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Covid-19: the new strategy to track down mutations – Coronavirus

No more “variants”, place for “mutations”: to track in a “more precise” and “more reactive” way the progression of worrying forms of the coronavirus on French territory, the strategy changes from this week.

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“Today we observe a growing variety of variants, which means that looking specifically for one, two or three variants no longer meets the need for monitoring the problematic “variants of Sars-CoV-2” “, explained Thursday an official of Public Health France, during a press point in line. “Any positive test must always give rise to a screening”, but the idea is now “to follow mutations of interest which are found in a large number of variants”, continued Sibylle Bernard-Stoecklin of the infectious diseases department. of the public agency.

Faster results

Screening involves the use of specific test kits, which “screen” positive PCR tests to see if the patient is a carrier of a form of concern of the Sars-CoV-2 virus. This method was implemented in January, to identify the emergence of the “Alpha” variant, identified for the first time in the United Kingdom in December 2020 and now in the majority in positive cases in France. The kits used were then adapted to detect the “Beta” (first spotted in South Africa) and “Gamma” (which emerged in Brazil) variants of concern, before the arrival of the “Delta” variant (subline from India).

If this strategy allows results to be obtained faster than by sequencing, which consists of analyzing the whole RNA of the virus, it has many limitations. First, French analysis laboratories are equipped with different kits, which do not all detect the same mutations. Then, a positive result means the “suspicion” of the presence of a variant of concern, but only sequencing can be sure. Finally, since the same mutation can be present on several variants, the same screening result could be attributed to different variants according to the laboratories.

New method launched this Thursday

For example, the variant responsible for a cluster in Bordeaux at the end of May, being related to the “Alpha” variant but having acquired several additional mutations, including E484Q, could be wrongly listed as “Beta” or “Gamma” variant, or as “undetermined variant” or in “absence of variant”. In recent weeks, Public Health France had warned that the distribution percentages of the various worrying variants were “to be interpreted with caution”.

Since the end of May, the laboratories have started to equip themselves with the new screening kits, which will become the only ones authorized from mid-June. And Public Health France stops this Thursday to publish the distribution of variants on the territory according to the old method, to switch to the new nomenclature.

Three mutations were selected, called E484K, E484Q and L452R. Present in particular on the “Beta”, “Gamma” and “Delta” variants, they are considered “of interest” because they can have an impact on immune escape, transmissibility or even the severity of the infection. The list is limited to three because “the more mutations are added in a screening kit, the more the sensitivity decreases”, underlined Sibylle Bernard-Stoecklin.

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