Launch of EMERGEN 2.0: To better prepare France for future epidemics and potential health crises

Review of EMERGEN: the genomic surveillance and research platform

Although France was already organized to monitor infectious diseases at national level, the scale of the Covid-19 crisis demonstrated the need to strengthen the country’s sequencing capabilities and support research activities to better respond to epidemics.

In January 2021, the Ministries of Health and Research entrusted Santé publique France and Inserm / ANRS Emerging Infectious Diseases with the creation and management of the EMERGEN consortium (or consortium for surveillance and research on EMERgENT pathogen infections via microbial GENomics). The aim of this consortium was to monitor the genetic evolution of the SARS-CoV-2 virus in order to detect the emergence and spatio-temporal distribution of variants

Since it was set up, EMERGEN has made an active contribution to COVID-19 surveillanceconducting and reporting the results of 135 flash surveys and producing 55 risk analyses on emerging variants of SARS-CoV-2, produced by Santé publique France in conjunction with the Centre national de référence (CNR) des viroses respiratoires. The consortium also enabled the rapid promotion and funding of 16 research projects, for a total of €9.3 million. The rapid results of the surveillance data and research projects supported by EMERGEN have made a major contribution to monitoring the evolution of the circulation of SARS-CoV-2 variants, and thus to guiding public health policies in the context of the Covid-19 epidemic.

From EMERGEN to EMERGEN 2.0: Extending the platform to other pathogens to prepare for future pandemics

Although initially focused on responding to the Covid-19 epidemic, EMERGEN was designed from the outset to evolve and support surveillance and research activities on other emerging infectious diseases, whether viral, bacterial, fungal, or parasitic.

In this context, and as part of the national effort to strengthen systemic preparedness for the risks of new health crises supported by the Emerging Infectious Diseases and Nuclear, Radiological, Biological, and Chemical Threats Acceleration Strategy, the project is now evolving towards EMERGEN 2.0 to consolidate and extend what was put in place during the Covid-19 pandemic, and to make the EMERGEN consortium a sustainable project.

The scope of EMERGEN 2.0 thus extends to other pathogens, preparing France for future emerging infectious diseases and potential health crises, regardless of the pathogen involved.

This expansion of scope involves identifying sequencing capacities that complement those of national reference centres and laboratories (for human and animal health, respectively), coordinated within a network integrated into the platform. It also includes a bioinformatics platform equipped with dedicated resources, to host the EMERGEN database.

EMERGEN 2.0 also plans to pursue the research initiatives launched during the Covid-19 crisis by supporting major projects and issuing calls for proposals, particularly to extend research efforts to other emerging or re-emerging pathogens. Furthermore, EMERGEN 2.0 will aim to strengthen collaboration between stakeholders promoting the “One Health” approach, initially focusing on viral genomics.

Under the leadership of the three coordinating institutions, EMERGEN 2.0 will not only strengthen links between the world of monitoring and the world of research, both academic and industrial, but will also play a crucial role in informing public authorities and civil society.

A strengthened “One Health” approach

From the outset, EMERGEN has adopted a “One Health” approach, considering human, animal and environmental health as interdependent. This approach is reinforced with EMERGEN 2.0 to better anticipate the emergence of zoonotic pathogens, and to rapidly adapt health surveillance and responses to emerging infectious disease crises.

Thus, EMERGEN 2.0 plans to:

• Strengthen collaborations with projects such as SUM’Eau and Obépine+, which play a key role in wastewater surveillance and research to enable early pathogen detection;
• Facilitate the sharing and joint analysis of sequences, whether of human, animal, or environmental origin;
• Organise access to its data for research teams while respecting the work of all stakeholders.

Implementation

EMERGEN 2.0 began in October 2024 with a €12 million funding over 5 years from the National Research Agency (ANR). The project will initially expand genomic surveillance to include mpox and zoonotic influenza. The launch meeting, scheduled for 19 March 2025, will bring together all partners to formalise the next steps.

“EMERGEN 2.0 enables the focus of sequencing activities, during inter-epidemic periods, on research projects expanded to include all infectious pathogens, beyond SARS-CoV-2. EMERGEN 2.0 will also continue the development of innovative bioinformatics tools.”
Hervé RAOUL, Deputy Director of ANRS Emerging infectious diseases

“In a world where 60% of infectious diseases are common to both humans and animals, and 75% of emerging infectious diseases have an animal origin—whether from livestock or wildlife—it is essential that health surveillance tools for humans, animals, and the environment be harmonised and shared between scientific communities. EMERGEN 2.0 represents a unique opportunity to bring together the scientific communities of ‘One Health’ to share genomic data on infectious agents from these different compartments and to jointly value the results produced, in support of ‘One Health’ public policies, while respecting each contributor’s input.”
Gilles Salvat, Deputy Director for Research and Reference at Anses

“EMERGEN 2.0 is now an essential platform for an integrated surveillance approach, enabling the epidemiological data produced by Santé publique France and ANSES and the sequencing data produced by the CNR, the LNR, the network of virology laboratories of the ANRS Emerging Infectious Diseases and the major high-throughput sequencing platforms. While genomics has accelerated dramatically during the COVID-19 crisis, the bringing together of these players and the pooling of their data has made it possible, and will make it even more possible in the future, to detect, characterise and monitor epidemics and future outbreaks in a reactive manner. Integrating from the outset a strong link with the ANRS Emerging Infectious Diseases, this platform will also continue to promote the reuse of the surveillance data thus produced for research purposes.”

Bruno COIGNARD, Director of Infectious Diseases, Santé Publique France