The rising incidence of public health emergencies driven by natural disasters, as well as emerging and re-emerging infectious diseases, remains a significant concern in Africa.¹ On average, the continent reports over 200 public health emergencies annually.² A substantial proportion of these events are outbreaks of emerging infectious diseases, which vary in magnitude, geographical distribution and complexity. These outbreaks, along with other health emergencies, exert considerable societal and economic impacts, often necessitating extensive human, financial and material resources, thereby further straining already overburdened health systems.³

The inherent unpredictability of infectious disease surges, coupled with resource constraints and limited capabilities for timely risk prediction, underscores the urgent need for a planned, targeted and evidence-based approach to public health emergency management. Implementing such an approach is essential for reducing response delays and mitigating the morbidity and mortality associated with outbreaks. The International Health Regulations (IHR) emphasise risk assessment and prioritisation as core components of an effective Public Health Emergency Preparedness and Response (PHEPR) framework.⁴

Risk prioritisation and ranking have long been recognised as essential for identifying diseases that warrant heightened attention and dedicated resources to strengthen preparedness and response strategies.⁵ This process involves systematically identifying hazards and assessing and categorising disease-related risks based on their potential impact, likelihood of occurrence and transmission capacity. It underpins strategic preparedness planning, facilitates informed resource allocation and supports the effective implementation of targeted interventions aimed at mitigating the adverse consequences of outbreaks and pandemics.^5,6,7 Furthermore, risk prioritisation provides a robust foundation for evidence-based decision-making, promotes dynamic and adaptive planning and ensures transparency and accountability in public health emergency management.

Given the dynamic nature of infectious diseases in Africa, continuous risk and disease prioritisation are imperative for the effective implementation of evidence-based preparedness strategies and response plans.

The Africa Centres for Disease Control and Prevention (Africa CDC) serves as the public health agency of the African Union, dedicated to strengthening the capacities of public health institutions and systems across the 55 African Union Member States.⁸ Its mission is to support the rapid detection and effective response to disease outbreaks and other health threats through an integrated, continent-wide framework encompassing surveillance, laboratory networks, disease prevention and control, emergency preparedness and response and public health research.

To enhance its operational efficiency and ensure timely support to Member States, Africa CDC established five Regional Coordination Centres (RCCs) in Eastern, Southern, Western, Central and Northern Africa (Figure 1),⁹ serving as decentralised hubs for implementing programmes and enabling regionally tailored responses to public health threats.

Building on the Africa CDC’s first continental-level prioritisation of epidemic-prone diseases in 2022,¹⁰ this process was adapted regionally to reflect diverse epidemiological profiles and public health challenges. Eastern Africa faces recurrent infectious disease outbreaks, impacts of natural disasters and climate change, zoonotic threats and a high burden of foodborne illnesses, compounded by limited resources, suboptimal surveillance, limited cross-border collaboration, fragmented data and inadequate public health infrastructure. In this context, a regional disease prioritisation exercise was carried out in 2023 to guide strategic planning, strengthen preparedness and enhance the capacity of Eastern Africa to respond effectively to emerging and epidemic-prone threats.

This paper presents the methodological approach employed for prioritising and ranking epidemic-prone diseases in Eastern Africa and summarises the key outcomes of the exercise.

The regional risk prioritisation process was adapted from the Africa CDC’s continental framework, which is based on the European Centre for Disease Prevention and Control (ECDC) risk ranking methodology utilising multi-criteria decision analysis (MCDA).^10,11 Multi-criteria decision analysis provides a structured, transparent and reproducible approach for evaluating and comparing options using multiple decision-making criteria.¹² To enhance the rigour of the process and ensure expert consensus, the modified Delphi technique was applied to systematically collect, review and harmonise expert input on disease selection, ranking criteria and prioritisation outcomes. The modified Delphi process is a systematic and structured method designed to facilitate consensus among a group of experts on a specific topic.¹³

The Africa CDC risk ranking methodology involves seven key steps: (1) Planning; (2) disease selection; (3) definition of ranking criteria; (4) scoring of diseases against the criteria; (5) disease ranking; (6) consensus building; and (7) evaluation of the process (Figure 2).

A total of 28 experts completed the online questionnaire. Their responses revealed marked variation in the perceived mean scores for epidemic potential, disease severity and preparedness across 22 priority infectious diseases. Cholera, coronavirus disease 2019 (COVID-19) and Ebola virus disease (EVD) were identified as having the highest epidemic potential (mean scores > 3.2), and EVD (3.8), Marburg virus disease (MVD) (3.7) and cholera (3.2) were rated as the most severe. The lowest preparedness levels were reported for unknown disease (mean score 1.6), mpox, Rift Valley fever (RVF) and Crimean-Congo haemorrhagic fever (CCHF) (each with a mean score of 2.0), highlighting critical gaps in readiness for these threats (Table 4).

