Viruses are constantly evolving genetically, at varying rates depending on the species. Certain genetic changes can alter their characteristics and affect their transmission dynamics, clinical impact, and the effectiveness of management measures (tests, vaccines, therapeutic agents, etc.). Continuous genetic surveillance, particularly through sequencing, can enable the timely detection of these evolutionary changes and help anticipate their impact.

Monitoring and understanding the genetic evolution of viruses, particularly emerging ones, is essential for assessing their impact, anticipating future epidemics, and informing public policy decisions. With this in mind, the ministries responsible for Health and Research asked Santé publique France and the ANRS Emerging Infectious Diseases (ANRS MIE) to establish, during the COVID-19 pandemic, the EMERGEN consortium (Consortium for Surveillance and Research on Infections Caused by EMERgent Pathogens via Microbial GENomics). It brings together the main French stakeholders in the surveillance and research of emerging infectious diseases.

Key Players and Roles in Genomic Surveillance

• National Reference Centers: They are responsible for developing sequencing techniques and implementing them according to genomic surveillance needs.

• The EMERGEN consortium, coordinated by Santé publique France and ANRS MIE: it aims to deploy a nationwide genomic surveillance system for infections to complement and strengthen the work of the National Reference Centers. It combines surveillance activities coordinated by Santé publique France and research activities coordinated by ANRS MIE.

Objective: to track the genetic evolution of viruses to detect the emergence and spatio-temporal distribution of variants—that is, viruses with mutations likely to have functional consequences, such as increased infectivity, transmissibility, virulence, or immune evasion.

Establishment of the EMERGEN Consortium

The EMERGEN consortium was launched in January 2021 in the context of the COVID-19 pandemic and following the emergence of the first variant of concern of SARS-CoV-2 (Alpha, first detected in the United Kingdom in November 2020). Its first mission was to deploy a SARS-CoV-2 genomic surveillance system across the entire country to monitor the emergence and/or introduction of variants of concern more proactively. While, at the time of its creation, the EMERGEN consortium focused its activities on SARS-CoV-2, it was designed from the outset to be able to evolve and support surveillance and research activities on other emerging infectious diseases (viral, but also bacterial, fungal, or parasitic).

Partner members of the EMERGEN Consortium

In 2021–2022

• Santé publique France

• ANRS Emerging Infectious Diseases

• CNR Respiratory Infections (Institut Pasteur) and its associated laboratories (Hospices Civiles de Lyon and Institut Pasteur de la Guyane)

• Expert laboratories supporting SARS-CoV-2 sequencing (APHP Henri Mondor, Créteil, and APHM, Marseille)

• ANRS Network of Virology Laboratories for Emerging Infectious Diseases

• French Institute of Bioinformatics (IFB)

• Inserm ITMO Technology

• ANSES

• National Center for Human Genomics Research (CNRGH/CEA)

• Emerging Viruses Unit (UMR UVE), Marseille

• Sentinelles Network

In 2022–2023

• Public Health France

• ANRS|Emerging Infectious Diseases, and its hospital virology network (AC 43)

• ANSES

• French Institute of Bioinformatics (IFB)

EMERGEN-DB: The National SARS-CoV-2 Sequencing Database

Upon the creation of the EMERGEN Consortium, the French Institute of Bioinformatics was tasked with developing, hosting, and maintaining a SARS-CoV-2 sequencing database, named EMERGEN-DB. All sequences generated as part of surveillance efforts (along with associated metadata) are submitted to this database by the various sequencing laboratories. The purpose of this database is to make these sequences accessible for public health (surveillance) and research purposes within a secure digital environment.

Surveillance Activities

The EMERGEN-DB database enables epidemiologists at Santé publique France and the CNRs to continuously analyze the genomes produced each week. Over time, additional tools have been implemented and are currently used for sequence analysis, data visualization, and submission to international databases.

Where can I find surveillance data from genomic surveillance?

The SARS-CoV-2 genomic surveillance strategy is detailed on a dedicated page. Data from this surveillance are published in joint risk assessments conducted by Santé publique France and the CNR Virus des infections respiratoires. Some are available on the InfoCovidFrance dashboard. Since October 4, 2022, indicators tracking the sequencing activity of the EMERGEN consortium have been available on the EMERGEN-DB website.

Signals identified from these surveillance data are subject to further investigation, some of which are detailed on the page dedicated to SARS-CoV-2 variants.

Research Activities

EMERGEN promotes and funds research projects within the consortium related to the identification and characterization of new variants. The EMERGEN project’s research framework is aligned with Santé publique France’s genomic surveillance activities and enables the rapid acquisition of knowledge useful for public health decisions.

Four research areas have been defined:

• anticipating and analyzing the significance of variants through an “experimental research and animal models” component,

• the identification, characterization, and analysis of the evolution of new variants in cohorts,

• modeling the evolution and impact of these variants,

• the evaluation of wastewater as a tool for monitoring variants.

To coordinate this research component, a multi-institutional and multidisciplinary steering committee has been established by ANRS|MIE. Additionally, ANRS|MIE supports other research initiatives and efforts to strengthen genomic sequencing capabilities to monitor the evolution of SARS-CoV-2 and other emerging viruses at the international level.

Learn more:

• Emergen Project: ANRS Emerging Infectious Diseases (ANRS MIE) website

• Press release "Research at the heart of France’s genomic surveillance plan for SARS-CoV-2 variants" (January 11, 2022)

European Projects

The European Commission has invited Member States to respond to calls for proposals aimed at improving national sequencing capabilities and integrating these methods into surveillance and preparedness activities for health threats. The EMERGEN consortium has thus responded to two calls for proposals.

Learn more:

• Project: Enhancing Whole Genome Sequencing (WGS) and/or Reverse Transcription Polymerase Chain Reaction (RT-PCR) national infrastructures and capacities to respond to the COVID-19 pandemic

• SEQ4EPI Project