What we know about Omicron

In just a few weeks since its discovery, the Omicron variant has surged across the world faster than any other previous SARS-CoV-2 types.

The highly infectious variant is causing a sharp rise in infections globally, but the statistical risk of hospitalisation as a result of contracting Omicron is a third lower than the Delta variant.

Whether Omicron is a more benevolent virus or pre-existing immunity protects us from severe disease is still unclear. Either way, despite the variant causing milder symptoms in most people, Omicron is spreading so rapidly it’s putting healthcare systems in serious trouble.

“We keep saying that [Omicron] is causing milder disease, but the sheer number of infections is so large that even if a smaller percentage of people get sick enough to need hospitalisation, that’s still a huge number – probably a larger number than we saw in the previous waves,” says Professor Kanta Subbarao, an infectious disease expert and director of the WHO Collaborating Centre for Reference and Research on Influenza.

A milder disease might sound like good news, but the pandemic is far from over. Global vaccination remains a priority, and more evidence supports the need for booster shots.

Origin of the Omicron variant

Omicron was first reported in South Africa last November, but it’s still unclear exactly where it came from. This variant of SARS-CoV-2 contains many mutations rarely seen in other known human variants.

The most popular hypothesis is that Omicron emerged during a protracted COVID-19 infection in an immunocompromised patient. Usually, a functioning immune system suppresses the infection relatively quickly. In immunocompromised people, a viral infection can linger for months, allowing the virus to replicate again and again and undergo several mutations.

But a new study from the Chinese Academy of Sciences in Beijing has suggested that SARS-CoV-2 jumped from a human to a mouse in mid-2020, then back into a human in late 2021.

The researchers found that the Omicron mutations closely resembled those typically seen in a virus that has infected mice. They point out it is unlikely that the intermediate host was a laboratory mouse.

What are the symptoms of Omicron?

Some symptom differences have emerged.

Real-world data released in December from South Africa’s largest private health insurer suggested that most people developed cold-like symptoms such as sore throat and runny nose, fever, headaches and muscles aches, especially low-back pain.

Interestingly, Omicron may be less likely than earlier variants to cause a loss of taste and smell.

Spreading fast

“The big thing about this variant is that it’s highly transmissible,” says Dr Kirsty Short, a virologist at the University of Queensland.

In a pre-print study, researchers from the UK Health Security Agency observed how Omicron spread within 121 households. They found that the variant was 3.2 times more likely to cause a household infection than Delta.

Scientists don’t yet fully understand what makes Omicron so transmissible. They believe that the variant’s distinctive combination of more than 50 mutations, some carried by earlier variants such as Alpha and Beta, could enable a coronavirus to spread quickly.

“The changes in the spike protein do appear to cause more rapid infection and possibly provide higher amounts of virus,” says Professor William Rawlinson, a virologist and infectious disease expert at the University of New South Wales.

Researchers from Japan and the US found that Omicron attacks the lungs much less frequently in animal studies. Instead, the variant seems particularly good at infecting the nose, throat, and trachea cells.

Says Short, with Omicron the infection has moved from the lungs to the upper respiratory tract. This means when an infected person breathes, talks, sneezes or coughs, they can more easily release the virus than if it lived deep in the lungs.

Also, Omicron’s mutations make it adept at dodging antibodies produced by vaccines and previous infections.

The first indication that Omicron could evade immunity came from South Africa, where a large fraction of Omicron cases involved people who had previously been infected.

Several studies have demonstrated that Omicron is “markedly resistant” to neutralising antibodies found in serum from convalescent patients and vaccinated individuals.

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Antibody escape might explain why the rate of reinfections and breakthrough infections has skyrocketed.

There is also something else at play. While most countries tried to contain the Delta wave with lockdowns, the Omicron spread has been met with softer restrictions. Masks and vaccination certificates are still widely required, but mobility has increased globally within and through borders.

Many governments have been forced to change their quarantine policies, reducing the self-isolation period of positive cases from 10 days to as little as five days in the US.

The rationale behind a shorter isolation period policy is that a milder and shorter course of infection might suggest that the infectious period is also shorter compared to other variants.

But Rawlinson is not convinced that the scientific evidence strongly supports this thesis. “If somebody is symptomatic, is coughing, has a runny nose, touches their nose and then touches a surface, somebody else is more likely to transmit,” he agrees. “But just because you don’t have symptoms doesn’t mean you can’t spread the virus.”

