July 31, 2021

to better track variants, France is modifying its surveillance strategy

If the news is good on the front of the Covid-19 epidemic, still in decline, and on that of vaccination, with the threshold of 30 million first injections crossed this weekend in France, the new variant B.1.617.2, baptized Delta by the World Health Organization (WHO), disturbs the way out of the crisis. “We are not saved, the risk is still there”, said Daniel Lévy-Bruhl, head of the respiratory infections unit of the health security agency Public Health France (SpF), Friday June 11, describing a “Unstable situation” in France.

The Delta variant is more contagious than its predecessor – the Alpha variant -, by around 60%, according to the British, but mainly responsible for a rise in infections in the United Kingdom, which have tripled in three weeks, reaching almost 8 000 cases Friday June 11. It is also already present in France and among our border neighbors, Spain, Germany, Belgium… And it is undoubtedly responsible for a slight increase in cases in Portugal.

Read also Covid-19 around the world: the Delta variant is 60% more contagious than its predecessor, according to British health authorities

To better cope with this, SpF has decided to speed up the implementation of a new variant surveillance strategy, one of the weak points of the French system.

From Monday June 14, exit, in the test results, the reference to the “English”, “South African” variants, or, respectively, B.1.1.7, B.1.351, or even Alpha, Beta. Make way for the three mutations, E484K, E484Q, L452R. These “registrations” correspond to the position of amino acids, the molecules that make up proteins, within the portal of entry of the virus into the host, the spicule. The letters refer to the name of the modified amino acid. From now on, we will know if a virus carries one of its three mutations, by a so-called screening test, which is a second PCR test, carried out if the first is positive. This screening already existed, but the chemical reagents on which it was based, called kits, were used to spot a variant rather than a mutation.

Speed ​​up genomic surveillance of the epidemic

This modification brings several advantages. First, it corrects one of the shortcomings of the previous screening, which could not cope with the influx of variants, too numerous to be able to be grasped, with five “worrying” variants, and ten “to follow” or in evaluation course. Moreover, the method practiced until then did not differentiate a Beta from a Gamma (called “Brazilian”). Worse, in the current context of the emergence of the Delta variant, the technique classified it as “variant absence”, as if it were the original Chinese strain of Covid-19. At the last SpF score, for the first week of June, 19% of positive cases were neither Alpha, Beta or Gamma.

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