How to better track the Delta variant? The question arises today in France, while the United Kingdom is delaying its deconfinement protocol by one month, because of the spread of this so-called “Indian” variant.

And to respond, Public Health France has implemented a new variant surveillance strategy. The objective: to track in a “more precise” and “more reactive” way the progression of worrying forms of the coronavirus on the territory.

Three targeted mutations

Since June 14, there is no longer any question of an “English”, “South African” or “Indian” variant, but of three mutations of interest, present in several variants: E484K, E484Q and L452R. These mutations will be identified using a screening test.

What is it about ? Screening is a technique known as “acrobatic PCR” which consists in roughly recognizing one strain of virus in relation to another. Concretely, it indicates whether or not one of the three mutations sought is present in the sample analyzed. The screening test will therefore be positive or negative for a given mutation.

Read also: Covid: which screening tests to use against variants?

Detect the Indian variant

This is not new: since the arrival of the Alpha variant (British) last January on French territory, any positive PCR test gives rise to a second screening PCR test. But so far, the screening method used was far from precise and struggled to distinguish the new variants.

Worse, she could not detect the Delta variant yet at the center of current concerns. This will now be possible because one of the mutations targeted by the new screening, the L452R mutation, is carried by this variant.

“Suspicion” of presence

An improvement, therefore, but the method is still far from perfect. First, because a positive screening test is not synonymous with variant detection. It only indicates that there is “suspicion” of the presence of a variant of concern.

Then, the same mutation can be present on several variants. This is the case with the E484K mutation present in both the Beta (Brazilian) and Gamma (South African) variants. With a simple screening, it is always impossible to differentiate them and therefore to follow their evolution in an individualized way.

Sequencing versus screening

The best technique for spotting a variant remains sequencing, which involves analyzing all of the virus’s RNA. But this technology is more expensive, and much longer than screening. And in France, sequencing is rare and “lacking national coordination“, confided to Allodocteurs Professor Philippe Froguel, geneticist at Lille University Hospital.

The only count made is that of Inserm flash surveys, “performed every two or three weeks and which require three weeks to publish results“, observed the scientist.

Stop chasing variants

A race after variants, which he believes creates a risk of loss of control. This is for example what happened in Dax, “where the Indian variant was identified one month after the patient’s diagnosis“reminded Professor Froguel again.

Screening, which takes less than a day when sequencing requires a week, could be a stopgap to make up for this type of delay and activate in time a suitable strategy to break the chains of contamination of the variants of concern.