The EMERGEN consortium was launched in January 2021 in response to the COVID-19 pandemic and the emergence of the first variant of concern of SARS-CoV-2 (Alpha), first detected in the United Kingdom in November 2020. Its objective was to create a platform to strengthen the capabilities of the National Reference Center for Respiratory Viruses (CNR VIR) regarding the detection, characterization, and monitoring of new SARS-CoV-2 variants in France, including in the overseas territories.

The challenge was twofold: to establish a comprehensive nationwide genomic surveillance system and to facilitate research activities to anticipate or assess the public health impact of the emergence of new variants.

Given the effectiveness of this platform during the COVID-19 crisis and the risk of new epidemics or pandemics, it was essential to ensure its long-term sustainability beyond the COVID-19 crisis, to expand it to other pathogens, and, in particular, to maintain it during inter-crisis periods. It is also crucial to link this platform with other tools related to emerging infectious diseases that are currently being established through the national strategy for accelerating responses to emerging infectious diseases and CBRN threats (SA MIE MN).

From its inception, EMERGEN has adopted a "One Health" approach that views human, animal, and environmental health as interdependent. This approach is further strengthened in EMERGEN 2.0 through several key objectives:

• establishing links with wastewater surveillance activities, in conjunction with projects such as SUM’Eau and Obépine+;

• the integration of data from the sequencing of animal-borne pathogens to better anticipate the emergence of zoonoses.

These objectives aim to help health authorities respond quickly in the event of a new outbreak or risk of an outbreak, by adapting human surveillance to the risks posed by pathogens of animal or environmental origin.

Strengthening and Expansion of the UMS 56 Bioinformatics Platform

The INSERM UMS 56 unit now hosts the national database of sequences used in the activities of the EMERGEN platform. This database, initially developed in 2021 by the French Institute of Bioinformatics, collects and analyzes SARS-CoV-2 genomic sequences and their metadata generated by sequencing laboratories as part of COVID-19 surveillance. EMERGEN 2.0 aims to consolidate this database using the new capabilities provided by UMS 56, and to extend its use to other pathogens, whether of human, animal, or environmental origin. The platform also plans to develop tools to improve analysis, quality control, data sharing, and crisis management.

Technology and Skills Transfer

EMERGEN 2.0 also aims to serve as a platform for sharing the tools and expertise necessary for analyzing sequencing data among CNRs, LNRs, and other relevant laboratories (hospital laboratories or sequencing platforms). This transfer of expertise will improve preparedness for future health crises linked to emerging infectious diseases.

Sustainability and expansion of research

The project plans to continue the research initiated during the COVID-19 crisis and extend this research to other pathogens, particularly respiratory viruses. New research activities will be developed around issues related to genomic surveillance, particularly regarding emerging pathogens or those capable of causing new epidemics/pandemics. The implementation of this research program, in addition to public health activities in genomic surveillance, is essential for improving the knowledge needed for crisis management and for guiding public policies on health crisis management.

Facilitation and coordination of stakeholders in the field

EMERGEN 2.0 is committed to structuring and revitalizing the genomic surveillance landscape in France. A significant part of this coordination will be achieved through the establishment of a community of bioinformaticians to foster collaboration and knowledge exchange. This coordination will be carried out under the auspices of ANRS-MIE, Inserm, Santé publique France, and ANSES.

Founding members of the EMERGEN 2.0 Consortium

• ANRS-MIE

• Public Health France

• ANSES

Stakeholders of the Emergen 2.0 platform and their role in genomic surveillance

• The INSERM UMS 56 unit (based in Marseille): hosts the database associated with the EMERGEN platform and possesses bioinformatics capabilities.

• National Reference Centers (CNR): mandated by Santé publique France, they are on the front lines of genomic surveillance for the pathogens under their purview. They carry out surveillance, alert, advisory, and expert assessment missions.

• National Reference Laboratories (LNR) in animal health: dedicated to the surveillance of circulating animal viruses (influenza, coronavirus, West Nile, Usutu, and other arboviruses).

• The ANRS-MIE network of hospital virology laboratories: Specializing in surveillance and research on various viruses (HIV, hepatitis, respiratory viruses, etc.), they contribute their expertise and sequencing capabilities.

• Genomic sequencing platforms: distributed throughout the country, their purpose is to serve as a reserve of capacity that can be rapidly mobilized in the event of a crisis to support the CNRs and NRLs.

National and international partners

EMERGEN 2.0 relies on a diverse network of partners, both nationally and internationally, such as clinical research platforms, sequencing platforms, and global health organizations. Collaboration with these partners is essential for expanding genomic surveillance of emerging and re-emerging pathogens and better preparing for future epidemics and pandemics.

• I-REIVAC

• OPEN-ReMIE

• Obepine+

• SUM’Eau

• ECDC

• World Health Organization

• Isidore

• Afroscreen