Periodic Reporting for period 1 - GenPath Africa (GENOMIC SURVEILLANCE TO CONTROL PATHOGEN INFECTIONS IN AFRICA)
Période du rapport: 2023-05-01 au 2024-10-31
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 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.
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.
During the first 18 months, this project has achieved significant milestones in using genomic tools to combat epidemics, enhance public health, and build capacity in Africa.
Improving Genomic Epidemiology: Laboratory procedures were adapted to sequence multiple pathogens, aiding epidemic response in South Africa, Kenya, and Mozambique. Highlights include adaptations to sequence cholera, chikungunya, and hepatitis B, advancing tuberculosis (TB) genome analysis, and initiating HIV drug resistance surveillance in Mozambique. A low-cost Oxford Nanopore drug resistance test was validated to support future applications.
Fighting drug-resistant TB (DR-TB): Activities have focused on incorporating next-generation sequencing (NGS) into DR-TB management in South Africa, with personalized treatment aids and a clinical study framework developed. Key steps included stakeholder engagement and ethics approval for a clinical trial to enhance precision medicine approaches.
Set-up of early warning surveillance: Wastewater surveillance systems in Kenya are detecting pathogens of public health concern, while South Africa's samples focus on zoonotic mycobacteria. Notable findings include identifying Mycobacterium bovis in various domestic and wildlife animal populations and refining genomic tools for Rift Valley fever virus surveillance.
Advancing Data Integration: Activities have focused on developing systems to seamlessly integrate genomic, clinical, and epidemiological data to enhance tools like a metagenomics bioinformatics pipeline and an interactive dashboard for pathogen tracking.
Capacity Building: Workshops at Stellenbosch University and other institutions have contributed to the training of over 100 individuals in genomics and bioinformatics analysis. A structured Master's program in Pathogen Bioinformatics is under development and will be initiated in 2026.
This project underscores Africa’s leadership in leveraging genomic science for epidemic preparedness and response while fostering regional expertise and innovation.
Improving Genomic Epidemiology: Laboratory procedures were adapted to sequence multiple pathogens, aiding epidemic response in South Africa, Kenya, and Mozambique. Highlights include adaptations to sequence cholera, chikungunya, and hepatitis B, advancing tuberculosis (TB) genome analysis, and initiating HIV drug resistance surveillance in Mozambique. A low-cost Oxford Nanopore drug resistance test was validated to support future applications.
Fighting drug-resistant TB (DR-TB): Activities have focused on incorporating next-generation sequencing (NGS) into DR-TB management in South Africa, with personalized treatment aids and a clinical study framework developed. Key steps included stakeholder engagement and ethics approval for a clinical trial to enhance precision medicine approaches.
Set-up of early warning surveillance: Wastewater surveillance systems in Kenya are detecting pathogens of public health concern, while South Africa's samples focus on zoonotic mycobacteria. Notable findings include identifying Mycobacterium bovis in various domestic and wildlife animal populations and refining genomic tools for Rift Valley fever virus surveillance.
Advancing Data Integration: Activities have focused on developing systems to seamlessly integrate genomic, clinical, and epidemiological data to enhance tools like a metagenomics bioinformatics pipeline and an interactive dashboard for pathogen tracking.
Capacity Building: Workshops at Stellenbosch University and other institutions have contributed to the training of over 100 individuals in genomics and bioinformatics analysis. A structured Master's program in Pathogen Bioinformatics is under development and will be initiated in 2026.
This project underscores Africa’s leadership in leveraging genomic science for epidemic preparedness and response while fostering regional expertise and innovation.
There have not been any results beyond the state of the art produced yet.