With EMERGEN 2.0, this initiative is evolving to include other emerging pathogens and is strengthening its “One Health” approach with the addition of ANSES as a partner. The project is part of France’s 2030 strategy to accelerate research on emerging infectious diseases and nuclear, radiological, biological, and chemical threats, with €12 million in funding over five years from the French National Research Agency (ANR).

Feedback on EMERGEN: the SARS-CoV-2 genomic surveillance and research platform

While France was already organized to ensure the surveillance of infectious diseases at the national level, the scale of the COVID-19 crisis highlighted the need to strengthen the country’s sequencing capabilities and support research activities to better respond to epidemics.

In January 2021, the ministries responsible for Health and Research tasked Santé publique France and Inserm/ANRS Emerging Infectious Diseases with creating and leading the EMERGEN consortium (or consortium for surveillance and research on infections caused by EMERgent pathogens via microbial GENomics). The consortium’s objective was to track the genetic evolution of the SARS-CoV-2 virus in order to detect the emergence and spatiotemporal distribution of variants.

Since its establishment, EMERGEN has actively contributed to COVID-19 surveillance by conducting and reporting the results of 135 rapid surveys and producing 55 risk assessments on emerging SARS-CoV-2 variants, generated by Santé publique France in collaboration with the National Reference Center (CNR) for Respiratory Viruses. The consortium also enabled the rapid promotion and funding of 16 research projects, totaling €9.3 million. The rapid results from surveillance data and research projects supported by EMERGEN have significantly contributed to tracking the evolution of SARS-CoV-2 variant circulation and, in doing so, guided public health policies during the COVID-19 pandemic.

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

Although initially focused on the response to the COVID-19 pandemic, EMERGEN was designed from the outset to be scalable and to support surveillance and research activities on other emerging infectious diseases—not only viral but also 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 strategy to accelerate responses to emerging infectious diseases and nuclear, radiological, biological, and chemical threats, the project is now evolving into EMERGEN 2.0 to consolidate and expand what was established during the COVID-19 pandemic and to make the EMERGEN consortium a sustainable project.

The scope of EMERGEN 2.0 is thus being expanded to include other pathogens to prepare France for future outbreaks of infectious diseases and potential health crises, regardless of the pathogen involved.

This expansion of the scope of action involves identifying sequencing capabilities complementary to those of national reference centers and laboratories (in human and animal health, respectively), coordinated within a network on the platform. It also involves a bioinformatics platform equipped with dedicated resources to host the database associated with EMERGEN.

EMERGEN 2.0 also plans to continue the research initiatives launched during the COVID-19 crisis through support for foundational projects and the launch of calls for proposals, notably extending research efforts to other emerging or re-emerging pathogens. Furthermore, EMERGEN 2.0 will aim to strengthen coordination among stakeholders promoting the “One Health” approach, initially focusing on genomic and viral issues.

Under the leadership of the three coordinating institutions, EMERGEN 2.0 will strengthen ties between the surveillance sector and the academic and industrial research sectors, while also playing a crucial role in providing information to public authorities and civil society.

A Strengthened “One Health” Approach

From its inception, EMERGEN has adopted a “One Health” approach that views human, animal, and environmental health as interdependent. This approach is being strengthened 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:

• strengthening collaborations with projects such as SUM’Eau and Obépine+, which are active in wastewater surveillance and research to detect pathogens early;

• the sharing and joint analysis of sequences, whether of human, animal, or environmental origin;

• organizing access to its data for research teams while respecting everyone’s work.

Deployment

EMERGEN 2.0 launched in October 2024 with €12 million in funding over five years from the French National Research Agency (ANR). The project will initially expand genomic surveillance to include Mpox and zoonotic influenza. The kick-off meeting, scheduled for March 19, 2025, will bring together all partners to formalize the next steps.