Circulating Variants — Sequencing Indicators (EMERGEN)

The **Flash surveys** consist of randomly selecting positive samples for SARS-CoV-2 for which the viral genome is sequenced. Repeated at regular intervals, they aim to map the SARS-CoV-2 strains circulating in France. They also detect the emergence of new variants. The sampling fraction prescribed by Public Health France for each Flash survey is determined each week according to the incidence of the epidemic, in order to ensure an optimal detection capacity for emerging variants (according to the ECDC recommendations), and on the other hand to remain compatible with the consortium’s sequencing capabilities. The number of sequences obtained in the end depends on several factors: the proportion of RT-PCR in the diagnosis of SARS-CoV-2 infection, adherence of the sampling laboratories to the protocol, the proportion of samples with a viral load (Ct) sufficient to allow sequencing, the quality of the sequencing itself (sometimes subject to technical aleas). The indicators are updated weekly according to the reports of the sequencer laboratories. They are gradually consolidated taking into account sequencing times that may vary over time or depending on the laboratories. For reasons of representativeness, the data presented here include only Flash surveys for which the results of at least 500 sequences are present in the database. The **variables present** in these datasets are as follows: Reg = Region of residence of the patient taken or, if missing, from the sampling laboratory deb_periode = Date of the beginning of the Flash survey week considered flash_variants = Variant obtained as sequencing result cage10 = Age class (slices of 10) N = Number of samples resulting in the variant in question N_tot = Number of samples for date and region or age group considered The _age classes_ used are the following: • 0 = all ages • 09 = 0 @-@ 9 years • 19 = 10 @-@ 19 years • 29 = 20 @-@ 29 years • 39 = 30 @-@ 39 • 49 = 40 @-@ 49 years • 59 = 50 @-@ 59 years old • 69 = 60 @-@ 69 • 79 = 70 @-@ 79 years old • 89 = 80 @-@ 89 years old • 90 = 90 years and over The _region_ (column “reg”) follows the codification of the Official Geographical Code of INSEE and is codified as follows: • 01: Guadeloupe • 02: Martinique • 03: French Guiana • 04: Réunion • 05: Saint-Pierre and Miquelon • 06: Mayotte • 07: Saint Barthélemy • 08: Saint Martin • 11: Ile-de-France • 24: Centre-Val de Loire • 27: Burgundy-Franche-Comté • 28: Normandy • 32: Haut-de-France • 44: Great East • 52: Countries of the Loire • 53: Brittany • 75: New-Aquitaine • 76: Occitanie • 84: Auvergne-Rhône-Alpes • 93: Provence-Alpes-Côte d’Azur • 94: Corsica The _variants_ represented in these data are the variants classified as of concern (VOC) by the WHO and the variants to follow (VOI) circulating in France. Variants of Concern (VOC) according to the WHO classification are those that have an impact on public health (whether in terms of communicability, severity, or risk of escape to the immune response) more important than previously circulating variants. Variants of Interest (VOI) are those whose public health impact is not formally demonstrated, but with virological, clinical and/or epidemiological characteristics that justify their classification as “variants to follow”. Additional information about the classification of variants is available on the website of Santé publique France: Coronavirus: circulation of SARS-CoV-2 variants (https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/coronavirus-circulation-des-variants-du-sars-cov-2). Variants are codified as follows in the files: • 1 = Alpha • 2 = B.1.640 • 3 = Beta • 4 = Delta • 5 = Gamma • 6 = Omicron • 7 = Other variants The content of each of the available files is listed below: _Global data_ Files with the number of samples sequenced for each variant, per Flash survey: • Flash @-@ fra @-@ YYYY @-@ MM @-@ DD @-@ HHhmm.csv (national scale) • Flash @-@ reg @-@ YYYY @-@ MM @-@ DD @-@ HHhmm.csv (regional scale) _Data by age class_ Files with the number of samples sequenced for each variant, by age classes and Flash survey: • Flash @-@ cage10 @-@ fra @-@ YYYY @-@ MM @-@ DD @-@ HHhmm.csv (national scale) _To know +_: https://www.santepubliquefrance.fr/etudes-et-enquetes/enquetes-flash-evaluation-de-la-circulation-des-variants-du-sars-cov-2-en-france