Covid-19: this army of new Omicron sub-variants threatening winter

Is Sars-CoV-2 playing a new trick on us? Since the end of 2020, the same story has been repeating itself over and over again: an option appears, supplants the previous one, and imposes itself before replacing itself. After the original strain, Alpha, Delta, Omicron, then BA2 and BA5 re-introduced significant waves of infections. But in recent weeks, scientists have seen an unprecedented trend. “Perhaps for the first time we are seeing a shift in the epidemiological landscape, with multiple sub-variants of Omicron appearing around the world at the same time, some of which live within the same country,” said Professor Antoine Flahaud, epidemiologist and director of the Institute. Global Health at the University of Geneva (Switzerland).

BQ.1.1, BQ.1, BA.2.3.20, BA.2.75.2, BF.7, BJ.1, XBB… This is a whole viral menagerie that people are starting to talk about. How to explain this sudden abundance? By the origin of these sub-variants, most likely. Alpha, Delta, Beta or even the first Omicron, very different from each other, appeared in immunocompromised people. Without being able to rid their body of the virus, they would give it time to accumulate many mutations, up to the creation of a new branch in the Sars-CoV-2 family tree. Everything is different here, since all these descendants belong to the Omicron family – most come from BA.2 or BA.5. This time, only the very wide distribution of the virus will be involved in these developments: “The more it circulates, the more opportunities it has to mutate. Modifications to its genome happen randomly, but then some of them are selected when they give it an advantage,” says T. Ryan Gregory, professor of evolutionary biology at the University of Guelph in Canada.

In a population already heavily infected and/or vaccinated, the most important thing for our tiny enemy is to successfully bypass the defenses we have erected against it. Here’s how we repeatedly find “immune escape” mutations in its new descendants: “It’s always the same four or five, singly or in combination, depending on the subvariants,” confirms Etienne Simon-Laurier, head of evolutionary genomics. RNA Virus Division at the Pasteur Institute. Experts talk about “evolutionary convergence”: “Different variants of Omicron circulate throughout a population that has developed similar antibodies, resulting in the selection of the same elusive mutations,” explains virologist Etienne Decroly, director of research at CNRS at the University of Aix. -Marseilles.

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“The virus has already gained a head start”

This “soup” of sub-options, as the experts call it, poses a clear threat anyway. A group of Chinese researchers have evaluated the ability of the sera of people already infected or vaccinated to withstand their onslaught, and the results are hardly encouraging. “The immunity acquired by a population after infection or revaccination may not be sufficient to provide broad protection against infections,” they write in their study, available in a pre-publication (not peer-reviewed). They also show that most of the monoclonal antibodies, which are valuable in treating infected people and who are at risk of developing a severe form, partially or completely lose their effectiveness. “In the race between Sars-CoV-2 and our immune system, the virus has already regained its lead,” summarizes Professor Olivier Schwartz, head of the department of viruses and immunity at the Pasteur Institute.

It remains to be seen if these newcomers will continue to circulate together, or if one of them will end up crushing the others. “I won’t risk betting. It’s like asking the result of a race beforehand: the task is just as difficult for a race participant as it is for a virologist,” smiles Etienne Decroly. With luck, these sub-options may even disappear like the others before. However, at this stage, this scenario does not seem to be favored by scientists…

At the moment, this new virus battalion has not yet arrived in France. Our current wave is driven by BA.5, which continues to spread among people who have not yet encountered Omicron. “Added to this is a decrease in immunity over time, which leads to an increase in infections and re-infections. We have shown that after the third injection, vaccinated subjects lose their neutralizing antibodies against BA.5 after five months,” explains Olivier. Schwartz. It seems that the situation is similar in Germany. “On the other hand, we see this constellation of sub-options starting to increase in the United States, Great Britain or Denmark,” notes Professor Antoine Flao. However, the absolute number of sequenced viruses is still too small to draw conclusions about their real potential for spread. “We will know more in a few weeks,” says Étienne Simon-Laurier.

On the plus side, three doses of the vaccine continues to protect against serious forms, regardless of the virus. Except, of course, for people who are immunosuppressed or very old, who absolutely need a new injection if the previous one is more than six months old (or three months for those over 80). But between the lack of barrier gestures, the winter season, the decline in immunity in the general population, and these new sub-options, all the bricks seem to be coming together to make the next few months even more challenging.