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Africa CDC Institute of Pathogen Genomics (IPG) was launched in November 2019 and operates under the Division of Laboratory Systems and Networks.
IPG coordinate the implementation of molecular diagnostics, pathogen genomics and bioinformatics in National
...
Public Health Institutions (NPHIs) and/or Refe-
-rence Laboratories (NRLs) across Africa.
Africa CDC and APHF are coordinating a continental initiative to maximize the benefits of molecular approaches and pathogen genomics for more effective
outbreak preparedness, prevention, response, and for the control and elimination of endemic diseases in Africa. One of Africa CDC’s flagship initiative is the Africa
Pathogen Genomics Initiative (Africa PGI), a partnership that aims to strengthen laboratory systems and enhance genomic surveillance by equipping the continent’s
public health institutions with the tools, training, and data infrastructure.
About the Project
In 2023, 166 outbreaks and public health events were reported in Africa. This calls for a resilient laboratory systems for timely detection and reporting of current and future outbreaks. This project aims to scale up molecular diagnostic and genomic sequencing-based detection and characterization of outbreaks.
Africa CDC is working with Member States to develop guidance, diagnostic algorithm, training and capacity building to enable outbreak detection, and reporting to inform public health response.
more
The burden of diabetes is enormous, positioning it as one of the main challenges facing public health today. Currently, it is estimated that 62 million people are living with diabetes in the Region
...
of the Americas and projections show its prevalence will continue rising over the following years. The Region shows the highest number of years of healthy life lost (through either disability or premature death) due to diabetes worldwide. The high costs associated with its treatment produce a heavy economic burden. Its complications can seriously affect the quality of life of people living with diabetes, their families, and society and overload health systems. This report shows the latest internationally comparable data on diabetes and its main risk factors by year, country, and sex. It also includes a summary of the countries health systems’ response to diabetes, including national plans, targets, surveillance, guidelines, and access to essential drugs and technologies, and synthesizes information about diabetes-related complications and the close relationship between diabetes and other pathologies, such as cardiovascular diseases, tuberculosis, and COVID-19. The data presented here reveal that, despite advances in national responses, diabetes continues to expand, and our response remains insufficient. This report aims to draw attention to the urgent need to strengthen efforts to prevent, diagnose, and control diabetes in the Region of the Americas.
more
Epidemiologisches Bulletin ; 12. Dezember 2016 / Nr. 49 aktuelle daten und informationen zu infektionskrankheiten und public health
A variety of international organizations are involved in mobilizing resources from both public and private
sources and using them to extend development assistance to low-and middle-income countries around the world. They provide country-focused fin
...
ancial and technical assistance to developing countries, and contribute to the generation of global public goods,
such as disease surveillance, norms and standards,
data and knowledge, and aid coordination
more
Event-based surveillance (EBS) is defined as the organized collection, monitoring, assessment and interpretation of mainly unstructured ad hoc information regarding health events or risks, which may
...
represent an acute risk to health. Both indicator-based and event-based surveillance components serve the early warning and response (EWAR) function of the public health surveillance system. The Framework for Event-based Surveillance offers guidance to public health practitioners seeking to implement EBS at each administrative level in healthier countries.
more
The text “Pathogen Genomic Surveillance Policy Framework (2023)” is a strategic framework developed by Africa CDC to strengthen genomic surveillance of pathogens in the Member States of the Afri
...
can Union.
Its content focuses on how African countries can systematically integrate genome sequencing into their public health systems in order to detect infectious diseases more rapidly, monitor outbreaks more effectively, and support evidence-based public health decision-making.
