How are infections with the omicron variant recorded in France?

Question asked by Robert, on December 12, 2021.


Gabriel Attal was questioned Tuesday morning on the progression of the omicron variant in France. “We are at just over 130 cases, I believe, 133 cases that have been detected. We sequence a lot, we screen most of the positive cases that are detected in France. We do more than 10,000 sequencings per week, which allows us to identify fairly widely the cases on our soil, ”detailed the government spokesperson.

This figure, which comes from Public Health France (SPF), has since evolved. As of December 13, the number of omicron cases has risen to 170. While the United Kingdom recorded its first death due to omicron on Monday, SPF explains that it does not have further information on the status and state of health of the patients. infected with this variant.

"A little time"

In order to monitor the circulation of variants in France, additional screening tests are carried out on some of the samples positive for Sars-Cov-2. Until May, these tests aimed to identify suspicions of already known variants. "This screening strategy targeting VOCs [variants of concern, "variants worrying", editor's note] alpha, beta and gamma is no longer suited to the growing diversity of emerging variants of Sars-Cov-2", explains Public Health France in a methodological note. Since June, the strategy has evolved and the screening PCRs now target certain mutations of the virus (L452R, E484K and E484Q) selected because “they are potentially linked to immune escape and/or an increase in transmissibility and are found in the majority of VOCs to date,” comments SPF. About 27% of the positive results were thus analyzed by December 10.

Problem: the omicron variant does not carry the mutations currently targeted by the screen (even if it presents many others). “Today, there is no specific solution to characterize the presence of the omicron variant by RT-PCR. The health authorities are currently studying a screening scheme which would make it possible, from a combination of three mutations, to filter out suspected cases of omicron among the positive samples", explains the Eurofins Biomnis laboratory group, one of the main players of the sector, to CheckNews. “We have to be able to have a screening and that takes a bit of time. At the same time we always have delta, so we will have to choose the right mutations”, observes Lionel Barrand, president of the Syndicate of medical biologists for whom this technique is “the best way to quickly detect the omicron variant”.

Water drop

Comment sont recensées les infections au variant omicron en France ?

In the meantime, "as this variant does not possess any mutations of interest currently screened for (L452R, E484K /Q), a negative screening result for these three sought mutations may suggest its presence but is not specific", explains the band. To adapt the screening strategy to the arrival of omicron, in France, the General Directorate of Health gave new instructions in this direction, on December 2, in an urgent note intended for health professionals. Thus, a negative screening PCR result for the three mutations currently being sought is considered a "possible case" of an omicron variant and must therefore "be subject without delay to interventional sequencing, the only way to provide diagnostic confirmation. “, can we read.

The analysis of the virus genome – sequencing – is indeed the only technique to officially identify a variant. France, long behind on the subject, created in January the Emergen consortium, coordinated by Public Health France and the National Agency for Research on AIDS and Viral Hepatitis (ANRS), “to strengthen French capacities for genomic surveillance and research on Sars-Cov-2 variants”.

According to the latest figures available, covering the week of November 29 to December 5, 9,490 sequences were produced. Note that there is a delay of several days between the time of the PCR test, the sequencing and the results. A drop of water compared to the number of cases identified during this period. The number of 170 positive cases identified by sequencing on December 13 “is piecemeal and biased information”, believes Lionel Barrand, even if it makes it possible to “follow the dynamics” (with some precautions). According to the Eurofins Biomnis group, which sequences some of the positive samples, the analysis capacities will increase “very quickly”.