Since 2022, the response to COVID-19 pandemic gradually abandoned the domain of crisis management and is becoming part of the routine surveillance activities. With this optic, the surveillance systems implemented during the crisis (comprised the SARS-CoV-2 variant surveillance systems) must be integrated within the existent structures and be prepared for future emergencies, adapting them to other pathogens.
Funding
In April 2022, the European Commission, via their executive agency HaDEA, invited the countries that had previously been financed via the HERA incubator (France among them) to submit a project to their call for proposals EU4Health. This new call had as main objective to consolidate the whole-genome sequencing and RT-PCR activities in countries having benefited from financing in 2021, in order to ensure the sustainability of their capacities and the integration of the developed infrastructures into the epidemic surveillance and investigation systems, in synergy with the ongoing efforts taking place at an international scale. The activities financed by this project must allow to reinforce capacity-building in the involved countries outside of a crisis context and be extended to other pathogens other than SARS-CoV-2.
Objectives of the project: SEQ4EPI, pathogen sequencing for epidemiology
The SEQ4EPI project, carried by Santé Publique France and the National Reference Centre for Respiratory Infections, aims to support the sustainability of the genomic surveillance systems built during the pandemic and prepare them for future crisis, reinforcing the genomic surveillance activities in different dimensions (extension to other pathogens, development of genomic analysis tools, reinforcement of the epidemiological analysis capacities) during a period of 3 years (01/01/2022 – 30/09/2025). The objectives of SEQ4EPI are structured in two different time horizons:
- Between 2022 and 2024, the sustainability of the SARS-CoV-2 genomic surveillance and its integration in the routine activities.
- Between 2023 and 2025, the extension of the existing systems that were implemented for SARS-CoV-2 to other pathogens with strong emergence potential. This extension will begin with other respiratory viruses (influenza, RSV) but will not be limited to them.
The activities planned in the SEQ4EPI project aim to:
- Strengthen the coordination activities of Santé publique France to consolidate the existing genomic surveillance activities established for SARS-CoV-2 and gradually expand them to other emerging pathogens, including other respiratory viruses.
- Define and implement analytical tools to better monitor viral epidemics, for SARS-CoV-2 and other viruses, based on bioinformatics, phylogenetic, and phylodynamic techniques.
- Maintain a team of epidemiologists at the national and regional levels for signal investigation, laboratory network coordination, and risk analysis.