Circulating Variants - Sequencing Indicators (EMERGEN)
Description
**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 SARS-CoV-2 strains circulating in France. They also make it possible to 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 impact of the epidemic, in order to ensure an optimal detection capacity for emerging variants (following ECDC recommendations) and to remain compatible with the consortium’s sequencing capacities.
The number of sequences obtained in the end depends on several factors: the proportion of RT-PCRs in diagnoses of SARS-CoV-2 infection, adherence of 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 every week according to the reports of the sequencer laboratories. They are gradually consolidated taking into account sequencing times which may vary over time or depending on the laboratory.
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 sampled patient or, if missing, of the sampler laboratory
deb_periode = Start date of the week of the Flash survey considered
flash_variants = Variant obtained as a result of sequencing
cage10 = Age class (slices of 10)
n = Number of samples resulting in the variant in question
n_tot = Number of samples for the date and region or age group considered
The _age classes_ used are as follows:
0 = tous âges
09 = 0-9 ans
19 = 10-19 ans
29 = 20-29 ans
39 = 30-39 ans
49 = 40-49 ans
59 = 50-59 ans
69 = 60-69 ans
79 = 70- 79 ans
89 = 80-89 ans
90 = 90 ans et plus
The _region_ (column ‘reg’) follows the codification of the Official Geographic 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 - Loire Valley
27 : Burgundy-Franche-Comté
28 : Normandy
32 : Hauts-de-France
44 : Grand Est
52 : Pays de la Loire
53 : Brittany
75 : New Aquitaine
76 : Occitania
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 be followed (VOI) circulating in France.
Variants of concern (VOCs) according to the WHO classification are those with a greater impact on public health (whether in terms of transmissibility, severity, or risk of escape to the immune response) than previously circulating variants. Variants of Interest (VOI) are those whose impact on public health is not formally demonstrated, but which have virological, clinical and/or epidemiological characteristics that justify their classification as ‘variants to be followed’.
Additional information on the classification of variants is available on the Public Health France website: Coronavirus: circulation of SARS-CoV-2 variants (https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/coronavirus-circulation-des-variants-du-sars-cov-2).
The variants are coded as follows in the files:
1 = Alpha
2 = B.1.640
3 = Beta
4 = Delta
5 = Gamma
6 = Omicron
7 = Autres variants
The content of each of the available files is listed below:
_Global data_
Files with the number of samples sequenced for each variant, by Flash survey:
flash-fra-YYYY-MM-DD-HHhmm.csv (échelle nationale)
flash-reg-YYYY-MM-DD-HHhmm.csv (échelle régionale)
_Data by age group_
Files with the number of samples sequenced for each variant, by age group and by Flash survey:
flash-cage10-fra-YYYY-MM-DD-HHhmm.csv (échelle nationale)
_For more information +_: https://www.santepubliquefrance.fr/etudes-et-enquetes/enquetes-flash-evaluation-de-la-circulation-des-variants-du-sars-cov-2-en-france
Resources
| Name |
Format |
Description |
Link |
|
8 |
|
https://www.data.gouv.fr/api/1/datasets/r/fd772cf2-f03c-4ee5-ad6d-1b1b0289a5c2 |
|
8 |
|
https://www.data.gouv.fr/api/1/datasets/r/c68e73c2-5045-4ee2-ac50-bd1c39ff3175 |
|
8 |
|
https://www.data.gouv.fr/api/1/datasets/r/61aece05-1df1-4cdf-8755-f27913653e94 |