Institute of Pathogen Genomics (IPG)

Africa PGI

Africa CDC Institute of Pathogen Genomics, through the Africa Pathogen Genomics Initiative (Africa PGI) aims to enhance disease surveillance and public health partnerships through integrated, cross-continent laboratory networks equipped with the tools, human resource capacity and data infrastructure to fully leverage critical genomic sequencing technologies.

Why is pathogen genomics important for public health?

Nearly 140 disease outbreaks are detected annually across Africa. Genomic sequencing technology will provide the scientific evidence needed for health systems to better prevent, identify and track these outbreaks, thus helping public health experts to stay ahead of novel pathogens and re-emerging diseases. It will allow health systems to better tackle pathogens that cause diseases like COVID-19, polio, malaria, tuberculosis, HIV/AIDS, cholera, Ebola, and emerging health threats. In resource-limited environments, the near-real-time insights from pathogen genomics can inform the allocation of precious medical commodities like diagnostics, drugs and vaccines. Through improved surveillance that provides insights into local disease transmission, pathogen genomics can inform data-driven public health action tailored to meet local needs. 

Public health benefits of pathogen genomics

  • Surveillance: Genomic sequencing enhances the ability to detect emerging disease threats, bolster pandemic preparedness and monitor endemic disease control efforts.
  • Pathogen characterization: It helps in the identification of variation among pathogen strains for the prevention and control of antimicrobial resistance.
  • Product development: Genomic sequencing informs research and development of vaccines, therapeutics and diagnostics, and enhances monitoring of efficacy in diverse populations.
  • Delivery programmes: It helps in the optimization of vaccination campaigns and medical product introductions to at-risk populations.

Genomic sequencing technologies “read” genetic materials such as DNA and RNA and help researchers analyse changes in these materials over time. Next-generation sequencing (NGS), developed over a decade ago, allows researchers to ask more complex questions and obtain answers much faster and cheaper than was previously possible, enabling rapid, effective and data-based public health decisions.

COVID-19 has been a powerful reminder of the importance of disease surveillance systems and genomic sequencing technologies in advancing public health. However, this potential is still far from being realized in Africa due to the high costs of NGS equipment and tools, limited funding, and inadequate infrastructure and framework for data-sharing. Democratizing the use of next-generation sequencing technology in Africa and other low and middle-income regions will enable partnerships and upend the decades-old paradigm of reliance of cutting-edge global health innovation on technical or academic partners from the global north.


Spotlight on COVID-19

COVID-19 has been a powerful reminder of the importance of integrated molecular disease surveillance systems in advancing public health systems. Scientists from around the world have published open-source analyses of next-generation sequencing data for SARS-CoV-2, the virus that causes COVID-19, collaborating to further track the spread of the pathogen and to provide information for critical response efforts. In the coming months and years, NGS will continue to contribute to better understanding of SARS-CoV-2 including how it may evolve over time, which has important implications for vaccine and drug development.

Broader health goals and the Africa CDC

The Africa Health Strategy 2016-2030 aims to strengthen health systems to achieve global development goals, Universal Health Coverage (UHC) and the health security agenda. Establishing effective systems for disease surveillance is a critical piece of the strategy, and pathogen genomics technology can help enhance this. Pathogen genomics will strengthen the infrastructure established by Africa CDC, the continent’s leader in disease surveillance and key implementer of continent-wide health sector strategies.

Core components of the Africa PGI

Africa PGI is an initiative of the Africa CDC Institute for Pathogen Genomics, a continent-wide leadership initiative established in 2019 to support public health pathogen genomics and bioinformatics across Africa. Africa PGI aims to maximize the benefits of next-generation genomic sequencing tools by empowering public health experts in the continent with the tools, training and coordination needed for data-driven decision-making for preventing and responding to disease threats. 

The initiative consists of four key components to ensure impactful, sustainable and interconnected use of NGS technologies across the continent:

Africa PGI aims to build a continent-wide functional and operational network of pathogen genomics and bioinformatics. This includes building NGS capacity in 20 national public health institutes (NPHIs) across Africa by supporting laboratory upgrades and enhancing the technical capacity of laboratory staff. Under the initiative, Africa CDC will create regional hubs of laboratories in the five geopolitical regions to facilitate coordination as well as training, knowledge-sharing and technical support. Africa CDC will coordinate laboratory upgrades by equipping these laboratories with essential diagnostics and equipment and support the deployment of technical staff.
The NGS Academy is being developed in collaboration with key partners engaged in genomic sequencing. Organized in partnership with the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) and the African Academy of Sciences (AAS), this academy will adopt a blended learning approach to develop a semi-standardized, end-to-end curriculum, synthesizing in-person and online training that already exist in and outside the continent for such topics as: research study design, intelligent sampling, sample preparation methods, sequencing techniques (amplicon, whole genome, unbiased metagenomic), NGS data analysis, visualization and interpretation. This curriculum will include a menu of courses and certifications that will serve as important credentials to foster pathogen NGS research.
The data architecture of Africa PGI will include (1) a digital “bazaar” of interoperable software packages for pathogen NGS data analytics and visualization, including a “digital backbone” that connects into; (2) a continental, cloud-based data repository for pathogen NGS data, called the African Pathogen Genomics Archive.
Africa PGI will help develop public health use cases for pathogen genomics sequencing that is most relevant for each geographical entity. This will enhance sustainability of the Africa PGI and make it fit-for-purpose and focused on the highest-priority public health challenges and emerging biosecurity threats of African Union Member States. Africa PGI will incorporate access to expertise in epidemiology to support the design of sampling strategies as part of the development and implementation of use cases for pathogen genomic sequencing most relevant to target locations.


The following partners support the work of the Africa Pathogen Genomics Initiative:

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