capacity building activities by Africa CDC and other partners focused on regional training aimed at strengthening a countries' surveillance capacity to quickly detect and contain cases at points of entry and within the community.³⁷ The high tests per reported case ratios (>50) reported from several Member States in the Eastern (Ethiopia, Eritrea, Uganda, and Rwanda) and Southern (Angola, Lesotho, and Zimbabwe) regions at the start of their initial wave of cases could indicate a focus on points of entry surveillance as the countries were likely to be testing more people at the borders and ports before entering the country. Although it is recommended that countries transition from border screening to active case finding in the community via contact tracing or other surveillance efforts once local transmission occurs,³⁸ countries might be reluctant to abandon aggressive border screening efforts if they border or continue to receive travellers from countries that either report many cases or are not transparent about reporting or tracking cases.39, 40, 41 To address these concerns, cross-border COVID-19 management and data sharing efforts are underway for the Eastern and Southern regions.⁴²

Early PHSM implementation is assumed to have slowed the pandemic in Africa; however, this analysis suggests that it is necessary to review multiple indicators down to the country level to fully understand the situation.4, 7 Despite facing a second wave of cases and new, more transmissible variants of the virus,43, 44 many countries had not implemented the same degree of PHSMs as they had early on in the pandemic. Additionally, for some countries where cases continue to increase despite maintaining most of their stringent PHSMs, other factors like changes in population behaviour are likely to be present. Increasing reports of PHSM adherence fatigue45, 46 leaves the continent's population at risk and highlights the need to reinvigorate and update existing communication strategies. These data indicate that Member States not only need to remain vigilant in collecting and analysing COVID-19 data to inform PHSM adjustments in place, but they also need to monitor PHSM adherence and ensure public health and case management capacities are sustained as cases rise.

Most of the countries reporting higher CFRs than the continental and global ratios also simultaneously reported having decreased testing capacity. This result suggests that limited surveillance and testing capacity might have played a role in the observed higher CFRs as not all cases were identified. The Northern and Southern regions reported the highest regional CFRs despite typically having better developed health systems than the rest of the continent.⁴⁷ The higher CFRs in the Northern region might also be explained by truly high CFRs due to an older population and a higher prevalence of non-communicable diseases (comorbidities), which can both contribute to poorer clinical outcomes.⁴⁷

This study has some limitations. Although Africa CDC was able to collect basic epidemiological data from Member States, absence of case-specific information regarding age, gender, occupation (eg, health-care workers), comorbidities, and clinical outcomes for all Member States limited our ability to provide regional or Africa-wide information regarding these variables. Additionally, not all countries reported COVID-19 case and testing data daily, which might have skewed growth rate calculations, CFRs, active cases, and tests per case ratios. Further, our understanding of the dynamics for the spread of COVID-19 was limited by the different testing approaches used to diagnose COVID-19. Some countries started using rapid antigen tests on a limited basis to diagnose cases, which might have higher false negative results; and some countries included repeat tests in the numbers they reported, which could lead to elevated testing numbers and tests per case ratios. Additionally, some regional trends might have been affected by variance within the region, which might misrepresent the situation seen across that region as a whole (eg, cases, deaths, and tests in South Africa compared with other countries in the Southern region). Although the intent of this analysis was to provide a high-level understanding of the COVID-19 situation across the continent, future analyses could benefit from inclusion of additional variables that measure the effect of COVID-19 within the Member States.

Despite the limitations, these regional and country-specific analyses have helped inform the joint continental response efforts in the allocation of testing reagents and equipment, deployment of response staff, and identification of areas requiring training. For example, in countries without existing COVID-19 PCR capacity, the repurposing of existing GeneXpert platforms for COVID-19 has improved testing capacity.48, 49, 50 In addition to supplying the SARS-CoV-2 GeneXpert cartridges to these countries, Africa CDC and WHO also provided traditional PCR equipment to address the poor capacity. As part of the Partnership to Accelerate COVID-19 Testing initiative,³⁵ a continental procurement platform, Africa Medical Supply Platform, has been put in place to allow Member States to collectively purchase commodities needed for their own response efforts. The recruitment and deployment of community health workers, epidemiologists, risk communicators, and laboratory staff for this initiative are being driven by the epidemic situation and capacity needs of each Member State. As surveillance and testing efforts transitioned from border-focused to communities, training opportunities and guidance materials were produced to help meet the Member State demands. Further, collaborations like the Partnership for Evidence-Based Response to COVID-19 are using these epidemiology, testing, and PHSM data along with qualitative measures such as survey data to inform Member States' response efforts and improve risk communication regarding best practices that should be put in place.⁴

In the face of a second and possibly third wave of cases, Africa CDC remains vigilant in monitoring the COVID-19 outbreak on the continent. Although rapid PHSM implementation probably contributed to the relatively low initial continental case numbers being reported, several factors are likely to have led to a larger second wave of cases. Anecdotal evidence from across the continent indicates mask wearing and physical distancing behaviours are markedly decreasing, probably from adherence fatigue and economic necessity. Additionally, new variants of concern—reported to be more transmissible,⁴⁴ more deadly,⁵¹ and with the potential to escape existing immunity52, 53—are circulating among Member States and likely to be changing disease dynamics.

Efforts to better understand the true burden of COVID-19 and the outcomes associated with new circulating SARS-CoV-2 variants and their effect on vaccine efficacy are needed, along with campaigns to maintain population practices to prevent spread. Africa CDC is supporting Member States with the implementation of seroprevalence surveys, excess mortality surveillance, and genomic surveillance to better understand some of these outstanding questions. We want to highlight the need to measure the effect of COVID-19 intervention measures on other communicable diseases such as malaria and tuberculosis, which are prevalent in many countries across Africa. Having a holistic, data-driven understanding of the situation across, as well as within, the continent is imperative for preventing transmission, severe illness, and death from COVID-19; informing vaccination and other intervention strategies; and minimising the social and economic harms associated with the pandemic.⁵⁴

Data sharing

All COVID-19 case, death, recovery, testing, and PHSM data collected by Africa CDC are posted daily on our website. To gain access to a complete export of our dataset, please contact AfricaCDCEBS@africa-union.org to sign a data access agreement.

Declaration of interests

We declare no competing interests.

Supplementary Material