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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 Re
...
fe-
-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
Responding to a polio outbreak. Guidelines
recommended
The occurrence of a case of wild polio in a previously polio free area as presently in Syria, whether through importation, laboratory accident, or mutation of vaccine virus (VDPV), should be considered a public health emergency, that requires a rapid and high quality
...
response as utmost priority
more
Overview: Risk communication and community engagement are essential for any disease outbreak response. This is particularly critical during outbreaks of Ebola which may create fear in the public and
...
frontline responders alike due to severe presentation of symptoms, misunderstanding of the causes of illness and high fatality rates. This document outlines some of the key considerations for risk communication and community engagement response to Ebola outbreak in Democratic Republic of the Congo.
Ebola outbreaks have been associated with misinformation and false rumours. In the context of RCCE, rumours refer to unsubstantiated information, claims or beliefs about what is causing the disease or how it can be treated/cured. If not proactively addressed in culturally appropriate ways, misinformation and rumours can lead to the further rapid spread of the disease and unnecessary deaths, severe disease, suffering, and societal and economic loss.
The publication includes a 'Rumour Tracking Tool' (Annex II).
more
his Inter Action Review report for the COVID-19 outbreak in Mauritius documents and assesses the country’s capacity to respond to the outbreak and identifies the best practices, strengths, gaps an
...
d challenges of the national response. Areas requiring improvements or sustained actions have been identified across the 9 strategic pillars of World Health Organization (WHO)’s COVID-19 Strategic Preparedness and Response Plan and an additional pillar for the country’s response beyond health. On an overall, the review aims to enhance and sustain the national response with a particular focus on strengthening the health systems.
more
Integrating Clinical Research into Epidemic Response: The Ebola Experience
Gerald Keusch, Keith McAdam, Patricia Cuff, Michelle Mancher, and Emily R. Busta
National Academies of Sciences, Engineering, and Medicine
(2017)
C1
The 2014–2015 Ebola epidemic in western Africa was the longest and most deadly Ebola epidemic in history, resulting in 28,616 cases and 11,310 deaths in Guinea, Liberia, and Sierra Leone. The Ebola virus has been known since 1976, when two separate outbreaks were identified in the Democratic Repub
...
lic of Congo (then Zaire) and South Sudan (then Sudan). However, because all Ebola outbreaks prior to that in West Africa in 2014–2015 were relatively isolated and of short duration, little was known about how to best manage patients to improve survival, and there were no approved therapeutics or vaccines. When the World Heath Organization declared the 2014-2015 epidemic a public health emergency of international concern in August 2014, several teams began conducting formal clinical trials in the Ebola affected countries during the outbreak.
more
The exercise was convened by the East Africa Community (EAC) and implemented by the World Health Organization (WHO) to test both countries’ preparedness and response to disease outbreaks. It covered various real-life simulations involving the heal
...
th, livestock, agriculture, tourism and environment sectors. The simulation that was presented was not unusual in the region, and highlighted the daily challenge of managing the risk of disease outbreaks.
more
This document summarizes preparedness and response activities to address the coronavirus disease (COVID-19) outbreak in South Sudan through the end of 2020. The addendum includes the activities and
...
financial requirements of the updated National COVID-19 Response Plan. Originally issued in March prior to identification of the first person confirmed with COVID-19 in South Sudan and with a focus on preparedness, the updated plan encompasses a significantly scaled-up national response.
more
The document is a World Health Organization publication about communicable disease surveillance and response systems. It explains that communicable disease surveillance is a core public health function used to collect, analyse and interpret health
...
data so that outbreaks and other health threats can be detected early, monitored and responded to appropriately. The guide describes how surveillance systems help provide early warning of potential threats, support programme monitoring, enable outbreak detection and facilitate timely public health action to prevent disease spread. It also discusses the design and evaluation of surveillance systems and how the information they generate is used for decision-making in public health practice.
more
On October 6, 11 cases of Cholera were confirmed positive in one neighbourhood of the capital Sana’a. No confirmed cases have been reported in other locations in Yemen. UNICEF, together with WHO and Health authorities, have initiated a rapid response
...
setting up a treatment centre as well as dispatching an investigation team to the affected neighbourhood. The source of infection was identified as water and commercial food contamination.
more
The main objectives of the SOPs are to: (i) establish standards and timelines for response activities; and (ii) guide national governments and GPEI partners in key support functions.
This new version of the SOPs presents overall
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response requirements for dealing with type 1, 2 and 3 poliovirus following monovalent type 2 oral polio vaccine (mOPV2) cessation. Version 2.4 will be valid until release of revised version 3.0 (anticipated May 2018).
