Since its establishment, more than 79,000 sequences¹ have been generated in France by members of this consortium, enabling the detection, classification, and tracking of SARS-CoV-2 variants across the country. To expand the consortium’s surveillance capabilities and improve coverage of the entire national territory, Santé publique France has issued a call for expressions of interest. Furthermore, at the request of the ARS, private medical laboratories can now also contribute to this sequencing activity during investigations (so-called interventional sequencing). Several research areas have also been identified to launch research projects whose results will help strengthen our understanding of variants.

EMERGEN: A Surge in Sequencing Capacity in France

The first phase of EMERGEN was to bring together all public capabilities in virology and SARS-CoV-2 sequencing and to create an operational bioinformatics infrastructure to centralize sequencing results and share them with all consortium members. This phase, currently being finalized, now makes it possible to add additional sequencing capabilities to those already in place, in order to track the circulation of variants across the country more precisely. In collaboration with the two laboratories of the National Reference Center (CNR) for Respiratory Infections (Institut Pasteur and Hospices Civils de Lyon), two CNRs —expert laboratories supporting SARS-CoV-2 sequencing (Henri Mondor University Hospital (AP-HP) and APHM in Marseille)—the laboratories of the ANRS | Emerging Infectious Diseases virology network, the French Institute of Bioinformatics (IFB), and Inserm, several surveillance initiatives have consequently been launched. Starting in January, so-called “Flash” surveys—initially conducted every two months and now weekly—were implemented to map the various viruses circulating in the country. On a daily basis, the sequencing results thus generated also help guide investigations by the ARS and regional units of Santé publique France regarding clusters or any other situation deemed abnormal. Also based on this sequencing activity, risk analyses—updated twice a month—help classify the various variants—according to the risk they pose—and prioritize public health actions implemented on the ground. The rapid and effective increase in sequencing activity in France thus contributes to better surveillance and better control of the pandemic.

A Call for Expressions of Interest to Expand Genomic Surveillance Capabilities

From its inception, the EMERGEN Consortium has mobilized the leading virology laboratories with strong sequencing capabilities (CNR Institut Pasteur, CNR Hospices Civils de Lyon, CNR-Expert Laboratories for SARS-CoV-2 Sequencing Support: APHP Mondor and APHM Marseille) and the hospital laboratories of the ANRS|Emerging Infectious Diseases virology network. In five months, more than 79,000 sequences were produced in France, compared to fewer than 3,000 in 2020. Within the European Union, France ranks fourth among countries submitting the highest number of SARS-CoV-2 sequences to GISAID (nearly 49,700 sequences submitted since January 2021). However, this sequencing activity is set to expand further, particularly by strongly encouraging all testing laboratories to submit their positive samples as part of Flash investigations, as current platforms are not yet utilizing their full capacity. Furthermore, on May 26, 2021, Santé publique France published a call for expressions of interest (AMI) with the aim of expanding this genomic surveillance activity, notably by involving private clinical laboratories. The successful applicants following this AMI will be announced in late July. Finally, since June 19, 2021, private medical biology laboratories have also been able to contribute to this sequencing activity during investigations (so-called interventional sequencing), at the request of the ARS.

Research activities within the EMERGEN consortium

Beyond this surveillance activity, EMERGEN’s other objective is to promote and fund research projects within the consortium related to the identification and characterization of new variants. Four research areas have been defined: anticipating and analyzing the significance of variants through an “experimental research and animal models” component; identifying, characterizing, and analyzing the evolution of new variants in cohorts; modeling the evolution and impact of these variants; and finally, evaluating the use of wastewater as a tool for monitoring variants.

It has indeed become essential to establish a research pathway in coordination with public health genomic surveillance activities. This “research” pathway will enable the rapid acquisition of knowledge useful for public health decisions, notably through projects focused on:

• The discovery of new variants

• The biological significance of mutants and the impact of genetic and phenotypic changes in this new virus

• The possibility of anticipating the emergence of escape mutants

• The clinical and virological characterization of patients infected with variants (severity, kinetics, and sites of viral shedding of the variants)

• Immunity and the circulation of variants in the context of the vaccination campaign and control measures

• Virological and immunological investigation in cases of vaccine failure or reinfection

• Anticipating the circulation dynamics of different variants and the risk of introducing new variants

• The relevance of wastewater surveillance in monitoring circulating variants in the general population.

To coordinate this research initiative, a multi-institutional and multidisciplinary steering committee has been established by ANRS | Emerging Infectious Diseases.

In addition, ANRS | Emerging Infectious Diseases supports other research initiatives and efforts to strengthen genomic sequencing capabilities to monitor the evolution of SARS-CoV-2 and other emerging pathogens at the international level.

List of EMERGEN Consortium Partners

The EMERGEN consortium brings together the expertise and capabilities of the following institutions:

• Santé publique France

• ANRS | Emerging Infectious Diseases

• CNR Respiratory Infections Virus (Institut Pasteur and Hospices Civils de Lyon)

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

• ANRS Network of Virology Laboratories | 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