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EMERGEN Consortium : sequencing for public health to control the COVID-19 pandemic


Genomic surveillance of SARS-CoV-2 is now one of the pillars of the fight against the epidemic on a national and global scale. Since January 2021, the Ministries of Health and Research have entrusted Santé publique France and ANRS│Emerging Infectious Diseases with the creation and management of the EMERGEN consortium to deploy a genomic surveillance system for SARS-CoV-2 in France for public health and research purposes


EMERGEN integrates surveillance activities conducted under the aegis of Santé publique France and the CNRS, and research activities conducted under the aegis of the ANRS│ Emerging Infectious Diseases (EID). The project has three main focuses:

  • Identify the share of different variants circulating in the territory
  • Identify new variants by analysing the national database of sequencing data
  • Nourish research projects based on enhanced sequencing capacities and standardised, centralised and shared genomic data.


A multidisciplinary consortium


An efficient sequencing programme relies on the coordination of different steps that require complementary expertise: sample collection, sample preparation for sequencing and sequencing, bioinformatics analysis of genomes, publication of data in national and international databases, monitoring of variants of interest, possible discovery and characterisation of new variants, and in-depth research on their epidemiological and functional impact.


The EMERGEN consortium involves many partners, including in particular four sequencing platforms (CNR Institut Pasteur, CNR Hospices Civils de Lyon, CNR- Laboratoires experts pour l'appui au séquençage du SARS-CoV-2: APHP Mondor (Créteil) and APHM Marseille), the network of virology laboratories of the ANRS│MIE, the French Institute of BIoinformatics (IFB), Inserm, and about fifteen research teams affiliated to different organisations and institutes (Inserm, CNRS, CEA, ...), the National Centre for Research in Human Genomics (CNRGH/CEA) in Evry, and ANSES. 


EMERGEN: when research and monitoring are closely linked

The aim of the project is to monitor the genetic evolution of pathogens in order to identify the emergence and spatio-temporal distribution of viruses with mutations likely to have functional consequences. As part of the global strategy for monitoring variants, EMERGEN will strengthen French capacities in the fight against variants and, in the future, against other emerging infectious diseases.



Press kit

Press release


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