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Covid-19: how the new French variant screening strategy works

This is an old strategy for screening positive tests. She gave “suspicions” of variant. It was abandoned in favor of a new method of targeting three specific mutations. On Tuesday, this new technique made it possible to have more precise information on the circulation of the Delta variant, originally identified in India. This variant currently represents “between 2 and 4% of positive cases” of Covid-19 detected in France, said the Minister of Health, Olivier Véran, during a trip to a vaccination center in Paris.

“Currently in France, 2 to 4% of the positive tests that we screen correspond to the Indian variant, which nevertheless represents a fairly wide range, of the order of 50 to 150 new diagnoses of the Delta variant in our country. “, declared Olivier Véran. As recalled The Parisian, 2 to 4%, is much more than what was estimated via the Flash sequencing surveys, 0.5% in that of May 25th.

“It may still be little, but it was the English situation a few weeks ago,” said Olivier Véran, recalling that the Delta variant “represents more than 90% of cases in circulation” across the Channel. Faced with the increase in the number of cases in the United Kingdom, British Prime Minister Boris Johnson announced on Monday evening the postponement of the lifting of the last restrictions in England.

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The new French strategy for systematic screening by RT-PCR of positive tests for SARS-CoV-2 was put in place from May 31, specifies Public Health France. It replaced a strategy which “no longer allowed precise monitoring of the evolution of the variants of interest”, indicates Public Health France. In other words, 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.

“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 ‘SARS-CoV-2 variants'”, explained last Thursday an official of Public Health France, during an online press point. “Any positive test must always give rise to a screening”, but the idea now is “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.

The three mutations retained, called “of interest”, are E484K, E484Q and L452R. Present in particular on the variants “Beta” (spotted for the first time in South Africa), “Gamma” (which emerged in Brazil) and “Delta” (the subline coming from India), they are considered “d “interest” because they can have an impact on immune escape, transmissibility or 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. The new screening strategy by looking for mutations of interest “allows more reactive monitoring of the dissemination of variants carrying these mutations of interest at the national level and in the most affected territories”, notes Public Health France.

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” and “Gamma” variants of concern, before the arrival of the “Delta” variant.

The many limitations of the new strategy

This strategy makes it possible to obtain results more quickly than by sequencing, which consists in analyzing all of the virus’s RNA: if the old method could take a week, only a few hours are now necessary, recalls RFI. But the new method has many limitations. First, French analysis laboratories are equipped with different kits, which do not all detect the same mutations. Then, a positive result signifies the “suspicion” of the presence of a variant of concern, but only sequencing makes it possible to 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. For example, the variant responsible for a cluster in Bordeaux at the end of May, similar to the “Alpha” variant but having acquired several additional mutations, including E484Q, could be wrongly listed as a “Beta” or “Gamma” variant, or in “undetermined variant” or in the “absence of a variant”. In recent weeks, Public Health France had warned that the distribution percentages of the various worrying variants were “to be interpreted with caution”.

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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 has stopped since last Thursday to publish the distribution of variants on the territory according to the old method, to switch to the new nomenclature.


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