Mutations may have accumulated in an immunosuppressed patient, in a population with poor viral surveillance or in an animal reservoir (possibly rats) giving rise to a ‘reverse zoonosis’
Ever since South African scientists announced they had identified a disturbing new variant, later dubbed Omicron by the World Health Organization, the world has been eagerly awaiting how dangerous this new strain really is, what impact it will have on the pandemic and vaccines. . But there is another question that scientists all over the world are asking: where does Omicron come from? For now, scholars are formulating hypotheses and it is not taken for granted that one day we can really shed light on the origin of a variant with such strange characteristics.
Evolution under the radar
It seems quite evident that Omicron did not develop from one of the previous concern variants such as Alfa O Delta. In fact, Omicron looks very different from the millions of Sars-CoV-2 genomes that have been shared over the months. Based on the genetic profile, Emma Hodcroft, a virologist at the University of Bern, speculates that Omicron may date back to mid-2020, writes Science. It seems that Omicron does evolved in parallel with the other variants, concealed. “It is difficult to find a close relative of hers, she probably soon diverged from the other strains,” comments the virologist.
The three hypotheses
But where did Omicron’s predecessors hide for over a year? There are three possible explanations according to scientists.
1- The virus may have circulated in one population with poor viral surveillance and no sequencing
2- The virus may have had origin from an immunosuppressed patient, unable to eradicate Covid
3- The virus may have occurred andwanted in a non-human species and only recently would it have made the species leap into humans (reverse zoonosis)
The hypothesis of the inverse zoonosis
Some scientists think the virus may have hidden in rodents or in other animals rather than in man and has therefore undergone several evolutionary pressures which give rise to new mutations before returning to man. Kristian Andersen, an immunologist at the Scripps Research Institute, is among those who have raised the hypothesis that Omicron may have emerged from a reverse zoonosis (a zoonotic event is when an animal pathogen begins to spread to humans and a reverse zoonosis is when that virus returns to an animal species). “I know that most scientists think – Andersen told STAT – that the variants come from immunosuppressed individuals, and this is plausible.” But to be honest I think a new zoonosis is more likely taking into account that many mutations are somewhat unusual and that the strain appears to have undergone an early split from other coronavirus variants. This possibility is not to be discarded ».
Adaptation to rodents
According to investigations by Robert Garry, professor of microbiology and immunology at Tulane Medical School, Omicron presents seven mutations that would allow the variant to infect rodents such as mice and rats and similar species. Other variants such as Alfa for example carry only some of these mutations. In addition to the ‘rodent adaptation’ genetic mutations, Omicron brings about a number of changes not seen in any other version of Sars-CoV-2, and many scientists see this as potential evidence that the variant emerged in an animal. guest.
The case of the white-tailed deer
“It is interesting to observe how incredibly different Omicron is from the other variants,” comments the evolutionary biologist in Science Mike Worobey of the University of Arizona in Tucson, pointing out as 80% of white-tailed deer championships in Iowa between late November 2020 and early January 2021 was a carrier of Sars-CoV-2. There may be – some scientists speculate – other animal species, besides the white-tailed deer, also chronically infected and this could lead to selective pressure over time. A study published online a month ago suggests that the white-tailed deer could become what is known as a reservoir for Sars-CoV-2: animals could carry the virus indefinitely and periodically spread it to humans. “If this is the case, it would destroy any hope of eliminating or eradicating the virus in the United States and therefore from the world” – says the veterinary virologist Suresh Kuchipudi of Penn State, who co-directed the study. “It’s too early to rule out any theory about Omicron’s origin,” he says Aris Katzourakis, an evolutionary biologist from the University of Oxford who is skeptical of the animal scenario given the high number of human infections. “I would start to worry more about animal reservoirs if we were able to kill the virus and then it could find a place to hide in animals.”
Omicron hunting in animals
Scientists are already examining various animal species to see if they can be infected with Sars-CoV-2 and to look for traces of Omicron. To understand if Omicron could really be the result of a reverse zoonosis Michael Worobey suggests experimenting on selected species of wild animals to see if they can become infected and, once infected, if viral evolution patterns similar to those observed in Omicron occur. One of the hallmarks of Sars-CoV2 is that, as virologists describe it, it is a promiscuous virus capable of infecting a number of species, including domestic dogs and cats, minks, white-tailed deer and given the ease with which the virus appears to pass from one species to another it is possible that the list of animals capable of hosting the coronavirus will grow.
The hypothesis of poor viral surveillance
Some other scientists like Christian Drosten, a virologist at the Charité university hospital in Berlin, support the theory that Omicron circulated “in sleep” for quite some time. “I assume this new strain did not evolve in South Africa, where a lot of sequences are going on, but somewhere else in southern Africa during the winter wave.” Andrew Rambaut, evolutionary biologist
The University of Edinburgh, on the other hand, believes it unlikely that the virus could have remained hidden in a group of people for so long: “I’m not sure there really is a place in the world isolated enough to allow this type of virus to be transmitted for so long before that emerges in other areas “.
The Chronic Infection Hypothesis
Instead, Rambaut and several other scientists suggest that the virus most likely developed in a patient with chronic Covid-19 infection, possibly someone whose immune response has been compromised by another disease or drug. When Alpha was first discovered in late 2020 it appeared to have acquired numerous mutations at the same time, leading researchers to speculate that it resulted from a chronic infection. In South Africa, there was a documented case of an untreated HIV-infected woman who remained positive for Sars-CoV-2 for over six months. The virus has accumulated a number of mutations observed in the variants of concern. Immunocompromised people could indeed act as a ‘reservoir’ for variants, as they can harbor the virus for several weeks – enough time to mutate.
December 3, 2021 (change December 3, 2021 | 13:38)
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