BUILDING SCALABLE PATHOGEN GENOMIC EPIDEMIOLOGY FOR ETHIOPIA

Project Information

EpiGen Ethiopia

Grant agreement ID: 101103188

DOI

10.3030/101103188

EC signature date 29 June 2023

Start date 1 June 2023

End date 31 May 2028

Funded under

• Health

Total cost

€ 5 499 097,50

EU contribution

€ 5 499 097,50

Coordinated by

STICHTING AMSTERDAM INSTITUTE FOR GLOBAL HEALTH AND DEVELOPMENT
Netherlands

Periodic Reporting for period 1 - EpiGen Ethiopia (BUILDING SCALABLE PATHOGEN GENOMIC EPIDEMIOLOGY FOR ETHIOPIA)

Reporting period: 2023-06-01 to 2024-11-30

Summary of the context and overall objectives of the project

The EpiGen project aims to address the growing public health challenge of infectious diseases in Ethiopia, a country of over 110 million people. With a high burden of epidemic-prone diseases and antimicrobial resistance (AMR), there is an urgent need for robust genomic surveillance. Recent outbreaks such as COVID-19 have shown the limitations of traditional surveillance and highlighted the potential of genomic epidemiology to transform public health responses. However, in Sub-Saharan Africa, including Ethiopia, the adoption of genomic tools has been hindered by insufficient infrastructure, expertise, and integration between clinical, epidemiological, and genomic data. EpiGen tackles these challenges through a multidisciplinary approach, combining expertise from both European and African institutions to strengthen Ethiopia’s genomic surveillance capacity. Activities include improving data collection, upgrading laboratory infrastructure, training a skilled workforce, and integrating digital diagnostic tools for real-time decision-making. The project promotes collaboration among policymakers, researchers, and public health entities to create a scalable, sustainable model for genomic epidemiology that can be replicated across Africa. Through these efforts, EpiGen aims to enhance Ethiopia’s capacity to detect and respond to infectious diseases, reduce AMR spread, and inform policy decisions with timely, high-quality data. EpiGen also envisions fostering local production of diagnostics, supporting long-term self-sufficiency in healthcare technologies. The ultimate goal is to improve health outcomes, reduce economic burdens, and build resilience against emerging and re-emerging diseases in Ethiopia and beyond. Objectives of EpiGen: Strengthen the collection and analysis of clinical and epidemiological data, demonstrating the application of genomic epidemiology to inform public health decision-making. Enhance pathogen genomic sequencing capacity in Ethiopia, including strengthening laboratory infrastructure, the workforce, data analysis, and integrating metadata with genomic data. Develop and implement innovative digital diagnostic platforms and mobile applications for real-time public health decisions. Promote African collaboration and knowledge exchange in pathogen genomic surveillance, fostering surveillance and research opportunities.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Despite efforts at various levels, EpiGen did not receive sequencing reagents from Africa CDC during the first 18 months, delaying the production of results. However, hundreds of patient samples for diseases such as cholera, leishmaniasis, dengue, tuberculosis, malaria, and salmonella are ready for sequencing, with several Terms of Reference (ToRs) approved. Additional ToRs for diseases like HIV, anthrax, and measles are under approval. In the absence of reagents, EpiGen scientists analyzed previously collected sequencing data, leading to two scientific papers on leishmaniasis and dengue outbreaks. The first paper identified a new drug-resistant Leishmania tropica variant in Ethiopia’s Somali region, signaling an outbreak. The second paper on the 2023 dengue outbreak in Ethiopia found two dengue serotypes (DENV1 and DENV3) and identified transmission clusters related to outbreaks in Italy and India. This highlights the need for intensified surveillance and public health responses to prevent severe dengue outbreaks. In November 2024, EpiGen launched a measles genomic surveillance subproject, establishing a Nanopore sequencing workflow in Asella. In December 2024, 152 samples collected from the 2023-2024 measles outbreak were sequenced. Preliminary results show the feasibility of genomic surveillance in resource-limited settings. Sequencing depth varied across samples, but many achieved high resolution, with most samples identified as the B3 genotype. Ongoing analysis is refining bioinformatics tools and parameters for optimal results.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Five ToRs for EpiGen research have been approved and will roll out in 2025, with additional ToRs in development. These studies will address diseases such as leishmaniasis, MDR/XDR tuberculosis, dengue, malaria, and cholera, using genomic technologies to tackle public health challenges. For example, whole-genome sequencing (WGS) of Leishmania and tuberculosis isolates will reveal strain diversity and resistance mechanisms, guiding targeted treatments and vaccine development. Similarly, genomic analysis of dengue and malaria will help refine diagnostics and control strategies. The project aims to strengthen Ethiopia’s genomic surveillance, enhance health system capacity, and generate evidence for global interventions in tropical diseases. Key success factors include scaling laboratory capabilities, improving sequencing access, securing sustainable funding, and fostering international collaboration, which will impact global health by advancing precision medicine and data-driven public health strategies.

Lab coats at EPHI lab

Dr. Rajiha Abubeker Ibrahim, an EpiGen researcher at the Ethiopian Public Health Institute

HHU gives sequencing workshop at EPHI

PAI members visit EPHI lab