The report was developed in the context of the COVID-19 pandemic, which demonstrated the importance of genomic surveillance for identifying virus variants and enabling effective crisis management. The aim of the framework is to sustainably expand the capacities built during the pandemic and to apply them to additional pathogens beyond COVID-19.
more
Event-based surveillance (EBS) is defined as the organized collection, monitoring, assessment and interpretation of mainly unstructured ad hoc information regarding health events or risks, which may
...
represent an acute risk to health. Both indicator-based and event-based surveillance components serve the early warning and response (EWAR) function of the public health surveillance system. The Framework for Event-based Surveillance offers guidance to public health practitioners seeking to implement EBS at each administrative level in their countries.
more
The document “Strategic Framework for Strengthening Cross-Border Surveillance and Information Sharing in Africa” outlines a coordinated strategy developed by Africa CDC to improve public
...
health surveillance and collaboration across national borders in Africa. It addresses the challenge that infectious diseases often spread across borders due to population movement, trade, and migration, while surveillance systems and data-sharing mechanisms frequently remain nationally focused and fragmented.
The framework proposes strengthening regional coordination, harmonizing surveillance systems, enhancing information sharing between countries, and building laboratory and workforce capacity. It also emphasizes timely detection of cross-border health threats, joint outbreak investigations, and improved communication among Member States. Overall, the document aims to enhance preparedness, early warning systems, and collective response to public health threats across the African continent.
more
The document “Strategic Framework for Strengthening Cross-Border Surveillance and Information Sharing in Africa” outlines a coordinated strategy developed by Africa CDC to improve public
...
health surveillance and collaboration across national borders in Africa. It addresses the challenge that infectious diseases often spread across borders due to population movement, trade, and migration, while surveillance systems and data-sharing mechanisms frequently remain nationally focused and fragmented.
The framework proposes strengthening regional coordination, harmonizing surveillance systems, enhancing information sharing between countries, and building laboratory and workforce capacity. It also emphasizes timely detection of cross-border health threats, joint outbreak investigations, and improved communication among Member States. Overall, the document aims to enhance preparedness, early warning systems, and collective response to public health threats across the African continent.
more
On 13 August 2024, the Africa Centres for Disease Control (Africa CDC) declared the multi-country mpox outbreak a public health emergency of continental security, with strong recommendations to impr
...
ove surveillance and vaccine deployment in all AU Member States. On 14 August 2024, the WHO Director-General declared mpox outbreak a public health emergency of international concern (PHEIC).
more
Surveillance of influenza virus infection at the European level requires close collaboration between virologists, epidemiologists and sentinel GP networks to generate the data necessary to inform a timely
...
public health response.
more
The webpage “Health emergency preparedness, response and resilience” on the OpenWHO platform presents an online learning channel developed by the World Health Organization (WHO). It provides edu
...
cational resources and training materials aimed at strengthening knowledge and skills related to preparing for, responding to and recovering from health emergencies. The content introduces key concepts such as risk assessment, emergency coordination, surveillance systems, community engagement and resilient health systems. The courses are designed to help public-health professionals, responders and policymakers better understand how to prevent, detect and manage health threats and build stronger systems that can withstand future crises. Overall, the webpage serves as a global training resource to improve preparedness and resilience in public-health emergency management.
more
The importance of robust mortality surveillance systems cannot be overstated in an era marked by increasing global health challenges where health t
...
hreats loom large and population dynamics continue to evolve. Accurate and timely mortality data is essential for identifying trends and detecting emerging health threats, evaluating the impact of interventions, and guiding evidence-based policy decisions.
This framework outlines a holistic approach to strengthening routine mortality surveillance systems, considering the unique contextual factors and challenges faced by African countries. It emphasizes the importance of establishing efficient data collection mechanisms, enhancing data quality and completeness, and promoting data sharing and collaboration among stakeholders.
Moreover, the framework recognizes the pivotal role of technology in the integration of data from fragmented mortality data sources. It highlights the potential of innovative data capture methods, advanced analytics, and real-time reporting systems to enhance mortality data’s accuracy, efficiency, and timeliness.
