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HORIZON-JU-GH-EDCTP3-2022-OA2 Collaboration between GH EDCTP3 and the contributing Partner Bill & Melinda Gates Foundation: Genomic epidemiology for surveillance and control of poverty-related and emerging/re-emerging infections in sub-Saharan Africa

The collaboration between the Global Health EDCTP3 and the Bill & Melinda Gates Foundation Joint Undertaking aims to leverage the genomic sequencing capacity being built in Africa to support epidemiology and surveillance of endemic and epidemic pathogens. In order to achieve this, partnerships between epidemiology sites (such as population cohorts and clinical trial sites) and genomic sequencing labs in national public health institutes (NPHIs) are needed, sharing and leveraging resources and expertise.

The establishment of the Africa Pathogen Genomics Initiative (Africa PGI) with Africa Centre for Disease Control and Prevention (Africa CDC), coupled with the accelerated interest in genomic surveillance due to the COVID-19 pandemic has led to increasing capacity for genomic sequencing in Africa. There is an opportunity to advance the impact of genomic surveillance in Africa by better integrating it with epidemiology expertise and study infrastructure. The integration of epidemiology and genomics, so-called ‘genomic epidemiology’, would enable countries and regional health organizations in Africa to better understand the epidemiology of infectious pathogens, characterize pathogens, and support public health product and intervention design and effectiveness monitoring. While there exist many expertise and resources for both epidemiology and genomics in Africa, linking the Africa PGI to the Global Health EDCTP3 Joint Undertaking presents an opportunity to support better integration through partnerships between African and European organizations working on collaborative research. A key element of the partnership will be the Global Health Network (tGHN)’s support to Global South leadership and the creation of an enabling environment for improved health research and data science capabilities through tGHN’s ‘Ecosystem for Health Research & Data Science’ initiative.[[]]

This partnership aims to:

  1. Increase the use of genomic epidemiology by Africa CDC and NPHIs across Africa to answer public health questions of most concern nationally and regionally.
  2. Create data platforms through which integrated epidemiologic, clinical, and genomic data can be collected and combined by African researchers and NPHIs.
  3. Pilot selected projects of translational research for the application of genomic epidemiology for specific pathogens/disease areas in low- and middle-income countries (LMICs), translating these applications to inform public health decision-making and/or product development.
  4. Establish a community of practice, training programmes, and fellowship opportunities in genomic epidemiology, increasing the literacy of genomics experts in the principles and methods of epidemiology and of epidemiologist in the use of genomic data.

The partnership is being implemented through two topics.

The grant agreement to be concluded under this Other Action 2 topic HORIZON-JU-GH-EDCTP3-2022-OA2 brings together the contribution from the Bill & Melinda Gates Foundation and supports coordination activities for the collaboration. Through the second topic within this partnership GH-EDCTP3-2022-CALL1-01-03, Research and Innovation Actions in the area of genomic epidemiology research are supported by the Global Health EDCTP3 JU. Applicants to each of the topics are strongly encouraged to read the topic description for both topics: GH-EDCTP3-2022-CALL1-01-03 and Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2.

Specific conditions

Expected EU contribution per project

GH EDCTP3 estimates that an EU contribution of around EUR 0.05 million would allow these outcomes to be addressed appropriately. Nonetheless, this does not preclude submission and selection of a proposal requesting different amounts.

Indicative budget

The total indicative budget for this topic is EUR 50,000

Type of Action

Coordination and Support Action

Eligibility and admissibility conditions

Due to the focus on leveraging the African side of the established Africa Pathogen Genomics Initiative (PGI) and the Global Health Network (tGHN) platforms and the policy objectives of the GH EDCTP3 JU programme, legal entities forming a consortium shall be eligible for participation in actions under this topic provided that the consortium includes at least two independent legal entities established in two different sub-Saharan African countries that are member of the EDCTP Association.

Legal and financial set-up of the Grant Agreements - Costs for providing financial support to third parties allowed

Beneficiaries may provide financial support to third parties. The maximum amount to be granted to each third party is EUR 1,000,000 due to the need to directly support genomic sequencing at centres throughout Africa.

