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Disease Surveillance, Emergency Preparedness and Response in Eastern and Southern Africa

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A Situational Assessment and Five-Year Action Plan for the Africa CDC Strengthening Regional Public Health Institutions and Capacity for Surveillance and Response Program

Executive Summary

The Role of the Africa CDC’s Regional Integrated Surveillance and Laboratory Network (RISLNET) in Mitigating the Transnational Threat of Infectious Disease The mounting human and economic toll of COVID-19 has brought the challenge of regional disease surveillance and control to the forefront of the policy discourse around global public health. This report was commissioned in 2019, several months before the first cases of COVID-19 were identified. The rapid global spread of the virus over the following year prompted the team to adapt its analytical approach to reflect the evolving reality on the ground. The report’s findings identify the medium- and long-term investments necessary to build a comprehensive framework for monitoring, containing, and addressing infectious disease outbreaks. African countries have battled many outbreaks in the past, including several devastating Ebola virus disease epidemics and the recurrent ravages of cholera, yellow fever, and meningitis, among others.

These outbreaks compound the persistent burden of endemic diseases such as malaria, typhoid, and HIV. However, the damage inflicted by the COVID-19 pandemic and ensuing economic crisis exceeds all modern disease outbreaks in terms of the scope, extent, and persistence of its effects, which could undo decades of gains in public health and poverty reduction in countries across the region. The African continent is more integrated than ever before, with free trade across countries and open borders allowing the large-scale movement of people and goods; but while greater connectivity creates new economic opportunities, it also heightens the risk posed by communicable diseases. The worldwide spread of COVID-19 starkly illustrates how the undetected transmission of pathogens across borders can transform a local disease outbreak into a regional health emergency or even global crisis. The Africa Centres for Disease Control and Prevention (Africa CDC), which is the apex body for regional cooperation on disease control and prevention in Africa, has played a crucial role during the ongoing pandemic. The Africa CDC established the Africa Taskforce for Corona Virus (AFTCOR) in cooperation with the African Union Commission and the WHO.

Under the Africa Joint Continental Strategy for COVID-19, the AFTCOR and the Africa CDC’s Incident Management System moved swiftly to implement a continent-wide approach to combatting the virus, working in close coordination with the Africa CDC’s Regional Collaborating Centers (RCCs) and the national public health institutions (NHPIs) of African Union (AU) member states. The AFTCOR and the RCCs provided technical guidance and policy recommendations, supported the deployment of on-site technical assistance, and coordinated with stakeholders to align strategies and exchange information on best practices. The Regional Integrated Surveillance and Laboratory Network (RISLNET) was envisaged as a network of networks that would coordinate and connect the continent’s analytical, surveillance, and emergency-response assets. RISLNET is designed to leverage economies of scale and institutional complementarities to strengthen disease prevention, rapid detection, and response capacity across African sub-regions.

