EMERGEN project

Two short-term objectives of EMERGEN

• To describe and monitor the circulation of known SARS-CoV-2 variants down to the smallest possible territorial scale. To detect, identify and then monitor as quickly as possible the circulation of new variants of interest (i.e., those with functional consequences, in terms of transmissibility or pathogenicity for example). A list of priority targets is used to explore different populations (in towns and cities, in medico-social establishments, in health establishments) and to obtain the biological material and metadata required for sequencing activities and data interpretation.
• To promote and fund research projects within the consortium, in connection with new SARS-CoV-2 variant sequencing, focusing on certain aspects over others: experimental approach, animal models, cohorts, modelling studies  and environmental aspect (waste water).

Three key pillars to implement this system

1. A sampling and collection strategy:

• Representative Flash surveys carried out across France (including overseas departments): in towns (samples from specialised biology laboratories; from the Sentinelles Network; from certain screening tests conducted in schools or universities; at borders, ports and airports), in social or medico-social establishments (EHPAD) or in hospitals (serious cases, carers).
• Particular attention paid to certain patient populations or infection profiles (immunocompromised patients, patients who have failed to respond to vaccines or antibody treatments, reinfections).
• Consideration of the environmental dimension (waste water), which is still a subject of study.

2. Setting up sequencing platforms to perform sample analysis:

• Four national sequencing platforms collect and analyse samples centrally for surveillance purposes (Flash surveys): two CNR respiratory infection virus laboratories (Institut Pasteur and Hospices Civils de Lyon laboratories), and two CNR expert laboratories for support in sequencing SARS-CoV-2 (Henri Mondor University Hospital (AP-HP) and the APHM infectious diseases unit in Marseille).
• The nationwide network of virology laboratories receives samples for sequencing in response to clinical needs (e.g., cluster cases) or clinical indications (e.g., re-infection, hospitalised cases, etc.): this local network, coordinated by ANRS MIE, is composed of around forty laboratories (university hospitals, hospitals, SSAs).
• Since 19 January 2021, some private medical biology laboratories have been able to enhance their local genomic sequencing capacity, at their ARS’ request. In addition, on 26 May, a call for expressions of interest was issued by Santé publique France, inviting private laboratories to take part in genomic surveillance using their sequencing capabilities (random selection).

Consult the call for expressions of interest

3. Organisation of data management and integrative analysis:

• A secure bioinformatics infrastructure, commissioned by Santé publique France. It was developed  by the Institut Français de Bioinformatique (IFB), enabling data to be collected and shared for surveillance and research purposes, with timeframes adapted to each of these two segments of the project.
• Making data available to national and regional surveillance and research teams.
• Feeding into international databases (GISAID, ENA) according to defined data standards and Open Science principles

The infrastructure must be secure and allow data to be collected and shared for monitoring and research purposes, with timeframes tailored to each of these two segments of the project.

Key achievements of EMERGEN

National genomic surveillance of SARS-CoV-2

During the COVID-19 pandemic, a national surveillance system covering mainland France and overseas territories was coordinated by Santé publique France. The aim was to monitor the genetic evolution of the SARS-CoV-2 virus in order to detect the emergence and spatio-temporal distribution of variants. Weekly surveillance of SARS-CoV-2 variants and mutations was put in place, with the production of risk analyses on emerging variants and flash surveys.

Research funding and scientific coordination

The EMERGEN platform quickly funded research projects on SARS-CoV-2 variants, based on four defined areas:

• Anticipation and analysis of variants, based on experimental aspects and animal models;
• Identification, characterisation and analysis of the evolution of new variants in cohorts;
• Modelling of the evolution and impact of these variants;
• Evaluation of the use of wastewater as a tool for monitoring variants.

Following scientific evaluation, 15 research projects and 1 infrastructure project were funded for a total of €9.3 million.

These projects have provided new insights into SARS-CoV-2 variants. In particular, they have promoted:

• In-depth analysis of viral evolution and phylogeny data;
• Their integration into epidemiological modelling activities;
• Monitoring and understanding of antiviral resistance and immune response evasion phenomena;
• The detection of variants capable of crossing the species barrier.

EMERGEN has supported consensus-based projects and innovative approaches to address complex questions, yielding rapid results that have greatly contributed to crisis management, with numerous high-impact scientific communications.

Find out more about the project with EMERGEN 2.0

Members of EMERGEN Consortium

Laboratories in the ANRS EMI network involved in the sequencing of SARS-CoV-2

Please note: Laboratory contact details are intended for healthcare professionals carrying out SARS-CoV-2 screening and who need to send their samples for sequencing to one of the ANRS network laboratories. To obtain this information, please send a request by e-mail to: ssr@anrs.fr