Sequencing pathogens for Epidemiology

ended

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 (ANRS | MIE), 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 control of sequencing data, enhanced 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 7600 000 sequences milestone was reached in June December 2022. EMERGEN was built as the first stage of a sequencing network for emerging pathogens, complementing NRL capacities, and its scope is now expands its scope to expand beyond SARS-COV-2 to other pathogens, starting with 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 20223/20254 both to ensure the sustainable use and integration of EMERGEN into routine surveillance and investigation activities and to progressively expand genomic surveillance to other emergence-prone pathogens. We defined two objectives, focusing on metadata and sequence data use and valorisation. The first objective is to implement methods to better monitor viral epidemics, ensure the accurate detection of variants or mutations of interest (in the context of international efforts) and use molecular data in order to monitor within-outbreak pathogen dynamics using phylodynamics and to investigate clusters. This first objective will focus on SARS-CoV-2 and other respiratory viruses (Influenza, RSV) for the first two years of the project ; the adaptation of methodologies to other viruses (framework for detection of variants or mutations that may cause detection or sequencing issues for instance) will be explored in the 3rd year, in collaboration with the NRLs in charge of their microbiological surveillance. The second objective is to continue efforts for to integrateing genomic and epidemiological data at regional and national level for investigations and to animateing lab networks, with an emphasis on French overseas territories, with a similar timescale regarding the extension to other pathogens. Another transversal objective concerns the reinforcement of coordination activities, to accompany the strengthening of existing genomic surveillance activities and their progressive integration into a wider genomic surveillance system, including other laboratories from the French NRL network, specifically the 8 NRLs in charge of pathogens considered as priority ones in terms of emergence-risk (respiratory viruses, arboviruses, viral haemorrhagic fevers, tularaemia, hantaviruses, anthrax, orthopox viruses and plague) and new partners. T; the One Health dimension is incorporated into this evolution, with specific linkages to be developed with sequencing activities and actors in the animal health and environmental (waste water) sectors.