Scientists puzzled over when, how Omicron emerged

London, Dec 11:  Amid the unprecedented spread of Omicron variant, scientists ponder over several competing theories on the heavily mutated strain's origins, the media reported.

The coronavirus variant, which first surfaced in late November, has so far been detected in more than 60 countries, as health officials worldwide try to contain its rapid spread.

What was surprising to scientists was that Omicron's genetic traits bore more similarity to forms of the virus circulating last year than more recent strains, such as Beta and Delta, the Financial Times reported.

The mystery stems from the question of how "a whole raft of mutations" emerged "under the radar", David Stuart, professor of structural biology at Oxford university was quoted as saying.

"It seems to have been hiding for a year," added Sarah Otto, professor of evolutionary biology at the University of British Columbia.

The puzzle gave rise to competing theories -- the virus emerged in an immunosuppressed person with HIV, anti-Covid drugs accelerated its evolution, and it crossed over into an animal species that later jumped back into humans.

According to Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal in Durban, Omicron has its roots somewhere in South Africa.

Late last year, an untreated HIV patient who was infected with Covid-19 for more than six months was discovered by a South African research team. The team found that the person had a string of mutations that affected the spike protein. A UK study observed a similar process in a Covid patient with blood cancer, the report said.

The immune response of an untreated HIV patient would be "too weak to clear the virus but strong enough to drive the process of evolution", explained Lessells.

"This evolutionary pathway is likely to be rare but it's a plausible reason for the emergence of Omicron," he said.

The concern was echoed by Jonathan Li, director of the Harvard/Brigham virology specialty laboratory in Boston. He said that it was "striking" that two variants of concern - Beta and Delta - had arisen in southern Africa, a region with "large numbers of immunosuppressed individuals as a result of HIV infection".

"The collision of high case numbers, low vaccine availability and decades of an HIV crisis means that the chance immunocompromised individuals have been carrying Covid for a while is very high," said Otto.

Another theory speculates that mutations could have been caused by Merck's Covid-19 antiviral pill, as South Africa was among the locations chosen for clinical trials of the drug molnupiravir, which began in October 2020, William Haseltine, a virologist was quoted as saying.

The drug causes an explosion of errors to prevent the virus' ability from spreading.

"The timing is right. I'm not saying it happened, but it could have happened," Haseltine told FT.

However, Merck has refuted the claim. The company told the FT that Haseltine's "unfounded allegation has no scientific basis or merit".

Further, the theory that the mutation arose in animals before being passed back to humans "is not completely implausible but there is very little reason to believe that happened", according to Stuart Ray, professor of medicine at Johns Hopkins University.

"When you look at the passage of human viruses in animals, they accumulate mutations that are suited to that host, not to humans."

Meanwhile, medics and scientists have stressed that, regardless of how Omicron emerged, richer, western nations should focus on the need for vaccine equity for the pandemic to end.