OLD French Coronavirus Screening Data (OLD (France) Données de laboratoires pour le dépistage : Indicateurs sur les mutations SI-DEP)

The RT-PCR screening tests used and the results of which are reported in SI-DEP made it possible to suspect the presence of the worrisome variant (VOC) Alpha (20I/501Y.V1) and indistinctly from the VOC Beta (20H/501Y. V2) or Gamma (20J/501Y.V3). This screening strategy targeting Alpha, Beta and Gamma VOCs is no longer suited to the increasing diversity of emerging SARS-CoV-2 variants. Since 05/31/2021, the screening strategy has evolved to search for certain mutations of interest that can be found in different variants. It therefore no longer makes it possible to assign the infection to a specific variant but makes it possible to follow the evolution over time and in the territory of the proportion of infections due to a virus carrying these mutations.

For the first phase of deployment, the E484K, E484Q and L452R mutations were selected because they are potentially linked to immune escape and/or increased transmissibility and are found in the majority of VOCs to date. Due to the rendering of the results of these PCRs in shorter delays than sequencing, specific measures can be implemented as soon as cases carrying mutations of interest are detected in order to slow down their dissemination (reinforcement of contact tracing, screening or vaccination campaign).

The emergence of the B.1.1.529 variant, known as Omicron, implies an evolution of the current doctrine with regard to the mutations sought during screening, this variant not presenting any of the 3 mutations cited above. Between 29/11 and 19/12, three targets were sought by the new screening strategy: the 69/70 deletion and the N501Y and K417N mutations, carried by the Omicron variant. Since 12/20, the 69/70 deletion and the K417N, S371L-S373P and Q493R substitutions are searched and the E484Q and N501Y mutations are no longer searched. The presence of the 69/70 deletion or the K417N, S371L-S373P or Q493R substitutions remains to be interpreted with caution, however, the new, more specific screening strategy currently being deployed will make it possible to suspect the Omicron variant more precisely.

REPORTING OF RESULTS IN SI-DEP

The screening results are entered by following a nomenclature in the form of a succession of alphabetical characters representing the mutation(s) sought and numbers representing the result. Since 29/11/2021, a new variable "D" has been created in order to report results on mutations DEL69/70 or N501Y or K417N. Retrospective tests have been carried out on samples since 01/11/2021 to search for these three mutations. Then, since 12/20/2021, variable “D” reports results on mutations DEL69/70 and/or K417N, and/or S371L-S373P and/or Q493R.

Codes and associated mutations of interest A = E484K C = L452R D = DEL69/70, K417N, S371L-S373P and/or Q493R

1 = Presence of the mutation sought 0 = Absence of the mutation sought 8 = Uninterpretable 9 = Not sought

For mutations associated with code D:

A "D1" result means that at least one of the mutations associated with this code is positive; A "D0" result means that at least one of the mutations associated with this code is negative, and that none are positive

ANALYSIS OF DATA TRANSMITTED IN SI-DEP

The data is reported to all positive tests carried out (RT-PCR + TA), and not to the number of people tested or positive. In fact, the definition of persons for the calculation of the indicators retains only one test for a person in a given period, whereas the latter may have been tested several times (antigen test, followed by a PCR, for example). This methodology could result in not counting a test that provides information on the presence of a mutation, and therefore underestimating their representation. All of the positive tests in the SI-DEP database are the subject of a search for information on one or more mutations, with the application of a cleaning procedure concerning strict duplicates, based on a corresponding key:

au pseudonyme de la personne (code anonymat individuel basé sur les traits identifiants de la personne) à la date et l’heure du prélèvement au type d’analyse DATA AVAILABLE

The data is available at department, region and France level.

Available variables:

nb_pos: Number of positive tests nb_crib: Number of tests screened tx_crib: Rate of tests screened nb_A0: Number of positive tests for which the search for mutation A is negative nb_A1: Number of positive tests for which the search for mutation A is positive tx_A1: Proportion presence of mutation A nb_C0: Number of positive tests for which the search for mutation C is negative nb_C1: Number of positive tests for which the search for mutation C is positive tx_C1: Proportion of presence of mutation C nb_D0: Number of positive tests for which the 'one of the following mutations: DEL69/70, K417N, S371L-S373P or Q493R is absent nb_D1: Number of positive tests for which one of the following mutations: DEL69/70, K417N, S371L-S373P or Q493R is present tx_D1:Proportion of tests with the presence of one or more of the following mutations: DEL69/70, K417N, S371L-S373P or Q493R nb_A0C0: Number of tests for which mutations A and C are absent nb_A01C01: Number of tests for which mutations A and C are searched for and interpretable tx_A0C0: Proportion of tests with absence of the two mutations A and C

The complete methodological note is available.