Africa Centres for Disease Control and Prevention Is Closing Gaps in Disease Detection

Introduction

For millennia, people living in Africa have suffered high rates of infectious disease because of the continent's unique geography, climate, ecology, and cultural diversity. ¹ Reductions in child mortality and vaccine-preventable disease are now helping drive the most rapid human population growth ever on the continent. ² The number of Africans is expected to double from 1.2 billion in 2016 to 2.5 billion by 2050. ³ Despite public health successes, the 2014-2016 West Africa Ebola outbreak demonstrated to African leaders that infectious disease outbreaks remain a major threat to health, economic growth, and development. ⁴

The African Union (AU) is an intergovernmental organization that represents all countries in Africa and works to develop an integrated, prosperous, and peaceful continent. Its signature initiative is a continental free trade agreement that will allow people to move without visas and goods to move without customs checks. ⁵ Recognizing the unique and persistent vulnerability to infectious diseases and imminent free movement of people and goods, the AU established a new continent-wide public health agency, the Africa Centres for Disease Control and Prevention (Africa CDC), in 2017. ⁶

After the 2014-2016 West Africa Ebola outbreak ended, 4 comprehensive analyses concluded that earlier detection of the outbreak and subsequent cases by public health officials could have reduced transmission, illnesses, and deaths. ⁷ From 2016 to 2019, 49 countries in Africa completed a joint external evaluation to assess their capacity to prepare, detect, and respond to epidemics. Findings from the evaluation found major gaps across all 3 of these areas.^8,9 The first strategic objective in the statute that established Africa CDC was, therefore, to establish “early warning and response surveillance platforms to address in a timely and effective manner all health emergencies.” ³ There are 2 central challenges to early detection of outbreaks in Africa. First, most outbreaks on the continent are never detected. People may not have access to healthcare, high-quality laboratory testing performed, or their laboratory tests reported.^10-13 Moreover, public health officials often do not analyze reports for aberrations and act on them. ¹⁴ Second, among outbreaks that are detected, public health agencies often respond late and with minimal resources. Outbreaks may end naturally rather than by government intervention—that is, susceptible people become infected and either recover with immunity or die. ¹⁵ In this article we describe Africa CDC's strategy to close the gaps between what is not detected versus what is detected, and what is detected versus what is done by public health agencies, including enabling policy and practice.

What Is and What Is Not Detected

In Africa, as in most of the world, infectious disease surveillance relies primarily on healthcare delivery systems that are accessible and sufficiently resourced and on public health systems that are sufficiently resourced and empowered by law. For diseases to be measured accurately, people who are ill must first access care at a health facility. At the health facility, a clinician use signs and symptoms to diagnose a disease of public health interest and may perform a laboratory test. Public health officers use the records from these encounters to measure disease occurrence and submit reports to a higher-level public health office. In sub-Saharan Africa, most countries use a surveillance approach called Integrated Disease Surveillance and Response. ¹⁶ Promoted by the World Health Organization (WHO) for use in resource-limited settings, this approach uses standardized definitions of selected priority diseases of public health interest—relying primarily on clinical syndromes and minimally on laboratory testing—and structured forms for recording individual cases and reporting aggregate cases.

For the healthcare delivery system, closing the gap in detection will require African countries to achieve universal health coverage, a global movement championed by WHO to increase access to healthcare while also decreasing out-of-pocket costs among all people in all countries.^17,18 In 2001, the heads of state and government members of the AU committed to spend at least 15% of their annual budget on improving health services. ¹⁹ As of 2019, only 3 AU member states had allocated at least 5% of their gross domestic product to health, and between 2016 and 2019, 21 countries actually decreased their financing for health. ²⁰ In February 2019, African leaders and donors pledged over US$200 million to increase access to essential health services. ¹⁸ Even if people have access and can afford healthcare, clinicians in many parts of Africa rarely perform diagnostic testing for infectious diseases, and tests are rarely performed in accredited laboratories. ²¹ Failure to perform high-quality diagnostic testing may lead to incorrect treatment, missed opportunities for treatment, and misuse of antimicrobial agents. ²² To address this, Africa CDC and the African Society for Laboratory Medicine are developing programs to expand access to essential laboratory diagnostics and improve the number of clinical and public health laboratories that perform quality-assured testing. ²³

