The origin of the omicron variant is under debate: while its existence was first reported in South Africa at the end of November, analysis of its genetic history suggests that it diverged as early as June 2021. According to Danielle Perez Bercoff, virologist and researcher at the Luxembourg Institute of Health (LIH), there are three possible explanations for this jump in time and the very high number of mutations in this variant: emergence from an immunosuppressed individual, the influence of a drug or a jump between species from an animal.
The hypotheses could help us to better understand the high contagiousness of omicron, which has led to stricter measures in European countries, and to better respond to the threat of potential new variants.
What characterises the omicron variant compared to other covid-19 variants?
Danielle Perez Bercoff: Three aspects characterise the omicron variant: the quantity and quality of the mutations, and the time factor. If we compare it to the original Wuhan strain of 2020, the omicron variant is extremely mutated, much more than the other variants in circulation. Where there are about ten mutations for the beta or delta variants linked to the Spike protein (the key that allows the covid virus to penetrate our cells, editor’s note), there are 32 for omicron. And that's without counting mutations in the genome other than those affecting the Spike protein.
Are these many mutations different from what we have seen before?
The DNA of the virus is made up of four bases (A, T, C and G; or A, U, C and G for RNA, editor’s note) that code for the message that makes the virus’ proteins. Most often, these mutations go from C to U. With omicron, however, they went from G to A. This difference leads scientists to believe that the cause of the mutations is probably not the same as for the previous variants.
When reconstructing its genetic history, it was found that omicron is not a direct descendant of the alpha, beta or delta variants. It is estimated to have diverged in mid-2021, around June.
Finally, one of omicron’s particularities is the time factor...
In reconstructing its genetic history, it was found that it is not a direct descendant of the alpha, beta or delta variants. It is estimated to have diverged in mid-2021, around June. However, South Africa reported its existence to the World Health Organization (WHO) on 24 November, almost six months later.
That’s a jump of almost six months. Why wasn’t it detected earlier?
There are three possible explanations. The one that seems most likely to me is that of an immunosuppressed human host. As a rule, the virus does not remain in the host for more than three weeks, which is not enough time for many mutations to take place. Consequently, the virus that emerges does not escape the immune response conferred by an infection or a vaccine very well.
But in an immunosuppressed individual--who does not have an optimal immune response, because of chemotherapy or Aids, for example--the virus can stay longer, for three, four or five months. It then has time to acquire many mutations.
In an immunosuppressed individual, the virus can stay longer... It then has time to acquire many mutations.
The antiviral treatment molnupiravir, developed by the American laboratory Merck to combat covid-19, has also been singled out...
The aim of such a drug is to mutate the virus to such an extent that its proteins become so wobbly that it can no longer replicate itself. This could explain the presence of many G-to-T mutations, which is the signature of molnupiravir. I don’t believe it 100%, but it is a theory that exists.
Another hypothesis is that omicron came from another animal species...
Most viruses are linked to species jumping. In 2021, one or more individuals would have infected other animal species--mice, rats or lemurs. Then the virus would have jumped to humans. This would be a reverse species change. This would explain the six-month jump and the quality of the mutations. But it has never been proven that there were transmissions from these species to humans…
Why is it important to find out the origin of omicron?
Knowing where it comes from is necessary to learn how to manage it. If molnupiravir was involved, it should no longer be given to patients. If it’s species transmission, then infected people need to protect their pets…
Omicron is more infectious, so that means more people infected, so more people hospitalised.
Is the appearance of a variant like omicron worrying?
Yes, it is worrying. Omicron is more infectious, so it means more people are infected, so more people are hospitalised. But we have to weigh this up: this variant worries us because it escapes the vaccines in part, but not totally. Because, if these vaccines protect less well against omicron infections, they still protect against the severe forms.
What can be done to protect against it?
You need a third dose as soon as possible, because it increases the protection against infection to 70%. And, in general, the most important thing to do is to vaccinate. With good vaccines, for all populations, especially in developing countries. There is a need for global protection.
We will not return to normal in the next few years, despite the vaccines.
The situation was already precarious with delta. It is getting worse with omicron. Is there a way out of the crisis?
Unfortunately, we will not return to normal in the next few years, despite the vaccines. I think we have to change our lifestyles and accept that our behaviour has to change. Summer is certainly a good time to relax. But during the winter, when there are many people in closed rooms, I think we have to stop that. We have to be more responsible, respect the barrier gestures and the wearing of masks. Several factors will help: mass vaccination and careful behaviour during the winter.
This story was first published in French on . It has been translated and edited for Delano.