EpiGen Ethiopia

The challenge

Ethiopia, the second most populous country in sub-Saharan Africa, is affected by multiple infectious diseases. These infections account for an estimated 85% of the country’s health problems. Ethiopia has introduced the WHO’s Integrated Disease Surveillance and Response (IDSR) system to track 19 priority infectious diseases across more than 900 districts.

Implementing the IDSR system is challenging for several reasons, including limited expertise and insufficient infrastructure. Furthermore, because it relies on microbiological methods, the IDSR approach does not provide comprehensive coverage of all pathogens.

Genomic approaches, based on whole-genome sequencing of pathogens, can provide more information across a wider range of pathogens to guide public health responses. Primarily in response to the COVID-19 pandemic, genome surveillance has become more widely used in sub-Saharan Africa. However, further development is required to underpin national surveillance systems. 

The project

The EpiGen Ethiopia project is bringing together academic and public health institutions in Ethiopia, as well as regional and European partners, to create a national genomics-based surveillance system. 

To this end, 30 sites within the existing IDSR network, including six regional public health laboratories, will share samples with two national sequencing centres, Ethiopia’s national public health institute (EPHI) and the Armauer Hansen Research Institute (AHRI), along with linked clinical and epidemiological data. Genome sequencing capacity will be built at additional sites, and the EPHI data management platform will be strengthened and adapted to integrate TB diagnostic data into a single repository. The project will extend the platform to include data from malaria diagnostic tests and assess the feasibility of integrating additional point-of-care tests, such as for typhoid fever. 

The project will build on experience in Kenya, where dashboards have been created using location- and time-tagged data, enabling near-real-time disease information to be viewed by policymakers and other stakeholders on mobile phones. The information generated will be available to support policymaking and local treatment decision-making. 

Data visualisation tools will be co-developed with national policymakers to ensure that they meet user needs. These efforts will also benefit from input from experts at the Africa Centre for Disease Control and Prevention (Africa CDC), which has experience in dashboard development. The Africa CDC is a core project partner, and the project’s work will feed into the Africa CDC’s African Pathogen Genomics Initiative. This linkage will also help to disseminate learnings and tools emerging from the project across sub-Saharan Africa. 

The project will also generate a biobank of samples to support further research and establish a comprehensive training programme to build capacity in sequencing, bioinformatics and data management. 

Impact

The EpiGen Ethiopia project will establish the foundation for a genomics epidemiology platform for infectious disease surveillance in Ethiopia. It will:

• Enhance the country’s ability to gather information on pathogens and use it in clinical practice and disease control.
• Bring together many partners in a community of practice, catalysing local innovation in the application of genomic technologies to infectious disease surveillance.
• Provide a model that can be replicated in other countries, via links with the Africa CDC.
• Create a centre of excellence in the Horn of Africa and promote wider adoption of genomic technologies.

A functioning genomic surveillance system will deliver multiple benefits to Ethiopia, including the potential to limit indiscriminate use of therapeutics and reduce the drivers of drug resistance, to target disease control efforts where they are most needed, and to support research into the key factors driving the spread of key infectious diseases.