EMERGEN 2.0 Consortium: A platform for genomic surveillance and research on emerging pathogens

From EMERGEN to EMERGEN 2.0: From the COVID-19 crisis to preparedness for future pandemics

The COVID-19 pandemic and the successive appearance of numerous SARS-CoV-2 variants – Alpha, Beta, Gamma, Delta and finally Omicron – have highlighted the necessity to support epidemiological and virological surveillance by strengthening molecular surveillance, particularly through sequencing. Given that the variants may have characteristics likely to modify the dynamics of the epidemic, such as transmissibility or pathogenicity different from that of the wild strain of the virus, it is essential to monitor their circulation to strengthen control of the infectious risk in the population and to inform public decisions. The characterisation of these variants is equally important in evaluating the efficacy of the vaccines and treatments used.

While France is already organised when it comes to the surveillance of infectious diseases at national level, particularly thanks to Santé publique France and the network of National Reference Centres for communicable diseases, the scale of the COVID-19 crisis has shown the necessity to strengthen the country’s sequencing capacities, and to support research activities to better respond to epidemics.

To remedy this situation, the EMERGEN project was launched in early 2021, thanks to special funds from the French Ministries of Health and Research. Initially focused on the response to the COVID-19 epidemic, this Consortium has worked to:

• Describe and monitor the circulation of known SARS-CoV-2 variants at the most detailed territorial level possible, but also detect, identify and then monitor the circulation of novel variants of interest as soon as possible;
• Promote and fund research projects within the consortium, linked to the sequencing of novel SARS-CoV-2 variants, particularly in relation to experimental studies and animal models, cohorts, modelling studies and environmental aspects (wastewater).

EMERGEN 2.0: A One Health approach

Since its inception, EMERGEN has adopted a One Health approach that considers human, animal and environmental health as interdependent. This approach is reinforced with EMERGEN 2.0 through:

• The strengthening of links with stakeholders in wastewater surveillance and epidemiology research (projects SUM’Eau and Obépine+);
• The extension to include the sequencing of strains of animal origin;
• The intersectional sharing of surveillance and research data and analysis tools.

These developments will enable better anticipation of the emergence of zoonotic pathogens, and the rapid adaptation of health surveillance and responses to emerging infectious disease crises.

EMERGEN 2.0: Operational and scientific developments

Creation of UMS 56

In order to facilitate the management and utilisation of EMERGEN data, and in compliance with the regulatory framework, the bioinformatics platform developed by the French Institute of Bioinformatics (IFB) was transferred to JRU 56, which was created on 1 January 2024. As part of EMERGEN 2.0, this unit will be responsible for maintaining and upgrading the platform, helping to organise the flow of data, and developing analysis methods and tools for the use of this data by the scientific community.

Transfer of technologies and skills

To better prepare France for future infectious disease emergences and potential health crises, regardless of the pathogen concerned, EMERGEN 2.0 plans to extend sequencing capabilities in terms of expertise and the volume of sequences to produce. This will involve identifying and reinforcing a network of expert laboratories, with skills transfer through the dissemination of sequencing and data analysis knowledge and tools, from the National Reference Centres and National Reference Laboratories to the other sequencing platforms.

Continuation and expansion of research support

The project plans to continue the research undertaken during the COVID-19 crisis, particularly in connection with ANRS EID’s missions of facilitating, coordinating and funding research, and to extend these activities to other emerging or re-emerging pathogens. Support for structuring projects, making it possible to provide answers to the scientific questions raised by these emergences in order to support crisis management, the organisation of calls for proposals, and support for the use of surveillance data in research, will be key actions of EMERGEN 2.0.

Facilitation and coordination of stakeholders

EMERGEN 2.0 will be tasked with strengthening the link between health stakeholders (human, animal, environmental) around genomic issues, initially viral. Under the auspices of the three coordinating institutions, the project will not only strengthen the links between the worlds of surveillance and academic and industrial research but also play a crucial role in informing public authorities and civil society.

EMERGEN 2.0: Coordinators, players and partners

EMERGEN 2.0 coordinators

• Inserm/ANRS MIE
• Santé publique France
• Anses (French Agency for Food, Environmental and Occupational Health & Safety )

EMERGEN 2.0 players and their role in genomic surveillance and research

• UMS 56: hosts the database associated with the EMERGEN platform.
• National Reference Centres (Centres Nationaux de Référence (CNR)): responsible for the genomic surveillance of pathogenic organisms, especially those centres for pathogens that could cause a potential health crisis. They develop and apply sequencing techniques for public health.
• National Reference Laboratories (Laboratoires de Référence Nationaux (LNR)) for human and animal health: intended for the surveillance and research of circulating animal viruses, especially those laboratories that work with pathogens likely to emerge in humans and cause an epidemic.
• The ANRS MIE network of hospital virology and medical pharmacology laboratories: mobilised through hospital laboratories in France, specialising in surveillance and research, they provide their expertise and sequencing capabilities.
• High-throughput sequencing platforms: distributed across France, they increase sequencing capacity in support of the National Reference Centres during health crises, while playing a key role in research projects during inter-crisis periods.

National and international partners

EMERGEN 2.0 develops links with a diversified network of partners, both nationally and internationally, such as clinical research platforms, other sequencing platforms and international agencies and institutions. Collaboration with these partners is essential in expanding genomic surveillance of emerging and re-emerging pathogens and to improve preparedness for future epidemics and pandemics.

• I-REIVAC Emergence
• OPEN-ReMIE
• Obepine+
• SUM’Eau
• ECDC
• World Health Organization
• Isidore
• AFROSCREEN