The continental framework for mortality surveillance aligns with Africa CDC’s mission and strategic goal by serving as a fundamental component in strengthening public health systems, enhancing disease surveillance capacities and capabilities, informing evidence-based policies and interventions, and promoting collaboration and coordination among African countries to address health challenges and improve health outcomes on the continent.
The successful implementation of this framework requires collective commitment and concerted efforts from governments, health institutions, and the international community. We hope this document will serve as a catalyst for transformative change, enabling countries to build resilient mortality surveillance systems that protect public health, save lives, and contribute to evidence-based decision-making.
more
Despite the considerable improvement in global health, millions of people still lack access to quality health services, including access to effective antimicrobial medicines, or are impoverished as
...
a result of health spending. At the same time, antimicrobial resistance – a consequence of overuse and misuse of antimicrobials – is increasingly a barrier to accessing effective care. The declining effectiveness of antibiotics is driven by multiple factors, many of which can be addressed through well functioning primary health care. However, primary health care has not always had much attention in national health sector responses to
antimicrobial resistance, which often focus on tertiary care, laboratory detection and surveillance. The three pillars of primary health care (community engagement, front-line health services including primary care and essential public health, and multisectoral action on wider health determinants) are central not just to Universal Health Coverage and the Sustainable Development Goals, but also to an effective response to antimicrobial resistance.
more
Since the emergence of COVID 19 in December 2019, various public health responses measures have been implemented to control the pandemic. Among measures taken by the Africa CDC was the launch of PAC
...
T initiative to accelerate COVID 19 testing. Key to the initiative is the engagement of Community Health Workers (CHWs) in risk communication and community engagement (RCCE), surveillance activities for early case identification, contacts tracing and in facilitating referrals for testing and continuum of care.
As of 31 May 2021, Through PACT support, over 17154 CHWs have been trained and locally deployed in 24 AU Member states. The PACT supported CHWs visited more than 2,568,654 households for community engagement activities, active case search and contact tracing, identified 1,618,601 Contacts, 710,167 COVID 19 suspect cases based on the standard case definition and facilitated referrals for 553053 (78%) suspect cases for testing. These efforts were crucial for early identification and isolation of cases in limiting further transmission.
more
Surveillance Mpox. Protocole de notification pour les états membres de l'union Africaine
recommended
On 13 August 2024, the Africa Centres for Disease Control (Africa CDC) declared the multi-country mpox outbreak a public health emergency of continental security, with strong recommendations to impr
...
ove surveillance and vaccine deployment in all AU Member States. On 14 August 2024, the WHO Director-General declared mpox outbreak a public health emergency of international concern (PHEIC).
more
To guide One Health capacity building efforts in the Republic of Guinea in the wake of the 2014–2016 Ebola virus disease (EVD) outbreak, we sought to identify and assess the existing systems and structures for zoonotic disease detection and contro
...
l. We partnered with the government ministries responsible for human, animal, and environmental health to identify a list of zoonotic diseases – rabies, anthrax, brucellosis, viral hemorrhagic fevers, trypanosomiasis and highly pathogenic avian influenza – as the country's top priorities. We used each priority disease as a case study to identify existing processes for prevention, surveillance, diagnosis, laboratory confirmation, reporting and response across the three ministries. Results were used to produce disease-specific systems “maps” emphasizing linkages across the systems, as well as opportunities for improvement. We identified brucellosis as a particularly neglected condition. Past efforts to build avian influenza capabilities, which had degraded substantially in less than a decade, highlighted the challenge of sustainability. We observed a keen interest across sectors to reinvigorate national rabies control, and given the regional and global support for One Health approaches to rabies elimination, rabies could serve as an ideal disease to test incipient One Health coordination mechanisms and procedures. Overall, we identified five major categories of gaps and challenges: (1) Coordination; (2) Training; (3) Infrastructure; (4) Public Awareness; and (5) Research. We developed and prioritized recommendations to address the gaps, estimated the level of resource investment needed, and estimated a timeline for implementation. These prioritized recommendations can be used by the Government of Guinea to plan strategically for future One Health efforts, ideally under the auspices of the national One Health Platform. This work demonstrates an effective methodology for mapping systems and structures for zoonotic diseases, and the benefit of conducting a baseline review of systemic capabilities prior to embarking on capacity building efforts.
