Omicron has become a global public health threat thanks to a dangerous array of mutations, but where did it come from?
December 17, 2021
We don’t know for sure where or how the omicron variant of the coronavirus acquired such a large and dangerous set of mutations before it started spreading like wildfire around the world, and we may never know. It most likely developed in one immunocompromised person, possibly someone with HIV living somewhere in South Africa who was not receiving effective treatment, but there is no direct evidence for this.
How did we discover the alternative Omicron?
Researchers in South Africa noticed a slight 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 November 25th. Researchers elsewhere I noticed this variant About the same time sequences are uploaded to public databases.
What is different about it?
Omicron contains about 50 mutations compared to the original virus discovered in Wuhan, China, with 30 in the outer spike protein alone. This is important because the spike protein is the target of our antibodies. Extensive changes in the spike omicron protein drastically reduce the effectiveness of antibodies that people get from vaccination or from infection with other variants.
How did you get so many mutations?
There are two main hypotheses. The first is that it originated in someone with a weakened immune system. Normally all viruses are killed when our immune response is fully in place, but if a person’s immune system is weak, some viruses can continue to multiply in their bodies and evolve over the course of several months to become much better at avoiding antibodies.
Is there evidence of this what happened?
There is no direct evidence but it has been observed that this process of accumulation of mutations occurs in an individual with HIV who was not responding to treatment. The researchers who discovered Omicron called for intensified efforts to tackle HIV.
What is the other main idea?
That the virus infected animals of some sort, acquired so many mutations that it spread between them and then jumped back to humans – a phenomenon known as reverse zoonosis.
What is the evidence for omicron evolution in animals?
Some of the mutations in the spike proteins are the same as those seen in the SARS-CoV-2 viruses that have adapted to spread in rodents, specifically mice. But this could be just a coincidence.
Could this happen in mice in the lab?
Most of the 7 billion people in the world have rodents that live near, if not inside, their homes, so there have been endless opportunities for this to happen with mice or rats. Very few labs conduct experiments involving mice with SARS-Cov2 virus and None of them are in South Africa. In other words, the idea of lab mice cannot be ruled out but seems highly unlikely.
Are there any other possibilities?
Omicron could have evolved gradually as it is spreading from person to person in one of many parts of the world where little or no sequencing is done. But given its prevalence, it is difficult to explain why its ancestors were not widespread enough to reach countries doing more sequencing. Another possibility is that molnopiravir, which works by inducing many virus-killing mutations, could have played a role but there is no evidence to support this speculation.
Where did Omicron originate?
The first confirmed omicron cases so far were in South Africa and Botswana in the first half of November. However, it is estimated that Omicron first began to spread in humans in early October. We don’t know where it happened. However, the fact that the first omicron wave was in South Africa indicates an origin somewhere in the region.
I read that omicron was discovered elsewhere before South Africa reported it?
Several countries, including the United States and the Netherlands, have reported cases of omicron as of mid-November, but these do not precede the first cases in South Africa and nearly all are associated with travel from the region. There was a report of an omicron in Nigeria in October, but it was later said to be a bug.
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