To improve public health systems in Africa, Africa CDC has prioritized establishing and strengthening national public health institutes (NPHI). NPHIs are institutions that lead and coordinate a country's essential public health functions, such as prevention, detection, and response to infectious and noninfectious health conditions. ²⁴ Public health systems function optimally when a single government entity is recognized as the authority for policy, practice, and information related to surveillance, preparedness, response, workforce development, and reference laboratory testing. ²⁵ NPHIs are also anticipated to play a critical role in coordinating and implementing national action plans for health security. ²⁶ In Africa, 35 of 55 countries have an NPHI or have initiated its development; of these 35 NPHIs, only 15 perform all the core functions (Africa CDC unpublished data, 2019). To help establish and progressively improve NPHIs, Africa CDC has developed a model legal framework for countries to use when establishing an NPHI and a “scorecard” to assess the functions it performs. One of the essential activities of an NPHI is to establish and run an applied epidemiology training program where health professionals receive on-the-job training in surveillance, disease control, outbreak investigation and response, and other core functions of public health. ²⁷ Placing graduates of such programs into government public health facilities at all levels accelerates the time to detection and control of emerging infections. ²⁸

Modernization and innovation have the potential to help Africa CDC fulfill its mandate as well. In many African laboratories, records are often maintained using paper ledgers or electronic spreadsheets, each dedicated to a single test. Africa CDC is working to evaluate whether internet connectivity can be added to instruments already present in laboratories; such instruments would then be able to directly transmit electronic data to public health officials. ²⁹ The GeneXpert instrument used almost exclusively for diagnosis of tuberculosis in Africa has proven how a test designed for point-of-care clinical use can also be a powerful instrument for monitoring disease occurrence and testing multiple pathogens. ³⁰ Similarly, advances in genomic sequencing technology now make it possible for African laboratories to test specimens they already receive with methods that were previously found only in advanced research laboratories. Genomic sequencing can help diagnose pathogens that were previously not detectable with classical microbiology methods (including novel strains) and help detect clusters (ie, a common strain of pathogen in 2 or more ill people, suggesting a common exposure).^31,32 In 2018-2019, Africa CDC assessed pathogen genomic sequencing capacity in all regions of Africa. This assessment found skilled laboratory personnel and modern laboratory equipment, but few personnel with skills to analyze data and weak connections between laboratories and disease control programs. Making pathogen genomic sequencing and other advanced diagnostic methods available at the point of care will enable more rapid, complete diagnosis of infections and detection of outbreaks and will depend on strengthening both technology and human resources.

For disease detection, studies have shown that digital disease surveillance—the analysis of data available through internet search engines, social media, mobile phones, and other internet-accessible sources—can estimate incidence, burden, and trends of selected infections in high-income settings. ³³ Africa CDC is collaborating with academic researchers to evaluate whether similar findings can be obtained in African settings and, even more important, whether such data can be used to guide disease control interventions, specifically for cholera and yellow fever.

What Is Detected Versus What Is Done

As a public health agency embedded within a political institution, Africa CDC has an opportunity to ensure that government leaders learn immediately about outbreaks and recognize them as threats, and, therefore, deploy resources for disease prevention and control. To accomplish this, Africa CDC aspires to have total health information awareness, including continuous receipt of real-time data about suspected public health threats, incident cases, mortality, and relevant social, economic, and political information.

For Africa CDC, the first component of total health information awareness involves scanning traditional media, social media, and other open sources for reports of public health events. In 2017, WHO developed a novel software application called Epidemic Intelligence from Open Sources that combines multiple media scanning and ontology systems to continuously receive and process reports of health-related events, which can be filtered by defined criteria of interest such as infectious disease outbreaks in Africa. ³⁴ Africa CDC is using this software application and informal reports from government personnel around the continent to develop a weekly report of public health events that is distributed to the AU's peace and security program and other leaders. The report includes a summary of up-to-date information about the event, an assessment of the risk to member states, and recommended actions for Africa CDC and the AU. In January 2018, Africa CDC provided the first update ever about public health threats to the AU Peace and Security Council, an entity akin to the United Nation's Security Council. The council “agreed to have regular briefings by the Africa CDC on public health threats to peace and security in Africa, at least once every year, and whenever the need arises, within the context of early warning.” ³⁵

