Coordinated by ANRS | Emerging Infectious Diseases, an autonomous agency of Inserm, and Santé publique France, the EMERGEN¹ consortium currently conducts genomic surveillance of SARS-CoV-2 variants throughout France. Created in January 2021 to strengthen genomic surveillance and research capabilities on SARS-CoV-2 variants in France, this consortium has generated a total of 317,521 sequences since its launch in January 2021, increasing the number of sequences generated by more than 100 times compared to 2020.

From its inception, the EMERGEN consortium has mobilized the leading virology laboratories with strong sequencing capabilities (CNR Institut Pasteur, CNR Hospices Civils de Lyon, expert laboratories supporting SARS-CoV-2 sequencing: AP-HP Mondor and AP-HM Marseille) and the hospital laboratories of the ANRS | Emerging Infectious Diseases virology network; since July 2021, a number of private clinical laboratories have also been participating in sequencing activities. This effort is being carried out in mainland France as well as in the overseas territories; the detection and identification of the Omicron variant of SARS-CoV-2 by the Joint Research Unit on Infectious Processes in Tropical Island Environments (PIMIT) at the University of Réunion is a concrete example of this.

Furthermore, in the context of a global pandemic, the French Development Agency (AFD) and ANRS | Emerging Infectious Diseases, in partnership with the Pasteur Institute, IRD, and laboratories in 13 African countries, have jointly launched the AFROSCREEN³ project. This project addresses an urgent need to monitor the evolution of SARS-CoV-2 variants and other emerging pathogens by strengthening laboratories’ genomic sequencing capabilities. This project, part of the Initiative Santé en Commun⁴ and championed by the President of the Republic, strengthens France’s contribution to the global response to the COVID-19 pandemic and aligns with the G20 strategy, in close coordination with the African Union’s CDC (Centers for Disease Control and Prevention).

In parallel with EMERGEN’s surveillance activities, coordinated by Santé publique France, the objective of the research component—coordinated by ANRS | Emerging Infectious Diseases—is to launch projects to advance knowledge regarding SARS-CoV-2 variants. To this end, the consortium’s first step was to rapidly propose research projects with high potential for impact, based on four areas defined in the EMERGEN project: anticipating and analyzing the significance of variants through an “experimental research and modeling” component; identifying, characterizing, and analyzing the evolution of new variants in cohorts; modeling the evolution and impact of these variants; and finally, evaluating the use of wastewater as a tool for monitoring variants.

In agreement with the Ministry of Higher Education, Research, and Innovation, ANRS | Emerging Infectious Diseases has identified various external scientific experts qualified to evaluate EMERGEN projects based on the topics addressed and the specific characteristics of the projects submitted under this research component.

Following a rigorous and transparent scientific evaluation, the Minister of Higher Education, Research, and Innovation approved funding for 15 research projects and 1 infrastructure project for a total amount of €9,313,060.

This research component will contribute to the acquisition of knowledge regarding SARS-CoV-2 variants and will, in particular, enable in-depth analysis of viral evolution and phylogeny data and their integration into epidemiological modeling activities, monitoring and understanding resistance to anti-infectives or immune escape, as well as the detection of variants that could potentially cross the species barrier.

In the longer term, the genomic surveillance and research system deployed under EMERGEN will be expanded to cover infections caused by emerging pathogens (viral, bacterial, fungal, and parasitic infections).

List of funded projects