Africa CDC Institute for Pathogen Genomics

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Africa CDC IPG

Pathogen genomics – harnessing genetic information of pathogens for enhanced disease epidemiology – is revolutionizing public health through early outbreak detection, enhanced disease surveillance, monitoring drug resistance, assessing the impact of infection prevention and control (IPC) programmes, and many other critical disease control activities. There is substantial interest in pathogen genomics among public health experts and institutions, but there are also substantial barriers to its implementation in Africa. Africa CDC is supporting a coordinated approach to address these challenges and maximize the benefits of new technologies for more effective disease prevention and control in Africa. 

The Africa CDC Institute for Pathogen Genomics (IPG) is a continent-wide leadership initiative established in 2019 to support public health pathogen genomics and bioinformatics activities in Africa. Through the Africa CDC Regional Collaboration Centres (RCCs) and its Regional Integrated Surveillance and Laboratory Network (RISLNET), this institute is facilitating close collaboration with NPHIs, academic institutions, private and public laboratories, and centres of excellence to support prevention, rapid detection and response to current and emerging public health threats across Africa. A key component of this institute is its early focus and pioneering investment in molecular sequencing, leveraging pathogen next-generation sequencing.

Africa Pathogen Genomics Initiative

Africa Pathogen Genomics Initiative Africa PGI is an initiative of the Institute for Pathogen Genomics, a new partnership that aims to enhance disease surveillance and public health partnerships by equipping the continent’s public health scientists with the tools, training and data infrastructure to fully leverage critical genomic sequencing technologies. This new initiative will establish a continental, integrated disease surveillance network, including capacity building for more than 20 NPHIs, to maximize the benefits of next-generation sequencing by providing data for public health decision-making. The Africa PGI laboratory network will provide scientific information for research and public health responses to COVID-19 and other emerging endemic diseases and public health threats that disproportionately affect Africa, e.g. malaria, tuberculosis, HIV and cholera.

Strategic priorities of the Africa CDC Institute for Pathogen Genomics

The Africa CDC IPG has the following three strategic priorities:

1. Governance and enabling mechanisms for public health pathogen genomics in Africa 

Under this priority, the institute:

  • facilitates the development and adoption of standards and policies for generating and sharing pathogen genomics data for public health use, ethical data sharing, biobanking, biological specimens transfer, and networking to leverage continental capacities;
  • convenes meetings and facilitates the creation of functional technical working groups to enhance the use of pathogen genomics in addressing public health priorities and needs;
  • strengthens collaboration within and between NPHIs, academia and industry;
  • supports sequencing and bioinformatic infrastructure development at selected sites in collaboration with partners; and
  • facilitates training of technicians, laboratory staff, bioinformaticians and molecular epidemiologists to integrate genomics into disease control and elimination programmes.

2. Mapping the landscape of pathogen genomics in Africa 

To support efficient use of existing capacities, IPG supports identification of existing institutional capacities and assessment of additional capacities needed to leverage and strengthen regional pathogen genomics laboratories and networks.

3. Facilitate the implementation of demonstration programmes 

IPG facilitates key demonstration programmes to build evidence for the scalable and sustainable application of pathogen genomics and pathways of integration into public health practice in Africa.

Operational strategy of the Institute for Pathogen Genomics

IPG leverages existing infrastructure in Africa and links these assets with the Africa CDC coordinating platforms, i.e. its five RCCs, RISLNET and Member States NPHIs. Technical assistance is delivered through the five strategic pillars of Africa CDC: surveillance and disease intelligence, emergency preparedness and response, laboratory systems and networks, information systems, and public health research.

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