In less than a month, the Omicron variant of the coronavirus concern has already been detected in 40 countries, including Argentina. It is known that it can increase the risk of reinfection in people who have already had COVID-19 and who are not vaccinated. There are global platforms that are compiling genomic surveillance data of coronavirus variants, and the great unknown of the moment is how the Omicron variant appeared, and there are already three hypotheses that researchers from different countries have raised as attempts to give an explanation.
Until now, it is suspected that the Omicron variant did not develop from one of the previous worrying variants, such as Alpha or Delta. In fact, the new variant is very different from the millions of genomes from COVID-19 patient samples from around the world that have been shared over the months.
According to scientist Emma Hodcroft, a virologist at the University of Bern, in Switzerland, suspects that the Omicron origin may date back to mid-2020. It could have evolved in parallel with the other variants. “It is difficult to find a close relative of yours, probably it soon separated from the other variants”, comments the virologist.
What are the hypotheses
1- One of the hypotheses is that the virus could have circulated in a population in which almost no genomic surveillance has been carried out. Therefore, the Omicron variant could have been generated and circulated without being detected earlier. Christian Drosten, virologist at the Charité University Hospital in Berlin, supports that hypothesis: the Omicron variant could have been running “dormant” for quite some time. “I guess this new variant didn’t evolve in South Africa, where a lot of sequences are taking place, but somewhere else in southern Africa during the winter wave.”
Instead, Andrew Rambaut, an evolutionary biologist at the University of Edinburgh, believes that it is unlikely that the virus has remained hidden in a group of people for so long.: “I’m not sure that there really is a place in the world that is isolated enough to allow this type of virus to spread, to be transmitted for a long time before it emerges in other areas.”
2- Another hypothesis is that the Omicron variant may have originated in an immunosuppressed patient, whose body was unable to eradicate the virus when it was infected. “A new and potentially disruptive variant has always been expected to emerge when the virus remains rampant in millions of people. It will continue to mutate and that is why we must remain vigilant and agile in our responses. This variant almost certainly arose in an immunosuppressed individual who was unable to clear the original infection. It is most likely an unvaccinated HIV patient in South Africa, where the virus can replicate and evolve, ”said Professor Jeremy Nicholson, from the Futures Director Center and Institute of Health at Murdoch University in Australia.
3- The third hypothesis is that the coronavirus, which was first identified in humans in January last year, could then have jumped onto an animal. From there it could have been modified and the Omicron variant could have been spawned. Some scientists think that the virus may have hidden in rodents or other animals rather than humans, and therefore suffered various evolutionary pressures that led to new mutations before returning to humans.
Kristian Andersen, an immunologist at the Institute of Scripps Research, in the United States, is among those who have hypothesized that Ómicron could have arisen from a process called “reverse zoonosis”: it occurs when this virus returns to an animal species. “I know that most scientists think that the variants come from immunosuppressed individuals, and this is plausible. But to be honest, I think a new zoonosis is more likely considering that many mutations are somewhat unusual and that the variant appears to have undergone an early split from other coronavirus variants. This possibility should not be ruled out ”.
According to research by Robert Garry, professor of microbiology and immunology at the Tulane School of Medicine in the United States, Ómicron has seven mutations that would allow the variant to infect rodents such as mice and rats and similar species. Other variants like Alpha, for example, carry only some of these mutations.
In addition to ‘rodent adaptation’ genetic mutations, the Omicron variant produces a number of changes not seen in any other version of the Sars-CoV-2 coronavirus, and many scientists believe that this particularity may be potential evidence that the variant arose in a guest animal.
“It’s interesting to note how incredibly different Omicron is from the other variants,” said evolutionary biologist Mike Worobey of the University of Arizona in Tucson in the journal. Science. It indicated that 80% of the white-tailed deer that have been studied in Iowa between late November 2020 and early January 2021 were carriers of the Sars-CoV-2 coronavirus.
A study published a month ago suggests that the white-tailed deer could become what is known as a reservoir for the Sars-CoV-2 coronavirus: Animals can carry the virus indefinitely and periodically transmit it to humans. If that idea were confirmed, “It would destroy any hope of eliminating or eradicating the virus in the United States and therefore in the world,” said Penn State veterinary virologist Suresh Kuchipudi, who co-led the study.
Ómicron has 32 mutations in its Spike protein alone, almost five times more than Delta, and it is feared that its highly divergent nature could make it more transmissible. The impact on the protection afforded by vaccines is still being investigated.
Professor Andersen then argues that Omicron could have evolved into rodents – known to carry the coronavirus – after an infected human transmitted the virus to them. This would explain why it broke away from its evolutionary branch and “faded” sometime in 2020 and reentered the population with so many very unusual mutations, many of them never seen before.
Omicron’s ancestor would then have adapted to infect the animal host. This would have resulted in its heavily mutated nature, before passing back to humans and then quickly spreading to other people. He bases his hypothesis on the fact that, while Ómicron diverged from other variants of the coronavirus in the middle of last year, genomic sampling suggested that it only began to circulate in people sometime in October this year.
What happened between those two periods is the mystery behind what has made Ómicron so different. According to Andersen, “the lineage is ancient and it seems unlikely that it has circulated undetected in immunosuppressed patients for so long” and the coronavirus has been shown to jump from one species to another “. Second is that several of the Omicron mutations have also occurred in rodent species such as mice and hamsters.
Instead, Professor David Livermore, a microbiologist at the University of East Anglia, in the United Kingdom, does not agree with the hypothesis of the jump of the coronavirus to an animal to explain the origin of the Omicron variant. Although he acknowledges that this variant had separated from its ancestors some time ago, Livermore defends the immunosuppressed patient hypothesis. “Ómicron is very remote from its ancestors and exhibits an unusual combination of multiple changes,” he said. “It is more likely that it was selected under strong selection pressure, for example in a chronically infected immunosuppressed patient,” he added.
Professor Lawrence Young, a virus expert at Warwick School of Medicine, UK, said: “We are in the early days of understanding Omicron and its mutations. However, my opinion is that these people can make all the models they want, but using them to try to predict the biological behavior of the virus is, at best, highly speculative. “
Studies are still ongoing on the new variant, but researchers are concerned that it could produce new waves of COVID-19. Currently, in the world the Delta variant predominates in the majority of patients with COVID-19. But the reproduction rate in the South African province of Guateng, at the epicenter of the Omicron outbreak, has gone from less than one to more than three in less than a month.
Public Health officials in the Guateng province estimated that the R value – a key measure used to gauge the growth rate of a wave – could be as high as 3.5. By comparison, the UK’s R index has never been higher than 1.6. In South Africa, Ómicron has become the dominant variant in just over a week since it was officially discovered, constituting 75% of the sequenced samples. Only a quarter of South Africans are vaccinated, compared to around 70% in the UK, US and Europe.
UKHSA epidemiologist Meaghan Kall cautioned that current data suggests that Ómicron may be “worse” than Delta, although the picture is still emerging. She said she was “very skeptical” that the new variant caused milder symptoms, stating that infections might appear less severe just because people have immunity against other variants, unlike the first wave.
Nevertheless, Doctors in Norway, where 60 people got Omicron at a Christmas party, say all those infected have mild symptoms, such as headaches and sore throats. But all those infected are young and believed to be vaccinated, which should mean they only experience mild symptoms anyway. Despite optimism, hospital admissions already appear to be on the rise in South Africa: Thursday’s 274 were up 180% from last week, albeit starting from a low base.