This study conducted trend analyses with longitudinal COVID-19 data from Our World in Data [43]. The study provides updates on traditional surveillance data and dynamic panel estimates from the original study by Post et al [7,40,41,44-46]. For the region of SSA, the data comprised an unbalanced panel of 47 countries and territories, running from December 11, 2020, to May 12, 2023. Because many countries around the world switched from daily to weekly reports at various points in 2023, we used a cubic spline to interpolate daily new cases and deaths if any country had 4 consecutive periods of nonzero new cases interspersed by 6 days of zero new cases.

To identify the appearance and duration of VOCs, we also used data on sequenced SARS-CoV-2 specimens from the Global Initiative on Sharing All Influenza Data (GISAID) [47-51]. We used Nextclade nomenclature [52] to collect clade designations from sequences and Pangolin nomenclature for lineage designations of SARS-CoV-2 [53,54]. Metadata for the study period were collected on June 22, 2023. To avoid low frequency or potentially erroneous samples, the data were filtered to exclude months with fewer than 100 available samples, variant groups with fewer than 5 samples in a month, and variant groups representing less than 0.5% of the total samples in a month. The final data set consisted of 184,386 total samples available on the GISAID platform [48-51].

This study employed the traditional surveillance metric, “speed” of spread, defined as the rate of new COVID-19 cases per 100,000 population. Additional enhanced metrics include acceleration, jerk, and 1- and 7-day persistence metrics. “Acceleration” is the change in speed from 1 unit of time to the next. Acceleration identifies whether the speed of spread is rising (positive acceleration), falling (negative), or stable (zero). “Jerk” is the change in acceleration over time. Its name comes from physics nomenclature. A large positive jerk can signal explosive growth in transmission rates. The 1- and 7-day persistence metrics are the statistical impacts of the 1- and 7-day lags of speed on the current speed. These measures capture an echo-forward effect of COVID-19 cases on cases either 1 or 7 days later. They are coefficient estimates from an Arellano-Bond dynamic panel data model [55]:

The data in this study are publicly available and contain no identifiable or private information. As defined by the 45CFR46:102 policy, the study does not qualify as human subjects research. Sources have been presented in the Data Availability statement.

The first objective of this study was to describe the status of the COVID-19 pandemic in SSA up to the point when WHO declared an end to COVID-19 as a public health emergency. The weekly transmission rate remained below 1 case per 100,000 population for over a year. Both dynamic and genomic surveillance methods suggested that COVID-19 transitioned from “pandemic” to “endemic” in SSA. For historical context, the overall region never reached the status of an outbreak. In general, SSA faced lower caseloads and fatalities from COVID-19 than the rest of the world. For example, during the first wave of the pandemic in early 2020, SSA as a region had significantly lower cases and deaths compared to individual countries such as Germany, Italy, and the United States. By early 2021, the region reported 3.2 million cumulative COVID-19 cases and 83,000 deaths, which accounted for only 2% of global cases and deaths despite the region hosting over 1.1 billion people or 14% of the global population [62].

One possible explanation for the low disease burden is undercounting driven by a lack of strong health care infrastructure in SSA [62-64]. The region went into the pandemic with limited health care facilities, personal protective equipment (PPE), and health care providers [65]. For example, in 2020, countries in SSA on average had 1.8 hospital beds per 1000 people compared to 4.41 hospital beds per 1000 people in Europe [66-68]. Some countries have also faced years of political instability. For example, South Sudan has dealt with nearly a decade of armed conflict, which has weakened the health care system and limited the ability to track outbreaks.

However, testing capacity in the region quickly expanded from a somewhat strong foundation, as the region had grappled with infectious diseases, such as malaria and Ebola, for years ahead of the COVID-19 pandemic [69,70]. Furthermore, estimates from several studies indicate that Africa had an undercounted death rate in line with the rest of the world [71-73]. The number of tests per COVID-19 case was also similar or higher in many African countries than in other countries around the world, even early in the pandemic [71].

