• Worried about the new Omicron variant, France is seeking to identify new cases positive for this mutation of the coronavirus as quickly as possible.

  • For this, the country uses sequencing, which allows to know which strain of the virus has infected the patient.

  • France suffers from a reputation for being slow in sequencing cases compared to other nations.

Nine positive cases for the Omicron variant have been detected in France so far. Potentially even more contagious than Delta, perhaps more resistant to the vaccine, this variant made public last week greatly worries the French authorities. Faced with the risk of seeing it sweep over the country, as Alpha and Delta had done before it, France - after having temporarily closed the borders with southern Africa - is determined to detect cases of this variant as soon as possible. in order to limit its spread. But in fact, how is a variant detected?

A PCR or antigen test provides information on being positive - or not - for the coronavirus, but it does not indicate which strain of Covid-19 has infected us: Delta variant, Omicron, Alpha, original strain?

It is this imprecision that makes it difficult to measure new variants in France.

To know the precise strain, it is therefore necessary to go to the further step, sequencing.

This is possible on any good quality PCR test having collected enough material, "which is the case in the majority of tests", notes the virologist Yannick Simonin of the University of Montpellier.

On the other hand, this is impossible with an antigen test.

Sequencing or screening?

That is the question

Sequencing is used to completely decipher the genome of an organism. "It thus makes it possible to determine the exact sequence - represented by a series of letters - composing the virus. This technique has the advantage of making it possible to identify the appearance of possible mutations compared to the original strain, ”says the virologist. Even if the genome of the viruses is not very long, the technique takes several days to give its verdict, which makes its deployment slower. This is why it takes several days each time to determine whether or not such a suspected case is indeed contaminated by Omicron. Not to mention a significant material cost when you want to identify a lot of cases, as currently.

In order to go faster, there is another technique once a variant is properly identified: screening. Unlike sequencing which reads the entire virus genome, the screening only focuses on defined mutations: either they are there, and the screening is positive, or they are not, and the screening is negative. It is therefore sufficient to identify the characteristic mutations of a variant, to note them in the screening to make it possible to detect this variant without having to go through sequencing, which is more tedious. The advantage of screening is that it is much faster. "We have the results in less than 24 hours," explains Sébastien Hantz, professor of virology at the University of Limoges. Very quickly, four characteristic mutations were, for example, identified in Delta,which made it possible to screen this variant and therefore to identify it more easily in positive cases.

France in search of lost time

However, the screening only works on a specific variant, and no longer reads the virus genome. It cannot therefore spot other variants, much less detect new ones. "These two tools are therefore complementary to assess the different versions of the virus circulating in France and study their evolution in terms of the proportion of positive samples", supports Yannick Simonin. The interest of sequencing varies over time. “For months, 100% of coronavirus sequencing in France indicated the Delta variant, recalls Sébastien Hantz. We can therefore wonder if it was really useful to sequence a lot. On the contrary, now that a new variant appears, sequencing is quite conducive to seeing its evolution, its dynamics, or even trying to slow it down by isolating people as quickly as possible.

France has a serious reputation for lagging behind on the issue of sequencing compared to other European countries. The country has nevertheless made efforts to adjust the target a little. “The EMERGEN program brings together eight laboratories - half belonging to the private sector. In particular, it sets up weekly "flash" surveys by regularly randomly sequencing samples of positive patients, "notes Yannick Simonin.

In the first week of November, just over 6,000 sequences were determined, representing approximately 10% of the cases identified.

"This remains insufficient for some specialists, especially when there is a sharp increase in the number of samples to be analyzed - as is currently the case - and de facto the percentage of samples sequenced is less important", supports the virologist.

Sequence a lot, but without a miracle

In comparison, Iceland sequences almost all of the positive samples by PCR, even if the performance should be put into perspective due to its small population.

On the continent and with larger populations, Denmark and the United Kingdom are leaders, far ahead of the average for European countries.

The United Kingdom currently covers around 20% of its positive cases, informs Yannick Simonin.

Our dossier on the Omicron variant

Really useful performance?

Sébastien Hantz recalls that the United Kingdom does not have better results on the epidemic front than France, despite its greater sequencing - 179.3 deaths per 100,000 inhabitants for France against 225 among the British -, and it is the case of most of the countries which sequence more than France.

If sequencing can therefore prove to be of great use, it is by no means a miracle recipe.


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  • Covid 19

  • epidemic

  • Research

  • Omicron variant

  • Delta variant

  • Coronavirus

  • Health

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