Sequencing pathogens for Epidemiology

The French EMERGEN Consortium was created in 2021 to scale up SARS-CoV-2 genomic surveillance and research. Coordinated by Santé publique France and ANRS|Maladies Infectieuses Emergentes, it is based on a network of public and private laboratories, including the National Reference Laboratory (NRL) for respiratory viruses, and a centralised database. Our priority in 2021 was to build the infrastructure and network, in a time of crisis with a huge pressure for results; more than 300 000 SARS-CoV-2 sequences were produced and analysed, a 100-fold increase when compared to 2020. In 2022, the ECDC/HERA grant was used to achieve new objectives: sequencing data quality, capacities in overseas territories, network animation, and timeliness of sequencing. These activities helped in better detecting and assessing new variants, from Delta to Omicron and its sublineages, and are still increasing; the 600 000 sequences milestone was reached in June 2022. EMERGEN was built as a first stage of a sequencing network for emerging pathogens, complementing NRL capacities, and its scope will expand to other respiratory viruses as a component of a new acute respiratory infections surveillance scheme. In addition to national funding, the EU4Health grant will help consolidating WGS activities in 2023/2024 to ensure the sustainable use and integration of EMERGEN into routine surveillance and investigation activities. We defined two objectives focusing on data use and valorisation. The first objective is to implement methods to better monitor viral epidemics, ensure the accurate detection of variants of interest (in the context of international efforts) and use molecular data to monitor within-outbreak pathogen dynamics using phylodynamics and to investigate clusters. The second objective is to continue efforts for integrating genomic and epidemiological data at regional level for investigations and animating lab networks, with an emphasis on French overseas territories.