Genomic epidemiology for surveillance and control of poverty-related and emerging and re-emerging infections in sub-Saharan Africa
The GenEpi Network is a collaboration between the Global Health EDCTP3 Joint Undertaking (EDCTP3) and the Bill & Melinda Gates Foundation (BMGF). The network consists of ten genomic epidemiology projects supported by these two funders which are described below in more detail. Cross-project collaboration is implemented via working groups which were initiated in 2024. This powerful new partnership aims to leverage the genomic sequencing capacity being built in Africa to support epidemiology and surveillance of endemic and epidemic pathogens.
Specifically, the GenEpi Network seeks 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.
EDCTP3- funded projects
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The aim of the EpiGen project is to build capacity for an integrated pathogen genomic surveillance system that can then inform public health decisions. The specific overarching objectives include strengthening the collection and analysis of clinical and epidemiological data, enhancing the capacity and capability for pathogen genomic sequencing, including strengthening the laboratory infrastructure, human workforce, pathogen genomic data analysis, and the integration of metadata with genomic data, developing and implementing innovative digital diagnostic platforms, creating mobile phone applications which update in semi-real time for policy decisions, and promoting communities of practice and knowledge exchange through fostering African collaboration and networking in the domain of pathogen genomic surveillance for infectious diseases.
Duration: 60 months (01/06/2023 - 31/05/2028)
Website: www.epigenethiopia.org
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The overall goal of GenPath Africa is to control pathogen infections in Africa. The project 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, and 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, GenPath Africa aims to make precision medicine and precision public health a reality in southern and eastern Africa.
Duration: 48 months (01/05/2023 – 30/04/2027)
Website: www.genpath-africa.org
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GREAT-LIFE has as the primary objective to establish capacity for using mobile nanopore sequencing combined with laptop analyses and sharing of summary data in real-time in the African Great Lakes Region. In GREAT-LIFE, we will establish sequencing across six countries in the region and use this to study the abundances of AMR in villages and refugee camps. Linking this with spatial and temporal epidemiological data will enable us to identify locally relevant drivers for AMR and provide data for changing empiric treatment and policies.
In addition, we will utilize sequencing directly on GI samples to identify the causative agents (and their AMR) both to provide data for policies, but also to provide immediate results for direct patient care in the frontline. We will educate a number of people in the very frontline to utilize field-sequencing and bioinformatics, as well as more advanced bioinformaticians and epidemiologist centrally. The data generated will be linked in real-time through a central hub in Tanzania to public health authorities for actions.
Duration: 48 months (01/07/2023 - 30/06/2027)
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The ODIN consortium is a collaborative research and capacity building effort bringing together a diverse group of leading institutions that aims to establish innovative and adaptable infectious disease surveillance in sub-Saharan Africa. Each institution in the consortium brings its unique expertise and perspective to the table, making ODIN a dynamic force in the realm of environmental surveillance and public health. Together, ODIN strives to enhance our understanding of environmental factors that impact public well-being and work towards innovative solutions for a healthier future.
Duration: 48 months (01/07/2023 - 30/06/2027)
Website: https://odin-wsp.tghn.org/
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The main purpose of this project is to increase Africa’s capacity in genomic epidemiology and to conduct genomic epidemiology of drug-resistant tuberculosis and malaria across 12 African countries. The capacity building strategy will include engagement of Post-docs, conducting of on-site workshops and development of free training virtual materials. The initiative will expand south-south research collaborations, train the next generation of African scientists with cutting-edge techniques, and develop advances in disease surveillance, contributing to the African Union Agenda.
Duration: 48 months (01/07/2023 - 30/06/2027)
Website: https://pangens.org
NGS4PH
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The EU-funded NGS4PublicHealth project aligns with the collaboration between the Global Health EDCTP3 and the Bill & Melinda Gates Foundation joint undertaking. The project will support the platforms to deliver expertise and resources in genomics and clinical trials research and data science to EDCTP grantees in genomic epidemiology. The grant will enable one full-time project manager to assist in coordination activities between EDCTP grantees and the participants. These platforms combined with the coordination activities will support relevant EDCTP3 grantees to implement use-cases in genomic epidemiology.
Duration: 40 months (08/09/2022 - 07/01/2026)
BMGF-funded initiatives
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Public Health Alliance for Genomic Epidemiology (PHA4GE) is a global consortium established in 2019, to ensure a rapid global genomic-driven public health response to disease outbreaks. Our community includes partners and stakeholders such as funders, public health organisations at international, regional and national levels; and non-specialist individuals across the world. Representative individuals, from the growing list of over 60 member countries and over 68 partner organizations, form the consortium's Working Groups. These Working Groups drive various activities to fulfil the consortium's mission. Our mission is to establish global consensus data standards, document and share best practices, improve the availability of critical bioinformatic tools and resources and advocate for greater openness, interoperability, accessibility and reproducibility in public health bioinformatics.
Website: https://pha4ge.org/
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The Global Health Network is a vast and trusted open knowledge community transferring know-how across disease areas, types of research and between organisations, networks and regions. This collective endeavour aims to enable research in every healthcare setting by driving equity in where research happens, who leads and who benefits from the evidence. Through research system strengthening programmes embedded within countries, diverse online knowledge hubs and training courses, The Global Health Network integrates research within healthcare practice by facilitating workplace-based learning, local research support activities and professional development for research teams. The Global Health Network is a WHO collaborating centre for research information sharing, e-learning, and capacity development.
Website: www.theglobalhealthnetwork.org
NGS Academy
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The NGS Academy forms part of the Africa CDC Pathogen Genomics Initiative (PGI) and is funded by the Bill & Melinda Gates Foundation. It aims to develop and deliver a comprehensive training framework for the implementation of next generation sequencing (NGS) for pathogen surveillance. This includes all aspects of NGS, from sample collection to sequencing and analysis to inform public health interventions. The NGS Academy is developing a competency-based curriculum for pathogen surveillance for public health. It also helps to implement the strategic plans of the PHA4GE training and workforce development working group, and organizes training events as required by the PGIs.
Duration: 50 months (01/11/2020 - 31/12/2024)
Africa PGI
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Africa PGI 2.0 is a flagship initiative of the Africa CDC to build and strengthen resilient, integrated, proactive, and sustainable, molecular diagnostic, genomic surveillance and epidemiology ecosystem in Africa. Africa PGI 2.0 will leverage on the progress and lessons learned from the implementation of the initial phases of the Africa PGI. It will also consider emerging needs, evolving priorities and national, regional and global changes on the perception, utility and application of genomic surveillance.
Website: https://africacdc.org/africa-pathogen-genomics-initiative-africa-pgi/