Launched in January 2021 in response to the COVID-19 pandemic and the emergence of the Alpha variant (first detected in the United Kingdom in November 2020), the EMERGEN consortium has established a national genomic surveillance system across the entire country to detect, characterize, and track the evolution of SARS-CoV-2 in France, including in the overseas territories. It was designed from the outset to be scalable and to support surveillance and research activities on other emerging infectious diseases (viral, but also bacterial, fungal, or parasitic).

Thus, the project is evolving into the EMERGEN 2.0 platform, launched on October 1, 2024, dedicated to surveillance and research on infections caused by EMERgent pathogens, using microbial genomics. This is a major evolution aimed at ensuring the long-term sustainability and expanding the activities of the initial project.