New mutations screened to better identify Omicron

Since December 20, 2021, screening has been based on a strategy targeting a combination of mutations that allow for more precise identification of the Omicron variant (such as the 69/70 deletion and the K417N, S371L-S373P, and Q493R substitutions). Screening results are entered into the SI-DEP information system. This system has been adapted to add a new code (D) to the three existing ones, which represent the mutations present in the three previously targeted variants of interest (A, B, and C, for the Alpha, Beta, and Delta variants). This new nomenclature allows clinical laboratories to enter the results of additional screening tests targeting mutations carried by Omicron.

Correspondence Table

How should these results be interpreted?

An "A0C0" result means that the E484K and L452R mutations are not present, suggesting the Omicron variant.
A "D1" result means that at least one of the mutations associated with this code is present, thereby confirming the finding.

These results are then confirmed by whole-genome sequencing of the virus, the gold standard for variant identification.

Five new indicators available as open data

After ensuring that the new screening strategy has been adopted by the largest number of laboratories and verifying the quality, reliability, and completeness of the reported data, Santé publique France is making the following new indicators available:

• Number of screening PCR tests and percentage of screened tests relative to all positive tests performed (RT-PCR + TA)

• Proportion of tests with the presence of E484K among screened tests where the mutation is sought and interpretable

• Proportion of tests with the presence of L452R among screened tests where the mutation is sought and interpretable

• Proportion of tests without the E484K and L452R mutations among screened tests where both mutations are tested for and interpretable

• Proportion of tests showing one or more of the following mutations: DEL69/70, K417N, S371L-S373P, or Q493R among screened tests where one of the mutations is tested for and interpretable

These 7-day rolling indicators are available daily on the Géodes platform and the data.gouv.fr website starting January 6, 2022, with historical data reconstructed back to November 1, 2021. They are broken down at the national and regional levels and will soon be available at the departmental level.

The InfoCovidFrance dashboard is also evolving. The graph for “Screening for Variants of Interest” now displays the Omicron monitoring indicators.

The following indicators will be presented:

• “Omicron Suspicion – Absence Rate of E484K and L452R Mutations”

• “Strong suspicion of Omicron – Rate of presence of one of the mutations K417N or del69/70 or S371L-S373P or Q493R”

• “Beta/Gamma Suspected – Rate of Presence of the E484K Mutation”

• “Strong suspicion of Delta – Prevalence of the L452R mutation”

• “Screening test rate”