Where did Omicron come from?

An Israeli doctor who was one of the world’s first confirmed Omicron cases says he believes he was infected with the Covid-19 variant while in London.

Cardiologist Elad Maor’s theory that he caught the virus while attending a medical conference in the English capital last month has raised fresh questions about the origins of Omicron, which has a high number of mutations.

The variant was first detected in a specimen collected on 9 November in South Africa, according to the World Health Organization.

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But the South African authorities have argued that this does not prove the new strain originated in their country, which they say “is being punished – instead of applauded – for discovering Omicron”, the BBC reported. As countries worldwide banned travellers from South Africa, the Foreign Ministry said the restrictions were “akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker”.

The other origin theories

Christian Drosten, a virologist at Charite University Hospital Berlin, told Science that he believed the variant evolved “not in South Africa, where a lot of sequencing is going on, but somewhere else in southern Africa during the winter wave”.

Leading US virologist Trevor Bedford also argued, in a series of tweeted posts, that the variant probably circulated initially in a “geography with poor genomic surveillance” and “certainly not South Africa”.

Speaking to US radio network NPR, Bedford said that other Covid variants with the closest genome sequences to Omicron “are back from mid-2020”.

In other words, said the broadcaster, “while scientists can tell that this variant evolved from a strain that was circulating in mid-2020, in the intervening months there's been no trace of all the intermediate versions that scientists would have expected to find as it morphed into its current form”.

Bedford added that it was possible, if unlikely, that an earlier strain infected an unknown animal population and evolved as it spread, before recently spilling back over into humans.

In some African countries and other nations, ongoing sampling of the coronavirus has been patchy. Some experts believe Omicron may have began circulating in such a region and was able to evolve without being noticed.

However, that theory was refuted by Richard Lessells, an infectious disease specialist at the University of KwaZulu-Natal in Durban, who was part of the team that first identified Omicron. The variant triggers a notable signature in the PCR tests routinely done to confirm infections, he told NPR, so “you’d have to have a pretty big blind spot to be missing something that's really evolving over a period of months”.

If the variant was not hiding inside a relatively unmonitored country, it may have evolved in a smaller entity: an individual with a weakened immune system.

Many experts, including US expert Bedford, believe the virus probably developed in a chronically infected Covid patient, such as someone whose immune response was impaired by HIV, or a drug. The virus could have lingered undetected and evolved in the patient.

Such a person’s immune system would be strong enough to prevent the virus from killing them but not to completely clear their body of the infection, creating a “kind of cat-and-mouse game where the immune response is chasing and the virus is running”, Bedford told NPR.

In cases of similar infections, he added, “over the course of the year, if you look in these individuals, you see, at the end of that time, generally a quite evolved virus”.

However, the plot thickens. Dutch health authorities announced on Tuesday that the new Omicron variant had been detected in samples collected in the Netherlands between 19 and 23 November, “indicating that it was already spreading in western Europe before the first cases were identified in southern Africa”, said CBS News.

Whether the mystery of the new variant’s origins will ever be solved is also a matter of debate. “It's unlikely we will ever know precisely when or where Omicron first emerged,” the BBC’s health editor Michelle Roberts concluded.