Legal and financial set-up of the Grant Agreements – linked action

Grants awarded under this topic will be linked to the following actions: Grants awarded under the corresponding topic under this collaboration HORIZON-GH-EDCTP3-2022-CALL1-01-03. Signing of a collaboration agreement as linked actions will be required in accordance with Article 7 of the Model Grant Agreement.

Expected outcome: Bringing together the Africa Pathogen Genomics Initiative (PGI) and the Global Health Network platforms enable the Global Health EDCTP3 Joint Undertaking-funded actions to access expertise and resources in genomics (from PGI) and clinical trials research and data science (from tGHN). Importantly, these platforms will also support important functions to help to coordinate and find synergies between pre-existing partners and initiatives (including those previously funded by EDCTP programmes) in their respective fields of genomics and epidemiology & data science. Such coordination would happen at the global level as well as regionally within Africa. Africa CDC are the lead partner for both Africa PGI and tGHN in Africa. Africa CDC also have existing partnerships in place with the European Union for health security and field epidemiology. The role of Africa CDC, therefore, presenting an opportunity to integrate and find synergies between multiple engagements with complementary objectives to advance genomic epidemiology and improve public health in Africa.

Expected outcomes from this topic are:

  • Through the Africa PGI, providing core capabilities to Global Health EDCTP3-funded actions in genomics through its (1) secretariat function at Africa CDC and the Africa Society for Laboratory Medicine (ASLM), (2) genomic laboratory network across NPHIs, (3) the NGS training academy, (4) genomic data architecture for Africa, and (5) close partnership with African Union member states to develop national strategic plans and use-cases for genomic surveillance;
  • Through the tGHN, providing important functions in supporting (1) research and data science capabilities, (2) coordination and strengthening of the data access, sharing, and use ecosystem, including support for data platform development as appropriate and (3) support for the partnership governance and administrative execution;
  • Support coordination with relevant activities in genomic epidemiology and data science.

Scope: Through this action the Bill & Melinda Gates Foundation will be contributing significant investments in the Africa PGI to the Global Health EDCTP3 Joint Undertaking, including but not limited to its Next-Generation Sequencing (NGS) Academy and the Public Health Alliance for Genomic Epidemiology (PHA4GE), and tGHN, to provide foundational platforms to achieve the programmatic partnership aims outlined in the introduction for this programme.

The proposal should address all of the following activities:

  • Encompass the secretariat to lead and manage the Africa PGI as well as providing financial means to laboratories across the continent to directly support genomic sequencing with the expectation to support African states and their national public health institutes;
  • Working with Africa CDC, synergize existing initiatives and partnerships in Africa related to epidemiology, data science, and genomics, including Africa PGI, and as well as other European Union and EDCTP-funded projects and initiatives where relevant, such as the EDCTP’s Networks of Excellence[[Networks of Excellence - EDCTP]], European COVID-19 Data Platform[[The European COVID-19 Data Platform : COVID-19 Data Portal (]] and BY-COVID project[[BY-COVID | BY-COVID]];
  • Develop curricula for training in genomic sequencing and provide training for genomic sequencing and genomic epidemiology, in partnership with the Calestous Juma Fellows, NGS academy, tGHN and, where possible, with other relevant projects funded under EDCTP2 such as EDCTP’s Networks of Excellence, EDCTP’s Knowledge Hub[[EDCTP Knowledge Hub - EDCTP]] and/or awarded projects under the EDCTP2’s CSA2020E[[Capacity development for disease outbreak and epidemic response in sub-Saharan Africa, in collaboration with Africa CDC - 2020 - EDCTP]];
  • Build consensus standards; document and share best practices; improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics;
  • Support research capacity building and communities of practice in data science, including increasing data access, sharing, and use.

Type of Action: Grant to identified beneficiary according to Financial Regulation Article 195(e) - and Article 24(3) (a) of the Horizon Europe Regulation - Coordination and Support Action

Indicative timetable: 3rd quarter 2022