It was only a matter of time. Two days after the announcement of a positive case with the Omicron variant in Reunion, the number of cases of infections with the Omicron variant detected in mainland France now stands at eight, according to the latest report from Public Health France, Friday, December 3 .
The first, a man in his fifties residing in Seine-et-Marne, had tested positive on November 25 when he got out of the plane that brought him back from Nigeria. He was not vaccinated, unlike the second case, detected in the Haut-Rhin: a woman between 40 and 50 years old, returning from a trip to South Africa, where the Omicron variant appeared in mid-November.
“Without doubt the first of a long series”
Both had been placed in solitary confinement pending sequencing of their sample. The comparison with the genetic code of the virus published by the South African authorities as of November 25 finally confirmed their infection with this new variant. “These cases are undoubtedly the first of a long series”, anticipates Laurent Kbaier, spokesperson for Biogroup. In these laboratories, where 20 to 30% of PCR tests are carried out in France, several suspected cases have been identified in recent days. “What alerted us each time was the result of the screening. “
→ TO READ. Omicron: what we know about the new variant of Covid
This did not recognize any of the characteristic mutations of the Delta variant.. “Concretely, this means that the strains collected have nothing in common with Delta, which leaves two possibilities: either it is the starting strain, which is very unlikely because it is no longer circulating, or it is ‘acts of Omicron’, explains Laurent Kbaier. The samples were sent to Tours, to one of Biogroup’s five sequencing platforms.
Still so many tests
Since January, the group has been one of eight French laboratories participating in “flash surveys”, piloted by the National Reference Centers (CNR) in order to measure the circulation of the various variants at regular intervals. “On the other hand, as soon as we identify suspected cases, we have an obligation to request authorization to sequence from the regional health agencies. It’s a waste of time “, deplores Laurent Kbaier, who nevertheless specifies that these cases are very rare, ruling out the hypothesis of a low noise circulation of Omicron as was the case for Alpha, the English variant, “Already in the majority in France when it was discovered”.
→ TO ANALYSE. Omicron: a new anti-Covid vaccine could be put on the market in three months
Can we be so certain, at a time when it is said that the delisting of tests would have caused screening to fall? “With us, the expected drop did not take place, we continue to test massively”, underlines Laurent Kbaier. And the recovery is visible: in one week, the number of positive PCR testsdoubled from 8% to 16%. But the biologist reminds us: the most telling indicator remains hospital admissions.
A still abstract variant
Hospitals which, for the time being, fear above all that the 5e wave linked to the spread of the Delta variant does not yet saturate their services. After Mulhouse and Colmar, the Strasbourg University Hospital again launched the white plan on Thursday 2. “The only instruction from the authorities is to ‘think Omicron’ as soon as you have a patient returning from South Africa or an affected area, reportDoctor Serge Alfandari, infectious disease specialist at the Tourcoing hospital. But for the moment, this variant remains very abstract. Like everyone else, we wait. “
→ EXPLANATION.Omicron and vaccination: the questions raised by the new variant
Is this variant more contagious? More dangerous ? Less sensitive to the vaccine? So many unanswered questions. According to the European Center for Disease Prevention and Control, it is likely to become the majority “In the next few months”. But nothing certain at this stage. “Omicron was only identified a fortnight ago. Studies have barely started ”, underlines Yannick Simonin, virologist at the University of Montpellier.
Responsiveness and prudence
The genome communicated by South Africa makes it possible to compare it with previous variants, but not to assess its dangerousness. To find out more, the Institut Pasteur urgently launched the synthesis of pseudo-viruses. “We can use it to study the attachment mechanisms of the variant to human cells”, explains Olivier Schwartz, head of the “virus and immunity” unit.
“The tools developed since the start of the pandemic allow us to respond much faster to questions about variants, argues Vincent Maréchal, professor of virology at Sorbonne-University. Scientific time has accelerated. The specialists communicate from the first results. This allows greater responsiveness but also forces caution.“
To go further, the researchers need the entire strain, that is to say the living virus. In the absence of cases in France, the specialists had, at first, solicited their colleagues abroad. The arrival of the variant in France should at least have the advantage of simplifyinglogistics, with the possibility of taking samples directly from patients. Samples which can then be distributed among the research laboratories. “The objective is to have as many teams as possible working on it“, confirms Yannick Simonin.
Two weeks for the first results
Despite this strong mobilization, the research will take time. Allow at least ten days for the first elements on a possible resistance of the variant to the available vaccines. “We must first isolate the virus, amplify it and put it in culture, details Olivier Schwartz. It takes four to six days before you can “harvest” it for testing., which also take several days. This involves, in vitro, bringing the variant into contact with serum from vaccinated persons. “ Scientists plan to study a variety of profiles, using blood samples from people who have received a particular vaccine, for such or such duration.
In parallel with public laboratories, vaccine manufacturers conduct their own research to find out whether they should adapt their products. Yannick Simonin warns all the same: “These tests will make it possible to see more clearly but will give only partial information, because the immune system of each one is much more complicated than just antibodies in test tubes. “
Hence the importance of field observation. “Always compare laboratory data with real life data, insists Vincent Maréchal. We move forward on two feet and yes, it takes time. “ Because here again, it is difficult to generalize from the South African case. Epidemiologist Arnaud Fontanet explained it at the end of last week during a point from the Scientific Council: “The Omicron variant appeared in a poorly vaccinated population and at a time when the Delta was very calm. ” A very different situation from France.
A peak of hospitalizations expected in January
49,610 new cases of Covid were registered on 1er December, according to Public Health France. The most affected are the 30-39 year olds (420.9 cases per 100,000 inhabitants), followed by the 0-9 year olds (389.5 cases per 100,000 inhabitants).
More than 8,500 people are hospitalized for Covid-19, and new critical care admissions are increasing.
The peak of hospitalizations of the fifth wave should be reached in January 2022, according to projections from the Institut Pasteur.
Its magnitude will depend on the vaccine booster but also wearing a mask, respecting barrier gestures and reducing contact in general, underline the modelers. In the “best” scenario, 1,250 people will be hospitalized each day, in the “worst” scenario, 2,250.
66.4% of adults always wear the mask in public places and 87.9% are vaccinated or intend to do so, reports the CoviPrev survey of November 19 on the evolution of French behavior.