more
Africa’s health sector is facing an unprecedented financing crisis, driven by a sharp decline of 70% in Official Development Assistance (ODA) from 2021 to 2025 and deep-rooted structural vulnerabilities. This collapse is placing immense pressure o
...
n Africa’s already fragile health systems as ODA is seen as the backbone of critical health programs: pandemic preparedness, maternal and child health services, disease control programs are all at
risk, threatening Sustainable Development Goal 3 and Universal Health Coverage. Compounding this is Africa’s spiraling debt, with countries expected to service USD 81 billion by 2025—surpassing anticipated external financing inflows—further eroding fiscal space for health investments. Level of domestic resources is low. TThe Abuja Declaration of 2001, a pivotal commitment made by African Union (AU) member states, aimed to reverse this trend by pledging to allocate at least 15% of national budgets to the health sector. However, more than two decades later, only three countries—Rwanda, Botswana, and Cabo Verde—have
consistently met or exceeded this target (WHO, 2023). In contrast, over 30 AU member states remain well below the 10% benchmark, with some allocating as little as 5–7% of their national budgets to health.
In addition, only 16 (29%) of African countries currently have updated versions of National Health Development Plan (NHDP) supported by a National Health Financing Plan (NHFP). These two documents play a critical role in driving internal resource mobilisation. At the same time, public health emergencies are surging, rising 41%—from 152 in 2022 to
213 in 2024—exposing severe under-resourcing of health infrastructure and workforce. Recurring outbreaks (Mpox, Ebola, cholera, measles, Marburg…) alongside effects of climate change and humanitarian crises in Eastern DRC, the Sahel, and Sudan, are overwhelming systems stretched by chronic underfunding. The situation is worsened by Africa’s heavy dependency with over 90% of vaccines, medicines, and diagnostics being externally sourced—leaving countries vulnerable to global supply chain shocks. Health worker shortages persist, with only 2.3 professionals
per 1,000 people (below the WHO’s recommended 4.45), and fewer than 30% of systems are digitized, undermining disease surveillance and early warning. Without decisive action, Africa CDC projects the continent could reverse two decades of health progress, face 2 to 4 million additional preventable deaths annually, and a heightened risk of a pandemic emerging from within. Furthermore, 39 million more
Africans could be pushed into poverty by 2030 due to intertwined health and economic shocks. This is not just a sectoral crisis—it is an existential threat to Africa’s political, social, and economic resilience, and global stability. In response, African leaders, under Africa CDC’s stewardship, are advancing a comprehensive three-pillar strategy centered on domestic resource mobilization, innovative financing, and blended finance.
more
Surveillance, prevention and control of leishmaniases in the European Union and its neighbouring countries
European Centre for disease prevention and control (ECDC)
European Centre for disease prevention and control (ECDC)
(2022)
C_CDC
This technical report presents the epidemiology of human and animal leishmaniases in the EU and its neighbouring countries and concludes that the disease remains widespread and underreported in many countries of southern Europe, northern Africa, and the Middle East and that there is a need to improv
...
e leishmaniasis prevention and control based on robust surveillance in humans, animals, and vectors, and to increase public awareness following a one health approach.
more
This document summarizes current WHO guidance for public health surveillance of coronavirus disease 2019 (COVID-19) in humans caused by infection w
...
ith severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
New elements include:
update of contact definitions, in line with latest contact tracing guidance
update of detection strategies in line with updated version of WHO SARS-CoV-2 testing guidance
reinfection evidence standardization and surveillance: molecular, genomic and immunological evidence of reinfection
inclusion of clinical case definition of Post COVID-19 condition as defined by WHO
definition of breakthrough infection
more
