They entered, despite us, into our daily lives.
Six months after the appearance of the first variant of SARS-CoV-2, easily qualified as “British” since it arrived from across the Channel and now called “Alpha” by the World Health Organization (WHO ), several dozen others have appeared.
All of them do not of course present the same level of risk: five are classified as “of concern”, five “to be monitored”, and nine others are “under investigation”.
Read also Covid-19: why the number of variants identified in the world is likely to multiply
We speak of a “variant” when SARS-CoV-2, whose genetic makeup consists of a long RNA sequence of 30,000 nucleotides, displays “mutations”.
These can appear when there are "errors" at the time of replication, which is expected.
The spread of each of them must be monitored as effectively as possible, in order to be able to react locally by intensifying screening, vaccination, or by imposing certain measures.
Two methods, qualified as “complementary”, are used: screening and sequencing.
But they do not work the same and do not achieve the same results.
Here's how to navigate it.
Screening: fast but not very precise
What's the point ?
To know if a positive test sample contains one or more mutations associated with a particular variant.
How it works ?
The laboratories use different screening “kits”, which make it possible to target a particular mutation in a very specific area of the virus genome.
The idea is to find out whether the mutation is present, via a “polymerase chain reaction” technique, known as PCR.
This is already used during a "classic" test, to find out if a sample is simply positive for SARS-CoV-2.
VIDEO.
How this laboratory manages to detect the English variant of Covid-19
We get “suspicions” of variants in a few hours, but this does not guarantee that it is a particular virus.
"Screening looks for mutations without being able to formally identify variants, but it can be done very quickly", summarizes Florence Debarre, CNRS researcher in evolutionary biology.
Where is France at?
Part of the positive samples, from 40 to 60% nationally for several weeks, is screened.
Only suspicions of Alpha, Beta (“South African”) and Gamma (“Brazilian”) variants appear for the moment in the data, and the other strains are grouped into two categories: “no variant” and “undetermined variant”. .
Read alsoCovid-19: E484K, the other variant mutation that worries
Until then, several mutations, including N501Y, were targeted and led to these “suspected variants”.
But they "no longer allowed precise monitoring of the evolution of variants of interest in France", indicates Public Health France.
Things are about to change, with new screening kits.
Deployed since May 30 and generalized from June 14, they allow the targeting of three particularly worrying new mutations: E484K, E484Q, and L452R.
This will “allow more reactive monitoring of the dissemination of variants carrying these mutations of interest at the national level and in the most affected territories”.
Sequencing: ideal, but France is lagging behind
What's the point ?
Sequencing
"
enables precise mapping of variants in France, ”replies Sybille Bernard-Stoecklin, from the Infectious Diseases Department of Public Health France. "Knowing whether a person has been infected with such or such a variant has no impact on their treatment, but sequencing allows them to be classified precisely", adds Jean-Michel Pawlotsky, head of the bacteriology and virology department. of the Henri-Mondor hospital.
How it works ?
The principle is simple on paper: "read" the entire genome of a virus, that is to say analyze its identity card. No possible mutation can escape. Concretely, the RNA of the virus is extracted from the sample then it is passed through a device called a sequencer. "It's like a big camera that will be able to read the genetic sequence and then transcribe all of this into data", describes Jean-Michel Pawlotsky. Analysis of the results makes it possible to establish which variant the genetic sequence corresponds to. In total, "between receipt of the sample and identification of the variant, it takes six days," says the doctor.
Where is France at?
In addition to Henri-Mondor, three sequencing platforms are operational (the national reference center for viruses at the Institut Pasteur, the Hospices Civils de Lyon and the IHU Marseille), as well as hospital virology laboratories. About 3,500 samples (on average) have been sequenced every week since the beginning of the year as part of genomic surveillance, indicates Public Health France. This is slightly less than the 5% sequenced positive tests recommended by the WHO.
Some of the sequences are deposited on the international GISAID platform. Too few, believe several researchers. “A few weeks ago, a new variant of interest (AV.1) had been identified in the United Kingdom and we were contacted by British colleagues who asked us if we had already seen this sequence apart from what is already shared on the international public platforms to which they have access. We were unable to answer them, ”remembers Florence Debarre. In a recent opinion, the Scientific Council considered that "the deposits on GISAID of sequences produced in France [still remained] to be encouraged".