The origin of omicron

Researchers around the world are busy trying to identify the specific characteristics of the omicron variant of coronavirus and its origin — its viral heritage, if you like.

That may sound academic. But knowing that will help scientists get a better understanding of when this pandemic might end and how we can best protect ourselves against future variants of the virus.

There's not a lot of data (at time of writing), but we do know that omicron is dangerous.

It is spreading fast, internationally. On December 14, 2021, the World Health Organization said 77 countries had reported omicron cases.

The variant has more than 50 mutations, with a majority of them in the virus' spike protein, which it uses to infect human cells.

Existing vaccines are less effective against omicron. Even vaccinated people can get infected with it. It can "evade" or escape our immune response.

The variant appears to be more infectious or transmissible than other variants of coronavirus, and some experts are concerned that many more infections in a short space of time may push health systems beyond their limits.

It's possible to have a severe infection with omicron — the WHO has warned against thinking it is milder than other variants. Some omicron patients are already being treated in hospitals. And the UK reported the first person to die with omicron.

That's why it's so important to get first, second and booster vaccines. Experts say omicron is likely to continue spreading quickly and may soon supersede delta, which currently remains the dominant variant in many parts of the world.

We're unlikely to eradicate the world of this novel coronavirus in the near future.

SARS-CoV-2 is more likely to become endemic. That's when a virus is no longer a worldwide pandemic, but one that crops up from time to time, locally, such as the seasonal, common flu. We protect ourselves against influenza with an annual flu jab and we may then do the same with COVID.

Evolved parallel with other variants

Scientists say the sudden emergence of omicron is interesting because the variant seems to have evolved in parallel to other variants — that is, it's not necessarily a straight evolution of the alpha, beta, gamma and delta variants.

That's one possible reason why omicron is so different from the other variants, and why it will probably be hard to predict its next evolution. That's according to Emma Hodcroft, a virologist at the University of Bern, who spoke to DW's COVID-19 Special.

Sequencing information hosted by the international "Nextstrain" database suggests that omicron may have started its progression in mid-2020 — and we still didn't see it coming.  

Three theories on omicron's origin

Researchers have so far come up with three theories to explain how "weird" omicron evolved.

Theory one: It evolved undetected in an isolated population

It's possible that omicron evolved in a population of living people among whom the virus had circulated for some time. Those people may have become infected and recovered without its being detected or diagnosed, and without any testing or sequencing of the strain of the virus that had infected them.

Christian Drosten, a virologist at Charité University Hospital in Berlin, told Science magazine that he thinks omicron "evolved not in South Africa, where a lot of sequencing is going on, but somewhere else in southern Africa during the winter wave. There were a lot of infections going on for a long time and for this kind of virus to evolve you really need a huge evolutionary pressure."

But Andrew Rambaut at the University of Edinburgh is not convinced. He told Science: "I'm not sure there's really anywhere in the world that is isolated enough for this sort of virus to transmit for that length of time without it emerging in various places."

Theory two: It evolved in a person with a weakened immune system

It's possible that omicron developed in a person whose natural immunity was suppressed, such as someone who was chronically ill or whose medication weakened their immune system.

That could be someone with a form of cancer or HIV. A suppressed immune system needs longer to fight viral infections. That in turn gives the virus more time to evolve and mutate in order to evade the person's immune response and defense.

Richard Lessells, an infectious disease researcher at the University of KwaZulu-Natal, supports this theory.

Lessells cites a young woman in South Africa who had an untreated HIV infection and carried SARS-CoV-2 for more than 6 months.

Science quotes him as saying: "The virus accumulated many of the same changes seen in variants of concern, a pattern also seen in another patient whose SARS-Cov-2 infection persisted even longer."

But Drosten says there's clear evidence, observed in people with HIV when they fight other viruses like influenza, to counter the theory. Drosten told Science that while those viruses developed mutations to evade the person's immune response, they also evolved to reduce their ability to transmit from person-to-person.

And compared to other coronavirus variants, omicron is significantly more infectious.

Theory three: It evolved in an animal host and jumped back

It is also possible that the virus hid itself in an animal host, evolved into omicron, and then transmitted back to a human host. 

Kristian Andersen, an infectious disease researcher at Scripps Research, and evolutionary biologist Mike Worobey of the University of Arizona, Tucson, support that theory.

The theory is further supported by the fact that we know that animals are susceptible to coronaviruses, such as SARS-CoV-2.

That's also why many researchers still believe that the first version of SARS-CoV-2, detected in Wuhan, China, over two years ago, originated in an animal.

In 2020, farmers had to cull millions of minks when a mutated version of the coronavirus was detected among them. Veterinary experts suspect the virus jumped from humans to the minks. There were then concerns that the "mink mutation" could jump back to humans again.

Experts say the virus experiences a totally different evolutionary pressure in animals (compared to human-animals) and that that could explain some of the unique mutations found in the omicron variant.

This article was translated from German