The top 10 highest risk-ranked diseases were EVD (risk = 12.7), MVD (11.8), cholera (11.1), COVID-19 (9.9), influenza (8.9), measles (8.6), yellow fever (8.5), CCHF (8.2), malaria (8.0) and RVF (7.9) (Table 4).

The results also showed a clear mismatch between risk and preparedness levels for several high-priority diseases, underscoring the need for targeted investment in medical and non-medical countermeasures, especially for emerging and re-emerging threats. EVD (risk = 12.7), MVD (11.8) and cholera (11.1) were ranked as the highest-risk diseases, yet showed only moderate preparedness levels (2.3, 2.1 and 2.7 respectively). Several emerging threats, including CCHF (risk = 8.2; preparedness mean = 2.0), RVF (risk = 7.9; preparedness mean = 2.0) and mpox (risk = 6.3; preparedness mean = 2.0), had relatively moderate risk scores but low preparedness, indicating major response gaps. Measles (risk = 8.6; preparedness mean = 3.0) and COVID-19 (risk = 9.9; preparedness mean = 2.9) showed better alignment between risk and preparedness, likely reflecting ongoing control efforts (Figure 3).

The boxplots illustrate variability in expert assessments of epidemic potential, disease severity and preparedness levels across 22 priority diseases. For epidemic potential, diseases such as COVID-19, malaria, mpox and rabies exhibited narrow interquartile ranges, indicating strong expert agreement. In contrast, anthrax, brucellosis, vaccine-derived poliomyelitis and unknown diseases showed wider distributions, suggesting lower consensus. The presence of multiple outliers for COVID-19 may reflect regional differences in experience or ongoing uncertainty regarding its future trajectory. Regarding disease severity, EVD, malaria, MVD and influenza demonstrated narrow interquartile ranges, reflecting consensus on their clinical impact. However, the frequent outliers for MVD and measles highlight divergent expert views, likely shaped by context-specific burden or prior experiences. Preparedness scores were broadly consistent across disease, clustering around moderate levels. Measles and COVID-19 received the highest ratings, while unknown diseases received the lowest, with the narrow interquartile range observed suggesting uniform expert concern regarding response capacity. These findings underscore the importance of accounting for both consensus and variability in expert assessments when informing preparedness and prioritisation strategies (Figure 4).

The top 10 ranked diseases in Eastern Africa included, in order: EVD, MVD, cholera, COVID-19, influenza, measles, yellow fever, CCHF, malaria and RVF. While most of these diseases are zoonotic in origin, others – such as cholera, measles and malaria – are not. Reports indicate that these diseases remain prevalent and continue to cause significant public health challenges in the region.^{14,15,16,17,18} This finding aligns with the 2017 World Health Organization’s recent list of viral and bacterial families with the highest potential to cause future epidemics and pandemics.¹⁸ The results also show similarities, with some distinctions, when compared to the continental-level risk prioritisation.¹⁰ Of note, in contrast to the continental prioritisation, measles, malaria and RVF ranked higher in the Eastern region’s prioritisation. These findings underscore the critical need to prioritise resources, workforce training and contingency planning tailored to the specific health threats and risks prevalent in Eastern Africa. The concurrent burden of emerging zoonotic diseases – such as EVD, MVD, CCHF and RVF – alongside persistent endemic diseases such as malaria, influenza and measles necessitates a dual-pronged approach. The findings further indicated that zoonotic diseases such as RVF, CCHF and mpox are associated with low levels of preparedness, highlighting systematic vulnerabilities. Therefore, strategies should integrate epidemic preparedness with the strengthening of routine disease control programmes. To improve regional response capacity, it is essential to ensure the prepositioning of critical supplies, including vaccines, therapeutics, diagnostics and personal protective equipment (PPE). Additionally, sustained investments in health infrastructure, workforce development and the establishment of clear policies and coordination frameworks are vital to enable timely and effective responses to these priority health threats. Strengthening collaborations and establishing research networks at both national and regional levels, as well as integrating a One Health approach, will be instrumental in enhancing preparedness and response capacities. Given the transboundary nature of many prioritised diseases, cross-border collaboration is particularly important. Coordinated surveillance, data sharing, joint outbreak investigations and harmonised response strategies among neighbouring countries are essential to contain outbreaks at their source and prevent wider regional transmission. Enhancing these mechanisms will contribute significantly to regional health security and build resilience against both current and future public health emergencies.

