Activities
The overall goal of GenPath Africa is to conduct and expand genomic surveillance of clinically important pathogens to better diagnose, monitor and manage current and future epidemics in Africa.
The work of the consortium is structured in six main areas of activity, which form the following key work packages of the project:
WP 1 Genomics Surveillance of Current and Emerging Pathogens
WP 2 Implementation: Drug Resistant TB
WP 3 One Health
WP 4 Bioinformatics and Digital Tools
WP 5 Capacity Building, Dissemination & Exploitation
WP 6 Project Management & Networking
WP 1 – Genomics Surveillance of Current and Emerging Pathogens
Lead: Tulio de Oliveira (SU)
This WP will help create effective response strategies to current and future epidemics by conducting genomic sequencing of multiple pathogens. Our team will adapt existing technologies and expand next generation sequencing to emerging pathogens, as well as conduct next generation sequencing to advance responses to current epidemics, particularly HIV-1 and TB. The goal is to strengthen countries’ response strategies to epidemics by supporting and developing diagnostic testing and biomarker capabilities.
Partners involved: SU, ILRI, INS, SU
WP 2 – Implementation: Drug Resistant TB
Lead: Annelies Van Rie (UA) together with Rob Warren (SU)
This WP will conduct next generation sequencing to identify the profile of current and emerging drug resistant TB strains (DR-TB) and will support their detection and containment through precision medicine and precision public health. The team will develop a novel strategy for DR-TB control and implement it in a cohort study to evaluate the use of optimal individualized rescue regimen for patients diagnosed with DR-TB in the WC Province of South Africa. The practice of next generation sequencing and the skills and knowledge acquired in this process will also be transferred to the National Department of Health, where they will be integrated into the routine diagnostic DR-TB algorithm, patient management, and public health activities. The long-term goal of this WP is to translate this research and practical experience into guidelines and policies for precision medicine and precision public health strategies for DR-TB control on a national level.
Partners involved: SU, ILRI, UA
WP 3 – One Health
Lead: Samuel Oyola (ILRI) together with Michele Miller (SU)
This WP will track pathogens through wastewater-based surveillance in Kenya and South Africa with the goal of optimising the genomic surveillance of Rift-valley-fever (RVF) virus in human and animal populations and the detection of Mycobacterium tuberculosis (M.tb) in domestic animal and wildlife populations. Using metagenomics approaches to analyse wastewater samples, researchers will develop a wastewater-based genomic epidemiology of zoonotic pathogens and establish surveillance systems in four cities. These surveillance systems will provide data to inform diagnoses and vaccine development initiatives in response to RVF virus present in both human and animal populations. Further, conducting genomic surveillance of domestic animals and wildlife populations will support the detection of zoonotic and anthropogenic pathogens of clinical importance, particularly the presence of pathogens that concern human health in HIV and M.tb burdened rural communities.
Partners involved: ILRI, SU
WP 4 – Bioinformatics and Digital Tools
Lead: Gerard Tromp (SU)
This WP will support effective data management across the entire GenPath Africa project by focusing on standardisation and harmonisation of data and the development of visualisation tools to aid the rapid dissemination of results. We will develop an overarching data management plan and establish a data integration platform to assist pathogen genomic and clinical data integration across countries and institutions. A wastewater dashboard, which will enable a more effective exchange of data across different geographical locations and institutions will be established and serve as an early warning system for public health action. Additionally, our team will develop reporting tools for rapid dissemination of epidemiological and genomic analyses results. These tools will enable agile programmatic responses to evolving epidemics.
Partners involved: SU, ILRI
WP 5 – Capacity Building, Dissemination & Exploitation
Lead: Samantha Sampson (SU)
This WP will facilitate the capacity building activities and develop dissemination and communication strategies across the entire GenPath Africa project. We will identify and implement key support mechanisms to strengthen the capacities of individual countries to conduct genomic surveillance. This will include the long-term degree training of young researchers, as well as short-term, hands-on genomic sequencing and analysis training. We will also develop a clear dissemination framework, provide guidance and support to ensure coherent communication amongst project partners, and enable quick uptake of knowledge and results by our target audience. Further, we will promote the integration of research with public health organizations, to maximize the project’s impact.
Partners involved: SU, ILRI, INS, UA, LINQ
WP 6 – Project Management & Networking
Lead: Claudia Schacht (LINQ)
This WP will ensure efficient management and networking infrastructure throughout the entire GenPath Africa Project. We will provide optimal managerial support for all project partners and support open communication between the consortium and the EDCPT to maximize the effectiveness of project activities. As GenPath Africa is part of a larger Genomic Epidemiology (GenEpi) cluster made up of six individual projects, this WP will also coordinate liaison with the other initiatives to enable effective collaboration between researchers across all projects.
Partners involved: LINQ, SU