Scientists at the Reykyavik lab are working on sequencing SARS-CoV-2.

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AFP

  • Concern is mounting in France over the spread of the English variant, which would make the coronavirus more contagious.

  • The sequencing of the SARS-CoV-2 virus, from PCR tests, makes it possible to detect the presence of possible variants.

  • But in France, very little sequencing.

    So this is a new challenge if we do not want to be overtaken by the epidemic once again, like our British neighbors.

This Wednesday morning, Jean-François Delfraissy was not there by four ways at the microphone of France Info: "I am very concerned about the English variant", assumes the boss of the Scientific Council.

Which gave an opinion Tuesday evening before possible announcements Thursday.

But to know if France is experiencing an “invasion” of this new variant - called for convenience “English”, but whose official name is actually Voc 202012/01 -, it would still be necessary to have the means to track it.

"The objective is to identify this variant to delay its dissemination as much as possible," explained Bruno Coignard, director of infectious diseases at Public Health France (SPF) last Friday.

I mean delay, not prevent.

"

How is the sequencing going?

First problem: France has a certain delay in sequencing.

To know if the English variant diffuses and where, it is necessary to sequence the positive PCR test samples.

And we are very far from the British and Danes, European champions in this area.

“The British sequenced 10% of their population infected with Covid-19, the Danes 5%, and us less than 1%,” regrets Gilles Pialoux, head of the infectious diseases department at Tenon hospital in Paris.

Who specifies that “a sequencing takes three days.

"We have room for progress," recognizes Daniel Lévy-Bruhl, epidemiologist at Public Health France.

Second challenge: to perform sequencing, you need a sample with a high viral load.

For some, it is not enough.

In addition, “sometimes, the samples are no longer available, underlines Bruno Coignard.

Laboratories typically store swabs for seven days.

But they are limited by their storage capacity, so the swabs are destroyed.

We have adopted guidelines to prioritize the RT PCR swabs from positive patients.

"

It will simply be impossible to sequence all the samples.

To get an idea, the United Kingdom manages to do 10,000 a week.

And there were nearly 100,000 positive tests in France between December 28 and January 3.

“We are in the process of identifying the people to be sequenced,” explains Bruno Coignard.

Guidelines for identifying suspected cases, including a history of travel within the past 14 days, were issued to all laboratories.

But this criterion of provenance will become less relevant.

The person affected by the English variant and tested in Bagneux had indeed no link with the Overseas Channel.

How to improve this monitoring?

However, France seems to be stepping up the pace.

Massive screening operations, for example in Roubaix, target this English variant.

Last week, the laboratories of the National Reference Center in Lyon could perform 400 sequences per week.

They made 100,000 in a few days.

"There are 46 hospital laboratories with sequencing capacity currently mobilized", insists Bruno Coignard.

"In our hospital group, the virology laboratory is sequencing the tests for December and January", adds Gilles Pialoux.

On the other hand, positive point, certain PCR tests, with a particular reagent (Thermo Fisher), make it possible to have a suspicion of the presence of this variant, and therefore to make a first selection.

"We should above all do genomic epidemiology: confront the analysis of the genome [sequencing] and epidemiological data", continues Gilles Pialoux.

Objective well understood by our health authorities, since a flash study was conducted last week, led by Bruno Lina at the CNR in Lyon.

Jean-François Delfraissy said on Wednesday on France Info that she revealed that out of 100,000 PCR tests scrutinized, 1% revealed the presence of this English variant.

And that it is present throughout the country.

But given the speed of propagation of the variant, this photograph is already obsolete.

Santé Publique France ensures that this flash survey will be repeated at regular intervals to monitor this development.

A centralized organization across the Channel

“Some labs are in the process of equipping themselves with platforms capable of sequencing 200 genomes per week,” continues Gilles Pialoux.

But to accelerate this hunt, we need resources and national governance.

Indeed, if we look again at our British neighbors, there is a centralized organization of the sequencing.

They have set up a consortium making it possible to bring together all the data reported by the laboratories of the country, to analyze them and to disseminate them in real time internationally.

At the end of December, on the international Gisead platform (initially developed for influenza, but used today for SARS-CoV-2) on the 322,000 genomes published, 146,000 came from Great Britain and 2,900 from France.

This fundraising effort seems necessary for today, but also for tomorrow.

Because the coronavirus will not stop mutating.

We already have three cases of the South African variant, which is also worrying health authorities.

And Jean-François Delfraissy warned this Wednesday that other strains have appeared, especially in Switzerland.

"It will be necessary to be able to detect the next variants that would raise questions", warns Bruno Coignard.

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