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Antimalarial drug resistance has emerged as a threat to global malaria control efforts, particularly in the Greater Mekong subregion. Drawing on data collected through more than 1000 therapeutic efficacy studies as well as molecular marker studies of Plasmodium falciparum drug resistance, the Report
...
on antimalarial drug efficacy, resistance and response: 10 years of surveillance (2010–2019) presents a decade’s worth of data on drug efficacy and surveillance, as well as recommendations to monitor and protect the efficacy of malaria treatment in the decades to come.
more
Effective response to an outbreak of COVID-19 requires detection in the very earliest stages of the outbreak when the number of cases is small, and the geographical extent of spread is limited. In order to achieve this, a sensitive
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surveillance system capable of detecting small scale, unusual events is necessary.
more
In response to the growing necessity for accurate and timely information regarding deaths categorized by age, sex, and cause of death, underscored by the profound impact of the COVID-19 pandemic, the Africa Centres for Disease Control and Prevention
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(Africa CDC) developed the Continental Framework designed to fortify mortality surveillance within the African Union Member States. This Operational Guide is a comprehensive companion, delineating specific activities harmonized with the framework.
more
Early Warning and Response to Outbreaks and other Public Health Events: A Guide provides practical guidance for strengthening early warning functions within existing public health surveillance syste
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ms in WHO’s South-East Asia Region. The document explains how countries can detect, verify, and respond rapidly to outbreaks and other unusual public health events in line with the International Health Regulations (2005). It describes the five key steps of an Early Warning and Response (EWAR) system—information collection, signal detection, event verification, response, and communication—and outlines how to set alert thresholds, identify signals, and ensure timely reporting. The guide also includes recommendations for monitoring and evaluating system performance to improve timeliness, sensitivity, and overall effectiveness in preventing and controlling public health threats.
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This document outlines minimum requirements of laboratory testing for COVID-19 and link laboratory testing with surveillance and contact tracing to guide the outbreak response by national health aut
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horities using a reduced number of tests performed. The strategies are organized according to stages of transmission: (1) No cases reported or observed (Stage 0); (2) Imported cases (Stage 1); (3) Localized community transmission (Stage 2); (4) Large-scale community transmission (Stage 3). For each stage, the recommended approaches indicate which testing strategy to prioritize when there are severe limitations on laboratory testing. The document is based on the current epidemiology of COVID-19 and available molecular testing methods.
more
Rabies is a fatal viral disease, but is preventable in humans. The rabies virus is transmitted to humans through virus-laden saliva from a rabid animal, mostly dogs. The virus is shed in the saliva of an infected animal and can be introduced into another body through bites, scratches and any other
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wounds that transect the skin. Contact of the infected saliva with mucous membranes is also thought to be a possible route of infection, whereas contact of infected saliva with intact skin is not considered an exposure. Rabies is preventable through pre-exposure prophylaxis (PrEP) for individuals at high and continual risk, and post-exposure prophylaxis (PEP).
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EWARS is a surveillance system developed by the World Health Organization to detect and respond quickly to disease outbreaks in emergency settings where normal health systems are disrupted. It allows health facilities to report priority diseases on
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a regular basis and generates alerts when unusual patterns or suspected outbreaks occur. The system is designed to be simple and fast to set up, even in remote areas, and supports rapid public health action to prevent the spread of disease during crises.
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The strategy focuses on mobilizing and coordinating partners, experts and resources to help countries enhance surveillance of the Zika virus and disorders that could be linked to it, improve vector control, effectively communicate risks, guidance an
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d protection measures, provide medical care to those affected and fast-track research and development of vaccines, diagnostics and therapeutics
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Early warning systems for disease outbreaks are surveillance systems that collect information on a selected list of epidemic-prone diseases in order to trigger prompt public health interventions. They function in humanitarian emergency situations wh
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en the routine public health surveillance systems of a country are underperforming, disrupted or non-existent. Early warning systems are often set up to fill such temporary gaps, while the routine systems recover from the effects of the disaster or a crisis. During humanitarian emergencies, detecting and responding swiftly to epidemics is key in order to reduce unecessary illness and death, especially among refugees and displaced people.
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Genomic sequencing has been an essential tool in generating virological data, driving the laboratory response, and better understanding the dispersal and evolutionary patterns of SARS-CoV-2. In addition to the characterization of the global circulat
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ion patterns, early detection of SARS-CoV-2 variants inside each country is critical to complement the epidemiological and virological surveillance
9 February 2021
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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
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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.
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Several tools are available to support and guide outbreak preparedness, investigation and response activities. These are open access and free to use.
A number of restricted platforms support early detection of public health threats and coordinate
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response activities between EU Member States, the European Commission and other partners. Access to these tools is limited to nominated users.
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The Strategy provides a high-level unifying framework to leverage existing capacities, address barriers and strengthen the use of genomic surveillance in the detection, monitoring and response to pu
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blic health threats. Genomic surveillance is part of the broader surveillance and laboratory system, and its implementation should reinforce end-to-end capacities including sample collection, diagnostics, data sharing and analysis. The strategy aims to facilitate the connectivity between different disease control programs and surveillance networks. This interoperability will strengthen the cross-cutting essential public health laboratory functions underpinning genomics holistically. The strategy articulates the overarching goal, objectives and strategic actions needed. These are dependent on commitments from countries, partners and WHO for their implementation.
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2nd edition. The Event-based Surveillance Framework is intended to be used by authorities and agencies responsible for surveillance and response. T
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his framework serves as an outline to guide stakeholders interested in implementing event-based surveillance (EBS) using a multisectoral, One Health approach. You can download the Training Manual and Framework in Arabic, English, French, and Portuguese
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his publication addresses surveillance and outbreak management of WRID associated with drinking-water supply systems, building on existing guidelines for infectious disease surveillance and outbreak
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response. It aims to help countries to build on and strengthen their systems by providing technical information on the specific features, activities and methodologies related to WRID surveillance and outbreak management.
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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
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response.
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The document provides a standardized protocol for evaluating the Early Warning Alert and Response Network (EWARN), a surveillance system used during humanitarian emergencies when regular national he
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alth surveillance may be disrupted. The purpose of EWARN is to detect outbreaks of communicable diseases early and enable rapid public health response. The guidance explains how the system should be assessed in terms of its structure, implementation, effectiveness, and usefulness. It outlines the key steps of evaluation: preparation, system description, data collection, and post-evaluation reporting. The protocol highlights common challenges observed in previous EWARN implementations, such as delays in establishing the system, limited data quality, weak outbreak response, and lack of clear transition plans back to routine surveillance systems. It emphasizes the need to evaluate both weekly disease reporting and alert verification processes, and to review attributes such as simplicity, data quality, timeliness, sensitivity, and stability. The document also provides templates for interviews, data review forms, and laboratory assessment, as well as guidance on conducting remote evaluations when access is limited. The overall goal of the protocol is to ensure that EWARN functions effectively to detect and respond to outbreaks and that practical recommendations are developed to improve the system’s performance and sustainability in emergency settings.
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