Old Laboratory Data for Screening: Indicators on variants

**Discontinuation of data update** Since 09/06/2021, the data for variants has not been updated anymore. Laboratory data for mutation screening are available on the dedicated dataset: https://www.data.gouv.fr/fr/datasets/donnees-de-laboratoires-pour-le-depistage-indicateurs-sur-les-mutations/ **Information of 20 May 2021** As of today, the indicators will be corrected in order to eliminate the double effect, when carrying out several tests by the same person. Since the beginning of the pandemic, the secure Si-DEP platform has recorded all the results of the tests. In order to guarantee the protection of the personal data of the persons tested, each result was linked to the issue of an anonymised pseudo. However, with the appearance of variants in the territory, some people are required to carry out two tests, so far counted twice. The algorithm used has therefore recently been updated so that it counts only one patient when tested several times in a short time interval, always respecting anonymity. Thanks to this new pseudonymisation, Santé publique France is able to increase its effectiveness and produce even more accurate data, which can be consulted weekly in its epidemiological point. ### Context SARS-Cov-2 is now circulating in the population in the form of many variants, which must be monitored in particular, both in terms of contact tracing and epidemiological, in order to contain the progression of the COVID-19 epidemic. To this end, SI-DEP has evolved from Monday 25 January 2021 to support information on these variants. ### Data analysis The analyses for the variants include data on suspicions or screening results following a PCR or an antigenic test (TA) positive. **Data are reported to all positive tests performed (RT-PCR + TA)**, not to a number of people. The definition of persons for the calculation of indicators uses only one test for a person in a given period, whereas the latter may have been tested several times (TA test, followed by a PCR for example). This methodology could lead to the non-recognition of a test that contains information on the presence of a variant, and thus underestimates their representation. All positive tests in the SI-DEP database are searched for information on the variant, with the application of a cleaning for strict duplicates, based on a corresponding key: — To the person’s Pseudonym (individual anonymity code based on the person’s identifying traits) — At the date and time of sampling — To the type of analysis The nomenclature of codes used for reporting information on the lineage of variants is that of the international database **_Nextstrain_**. This nomenclature is likely to evolve in line with international harmonisation requirements. The purpose of the analysis of these data is to monitor the movement within the territory of the variants of interest, which so far concern the following variants: — United Kingdom (UK): Nexstrain code = 20I/501Y.V1 — South Africa (ZA): Nexstrain code= 20H/501Y.V2 — Brazil (BR): Nexstrain code = 20J/501Y.V3 **Data by slippery week broadcast by department, region and france.** ### Variables: Week = slippery week cl_age90 = Age class Nb_tests_PCR_TA_crible = Number of PCR tests screened among positive PCRs Prc_tests_PCR_TA_crible = % of PCR tests screened among positive PCRs Nb_susp_501Y_V1 = Number of tests with suspicion of 20I/501Y.V1 (UK) Prc_susp_501Y_V1 = % of tests with suspicion of 20I/501Y.V1 (UK) Nb_susp_501Y_V2_3 = Number of tests with suspicion of 20H/501Y.V2 (ZA) or 20J/501Y.V3 (BR) Prc_susp_501Y_V2_3 = % of tests with suspicion of 20H/501Y.V2 (ZA) or 20J/501Y.V3 (BR) Nb_susp_IND = Number of tests with a detection of varying but not identifiable Prc_susp_IND = % of tests with a detection of varying but not identifiable Nb_susp_ABS = Number of tests with no detection of variants Prc_susp_ABS = % of tests with no detection of variants ### Age classes: • 0 all ages • 09 0 @-@ 9 years old • 19 10 @-@ 19 years old • 29 20 @-@ 29 years old • 39 30 @-@ 39 years old • 49 40 @-@ 49 years old • 59 50 @-@ 59 years old • 69 60 @-@ 69 years old • 79 70 @-@ 79 years old • 89 80 @-@ 89 years old • 90 years and over