The second component of total information awareness involves strengthening the capacity of member states to detect and report acute public health events. In November 2018, Africa CDC released its Event-Based Surveillance Framework, ³⁶ a guide for member states to detect public health events using 4 complementary approaches: (1) community surveillance, in which volunteers and/or local health workers report events; (2) health facility surveillance, in which hospital personnel report events; (3) telephone hotlines, in which any person can call a dedicated number to speak with public health personnel; and (4) scanning internet-accessible sources, such as media, to identify potential events. Of these approaches, community surveillance proved particularly effective at increasing case reporting during the 2014-2016 West Africa Ebola outbreak. It also has the intuitive appeal of expanding reporting to include events such as unexplained deaths that occur outside of healthcare facilities. ³⁷ While many countries have informed Africa CDC that they have begun implementing community surveillance, none have reported they are implementing all 4 approaches.

For Africa CDC, the third component of total health information awareness is to collect sufficient baseline data about illness and death to accurately determine whether a public health event is real, acute, unexpected, and likely to adversely affect a population. Africa CDC is collaborating with the Joint United Nations Programme on HIV/AIDS (UNAIDS) on the Situation Room, a software application that connects directly to 7 African countries' health information systems to analyze data about HIV cases and related services. ³⁸ A critical component of the Situation Room application is formal permission by these 7 governments for UNAIDS to access their electronic information systems directly, allowing both country officials and UNAIDS to produce HIV-related reports at any time using the most up-to-date data. In February 2019, Africa CDC met with member states to expand the Situation Room application to additional member states and to configure the software to produce similar reports of high-priority infectious diseases such as cholera, typhoid, meningitis, and viral hemorrhagic fever. ³⁹ As the program expands, Africa CDC will be able to obtain real-time reports about disease incidence in African countries on demand—by “pull”—rather than waiting for countries to “push” it out.

Understanding whether an event is increasing mortality requires high-quality data about the baseline numbers and causes of death in a population. According to a comprehensive study, 38 (69%) of 55 African countries did not produce any reliable data about numbers and causes of death from 2010 to 2016. ⁴⁰ The lack of reliable mortality data makes it impossible for the continent to monitor mortality and the impact of disease interventions. In February 2019, Africa CDC officially launched a program to improve mortality surveillance in Africa by statistically sampling populations and using a combination of verbal autopsy and data from Child Health and Mortality Prevention Surveillance to determine causes of death.^41,42 This initiative complements the AU's existing program to develop comprehensive civil registration and vital statistics programs in all member states. ⁴³

Enabling Policy and Practice

To achieve its ambitious agenda, Africa CDC aspires to change how public health agencies communicate and collaborate in Africa. Africa CDC is developing regional integrated surveillance and laboratory networks that coordinate and integrate data from all public health surveillance, laboratory, and emergency response organizations within a defined geographic area. ⁴⁴ Africa CDC has established regional collaborating centers in each of the 5 AU regions—Egypt in North Africa, Kenya in East Africa, Zambia in Southern Africa, Gabon in Central Africa, and Nigeria in West Africa—and across the regional economic communities of Africa to implement regional integrated surveillance and laboratory networks by: 1.

Collecting data about all public health partners and assets—both public and private—in their region regarding surveillance, laboratory, and emergency response capacity and personnel

Conclusions

Rapid economic and population growth, combined with the prospect of full integration into a common market, promise a future for Africa quite different from the immediate postcolonial period. The security of Africa will depend, in part, on Africa CDC's ability to build comprehensive, timely disease surveillance that rapidly detects and contains health threats.

The 2019 novel coronavirus disease (COVID-19) outbreak has presented both a risk and an opportunity for Africa CDC to advance disease detection. Although implementation of many activities has been delayed, Africa CDC immediately adapted its event-based surveillance materials to train member states in COVID-19 event detection and response, used the regional collaborating centers to track and verify reports of COVID-19 cases, and strengthened its presence online as a repository of trusted information about the epidemic in Africa. ⁴⁶

During and after the COVID-19 pandemic, Africa CDC will continue to strengthen diagnosis of diseases and electronically link the data to public health systems for immediate action, build central government institutions that perform essential core public health functions, develop the workforce to staff these institutions, and establish regional networks that connect existing public health assets. Achieving consensus, translating commitments to action, and building trust across public and private stakeholders for a large, diverse continent with 55 member states remains a daunting task.