visualize how Omicron and its sublines have supplanted other variants

The original SARS-CoV-2 virus, at the origin of the Covid-19 pandemic at the start of 2020, has long since disappeared in France, giving way to several successive variants, until the highly contagious Omicron , becomes mainstream at the end of December 2021. With its various sub-variants, it has largely contributed to three waves of infections.

The appearance of this variant, which has many mutations compared to the historical strain of the virus, was not a surprise: the detection by British laboratories of the Alpha variant at the end of 2020, the scientific community knows that SARS-CoV- 2 can mutate.

Strong progression of the BA.5 sub-lineage

It is possible to observe the circulation of a variant on French territory thanks to sequencing: carried out using RT-PCR samples from Covid-19 patients, this molecular biology technique makes it possible to read the complete genome of SARS-CoV -2 and to detect new mutations. The data can then be shared on the international Gisaid database (for global initiative on sharing avian influenza data“global initiative on sharing data relating to avian influenza”) or in the European surveillance system TESSy of the European Center for Disease Prevention and Control (ECDC).

The evolution of the estimated share for each variant remains subject to several biases (delay of publication, late development of sequencing and evolutions of the national strategy, etc.), but these data, updated each week, show the progression of the Omicron variant in metropolitan France. .

The evolution of variants in France

Proportion of samples sequenced and deposited in TESSy, by week and by variant classified as worrying. The graph below shows the number of sequences available. Data per week, ranging from that of to that of . The most recent weeks for which less than 200 sequences are available are not added to the graph.

Source: TESSy, data published by ECDC.

The views and opinions of the authors expressed herein do not necessarily state or reflect those of ECDC. The accuracy of the authors’ statistical analysis and the conclusions they report are not the responsibility of ECDC. ECDC is not responsible for any conclusions or opinions drawn from the data provided. ECDC is not responsible for the accuracy of the data and for data management, data merging and data compilation after data provision. ECDC will not be held liable for any misuse or misuse of the data.

The table below lists the characteristics of the main variants, according to the WHO classification, which baptizes each of them with a letter of the Greek alphabet, a denomination considered less “stigmatising” than their geographical origin. Most “worrying” (or VoC for variant of concern) are listed for their transmissibility, their virulence or even the lower efficacy of vaccines against them. There can be added variants to follow (VoI, for variant of interest). Sometimes the WHO downgrades certain variants when their circulation decreases.

To see the detail, click onselect a line.

Concerning variants including those that no longer circulate

Variations to follow

Likely to be more transmissible or more severe. Are at the origin of a “significant community transmission or several foci of Covid-19, in several countries”.

The screening technique, complementary to sequencing, makes it possible to directly monitor mutations and their evolution among infections, instead of reading the entire virus genome. This method does not make it possible to identify the variants, but has the advantage of being able to be used on a larger scale. At the beginning of August 2022, around a quarter of the positive tests for SARS-CoV-2 benefit from screening each week, according to data from SI-Dep, a file which lists PCR and antigen tests.

The latest results show the progression of the L452R (or L452Q) mutation. Previously, this mutation was mainly carried by Delta, and was used to identify it. It allows to follow the evolution of certain sub-variants of Omicron which circulate, like BA.4, BA.5 or BA.2.12.1.

The most watched mutations in France

Proportion of screened positive tests carrying the E484K, E484Q, L452R or L452Q mutations, and a combination of Omicron-specific mutations “among the screened tests where the mutation is sought and interpretable”. Rolling seven-day data from May 31, 2021 to . From the end of December 2021, this visualization uses data corresponding to the new screening doctrine (.PDF).

This article is a republication of a first version, published in September 2021, and updated regularly since.

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