One possibility for how a heavily mutated variant, such as Omicron, could have arisen
is that the virus began circulating and mutating in an isolated group of people, where it would have had an opportunity to change dramatically compared with variants outside of that bubble. It could then have gotten introduced, with its numerous mutations, into the larger population, where it was able to travel into different groups and countries, Bello says.
Alternatively, the virus
may have mutated significantly in a single individual before finding a new host. “This could happen in an immune-suppressed person,” such as someone with HIV, Anna-Lise Williamson, chair in vaccinology at the University of Cape Town, and Ed Rybicki, director of the university’s biopharming research unit, wrote in response to e-mailed questions. South Africa has the world’s largest HIV epidemic, with
more than seven million people infected with the virus. Neighboring countries also have widespread HIV infections. This has led some scientists to hypothesize that Omicron arose in Southern Africa because it was first identified there, but older cases have since been identified in European countries and the U.S.
Another possible hypothesis for how the virus rapidly gained so many mutations is that it spilled back into an animal reservoir before reinfecting humans, Bello says. Persuasive evidence suggests that the original SARS-CoV-2 likely
arose in a bat, and there have been
numerous cases of other wild and domesticated mammals contracting the virus. Last year, there were reports of coronavirus outbreaks
on mink farms in North America and Europe, and in the Netherlands there was a
confirmed case of the mink infecting a farm worker.
The numerous changes in the coronavirus’s spike protein could have arisen in an isolated population or an immunocompromised person—or animals
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