The 47 countries in SSA had fewer than 0.2 million cumulative deaths from COVID-19. At the time of writing this article in June 2024, the entire continent had approximately 250,000 deaths, according to Our World in Data [43]. In comparison, South America had 1.4 million deaths, North America had 1.7 million deaths, Europe had 2.1 million deaths, and Asia had 1.6 million deaths. The rounded population sizes of Africa, South America, North America, Europe, and Asia were 3.9 billion, 0.4 billion, 0.7 billion, 0.6 billion, and 4.7 billion, respectively. Without dramatic differences in death undercounts, other explanations must account for part of the relative performance of Africa.

If testing cannot explain such a large gap, another potential explanation for the low death rate in the region is its unique demographic and geographic profile. SSA has a significantly younger population than other areas of the world [64]. For example, individuals older than 65 years accounted for 16% of the United States population but 3% of the SSA population in 2020 [74]. COVID-19 is known to disproportionately affect the health of elderly people, and demographic differences may explain why some developed countries faced significantly higher rates of mortality compared with SSA [63]. Geographically, most of the region’s population (59%) lives in rural areas, and this proportion is greater than that in other global regions [64].

Given that the region hosts a variety of communicable diseases, including malaria, typhoid, and Ebola, it is also plausible that repeated exposures to various pathogens helped people in SSA build stronger immune systems that rendered them less vulnerable to COVID-19 [75]. Still, COVID-19 had long-term health and societal impacts in the region. Given the limited financial resources of many countries in SSA, prolonged containment strategies became unsustainable as millions of people were thrown into poverty [76]. The Delta variant, which was originally sequenced in India, became the dominant strain in the region by the middle of 2021 and contributed to a third wave of infections [77]. The first cases of the Omicron variant were discovered in Botswana and South Africa in November 2021. Immediately after the discovery, countries across the globe implemented travel bans to countries in SSA to stem potential viral spread. However, these efforts did not stop Omicron from spreading globally and led to negative socioeconomic impacts in the region [78].

The SSA economy was greatly affected by the pandemic. During 2020, the region experienced a 2.1% gross domestic product (GDP) contraction, which is largely attributable to decreased economic activity from COVID-19 restrictions [79]. Lockdowns disrupt daily life and potentially limit access to nutrition, education, and health services. The African Development Bank estimated that about 30 million people in the region were pushed into extreme poverty as a result of the pandemic [80]. Lockdowns had an especially large effect on urban centers where, due to high population density, governments used strict lockdown protocols to control the spread of the virus. Additionally, quarantine measures disrupted food supply chains and threatened food security for millions of people in SSA [81]. It is estimated that 19.3% of the population could no longer afford their prepandemic level of food consumption due to economic hardships brought on by lockdown measures [82].

In general, governments used economic packages to cushion the financial blow on individuals and businesses. These packages typically included direct cash transfers, tax relief, investment in health care infrastructure, and investment in specifically vulnerable sectors of the economy. For example, Nigeria announced on April 1, 2020, that it would make cash transfers of 20,000 Naira (US $52) to low-income households registered in the government’s National Social Register. On April 21, 2020, South Africa announced a massive US $26 billion (10% of GDP) stimulus package, most of which was allocated to health expenditure, wage protection through the Unemployment Insurance Fund, and financial support for small businesses [83]. Many SSA countries also implemented indirect forms of economic support. For example, Ghana provided all citizens with free water from April 2020 to June 2020 [84]. Some governments also took steps to ensure food security by providing food rations to vulnerable populations [85]. After the initial lockdown in 2020, Rwanda promptly began distributing several food staples, including rice, beans, flour, and cooking oil, to vulnerable households [86]. These supplies were delivered “door to door” in an effort to maintain social distancing and thus minimize the spread of the virus.

