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

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[[ec_rtd_edctp3-sria-2022.pdf (europa.eu)]]. 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[[The European COVID-19 Data Platform : COVID-19 Data Portal (covid19dataportal.org)]], the Public Health Alliance for Genomic Epidemiology (PHA4GE)[[PHA4GE - Genomic Epidemiology]], the Global Alliance for Genomics & Health (GA4GH)[[Data Use Ontology approved as a GA4GH technical standard]] and/or the European Union-funded BY-COVID project[[BY-COVID | BY-COVID]];
• 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[[Funding & tenders (europa.eu)]] 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[[Networks of Excellence - EDCTP]], and the African Society for Laboratory Medicine (ASLM)[[Home - African Society for Laboratory Medicine (aslm.org)]];
• 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[[Capacity development for disease outbreak and epidemic response in sub-Saharan Africa, in collaboration with Africa CDC - 2020 - EDCTP]], EDCTP’s Networks of Excellence, ECDC4Africa CDC initiative[[EU and AU sign partnership to scale up preparedness for health emergencies (europa.eu)]] and EDCTP’s Knowledge Hub[[EDCTP Knowledge Hub - EDCTP]], 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.