NGS4PublicHealth

The challenge

During the COVID-19 pandemic, genome sequencing provided a key tool for understanding the epidemiology of COVID-19 and tracking the evolution of SARS-CoV-2, including the emergence and spread of new variants. 

The pandemic led to a significant investment in sequencing capacity in sub-Saharan Africa. However, there are significant opportunities to extend the use of genome sequencing to other pathogens and to strengthen the linkage between genomic surveillance activities and disease control, so that data analysis informs policy and practical action. 

The Global Health EDCTP3 programme and the Bill and Melinda Gates Foundation collaborated on a joint call for proposals to strengthen the use of pathogen genomic surveillance in sub-Saharan Africa. This initiative is providing funding to five projects – EpiGen Ethiopia, GenPath Africa, GREAT LIFE, ODIN and PANGenS – which are applying genomic surveillance approaches to a range of pathogens across different geographic areas.

The project

The NGS4PublicHealth project is carrying out a coordinating role for the other genomic surveillance projects and providing them with access to additional expertise and resources.

It brings together two key bodies:

• The African Pathogen Genomics Initiative (Africa PGI), established by the Africa Centres for Disease Control and Protection (Africa CDC), to promote the use of genomics technologies in disease control in sub-Saharan Africa.
• The Global Health Network (TGHN), an open-access portal providing access to capacity-development resources and a virtual space for collaboration.

Project funding will primarily support a project coordinator, based in South Africa, who will liaise with the Africa CDC, coordinate support to the other projects, and promote cross-project collaborations.

Africa PGI and TGHN have been working together to strengthen capacity in genomics and bioinformatics in sub-Saharan Africa, and to promote their use in public health, mostly working through National Public Health Institutes. Key aims include sustaining and growing sequencing capacity in Africa and promoting linkage to clinical and epidemiological data to address key public health questions. 

Africa PGI will provide projects with access to additional expertise in pathogen sequencing, the experience of its laboratory network, encompassing 20 African National Public Health Institutes, its existing digital architecture, and technical training opportunities (for example, through its Next Generation Sequencing Academy).

A coordinated approach across projects will help to establish consensus standards, enable projects to document and share best practices, and support the development of communities of practice linked to pathogens or applications of sequencing.

Impact

The NGS4PublicHealth project will ensure that the other genomic surveillance projects are better able to meet their objectives and achieve greater public health impact. It will:

• Increase the literacy of genomics experts in the principles and methods of epidemiology, and of epidemiologists in the use of genomic data.
• Establish communities of practice linked to particular pathogens or applications of sequencing.
• Facilitate sharing of expertise and experience between projects.
• Ensure alignment in data standards and adoption of standardised methodologies.

By linking and coordinating other projects and providing access to additional expertise and resources, the project will magnify the impact of the individual projects, maximising impacts on public health and providing examples of how genomic surveillance can be applied within national public health systems.