Where did Omikron come from? Scientists had a big surprise

As Omicron spreads around the world, the “research frenzy” continues among scientists. All this to find out as soon as possible whether the superwariant is more infectious and whether and to what extent it is immune to vaccines. Scientists, however, are grappling with another mystery: where did Omikron come from? And here they came across a big surprise.

1. There are suspicions that Omikron did not develop from one of the earlier variants, such as Alpha or Delta, but evolved in parallel – unnoticed. “It doesn’t connect to anything that has been circulating recently,” notes virologist Trevor Bedford
2. When the scientists looked at the Omicron, they saw something surprising. – The closest genetic sequences come from mid-2020 – so they were created over a year ago
3. This means that although the variant evolved from a strain that was circulating in mid-2020, so far there has been no trace of intermediate versions that scientists could find as it transformed into its current form.
4. How to explain it? There are three hypotheses
5. More information can be found on the Onet homepage

Research on the Omicron. Scientists saw something surprising

While the emergence of the next mutation in the SARS-CoV-2 coronavirus was not a surprise for scientists, it might be surprising how much it differs from the variants discovered so far. It is not only about the unprecedented number of Omicron mutations (and there are about 50 of them, while in the case of Delta, for example, there were less than 20). It turns out that many of the changes in this mix were first seen (they were not seen in the other variants of the coronavirus). This would mean that the Omikron did not develop from one of the earlier variants, such as Alpha or Delta, but evolved in parallel unnoticed.

“It doesn’t connect to anything that has been circulating recently,” notes Trevor Bedford, an American virologist at the Fred Hutchinson Cancer Research Center in Seattle. “It’s interesting how wildly it is different from the rest,” says Mike Worobey, an evolutionary biologist at the University of Arizona.

All this raises the question of how the Omikron super variant was created and what could it mean for us and the future of the COVID-19 pandemic? While searching for answers to these questions, scientists came across a big surprise.

The rest of the article under the video.

One of the key tools scientists use to determine the origin of a particular variant of the coronavirus is to study its genetic code. Just like a person who wants to know their parentage. ‘By looking at the viral genome and seeing if a sequence is similar to those circulating in others, you can find out where these changes are coming from. As a result, scientists are able to see step by step how each particular strain begins to pick up additional – often mild – mutations, eventually transforming into another variant. However, when the scientists looked at the Omicron, they saw something surprising.

– The closest sequences are from mid-2020, so they were created over a year ago. It’s very rare, says Trevor Bedford. In other words, while scientists may conclude that this variant evolved from a strain that was circulating in mid-2020, in the meantime there was no trace of all the intermediate versions that scientists could find as it transformed into its current form. How to explain it? Where has Omikron been lurking for over a year? There are three hypotheses.

Where has Omikron been lurking for over a year? Animals and the “secret spread” theory

The first assumption is that the mid-2020 strain infected some unknown population of animals (e.g. rodents), as the pathogen spread in that group, it has evolved and recently spread to humans. That could explain where the new mutations came from. But Trevor Bedford thinks it’s rather unlikely. If that were the case, one would expect traces of the animal’s genetic material in the genome, and instead there is a “human RNA insert”.

The second hypothesis assumes the spread of the mid-2020 strain in an unmonitored region of the world. “Perhaps somewhere in South Africa,” Bedford says. This would allow the virus to evolve unnoticed. – After all, in 2021 it collected enough mutations that it became more contagious and began to spread rapidly around the world, the scientist says.

Christian Drosten, a virologist at the Charité University Hospital in Berlin, is behind this scenario. “I assume this has evolved not in South Africa, where a lot of sequencing is taking place, but elsewhere in the south of the African continent during the winter wave,” he says.

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For Bedford, however, this hypothesis – sometimes referred to by scholars as “mysterious spread” – has little credibility. If the strain did in this way evolve towards high-transmission, its individual versions would start spreading earlier. This, in turn, would be noticed in countries with solid surveillance systems, he notes. Andrew Rambaut from the University of Edinburgh also speaks in a similar vein, trying to understand how the virus could “hide” for so long in a group of people. “I’m not sure there is really a place in the world that is isolated enough for this type of pathogen to travel for such a long time without showing up in different places first.”

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The omicron evolved in the body of one man. «Cat and mouse game»

There is, however, a place where the virus may have hidden itself, evolving unnoticed into an Omicron. This place is the body of one specific person. Most likely, it was a person with a weakened immune system, for example as a result of untreated HIV infection.

As Trevor Bedford notes, in such cases the human immune system is still strong enough not to be destroyed by the pathogen, but too weak to completely remove the virus. Thus, the microbe could stay in the human body for many months, constantly reproducing. And with each replication, there is a chance that it will create a mutation that will more effectively avoid the “host” immune cells. “It’s kind of a cat-and-mouse game where the pathogen races against the body’s immune response,” says Bedford.

This scenario is the most likely explanation for the appearance of the Omicron, says Richard Lessells, an infectious disease specialist at the University of KwaZulu-Natal in South Africa, part of the team that identified the superwariant in South Africa and alerted the world. The scientist highlights an important point – to avert one of the possible sources of future variants, ‘we need to close the gaps in the HIV treatment process. So we have to diagnose everyone, we have to refer everyone to treatment, and we have to convert those who are currently ineffective to better treatment regimens ». The researchers emphasize that this is not about blaming or stigmatizing anyone, but rather showing that helping in such a situation is key to ending the coronavirus pandemic.

The advent of Omikron has made more and more talk about the huge gap in vaccination rates against COVID-19 in richer and poorer countries. Low vaccination rates in South Africa and Botswana “provided a fertile environment” for the evolution of the Omikron variant. However, some scientists argue that there is little evidence to support this claim.

– If we vaccinated more people in Africa, would we not have what we have? I wish it were true, but we have no way of finding out, says Aris Katzourakis, an evolutionary biologist at Oxford University. So for the moment, the lessons that can be learned from the appearance of the Omicron remain as unknown as its origin.

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