Sequencing of the virus: a French delay

The genomic sequencing platform at the Henri-Mondor hospital in Créteil will spin its machines to analyze hundreds of samples from Covid-19 patients to find out if the famous variant of Sars-CoV-2, responsible for the outbreak of cases in the south-east of England, has already arrived in France .

A welcome reaction, but late. Indeed, sequencing and sharing the genome of as many viruses as possible makes it possible to follow the epidemic and trace the path of certain strains.

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Unfortunately, France is not playing the game. Researchers around the world publish the sequences they find on an open access platform called Gisaid. At the time of writing, France points to 51e place in number of sequences published in relation to the number of cases in the country. It publishes less than one sequence per 1,000 declared cases of Covid-19 against 469 for Australia, 55 for the United Kingdom or 5.6 for Senegal.

These sequences must be filed with some information on the age of the patient, his location and the date of the sample. We quickly understand that the faster a sequence is filed, the more scientists can have access to real-time data and react, if, as is the case in the United Kingdom, a disturbing variant emerges. Here again, France is zero. When an average of 26 days pass between the collection of the sample and the publication of the genome across the Channel, 128 days pass in France …

Infographic: average time between sequencing and publication

From this observation, a question arises. Does France have little sequencing, or are national scientists playing the game of transparency and international aid? “It’s a bit of both”, plague the geneticist Philippe Froguel.

“Discredit”

Asked about the possibility that the English variant is present in the territory, Olivier Véran, Minister of Health, answered : “We will find out, we are launching genotypic studies. Over the past few days, 500 viral strains have been analyzed for genetics and this variant has not been found, which does not mean that it is not circulating. ” Sequences that cannot be found on Gisaid.

However, the alert on the subject was launched on November 3. A joint press release from the Académie des sciences and that of medicine explained that “Sequence data from a virus that has killed more than a million people can go a long way in saving lives. Not making them accessible as quickly as possible on INSDC or Gisaid has serious consequences. We appeal to the responsibility of researchers and to the vigilance of their scientific supervisors to put an end to this withholding of information which discredits our entire national scientific and medical community ”.

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The academicians had been received by the Ministry of Research. But if Minister Frédérique Vidal took any action after this alert, it did not materialize in an increase in sequence publications in Gisaid. Pity.

Massive sequencing campaign

To remedy the problem, we must therefore rely on individual initiatives. Philippe Froguel appealed to the President of the Republic to set up a consortium for sequencing the Sars-CoV-2 virus at the national level called Senticov. This initiative is supported by the CEA’s National Human Genomics Research Center in Evry, in collaboration with the Integrative Biology and Molecular Genetics Department.

Their goal is to start by relying on a massive sequencing campaign organized on January 11 in Roubaix. “The objective is to test at least 30% of the population, or 30,000 people and to sequence the positive cases”, explains Philippe Froguel.

He explains that he prefers to leave hospitals for two reasons. “If you only test hospitalized people, you can’t see a new strain emerging in the population. Moreover, the hospital only gives access to severe cases, so it is impossible to make a correlation between the clinical state and the emergence of a variant. ”


Olivier Monod

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