Genomic epidemiology for surveillance and control of poverty-related and emerging/re-emerging infections in sub-Saharan Africa

Whilst 2021 has seen an unprecedented expansion in global genomic sequencing capacity for SARS-CoV-2 also in Africa, many challenges remain. The translation of genomic data to inform public health decision making is needed to realize the full impact of this sequencing capacity. In order to achieve this public health impact, there needs to be improved integration of genomics capabilities with complementary disciplines, in particular epidemiology. Purposeful use of genomic sequencing beyond COVID-19 through improving the ability to link genomic sequencing data to clinical and epidemiological data has the opportunity to strengthen both epidemiological research and genomic surveillance in order to create integrated surveillance systems to monitor infectious diseases in sub-Saharan Africa.

This topic aims to support activities to strengthen genomic epidemiology and its application to inform public health decision making. To that end, proposals under this topic should aim to deliver results that are directed, tailored towards, and contributing to all of the following expected outcomes:

• Public health professionals and researchers in sub-Saharan Africa have a better understanding of poverty-related and emerging/re-emerging infectious diseases affecting these countries and use genomic epidemiology evidence as part of surveillance and disease control programmes;
• Public health authorities have access to genomic epidemiology data and evidence to better develop and implement informed public health policies in sub-Saharan Africa;
• More researchers and public health professionals (both genomics and epidemiology specialists) have competencies in genomic epidemiology, including how to design studies using genomic epidemiology and how to use and interpret data to answer questions of public health significance in sub-Saharan Africa;
• Researchers and public health professionals have access to improved and integrated research and surveillance infrastructure and capabilities that enables the combination of genomic and epidemiology data for the understanding of infectious disease epidemiology and the development of new, low-cost, easy-to-implement solutions for improved delivery of public health interventions for vulnerable populations in low-resource settings;
• Genomic epidemiology data are leveraged to help inform the design, development, and prioritization of public health products such as diagnostics, therapeutics, and vaccines that are affordable, accessible, and impactful for populations across sub-Saharan Africa;
• Genomic epidemiology capabilities and capacity are strengthened at National Public Health Institutions and regional public health organizations in sub-Saharan Africa;
• More researchers and public health professionals at the early stages of their research and/or public health career (e.g. Master’s, PhD or post-doctoral level) are able to develop their own scientific career in sub-Saharan Africa and/or establish themselves as scientific and public health leaders in sub-Saharan Africa.

Collaboration between the Global Health EDCTP3 JU and the contributing partner Bill & Melinda Gates Foundation

The collaboration between the Global Health EDCTP3 Joint Undertaking and the Bill & Melinda Gates Foundation 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)^[1] 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 in Africa to better understand the epidemiology of infectious pathogens, characterize pathogens, and support public health product and intervention design and effectiveness monitoring. While expertise and resources for both epidemiology and genomics exists 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.^[2]

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 epidemiologists in the use of genomic data.

The collaboration is being implemented through two topics.

Through the topic GH-EDCTP3-2022-CALL1-01-03 within this collaboration presented here, funding from the Global Health EDCTP3 JU is made available. This will be complemented by the grant to identified beneficiaries (Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2) which supports coordination activities for the collaboration and brings together the contribution from the Bill & Melinda Gates Foundation. 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.

Proposals should address all of the following:

