Flash Surveys: Assessment of the Circulation of SARS-CoV-2 Variants in France

Numerous variants of SARS-CoV-2 are circulating in the country, some of which are classified as "variants of concern" (VOC) ) or “variants of interest” (VOI) because their impact (in terms of transmissibility, virulence, or potential immune escape) warrants the implementation of specific surveillance and management measures at the national level, with the aim of containing their spread.

In this context, Flash Surveys have been implemented to map, at a given point in time, the SARS-CoV-2 variants circulating in France. To do this, sequencing laboratories use Next Generation Sequencing (NGS) technology to sequence the entire SARS-CoV-2 genome. This identification of variants through sequencing is complementary to and more robust than that based on screening tests (RT-PCR), which are limited to detecting only a few mutations.

The first surveys were conducted on January 7 and 8, 2021, and have since been repeated at regular intervals. The Flash surveys are among the priority targets of the national genomic surveillance strategy coordinated by Santé publique France and the ANRS | Emerging Infectious Diseases within the framework of the EMER-GEN consortium.

These surveys are part of a comprehensive surveillance system comprising:

The performance of RT-PCR screening tests; systematic screening of positive tests to enable more responsive surveillance of known variants of concern (VOCs) or certain mutations of interest.
The performance of whole-genome sequencing of the virus, as part of the national genomic surveillance strategy and particularly the Flash investigations.
Enhanced epidemiological surveillance across the entire country to identify any epidemiological signals that could also serve as an alert.

Learn more about the circulation and classification of variants

Objectives

Detect the emergence of genetic lineages (variants) with mutations that may affect transmissibility, virulence, or immune escape
Monitor their potential spread across the country or within specific populations

To track the molecular evolution of viruses circulating in the country, Santé publique France aims to collect sequencing results from the four sequencing platforms (CNR Institut Pasteur (Paris), CNR Hospices Civils de Lyon, AP-HP Henri-Mondor (Créteil), and IHU Méditerranée Infection) and the laboratories of the ANRS|MIE virology network. Analysis of these results enables the mapping of SARS-CoV-2 clades and variants circulating within the country. Surveillance data are compared with epidemiological data and the results of virological studies aimed at investigating the properties of the viruses in question.

How the Flash Surveys Work

The Flash surveys are based on the following methodology:

The first two surveys (Flash #1 on January 7–8, 2021, and Flash #2 on January 27, 2021) were based on a selection of RT-PCR-positive samples for which the screening results—specifically, the detection of variants of concern (VOCs)—were known.
Starting with Flash Survey #3, and in order to obtain a comprehensive map (not limited to known VOCs) of the different types of SARS-CoV-2 viruses circulating in France, the selection of samples with a positive RT-PCR result is based on random sampling, regardless of the screening result. These samples must not come from the investigation of a cluster to avoid selection bias, with the exception of Flash Surveys #12 through #15, which are based on the inclusion of all samples that received a positive RT-PCR result.

Public or private laboratories participate in these investigations under Article 1413-8 of the Public Health Code. These samples are then sent to the EMER-GEN consortium platforms. These Flash surveys have been conducted weekly since June 22, 2021.

Shipping label for positive samples (RT-PCR)

As part of SARS-CoV-2 genomic surveillance, positive (RT-PCR) samples to be sent to various sequencing laboratories must be accompanied by a shipping form. This shipping form must be included in the package containing the samples and must also be sent via secure messaging to the sequencing laboratory receiving these samples.

Download the sequencing shipment form (12/27/22).

What are the results used for?

The data generated by the Flash Surveys are intended to enhance COVID-19 surveillance, contribute to risk analyses that help characterize and classify the different variants circulating in France, and inform research efforts.

In addition, the data is compared with virological studies to link a mutation to transmissibility, virulence, or immune escape.

How are they analyzed?

The results of the Flash surveys are reported in the national epidemiological updates published weekly.

The consolidated results of Flash surveys #5 through #29 were reported in the summary documents titled "Le point sur," which are available online. Since Flash survey #30, the results of Flash surveys deemed sufficiently representative (more than 500 interpretable sequences) are available via the InfoCovidFrance dashboard (under the "Variants" tab).