Genomic surveillance to control pathogen infections in Africa
The overall goal of GenPath Africa is to control pathogen infections in Africa. The consortium of African and European investigators builds on their collective experience in responding to SARS-CoV-2 to better diagnose, monitor and clinically manage current and future epidemics in Africa.
GenPath Africa is funded by the European and Developing Countries Clinical Trials Partnership (EDCTP) and will run for 4 years, with planned completion in 2027.
GenPath Africa will expand genomics capacity to combat drug resistant HIV-1 and TB through precision medicine and by using genomic epidemiology to guide the public health response. Recent developments in wastewater and One Health surveillance will be applied to detect emerging pathogens. In addition, capacity development activities will include degree training in South Africa, the transfer of technology to the National Public Health Institute of Mozambique and the South African National Health Laboratory Service, and the collaboration with other key players and existing networks across the continent to harmonise training materials.
Through these activities we aim to make precision medicine and precision public health a reality in southern and eastern Africa.
In its mission to advance the impact of genomic surveillance, GenPath Africa has strong partners by its side. It is one of six projects that were created to form a Genomic Epidemiology Network in Sub-Saharan Africa. Together, this powerful new partnership aims to:
Increase the use of genomic epidemiology across Africa to answer critical public health questions.
Create data platforms through which integrated epidemiologic, clinical, and genomic data can be collected and combined.
Implement selected pilot projects that apply genomic epidemiology to specific disease areas and use the results to inform public health decision-making and product development.
Establish a community of practice, training programmes, and fellowship opportunities in genomic epidemiology on the continent.
Core activities overview
The work of the consortium is structured in six main areas of activity, whith the goal to conduct and expand genomic surveillance of clinically important pathogens to better diagnose, monitor and manage current and future epidemics in Africa.
WP 1 – Genomics Surveillance of Current and Emerging Pathogens
Creating effective response strategies to current and future epidemics by conducting genomic sequencing of multiple pathogens
Lead
Tulio de Oliveira, Stellenbosch University (SU)
WP 2 – Implementation: Drug Resistant TB
Conducting next generation sequencing to identify the profile of current and emerging drug resistant TB strains (DR-TB)
Lead
Annelies Van Rie, University of Antwerp (UA); Rob Warren, Stellenbosch University (SU)
WP 3 – One Health
Optimizing the genomic surveillance of Rift-valley-fever (RVF) virus and the detection of Mycobacterium tuberculosis (M.tb) in human and animal populations through wastewater-based surveillance
Lead
Samuel Oyola, International Livestock Research Institute (ILRI); Michele Miller, Stellenbosch University (SU)
WP 4 – Bioinformatics and Digital Tools
Supporting effective data management across the entire GenPath Africa project
Lead
Gerard Tromp, Stellenbosch University (SU)
WP 5 – Capacity Building, Dissemination & Exploitation
Facilitating capacity building activities and develop dissemination and communication strategies across the project
Lead
Samantha Sampson, Stellenbosch University (SU)
WP 6 – Project Management & Networking
Ensuring efficient management and a networking infrastructure throughout the entire project
Lead
Claudia Schacht, LINQ Management GmbH (LINQ)
Team
The Genomic Surveillance to Control Pathogen Infections in Africa consortium (GenPath Africa) connects African and European researchers from five organisations across five countries and two continents with a common goal: to increase the use of genomic epidemiology to address public health issues of importance in South Africa, Kenya and Mozambique.
The project brings together experts from multiple disciplines including epidemiologists, clinicians, bioinformaticians, immunologists, virologists, and public health and health policy specialists.
GenPath Africa is coordinated by Prof Tulio de Oliveira from Stellenbosch University (SU) and supported by LINQ management GmbH (LINQ).
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