The EMERGEN consortium is a platform for surveillance and genomic research on emerging pathogens, established in early 2021 by Santé publique France and the ANRS-Emerging Infectious Diseases (ANRS-MIE) to rapidly detect and characterize SARS-CoV-2 variants that have emerged during the COVID-19 pandemic.

It involved numerous partners, including the National Reference Center for Respiratory Infections (CNR VIR) and public and private medical biology laboratories with sequencing capabilities. Its infrastructure is based on a national database (EMERGEN-DB), bioinformatics tools, a network of laboratories, and research teams. The consortium has fostered collaboration among epidemiologists, microbiologists, and bioinformaticians, enabling better integration of epidemiological and genomic data.

Following an initial phase (2021–2023), SARS-CoV-2 sequencing was refocused at CNR VIR, and the expansion of EMERGEN to other priority pathogens was initiated, notably for Mpox (following the public health emergency declared by the WHO in 2024) and zoonotic influenza (given the growing threat it poses). As part of a proactive approach, these efforts are being strengthened to better prepare France for future public health emergencies.

Since 2021, Emergen has been supported by European funding (HERA and SEQ4EPI projects). Its evolution, Emergen 2.0, launched on March 19, 2025, is supported by the French National Research Agency (ANR) as part of the strategy to accelerate research on emerging infectious diseases and nuclear, radiological, biological, and chemical threats, as well as the France 2030 plan. Now coordinated by ANRS-MIE, Santé publique France, and ANSES, the platform incorporates a “One Health” approach for expanded surveillance of infectious diseases.

Three questions for Dr. Bruno Coignard, Director of Infectious Diseases at Santé publique France

Why is it important to continue and strengthen the work carried out during the COVID-19 pandemic?

The development of sequencing for the surveillance of SARS-CoV-2 variants was initiated in 2021, in response to the emergence of the Alpha variant. The goal today is to better anticipate and prepare for future crises in advance, relying on well-defined procedures and capabilities that can scale up rapidly in the event of the emergence of a new infectious agent.

The experience gained during the first phase of the EMERGEN project is essential and must be preserved. It has enabled:

• identify the teams and expertise available in France in this field (CNR, hospital laboratories in the ANRS-MIE virology network, private clinical laboratories, sequencing platforms in certain university hospitals or research institutes, bioinformatics and research teams), thereby facilitating their collaboration with Santé publique France and strengthening the interface between surveillance and research;

• create reference tools, notably the EMERGEN-DB database, hosted by Inserm in Marseille, serving as a model for other pathogens (Mpox, Influenza). Also tools and procedures for data submission by laboratories, bioinformatics analysis, and sharing in international databases (such as GISAID);

• to strengthen Santé publique France’s capabilities for analyzing and interpreting sequencing data by training our epidemiologists in their use and by developing ready-to-use procedures and algorithms.

It must now be strengthened to better integrate the “One Health” approach, given the very frequent zoonotic nature of emerging infectious diseases. It is within this framework that ANSES is joining forces with Santé publique France and ANRS-MIE to facilitate the exchange and joint analysis of human and animal data.

What is Santé publique France’s contribution within EMERGEN?

Santé publique France plays a central role within the EMERGEN Consortium by carrying out three main missions:

• surveillance: monitoring and reporting on indicators regarding the circulation of a pathogen and its impact; for SARS-CoV-2, activities within EMERGEN thus contribute to multi-source surveillance of acute respiratory infections, and the results are reported in the agency’s weekly bulletins;

• alert: detection of an outbreak or epidemic, risk analysis;

• investigation: characterization of a new pathogen (transmissibility, severity, potential evasion of existing preventive or therapeutic measures).

The agency funds the National Reference Centers (€28 million over 5 years) and, in particular, their sequencing activities, including SARS-CoV-2 sequencing since the end of its coverage by the National Health Insurance on March 1, 2025. Furthermore, the European funding received by Santé publique France has enabled support for the consortium’s surveillance activities until the transition to ANR funding.

In 2024, the inventory of sequencing capacities conducted by Santé publique France estimated a cumulative national capacity of approximately 15,000 sequences per month, which could reach 40,000 sequences per month in the event of a crisis, subject to additional funding. These capacities vary greatly from one CNR to another (not all have the same needs) and do not include those of other laboratories or platforms (outside the CNR network).

Finally, epidemiological and microbiological data from EMERGEN’s activities are published on the Santé publique France website, shared with the ECDC, and on other international databases (such as GISAID). Some are available as open data and are also intended to be shared with the research community via the ANRS-MIE as part of EMERGEN’s governance framework.

What are the challenges and contributions of genomics to public health more generally?

Genomics now plays a major role in infectious disease surveillance, and sequencing data from the National Reference Centers (NRCs) are used daily by Santé publique France epidemiologists, often within a “One Health” approach in collaboration with ANSES and its National Reference Laboratories (NRLs).

This practice is not new but has accelerated with the COVID-19 crisis. For example, teams at the Listeria NRL or the Escherichia coli, Salmonella, and Shigella NRL at the Pasteur Institute have been using sequencing for over 10 years to detect clusters early, enabling Santé publique France to investigate cases and identify sources of contamination. These sequencing data are also shared with ANSES’s LNRs to compare human-derived strains with foodborne strains. This increased use of sequencing has significantly contributed to strengthening food safety in France. Similarly, the CNR for Respiratory Infections sequences influenza viruses and shares this data with the WHO for vaccine formulation, while the CNR for HIV uses it to characterize viruses responsible for primary infections.

All CNRs now use sequencing because it allows for highly detailed characterization, at the genomic level, of pathogens (identification of virulence genes, genes conferring resistance to anti-infective agents, monitoring of their evolution, etc.). All of this contributes to strengthening their missions of expertise, surveillance, and early warning.

One of the objectives of EMERGEN 2.0, with the integration of ANSES, is to further strengthen collaboration between CNRs and LNRs. A current priority is the establishment of a shared database for influenza virus sequencing, in order to improve understanding and better anticipate the emergence of viruses of zoonotic origin.