International financial organizations also directed approximately US $230 billion during 2020 and 2021 to help countries in SSA mitigate the impact of the pandemic. For example, in April 2020, the African Development Bank Group created a US $10 billion COVID-19 Rapid Response Facility and a US $3 billion “Fight COVID-19 Social Bond” to help combat fiscal challenges [87].

SSA has several endemic diseases, such as Ebola, tuberculosis, HIV, and malaria, which have provided countries with valuable experience in how to combat disease outbreaks. For example, the African Union formed the Africa CDC in 2017 as a direct response to the 2014-2016 Ebola outbreaks. On February 22, 2020, the Africa CDC, in conjunction with the Southern Africa Center for Infectious Disease Surveillance (SACIDS), formed the Africa Taskforce for Coronavirus Preparedness and Response (AFTCOR) to create a continent-wide strategy for COVID-19 and bolster surveillance efforts in high-risk countries [88]. Surveillance efforts were built on existing systems in place for monitoring influenza and other severe acute respiratory diseases. Individual governmental responses in SSA involved travel bans, social distancing measures, public masking, contact tracing, and widespread lockdowns. Forty-four SSA countries closed schools, banned public gatherings, and enacted social distancing measures. Moreover, 11 SSA countries declared a state of emergency, and 15 countries closed their air, sea, and land borders [89]. South Africa, which had the region’s highest reported cases and deaths, was one of the first countries to implement strict lockdown measures. Within days of its first confirmed case, South Africa declared a national state of disaster [90]. By March 26, 2020, the government imposed a 21-day national lockdown, which restricted all nonessential movement of people and goods [91]. The government also used mobile testing units to reduce the movement of potentially infected individuals through communities [92]. Nigeria’s initial COVID-19 strategy included a nationwide curfew, public masking, and a ban on interstate travel. However, the country quickly shifted to a targeted lockdown strategy in specific areas with rapidly increasing COVID-19 cases. Kenya implemented a partial lockdown, with the government imposing a dusk-to-dawn curfew and restricting travel in and out of the capital, Nairobi, and other COVID-19 hotspots [93]. Uganda closed schools for almost 2 years to combat the pandemic, which is the longest school closure in the world [94].

Given the shortages of PPE and other essential medical equipment, such as ventilators, many countries shifted manufacturing to fill their gaps. A factory in Kenya was rapidly transformed from manufacturing clothes to producing 30,000 surgical masks a day [95]. The Central African Republic helped contract and support over 18,000 tailors and 300 firms by having them create protective face masks. This project not only bridged the gap in their PPE shortage but is estimated to have injected US $17 million into the economy [96]. South African manufacturers shifted tasks to address national shortages in ventilators [97].

Ultimately, countries focused on achieving herd immunity through widespread vaccination campaigns. However, the region faced difficulties accessing the limited global COVID-19 vaccine stockpiles, especially low-income countries [98]. It was estimated that US $12.5 billion would be required to vaccinate 70% of the SSA population and achieve herd immunity. This cost would equate to US $15.17 per person in the region, which is approximately 150% of the annual per capita governmental health care expenditure in the region [99]. As a result, many countries turned to international consortiums to fill the financial gap. For example, the African Vaccine Acquisition Team of the African Union and COVAX, a WHO-led consortium designed to ensure equitable access to vaccines, sought to acquire millions of vaccine doses [100]. However, vaccinations in SSA substantially lagged behind the rest of the world. By late 2021, when over 70% of high-income countries had over 40% of their populations vaccinated, Africa had only vaccinated 6% of its population [101]. As of March 24, 2023, just over 3 years after the start of the COVID-19 pandemic, less than 30% of the population of SSA had been fully vaccinated [102].