• Strengthen countries’ capacity for early detection and/or characterization of any poverty-related infectious diseases (PRDs) disease, group of PRDs or emerging or re-emerging infectious disease affecting sub-Saharan Africa and that are within the scope of the current EDCTP3 programme^[3]. In view of the amount of work already carried out, this call topic excludes proposals working on genomic epidemiology in the context of COVID-19;
• Implement at least one selected project of translational research demonstrating the application of genomic epidemiology to answer specific public health questions pertaining to infectious diseases. These projects should go beyond the generation of data. They should include translation to decision making through active engagement with public health officials and other stakeholders. Examples of potential projects demonstrating the application of genomic epidemiology to answer specific public health questions pertaining to infectious diseases could include investigation of the burden, transmission, or evolution of a pathogen, investigation of the pathogens causing a specific disease/clinical presentation, characterization of a pathogen to inform product development/ public health intervention design, evaluation of the effect of public health interventions (such as vaccination programmes) on the epidemiology of a pathogen. Public health areas that are not mentioned as an example but apply genomic epidemiology and are of relevance for public health decision-making and/or product or intervention design will also be considered;
• Proposals are expected to partner with National Public Health Institutes (with the support of the Africa Pathogen Genomics Initiative (PGI) as described in Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2);
• Proposals should explicitly outline how proposed partnerships with NPHI or other government entities will support definition of questions of greatest public health importance and allow applicants to leverage and integrate the use of genomic sequencing in Africa to answer the prioritized public health questions through integration with epidemiology data and approaches;
• Integrate epidemiologic, clinical, and genomic data through data integration platforms, with the need for this integration built into the design of the research study/surveillance programmes prior to data collection. Collaboration with the Global Health Network and harmonization across awarded projects (see Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2) is expected for the development of these data platforms, which should also leverage experiences and tools from existing initiatives such as the European COVID-19 Data Platform^[4], the Public Health Alliance for Genomic Epidemiology (PHA4GE)^[5], the Global Alliance for Genomics & Health (GA4GH)^[6] and/or the European Union-funded BY-COVID project^[7];
• Strengthen and harmonize data standards and tools to enable the integration of epidemiological and genomics data collection, storage, sharing, and analysis. Collaboration with the Global Health Network and PHA4GE is expected for this task (see Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2);
• Proposals should ensure that resulting data comply with the FAIR principles and collaboration with the future awardee of HORIZON-WIDERA-2021-ERA-01-41^[8] is encouraged to increase international cooperation on FAIR data;
• Establish a community of practice on genomic epidemiology including expertise in bioinformatics to increase the literacy of genomics experts in the principles and methods of epidemiology and the literacy of epidemiologists on the use of genomic data. This community of practice will be formed in collaboration with the consortium under the grant agreement of Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2 which could include : Global Health Network and the Africa PGI, as well as linking to existing communities of practice established through PHA4GE, the EDCTP’s Network of Excellence^[9], and the African Society for Laboratory Medicine (ASLM)^[10];
• Support the generation of harmonized training resources, including for young African scientists with gender balance through degree training in genomic epidemiology and/or hands on training during implementation of research projects to assist them in advancing their scientific careers. Training resources should be developed in collaboration with the consortium under grant agreement of Other Action 2 HORIZON-JU-GH-EDCTP3-2022-OA2 including Africa PGI’s Next-Generation Sequencing (NGS) Academy and the Global Health Network for: 1) genomic expertise in the principles, methods, and application of epidemiology methods; 2) epidemiologists in the principles, methods, and applications of genomics; 3) both communities in the combined principles, methods, and applications of genomic epidemiology and its use for public health decision making and surveillance programmes. It is expected that training will be harmonized across funded projects and collaboration with existing initiatives and projects, such as the awarded projects under the EDCTP2’s CSA2020E^[11], EDCTP’s Networks of Excellence, ECDC4Africa CDC initiative^[12] and EDCTP’s Knowledge Hub^[13], should be sought where possible;
• Promote the integration of research with public health organizations and disease control programmes at a national and regional level. Collaboration between relevant stakeholders in National Public Health Institutes and academic/research centres is expected at a national level. On a regional level, regional consortia and organizations such as Africa CDC, should be engaged where appropriate;
• Proposals should include organizations with expertise in epidemiology and those with expertise in genomics, with a willingness to work together to establish joint projects and achieve the aims outlined above;
• Proposals should consider gender equality in the design of their projects and justify how they will be gender intentional in their proposed aims and activities.

[1] https://ipg.africacdc.org/

[2] https://tghn.org/

[3] ec_rtd_edctp3-sria-2022.pdf (europa.eu)

[4] The European COVID-19 Data Platform : COVID-19 Data Portal (covid19dataportal.org)

[5] PHA4GE - Genomic Epidemiology

[6] Data Use Ontology approved as a GA4GH technical standard

[7] BY-COVID | BY-COVID

[8] Funding & tenders (europa.eu)

[9] Networks of Excellence - EDCTP

[10] Home - African Society for Laboratory Medicine (aslm.org)

[11] Capacity development for disease outbreak and epidemic response in sub-Saharan Africa, in collaboration with Africa CDC - 2020 - EDCTP

[12] EU and AU sign partnership to scale up preparedness for health emergencies (europa.eu)

[13] EDCTP Knowledge Hub - EDCTP