Covid-19 : visualisez comment Omicron et ses sous-lignages ont supplanté les autres variants

Covid-19 : visualisez comment Omicron et ses sous-lignages ont supplanté les autres variants

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

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

Strong BA.5 sublineage progression

It is possible to observe the circulation of a variant in French territory thanks to sequencing: carried out from RT-PCR samples from patients with Covid-19, this molecular biology technique makes it possible to read the complete genome of SARS-CoV-2 and detect new mutations. The data can then be shared in the international Gisaid database (for global initiative to share data on avian influenza“global initiative to share data related 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 is still subject to several biases (delay in publication, late development of sequencing and evolution of the national strategy, etc.), but these data, updated every week, show the progression of the variant Omicron in metropolitan France. .

The evolution of variants in France

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

Source: TESSy, data published by ECDC.

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

The following table 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 “stigmatize” than its geographical origin. The best “worrying” (or VoC for concern variant) are listed for their transmissibility, their virulence, or even the lower efficacy of vaccines against them. Variants can be added to follow (VoI, for interest variant). Sometimes the OMS degrades certain variants when their circulation decreases.

To see the detail, click onSelect A line.

As for the variants including those that no longer circulate

variations to follow

It is likely to be more communicable or more serious. They 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 between infections, instead of reading the entire genome of the virus. This method does not allow variants to be identified, but has the advantage of being able to be used on a larger scale. As of early August 2022, around a quarter of positive tests for SARS-CoV-2 benefit from screening each week, according to data from SI-Dep, an archive that lists antigen and PCR tests.

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

The most seen mutations in France

Proportion of screened positives carrying the E484K, E484Q, L452R, or L452Q mutations, and a combination of Omicron-specific mutations “among the screening tests in which the mutation is sought and is interpretable”. Seven days mobile data from May 31, 2021 to . As of the end of December 2021, this visualization uses data corresponding to the new detection doctrine (.PDF).

This article is a republished version of an earlier version, published in September 2021 and regularly updated since then.

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