Did the systems fail to detect the Omicron variant?

Barely discovered, the Omicron variant has already been detected in more than 240 people in 20 countries and territories around the world. Have the detection systems developed since the start of the pandemic failed? Guillaume Bourque, director of bioinformatics at the McGill University Genomic Center, and Benoît Barbeau, infectious disease specialist in the Department of Biological Sciences at UQAM, answer our questions.

Is it too late to block the arrival of the Omicron variant in Canada?

Guillaume Bourque : It’s too late to stop this variant. The objective is no longer to stop it, but to monitor its progress to give Public Health time to adjust its policies. It is clear that with cases detected in so many countries, it seems that community transmission was initiated long before the detection of this new variant.

Benoit barbeau : Once propagated in a multitude of countries, it is too late. It is not possible to block the road to the Omicron variant, but it is urgent to measure its presence to have a better idea of ​​its prevalence here. We know that we are dealing with a single variant with about thirty mutations, we should not be surprised that it is already widespread.

How did Omicron, first detected in South Africa, escape the detection systems of dozens of developed countries?

B. B. : We can say that we stumbled upon it a bit by chance. Because there is such a multitude of variants that before deciding to look at one of them, there must be a sudden emergence of cases, like the one observed in South Africa, to detect it. We cannot alert the planet to each new mutation. These are retrospective analyzes that make it possible to associate increases in cases with the peculiarities of a variant.

G.B. : The difficulty is that the propagation of a variant always starts without knowing it. The alarm is only sounded when there is sufficient evidence that it is a potentially problematic variant. There may be a delay between the propagation event and the detection of the variant. In this case, it is clear that the spread dates from a while.

How to explain that Omicron is already in 20 countries? Are we going to relive the same scenario as with the Delta variant?

G.B. : This time, the alarm signal was triggered faster than in the case of the Delta variant. The situation is very different, because a large part of the population is vaccinated, and our detection systems have been revised and are much faster than a year ago. The dilemma is always to cry wolf too quickly, or to delay in acting. Analysis of the impact of the variant [sur le sérum de personnes vaccinées] will tell us soon if we were right to be concerned.

B. B. : It was detected in South Africa, but this variant could come from elsewhere, from a country other than the one where it was detected. It is quite possible that it is already present in Canada, and that is why we must now seek its presence in samples already taken in Quebec.

Is the game lost in advance?

G. B. : It’s difficult to say, because we are still in a gray area as to the impact of this variant on the immunity of vaccinated people and on its dangerousness. If the variant causes a more severe form of the disease, it will be known quickly. But if its incubation is long and its symptoms are different, it will be longer before measuring the problematic potential of this variant. We cannot stop it, but we have important tools to slow it down. If we delay its spread in Canada by two to three weeks, that will allow us to learn from other countries and adjust our focus.

How could we adjust the shot?

G. B. : We will have to adapt our screening and sequencing measures. But screening more will not be enough. We could miss a new variant or a sub-strain. It will be necessary to sequence several lines to know if there was one or more sources of introduction of the variant in Canada. We have already received samples from the first two cases detected [en Ontario]. This will give us the fingerprint of the cases introduced here and allow us to know whether they are closer to those detected in Europe or to those detected in South Africa.

B. B. : It will take significant sequencing efforts. Because nothing tells us that other variants will not fall on us. Again, flaws in the global immunization effort mean that the virus always finds a way to mutate to spread. It will cause us concern as long as the entire population is not vaccinated.

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