Genome sequencing has brought about a revolutionary change in how we identify, investigate, and understand infectious disease outbreaks. To bolster genomics capacity-building, the Africa Pathogen Genomics Initiative (Africa PGI) has been actively supporting National Public Health Institutions (NPHIs) and National Reference Laboratories (NRLs) across the continent. Currently, these institutions are routinely conducting genome sequencing of priority pathogens, including Mpox, Lassa fever virus, Dengue virus, HIV, Vibrio cholerae, Mycobacterium tuberculosis, and Plasmodium falciparum, among others. As a result, these laboratories generate a significant amount of genomic data using high-throughput sequencing platforms.
Timely and efficient data transfer through the internet plays a critical role in establishing a real-time public health genomic surveillance system. However, limited bandwidth internet access remains a significant challenge in Africa, hindering the timely transfer of data and effective utilization of cloud-based or open-source web-based bioinformatics solutions and databases. To address this issue, the Africa PGI, in collaboration with ASLM, BMGF, and SpaceX, initiated a pilot project in September 2023. The primary objective of this project is to enhance access to high-speed satellite-based internet, enabling real-time, or near-real-time, transfer of pathogen genomic data and facilitating access to cloud-based resources. This high-speed internet service will not only improve data transfer but also enhance other internet-based operations such as communication, e-learning, virtual meetings, video conferences, and various other activities. The pilot project is being implemented in all Member States that have obtained regulatory approval for the operation of SpaceX’s satellite-based internet.
With the continuous expansion of the Africa CDC laboratory network, digital transformation becomes imperative to enhance efficiency. In November 2023, the Africa CDC introduced a laboratory network information management system (NIMS – https://www.pgi-nims-africacdc.org/) to monitor and facilitate informed decision-making on network operations. The NIMS system serves as a valuable resource for Africa CDC, centers of excellence, regional and national laboratories, enabling efficient tracking of biological sample shipments and ensuring their integrity during transit from referral sites to destination facilities across the network. This system also supports cross-border sample referrals for testing and sequencing. The NIMS system has undergone successful piloting for cross-border sample referral in four sites and is currently being implemented for in-country sample referral in one site. The integration of connectivity, digitization, and innovative solutions in public health genomics in Africa will contribute significantly to the detection, response, and control of infectious diseases. By strengthening genomics capacity, improving internet access, and digitizing laboratory operations, Africa is poised to harness the full potential of genomics for public health surveillance and outbreak management.
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Dorothy Njagi | Senior Communication Officer- Communication & Public Information directorate | Africa Centres for Disease Control and Prevention| African Union| email: email: njagid@africacdc.org | Website: www.africacdc.org| Addis Ababa| Ethiopia| Facebook | Twitter