Short says these policies are driven by a combination of practicality and the fact that the population now has some pre-existing immunity, whether through vaccination or previous infection. “You have so many people infected that it’s just not practical for everyone to quarantine for 14 days,” she says.

Milder disease or vaccines at work?

As mentioned, most Omicron infections centre on the upper respiratory tract rather than the lungs, which might explain why symptoms are generally milder.

Researchers at the University of Hong Kong found that although the Omicron variant infects the bronchus – the lungs’ major air passages – up to 70 times faster than the Delta variant, it spreads up to 10 times less in lung tissue, thus causing minor damage to the lungs.

“An infection in your lungs is much more problematic than a runny nose,” says Short.

But she says it is still not entirely clear whether the Omicron variant causes a milder disease per se, or if milder infections result from a change in epidemiology.

“When we compare the Omicron wave to the Delta wave, we are not just comparing different viruses, we are also comparing fundamentally different populations,” she says.

When Omicron emerged, wealthier countries had already reached high vaccinations rates, and in poorer countries, where vaccination rates are still low, most people had recently recovered from a Delta infection. In South Africa, where Omicron began to spread at first, scientists had estimated that at least 70% of the population had had COVID-19 at some point in the pandemic.

Compared to 2020 and the beginning of 2021, when Delta emerged, a large percentage of the world population has now some pre-existing immunity.

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Evidence suggests that antibodies elicited from a COVID-19 vaccine don’t do a great job at stopping the Omicron infection, causing many breakthrough infections. “That doesn’t at all mean that vaccines don’t work,” says Short.

Vaccines do more than elicit an antibody response.

“If you look at the virus’ mutations, particularly on the spike glycoprotein because that’s one of the drivers of the immune response, about 70% of those targets are still intact,” says Rawlinson. “So the T-cell response is very likely to be important in the longer term.”

Two new studies, not yet peer-reviewed, suggest that T-cells of vaccinated and recovered patients still recognise the Omicron variant nearly as well as the original SARS-CoV-2 variant, thus protecting us from the nastier symptoms.

Does a third dose make any difference?

Researchers at the University of Oxford found that the two doses of the AstraZeneca or Pfizer vaccines were less effective against stopping Omicron compared to previous COVID-19 variants. But in an extensive study of more than a million cases of COVID-19, researchers found that, compared to those unvaccinated, the odds of being admitted to a hospital were 65% lower for people who had received two doses of vaccine, and 81% lower for those who had received a booster shot.

“That leads to a very strong recommendation for the third dose of the vaccine because you push up the amount of antibodies and that reduced neutralisation effect is kind of cancelled out,” says Rawlinson.

Who is still most at risk?

“The story hasn’t changed at all,” says Short. The elderly, the immunocompromised, and those with underling conditions remain most at risk. “But a lot of those people are now vaccinated, thankfully,” she adds.

The unvaccinated are those who risk the most, agrees Subbarao, because they can still experience severe disease.

According to a report from New York state, US, since Omicron has begun to spread in the state, fully vaccinated New Yorkers have had between a 90% and 95% lower chance of being hospitalised with COVID-19 compared to unvaccinated New Yorkers.

Infections have also risen among children, who represent a large unvaccinated population. While they are yet less likely to experience severe disease, the large number of infections means that more of them will need hospital care. 

Kids older than five, those with underlying chronic illness or previous episodes of pneumonia are at higher risk of worse outcomes.

“They’re going to be really vulnerable because everyone else is vaccinated,” says Short. “That speaks to the benefits of rolling out paediatric vaccination.”

Is Omicron the beginning of the end?

“We all hope so,” says Subbarao. But she admits, this is something we still don’t know.

Pandemic viruses tend to evolve to become more transmissible but less lethal, and Omicron seems to head in that direction. But the path to endemicity is not entirely understood, she says.

We can certainly hope that Omicron is the beginning of the last chapter of the pandemic book. But what the following variant will be like “we have no way of knowing,” says Subbarao. “We just have to wait and see.”

“It is unusual that a more severe variant emerges as you go forward,” says Rawlinson reassuringly. “But it’s still possible.”

In the meantime, “vaccines are the way to go”, he says. And because vaccines do not offer 100% protection, “the old message about masks, wash your hands, don’t go to work if you are ill, it is still quite true”.

Rawlinson says good public measures can substantially lower people’s risk. “Just because it’s more transmissible doesn’t mean that you have to get it.”