One factor contributing to low vaccination rates was vaccine hesitancy due to a perceived lack of safety and efficacy [103]. Another limiting factor was the lack of resources and infrastructure in certain countries to effectively distribute the vaccine. For example, one report on public health care in SSA showed that 1 in 6 people in the region lived more than 2 hours away from the closest public hospital [104]. Governments ultimately turned to mass vaccination campaigns focused on community engagement and education. For example, Cameroon, which had one of the lowest COVID-19 vaccination rates as of November 2022, implemented a 10-day mass vaccination campaign that ultimately administered over 2 million doses, almost doubling the percentage of the population that had received at least one dose [105]. The campaign focused on mobilizing community leaders to disseminate accurate information regarding the effectiveness of the vaccines [105]. The Central African Republic carried out a similar 7-day mass vaccination campaign against both COVID-19 and tetanus during November 2022 [105].

Despite success in ramping up testing capacity in the region, economic constraints pose challenges for future pandemic readiness [106,107]. Regional cooperation is likely to be a necessity [106]. Meta-analyses suggest that population knowledge may have been an impediment to the use of PPE and other mitigation measures at the individual level [108]. A combination of economic resources to secure vaccines, coupled with information campaigns, may encourage the future uptake of vaccines, which has remained low in SSA as a whole over the course of the COVID-19 pandemic [102]. Still, while the region grappled with economic hardship from the pandemic, the disease burden in SSA was among the lowest in the world.

COVID-19 data became less frequently reported around the world by the time the WHO declared an end to the pandemic as a public health emergency [109]. The number of countries with zero reported cases around the time of the declaration suggests a regime change in data reports for the region (as well as for other global regions). Additionally, people began to use at-home tests as the pandemic evolved, though this change was less pronounced in SSA than in other parts of the world due to low rates of at-home tests [106,110]. Because the surveillance metrics of speed, acceleration, jerk, and 7-day persistence are based on rates and not total counts, statistical bias in regional estimates caused by countries moving in or out of the sample has been mitigated, but the omission of a country could still influence historical data comparisons. The persistence measures from dynamic panel estimates have been calculated from a 120-day window to limit intertemporal biases caused by changes in reporting or sample inclusion. Still, data availability remains a limitation. Continued reports on COVID-19 transmission after the middle of May 2023 would provide further insights into the status of the pandemic at the time. The team did not consider transmission data to be sufficient for conclusions beyond that point.

Although COVID-19 is now well contained in SSA, concerns about the potential resurgence of the virus remain valid. As long as COVID-19 continues to spread and mutate, the possibility of novel variants remains. Variants could potentially be more transmissible or resistant to vaccines, or cause more severe illness. This underlines the importance of continued vigilance, vaccination efforts, and global cooperation to control the spread of the virus [39].

SSA experienced a relatively low COVID-19 disease burden compared to other global regions, such as the Americas and Europe [43]. This relative performance may seem counterintuitive given the economic and health infrastructure disparities across regions, as well as the relatively low vaccination rates across SSA. However, SSA has several distinctive and protective factors. Demographics are the primary protective factors. The African continent as a whole has the youngest population in the world, and COVID-19 mortality rates rise exponentially with age [111-113]. Moreover, international trade and air pollution have been positively linked to transmission rates [114,115]. International trade between SSA countries remains stubbornly low [116], but as the region continues to develop economically, the risk of novel pathogen transmission through trade routes may grow. The climate may also be protective, but the relationship between climate and COVID-19 transmission is complex, and risk profiles will shift as climate change continues [117,118].

Several lessons for future pandemic preparedness have emerged. Perhaps the most pressing question is how to limit disease burden ahead of vaccines and treatment modalities. New technologies will renew the potential to improve early surveillance methods [119-121]. A combination of rapid widespread individual testing, together with epidemiological task forces, should be the first line of defense [122]. Lockdown policies, despite their economic cost, have also shown efficacy [123]. When vaccines do become available, measures of general governance are associated with vaccination rates, and individual countries with low general governance measures may be points of intervention to contain disease spread [124]. On that note, continued international cooperation will be necessary to mitigate the impact of future pandemics both inside and outside SSA [125,126].