How did Omicron evolve?

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The highly transmissible Omicron variant, which emerged with a host of unusual mutations in late November last year, has been detected in more than 120 countries. Now, scientists are trying to find out how it evolved.

The spread of the Omicron variant around the world has been the fastest than any previous versions.

While on one hand, there’s no transparent path of transmission linking Omicron to its predecessors, on the other, the variant has an unusual array of mutations, which evolved entirely outside the view of researchers, Nature reported.

In fact the variant is so different from earlier strains, such as Alpha and Delta, that evolutionary virologists estimate its closest-known genetic ancestor probably dates back to more than a year ago, some time after mid-2020.

“It just came out of nowhere,” Darren Martin, a computational biologist at the University of Cape Town, South Africa was quoted as saying.

Understanding the origins of Omicron might help scientists to understand the risk of new variants emerging, and suggest steps to minimize it, said Angela Rasmussen, a virologist at the University of Saskatchewan Vaccine and Infectious Disease Organization in Saskatoon, Canada.

“It’s very difficult to try to mitigate a risk that you can’t even remotely wrap your head around,” she was quoted as saying.

Scientists have explored three theories relating to the origins of Omicron.

Although researchers have sequenced millions of SARS-CoV-2 genomes, they might simply have missed a series of mutations that eventually led to Omicron. Alternatively, the variant might have evolved mutations in one person, as part of a long-term infection. Or it could have emerged unseen in other animal hosts, such as mice or rats, the report said.

But as of now, whichever idea a researcher favours “often comes down to gut feeling rather than any sort of principled argument”, Richard Neher, a computational biologist at the University of Basel in Switzerland, was quoted as saying.

Researchers agree that Omicron is a recent arrival. It was first detected in South Africa and Botswana in early November 2021; retrospective testing has since found earlier samples from individuals in England on November 1 and 3, and in South Africa, Nigeria and the United States on November 2.

An analysis of the mutation rate in hundreds of sequenced genomes, and of how quickly the virus had spread through populations by December, dates its emergence to not long before that — around the end of September or early October last year.

A study published in the journal Nature, suggested that the Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-2 variants as a result of adaptive evolution, in which beneficial mutations are passed onto future generations through natural selection, rather than through recombination between previous variants.

“The finding suggests that Omicron is likely the result of an evolutionary process that created a highly transmissible virus that partially evades our antibody responses,” the researchers said.

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