Omicron has become a global threat to public health thanks to a particularly dangerous set of mutations, but where did it come from?
17 December 2021
We do not know for sure where or how the omicron variant of the coronavirus acquired such an extensive and dangerous set of mutations before beginning to spread like wildfire around the world, and we may never know. It most likely evolved in a single immunocompromised individual, possibly an HIV-positive person living somewhere in southern Africa who was not receiving effective treatment, but there is no direct evidence for this.
How did we discover the omicron variant?
Researchers in South Africa noticed a small increase in cases in Gauteng province and decided to sequence more samples. They found a variant with a lot of worrying mutations and alerted the world on 25 November. Researchers elsewhere noticed this variant around the same time from sequences uploaded to public databases.
What’s different about it?
Omicron has around 50 mutations compared to the original virus discovered in Wuhan, China, with 30 in the outer spike protein alone. That matters because the spike protein is the target of our antibodies. The extensive changes in omicron’s spike protein greatly reduce the effectiveness of the antibodies people have from vaccination or from infection with other variants.
How did it acquire so many mutations?
There are two main hypotheses. The first is that it evolved in a person with a compromised immune system. Normally all viruses are killed when our immune response kicks in fully but if a person’s immune system is weak some viruses can keep replicating in their bodies and evolve over several months to become much better at evading antibodies.
Is there any evidence this is what happened?
There is no direct evidence but this process of accumulating mutations has been observed happening in an individual with HIV who was not responding to treatment. The researchers who discovered omicron have called for efforts to tackle HIV to be stepped up.
What’s the other main idea?
That the virus infected animals of some kind, acquired lots of mutations as it spread among them and then jumped back to people – a phenomenon known as reverse zoonosis.
What evidence is there for omicron evolving in animals?
Some of the mutations in the spike proteins are the same as those seen in SARS-Cov2 viruses that have adapted to spreading in rodents, and specifically mice. But this could just be a coincidence.
Could this have happened in mice in a lab?
Most of the 7 billion people in the world have rodents living near their homes, if not inside them, so there have been countless opportunities for this for this to happen with mice or rats. Very few labs are doing experiments that involve infecting mice with SARS-Cov2, and none of them are in southern Africa. In other words, the lab mice idea cannot be ruled out but seems highly unlikely.
Are there any other possibilities?
Omicron could have evolved gradually as it spread from person to person in one of the many parts of the world where little or no sequencing is done. But given how infectious it is, it’s hard to explain why none of its ancestors spread widely enough to reach countries that do more sequencing. Another possibility is that the drug molnupiravir, which works by inducing so many mutations it kills viruses, could have played a part but there is no evidence to support this speculation.
Where did omicron arise?
The earliest confirmed omicron cases to date were in South Africa and Botswana in the first half of November. However, it’s estimated that omicron first started spreading in people in early October. We don’t know where that happened. That said, the fact that the first omicron wave is in South Africa does suggest an origin somewhere in the region.
I read that omicron was detected elsewhere before South Africa reported it?
Several countries including the US and the Netherlands have now reported omicron cases from mid November but these do not predate the earliest southern African cases and are almost all associated with travel from the region. There was a report of omicron being found in Nigeria in October, but this was later said to be a mistake.
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