Africa Pathogen Genomics Initiative | Africa PGI 2.0

PGI2-01.0 web-01

Africa PGI 2.0 is a flagship initiative of the Africa CDC to build and strengthen resilient, integrated, proactive, and sustainable, molecular diagnostic, genomic surveillance and epidemiology ecosystem in Africa. Africa PGI 2.0 will leverage on the progress and lessons learned from the implementation of the initial phases of the Africa PGI. It will also consider emerging needs, evolving priorities and national, regional and global changes on the perception, utility and application of genomic surveillance.

Africa PGI 2.0 - Four Priorities and Enablers

The initiative consists of four key components and several enablers 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.

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