Despite substantial investments in vaccination and control efforts, experts continued to prioritise COVID-19, even though it was no longer classified as a global health emergency at the time of the workshop.¹⁹ This reflects ongoing concerns about its continued pandemic potential, given the virus’s capacity for rapid mutation, seasonal resurgence and antigenic variation – particularly in the context of limited vaccine access and the weakening of sustained control measures in many countries.^20,21,22 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus still evolves in humans and undergoes genetic mutations as a result of immune pressure exerted by factors such as herd immunity, prior infections, therapeutic interventions, vaccination and exposure to neutralising antibodies. These mutations can enhance viral infectivity and transmissibility while also reducing the efficacy of neutralisation by monoclonal antibodies, convalescent plasma or vaccine-induced immunity.²³ Furthermore, mutations may also lead to failure of detection by molecular diagnostic tests, leading to delayed diagnosis, increased community spread and delayed treatment.²³

The interplay between risk and preparedness is critical in guiding effective public health responses. High-risk diseases – characterised by their epidemic potential and severity – demand proportionately greater preparedness efforts, including robust surveillance systems, rapid response capacity, readily available medical and non-medical countermeasures and resource allocation. However, preparedness levels are not always commensurate with actual or perceived risk. In some cases, diseases with high perceived risk may be under-resourced, while others benefit disproportionately from pre-existing systems or global attention, e.g., measles and polio. This mismatch underscores the need for dynamic, evidence-based prioritisation frameworks that integrate both evolving risk profiles and existing preparedness capacity. For instance, the risk posed by filoviruses such as EVD and MVD in East Africa is high, with substantial response implications. However, preparedness for such outbreaks remains suboptimal, as demonstrated by recent epidemics in Uganda, Rwanda and Tanzania.^24,25,26 There is a need to improve access to prequalified vaccines and therapeutics and to strengthen research-embedded, One Health approaches to better understand the origins and drivers of outbreaks. Aligning preparedness with risk through such measures is essential to improving outbreak prevention, detection and response in the region. The outliers in disease severity scores reflect heterogeneity in expert perceptions, shaped by differences in professional background, field experience and contextual knowledge. This variation underscores the multi-dimensional nature of disease severity, encompassing clinical, economic and social impacts.

This exercise employed the MCDA methodology, which is well suited for prioritisation efforts involving multiple criteria. A range of criteria was selected to comprehensively reflect the objectives of the exercise, and the approach enabled multidisciplinary participation. The tool incorporated parameters to evaluate both risk and high-level emergency preparedness interventions. In settings where data may be limited, such risk-ranking tools are particularly valuable, allowing experts to apply their knowledge and judgement in prioritising public health threats. Extensive expert consultation contributed to stakeholder acceptance, endorsement and confidence in the results. This exercise complements existing risk-ranking frameworks, such as the WHO Strategic Tool for Assessment of Risks (STAR), by providing a more granular, disease-specific analysis using a multi-criteria decision approach. Its methodological innovation and contextual relevance make it both novel and fit for purpose in guiding evidence-based preparedness and response strategies.

Despite its usefulness, this exercise has some limitations. Firstly, the final risk ranking scores represent relative, not absolute, risk and are based on expert judgement rather than direct epidemiological measures. They reflect perceived threats informed by current knowledge, recent outbreak history and potential public health impact, rather than actual incidence rates. Secondly, assuming equal weights for all criteria may have reduced analytical precision. A weighted approach could yield more nuanced prioritisation. Thirdly, expert assessments may have been influenced by recent COVID-19 and EVD outbreaks in the region, introducing potential bias. Finally, the absence of real-time data and modelling constrained accurate risk estimation, increasing reliance on expert opinion. While the results reflect regional priorities, they may not fully capture country-specific needs. Even within a shared region, countries can vary significantly in disease epidemiology, health system capacity and contextual factors. This highlights the importance of conducting national-level disease prioritisation exercises. The knowledge and experience gained from this regional process can serve as a foundation for country-specific efforts, tailored to distinct objectives and contexts.

The findings of this exercise highlight priority diseases for Africa CDC and partners, providing critical evidence to strengthen preparedness and response in Eastern Africa. Institutionalising this prioritisation process across all levels and updating it every 2–3 years will ensure strategies remain targeted, adaptive and effective. Further analysis of capacity and capability gaps related to priority diseases is essential to inform evidence-based, coordinated and sustainable preparedness strategies.