GenPath Africa

The challenge

Pathogens rapidly evolve. Genetic variants may have different properties, affecting a pathogen’s ability to spread, its susceptibility to drugs and vaccines, and the severity of disease. Understanding which variants are in circulation is therefore critical to controlling diseases.

The COVID-19 pandemic emphasised the importance of tracking variants. During the pandemic, South Africa established a highly effective collaborative approach across institutions, known as the Network for Genomic Surveillance, to monitor SARS-CoV-2 variants and provide policymakers with up-to-date data to inform control efforts. 

Although the pandemic led to an expansion of genomic surveillance in sub-Saharan Africa, the potential of this new technology has yet to be fully exploited across the region.

The project

The GenPath project is leveraging the genomics capabilities established at two centres of excellence in sub-Saharan Africa: the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University in South Africa, and the International Livestock Research Institute (ILRI) in Kenya. Genomics surveillance platforms will be strengthened for HIV and TB in South Africa and for Rift Valley fever in Kenya. Additionally, the project will collaborate with authorities in Mozambique to enhance capacity for monitoring HIV and tuberculosis. 

For HIV, the focus will be on patients experiencing treatment failure. More portable technologies, such as Nanopore sequencing, will be piloted at central South African sites before being introduced more widely in other South African centres and Mozambique. The possible use at peripheral facilities will also be explored.

For TB, rifampicin-resistant isolates will be sequenced to generate information on resistance-associated variants, to inform treatment, to provide policymakers with data on the prevalence of drug-resistant strains and to alert them to highly resistant isolates. Factors associated with resistance will also be explored. 

In Kenya, the focus is on Rift Valley fever, a zoonotic infection. A One Health approach is being adopted, with surveillance activities spanning the medical and veterinary sectors. Veterinarians will collect samples from stillbirths and low-birth-weight animals at rural sites to complement hospital-based surveillance. 

In addition, a One Health approach will be introduced in two South African cities to investigate the transmission of different mycobacteria from domestic animals and wildlife to humans, as well as to explore factors associated with the transmission to humans. In both Kenya and South Africa, the project will extend wastewater surveillance systems to identify pathogens and genes associated with antimicrobial resistance (AMR). 

The work will be underpinned by the development of integrated data platforms that collate genetic, clinical, and epidemiological data. The project will engage with policymakers to develop dashboards to support decision-making, and an extensive training programme will be organised across the three countries.

Impact

The GenPath Africa project will have an immediate and long-term impact. It will: 

• Generate data on the drug resistance profiles of individual infections, guiding clinicians’ choice of treatment.
• Create an enhanced surveillance infrastructure, providing policymakers with information on geographical and temporal trends in drug resistance to support targeted control efforts.
• Integrate technologies and processes into national systems, building their capacity to apply genomics routinely in surveillance.
• Provide an early warning of Rift Valley fever outbreaks.

Ultimately, the project will ensure that patients with drug-resistant infections receive appropriate treatment rapidly, while also providing national policymakers with key insights to inform disease control activities.