France adopts 'more precise' strategy to track Covid-19 mutations

·2-min read

French health authorities have tweaked their procedures for tracking the progression of coronavirus variants in a "more precise" and "more reactive" way.

"Today there is an increasing variety of variants, which means that looking specifically for one, two or three variants no longer meets the need for surveillance of the 'SARS-CoV-2' variants problem," explained in a press conference Sibylle Bernard-Stoecklin, from the Infectious Diseases Directorate at Santé publique France.

From this week, health authorities will stop publishing information on the distribution of "variants" and instead switch to "mutations" (the process by which the coronavirus strain changes to take on new variants) in order to track worrying variants more precisely.

All positive test will continue to be screened, to detect "variants of concern" of the coronavirus. But new screening kits will focus on tracking specific mutations found in a significant number of variants.

Since the end of May, laboratories have started to equip themselves with the new kits, which will become the only ones authorised from mid-June.

Three mutations of interest

This method was introduced in January to identify the emergence of the Alpha variant, first identified in the UK in December 2020, and now the majority of positive cases in France.

Three mutations have been retained: E484K, E484Q and L452R. Present in particular in the Beta variant, (first identified in South Africa) and the Gamma variant (Brazil), before the arrival of the Delta variant (sub-lineage from India).

They are considered "of interest" because they may be able to evade immune response or present higher transmissibility or severity of infection.

The list is limited to three because "the more mutations you add to a screening kit, the more sensitivity decreases", Bernard-Stoecklin said.

Since the end of May, laboratories have started to equip themselves with the new screening kits, which will become the only ones authorised from mid-June.

Limitations

While this strategy allows results to be obtained faster than sequencing, which consists of analysing the entire RNA (ribonucleic acid) of the virus, it has many limitations.

Firstly, the French analysis laboratories are equipped with different kits, which do not all detect the same mutations.

Secondly, a positive result means that there is a "suspicion" of the presence of a worrying variant, but this can only be confirmed by sequencing.

Finally, as the same mutation may be present in several variants, the same screening result could be attributed to different variants depending on the laboratory.

For example, the variant responsible for a cluster in Bordeaux at the end of May (similar to the Alpha variant but with several additional mutations), could be wrongly classified as a Beta or Gamma variant – or as an undetermined variant or as no variant at all.

In recent weeks, Santé publique France had warned that the percentages of distribution of the different variants of concern were "to be interpreted with caution".

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