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This training is part of the national Rapid Response Team Training package, adapted to take into account specific issues pertaining to the COVID-19 outbreak. Several technical aspects presented here
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were developed and posted on different WHO platforms and for larger / different audiences. In this package, we have regrouped the essential elements that you, as a member of the national RRT, may wish to take into account as you perform COVD-19 related activities
The objectives of this online learning package is to provide National Rapid Response Teams members with the key knowledge and tools needed to early detect and effectively respond to a Covid-19 outbreak.
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AAll health workers deployed to measles outbreaks must complete the measles and rubella (MR) training to implement quality interventions and work safely and effectively in the field. This channel provides the essential preparedness, detection, investigation,
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response, and recovery skills required to contain the measles outbreak.
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The document Integrated Disease Surveillance and Response Technical Guidelines, Booklet Four: Sections 8 and 9 (Third Edition, 2019) provides guidance for strengthening public health surveillance and respo
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nse systems in the WHO African Region. It focuses on monitoring, supervision, evaluation, and feedback mechanisms to improve the performance and quality of Integrated Disease Surveillance and Response (IDSR) systems. The text outlines key surveillance core functions—such as case detection, reporting, data analysis, outbreak investigation, preparedness, response, and feedback—and introduces indicators to measure system effectiveness, including timeliness, completeness, and data quality. Additionally, it discusses the implementation of electronic IDSR (eIDSR) to enhance real-time reporting and outbreak management. Overall, the booklet aims to strengthen early detection, rapid response, and health security capacity across all levels of the health system.
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The document “Mpox Continental Response Plan 2.0” outlines the strategy developed by the Africa Centres for Disease Control and Prevention (Africa CDC) in collaboration with the World Health Organization (WHO) to respond to the ongoing mpox
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outbreak across Africa. The plan describes coordinated actions to strengthen surveillance, laboratory capacity, case detection and contact tracing in affected countries. It also focuses on improving access to vaccines, diagnostics and treatment, supporting healthcare systems, and enhancing risk communication and community engagement. In addition, the document highlights the importance of regional and international cooperation, resource mobilization and technical support to help African countries control the outbreak and prevent further spread. Overall, the plan serves as a continental framework to guide a coordinated public health response to mpox in Africa.
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The Coronavirus is spreading globally. How can individuals, communities and humanitarian actors best respond to the COVID-19 outbreak? How can the Sphere Handbook guide our response?
These guid
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elines are available in different languages
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The primary focus of the plan continues to be prevention, preparedness and treatment of the the Novel Coronavirus (COVID-19) outbreak. Central to the plan are the following overall objectives:
To prevent further transmission of COVID-19 in the
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oPt;
To provide adequate care for patients affected by COVID-19 and to support their families and close contacts; and
To mitigate the worst effects of the pandemic.
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The Coronavirus is spreading globally. How can individuals, communities and humanitarian actors best respond to the COVID-19 outbreak? How can the Sphere Handbook guide our response?
This docum
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ent has two sections: A. The first section covers fundamental principles which are crucial to a successful, holistic intervention. B. The second covers relevant standards and guidance in the handbook’s WASH and Health chapters.
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The Cholera Outbreak Guidelines: Preparedness, Prevention, and Control provide a practical field guide for responding to cholera outbreaks. Developed by Oxfam GB, the guidelines combine lessons from past cholera interventions and best practices for
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effective outbreak management. The document outlines key strategies, including preparedness planning, rapid response to outbreaks, water and sanitation improvements, hygiene education, and coordination among stakeholders. It covers both non-endemic and endemic cholera outbreaks, offering step-by-step guidance on surveillance, intervention, and monitoring. The aim is to ensure community-based, gender-sensitive, and rapid public health responses to control cholera and minimize mortality.
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Risk Communication and Community Engagement (RCCE) is an essential part of any disease outbreak response. Risk communication in the context of an Ebola ou
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tbreak refers to real time exchange of information, opinion and advice between frontline responders and people who are faced with the threat of Ebola to their survival, health, economic or social wellbeing. Community engagement refers to mutual partnership between Ebola response teams and individuals or communities in affected areas, whereby community stakeholders have ownership in controlling the spread of the outbreak.
It is intended to be used to guide RCCE work which is central to stopping the outbreak and preventing its further amplification. Unlike other areas of response, RCCE draws heavily on volunteers, frontline personnel and on people without prior training in this area. As such, the document provides basic background information, scopes the socio-economic and cultural aspects (that are known at the time of publication), and provides the latest evidence-based advice and approaches
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An example of integration of research into epidemic response.