Under the One Health approach, RISLNET aims to facilitate close collaboration among national public health institutions (NPHIs), academic institutions, private and public laboratories, centers of excellence, non-governmental and civil society organizations, and veterinary services to address regional challenges such as antimicrobial resistance (AMR), pandemic preparedness, and rapid disease detection and response. One RISLNET is planned for each RCC region: Central Africa, Eastern Africa, Northern Africa, Southern Africa, and Western Africa. The Central Africa RISLNET is currently active, and the others are in the process of being established. The World Bank, with financial support from the Korea-World Bank Group Partnership Facility, is providing Advisory Services and Analytics (ASA) to support the operationalization of the Africa CDC through knowledge transfer, technical assistance, and institutional capacity-building. The knowledge products generated through World Bank engagement will inform the activities of the Africa CDC, AU member states, and development partners as they work to enhance infectious disease control systems across the continent, and they will provide the analytical underpinnings for the World Bank’s Africa CDC Regional Investment Financing Program. This report presents a situational analysis of laboratories and disease-surveillance networks, AMR surveillance systems, human resources and capacity-building needs, emergency-response capabilities, and the role of the private sector in disease surveillance, prevention, and control in the Eastern Africa and Southern Africa RCCs. The Eastern Africa RCC is headquartered in Kenya, and member states include Ethiopia, Somalia, South Sudan, and Uganda. The Southern Africa RCC is headquartered in Zambia, and member states include Malawi, Mozambique, South Africa, and Zimbabwe. The member states described in this report are samples, and both RCCs encompass additional countries that are not included in the analysis. 7 Findings Existing laboratory networks have strengthened clinical and analytical capabilities at the country level while fostering cross-border collaboration, providing compelling proof of concept for RISLNET. Through the East Africa Public Health Laboratory Networking Project (EAPHLN), health authorities in Kenya, Uganda, Tanzania, Rwanda, and Burundi have developed a network of 40 well-equipped public health laboratories with trained personnel and robust diagnostic and surveillance capacity. The EAPHLN has significantly increased cross-border outbreak preparedness and response while enhancing the impact of national-level facilities, and it has played a crucial role in combatting the regional spread of COVID-19. In addition, about 187 laboratories connected through the WHO’s Global Influenza Surveillance and Response System (GISRS) were involved in COVID-19 testing during the initial phases of the pandemic. The African Network for Influenza Surveillance and Epidemiology (ANISE) brought together more than 30 African countries through a unified surveillance and testing platform. However, the existing laboratory networks do not cover all diseases or all countries, leaving ample scope for RISLNET to incorporate these networks into a comprehensive framework for disease surveillance and response. RCC member states vary widely in terms of strategic planning, laboratory capabilities, human resources, and surveillance and reporting mechanisms. States with limited institutional capacity, including Malawi, Mozambique, and Somalia, have not developed laboratory-specific strategic plans, while higher-capacity states such as Uganda and Zambia lack well-defined procedures to monitor the implementation of their plans. Across countries, laboratory personnel often lack the knowledge and skills necessary to adhere to biosafety guidelines, and such guidelines tend to be either unimplemented or legally unenforceable. Ethiopia, Kenya, Uganda, South Africa, and Zimbabwe have relatively strong specimen-referral mechanisms that include satellite-based vehicle tracking, hub-and-spoke models, and public-private partnerships. South Africa is a regional leader in quality control, with a wide range of tests covered under its external quality assessment (EQA) programs, but EQA coverage in other countries is limited. Most states have laboratory testing capabilities for endemic diseases such as cholera, diarrhea, measles, malaria, and HIV, but only South Africa and Zambia have the capabilities to perform all 12 laboratory confirmation tests for the priority diseases defined by WHO guidelines.

The RCC member states still lack a comprehensive platform for integrating epidemiological data with laboratory data. All countries are working to develop their capacity to address AMR, but progress has been uneven, and there are no standardized protocols for antimicrobial susceptibility testing (AST). Kenya and Uganda have begun developing the laboratory capacity to monitor and control AMR, but AST capabilities in Somalia, South Sudan, and Mozambique remain inadequate. Somalia and South Sudan have yet to develop national strategies for AMR surveillance, and countries that have AMR strategies face implementation challenges. Financing for AMR programming is limited, and the establishment of multi-sectoral governance and coordinating agencies is incomplete. Very few laboratories that have AST capabilities have enrolled in the WHO’s Global AMR Surveillance System (GLASS), and only a minority of the enrolled laboratories are reporting data to GLASS. Ethiopia, Kenya, Uganda, South Africa, and Zambia have well-functioning indicator-based surveillance (IBS) systems, and event-based surveillance (EBS) systems are operational in South Africa and Uganda, but EBS implementation is insufficient in all other countries. Infrastructure gaps, limited internet connectivity, and absence of clear policies and legislation weaken reporting, and despite the availability of electronic data platforms, empirical analysis is limited at the national and sub-national levels.

Most states rely on paper-based reporting. The use of Laboratory Information Management System (LIMS) software is limited, and the renewal of licenses is donor-dependent. Comprehensive multi-sectoral and multi-hazard risk assessments have yet to be conducted. The fight against COVID-19 has revealed significant gaps in national and regional defenses against the spread of infection. Supply chain management is a major weakness in most countries, risk assessments are inconsistent, and emergency-response capabilities vary substantially. However, regional collaboration is improving, and Ethiopia has participated in several emergency-management situations in neighboring Kenya and Somalia.