Did Omicron come from mice?

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They reported that the variant was spreading very rapidly in southern Africa and contained a large number of unusual mutations likely to make the virus more infectious than previous variants.

Confirming the scientists’ early fears, by early January 2022, Omicron was driving an unprecedented surge in cases worldwide.

This presents a puzzle for scientists because there are no known intermediate variants to reveal how Omicron evolved. It is almost as if the new variant appeared “out of nowhere.”

Many of the mutations that health experts identified in Omicron are rare among previously sequenced variants of the virus.

Story Highlights

  • On November 24, 2021, scientists in South Africa revealed that they had discovered a worrying new variant of SARS-CoV-2.

  • Within days of the scientists’ announcement, the World Health Organization (WHO) declared that the new variant, called Omicron, was a variant of concern.

There are three alternative theories for the origin of Omicron:

The variant evolved undetected in a population somewhere in the world where there was little COVID-19 surveillance and sequencing.It evolved in someone who remained with the infection for an unusually long time because their immunity was compromised, perhaps as a result of a concurrent HIV infection or treatment with an immune-suppressing drug.It evolved in an animal population before a human acquired the virus.

The second theory is the most popular among virologists and epidemiologists. However, some experts have argued that other viruses, such as the influenza virus, tend to become less infectious over time in individuals with compromised immune systems.

They cite evidence that while such viruses evolve adaptations to their host’s immune system, they accumulate other mutations that make them less able to cause infections in other people. However, Omicron appears to be more infectious than all previously known variants.

Researchers at the Chinese Academy of Sciences in Beijing have now found evidence that Omicron may have evolved its large collection of unusual mutations in mice. They believe that an earlier variant, from the lineage known as B.1.1, jumped from a human into a mouse in mid-2020. Over time, it evolved a range of adaptations to its new host before causing an infection in another human in late 2021.

Past research suggests RNA viruses tend to pick up more mutations in particular bases, according to which animal host they are replicating inside. Using this knowledge, the authors of the new paper have previously identified the mutation “signature” of different animal hosts of SARS-CoV-2.

Point mutations are substitutions of single chemical letters, known as bases, in the four-letter genetic code. They identified 45 “point mutations” in the RNA of Omicron that they propose occurred after the variant split from its last known common ancestor in humans.