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Omicron: University of Cambridge virologist on what we know so far about Covid-19 virus variant

The highly-mutated Omicron variant of the Covid-19 virus is circulating in the community and could become the dominant strain in England within weeks.

The first confirmed case in Cambridgeshire came on December 1 in South Cambridgeshire.

An illustration of the Omicron (B. 1. 1. 529) variant of the Covid-19 virus, showing the spike protein mutations. Image: COG-UK Mutation Explorer
An illustration of the Omicron (B. 1. 1. 529) variant of the Covid-19 virus, showing the spike protein mutations. Image: COG-UK Mutation Explorer

The government has moved to its Plan B restrictions in the wake of the variant, meaning work-from-home guidance is returning, face masks are required in more settings and NHS Covid Passes are required for certain events and locations.

On Thursday (December 9), the World Health Organization said: “While there seems to be evidence that the Omicron variant may have a growth advantage over other circulating variants, it is unknown whether this will translate into increased transmissibility.”

Equally, it is still too early to know whether it is more or less severe than the Delta variant.

All 212 confirmed Omicron cases across 18 European Union countries on December 6 had been classed as asymptomatic or mild - but that could be influenced by the age profile of cases.

“Even if the severity is equal or potentially even lower than for Delta variant, it is expected that hospitalisations will increase if more people become infected,” WHO noted.

Meanwhile, Pfizer said lab tests showed three doses of its jab could neutralise the variant, but the effectiveness of two doses was compromised by Omicron.

We asked University of Cambridge virologist Dr Jane Greatorex some key questions about what we know so far, and what we hope to learn in the coming weeks.

Please note that information on the variant is changing fast as more data comes in.

University of Cambridge virologist Jane Greatorex
University of Cambridge virologist Jane Greatorex

How dangerous is this new variant?

I can’t give a definitive answer, because it will still take several more weeks of work before we know. If you look on the government website you can find risk assessments for each variant, which look at whether a virus can escape natural immunity (due to infection) or vaccine-induced immunity. With Omicron, the tests are ongoing. Scientists follow every single variant that has occurred. They do a mixture of sequencing whole viruses, bits of viruses, and looking at antibodies in patient sera. Two years on from the start of the pandemic we have the techniques to be doing this in more or less real time. Even so, it takes a while to do the experiments.

Is the speed Omicron is spreading alarming?

It has moved remarkably quickly around the world – recorded in 57 countries as of December 8 – and you can see on the WHO website that South Africa and the UK have the most cases. But that is also where labs can sequence and detect it. It may have arisen in South Africa – it will be a long time before we know for sure, because not everywhere is sequencing the viruses in the same way. It seems to be spreading faster than Delta. But then, if you think about it, we are travelling more than when we first had the Delta variant.

Why is the Omicron variant being flagged?

It has more combinations of mutations. These viruses mutate all the time but the mutations that are selected for are the ones that make it more easy to transmit. There are subtle changes to the way they bind to us, to the way they dodge our immune systems. And we see the ones that get selected come and go. The government website is interesting because it’ll say a particular variant is ‘extinct’, because one will pop up, appear to transmit to a few people and maybe become a ‘variant under investigation’. Then it will vanish because it just didn’t cut the mustard.

Some media outlets are trying to reassure people saying that the virus will most likely mutate and become more like a cold. Are we kidding ourselves with this idea?

Yes, we are kidding ourselves. This idea that somehow viruses don’t want to kill you or don’t want to make you too ill, is wrong. They don’t want to do anything. They are not sentient; they are just a little bag of protein with some nucleic acid inside that has the capacity, because they have some enzymes as well, to replicate themselves. So we select them and if transmission just happens to coincide with more disease, then that happens. If you think of Ebola, that is successfully transmitted purely because it produces so much virus and it spreads even when its hosts are dead.

This idea comes from the fact we have lived with some viruses for millennia, since we were little four legged things that ran around on the ground. And those viruses become latent within us. The best example is the cold sore virus, herpes. Most of the time you don’t notice that virus, it just lives within you. But every now and again something happens – perhaps you get sunburnt – and you get another infection. Somehow people think that equates to viruses that have been around a long time evolving to cause not so much disease. I don’t think that’s necessarily true. There’s no evidence that it has happened with influenza, which has been with us since at least medieval times according to the literature. In 1918, it killed 10 times more people than Covid has so far.

When will we learn more about Omicron?

I do know that the government is planning to make an announcement on December 18. I think that they will be talking about Christmas and anything that might have to happen.

I’m relatively optimistic. If this had happened a year ago, we wouldn’t be having Christmas, but now we have vaccinations that are very successful and we have some people with booster jabs. There’s no evidence yet to show that this virus can dodge the immune system. That’s one of the things that they’re looking at. But a lot of the mutations in the virus are mutations we’ve seen before, and we know the vaccines work against them.

What is concerning people is that it’s got so many mutations at once, and we don’t know what these combinations of mutations will mean for the immune system. I think people understand now that vaccines don’t necessarily stop you getting the infection but certainly attenuate it.

Is there a risk of another Christmas being cancelled?

I would hope not. I remain optimistic. There will possibly be more mitigations put in place. We know face coverings are more effective than social distancing. We need to make sure people wear face coverings where they can, perhaps in public spaces like train stations, museums, or other places people are gathering. We are used to masks – it shouldn’t be such a big deal. Our students at Lucy Cavendish College have been brilliant. We have just asked them to wear a face covering in college because a lot of people are coming and going, travelling and meeting friends.

We need to be sensible. If you really want to take yourself on a long journey on a plane or a train and people might be talking to you or close to you, it would be a good idea to wear a high quality mask such as an FFP2, which are like a notch down from the clinical masks used in hospitals.

I think we have to have Christmas, but do a lateral flow test first if you want to see your mum or grandma or an immuno-suppressed friend. I use them whenever I’m meeting people if I go to dinner or meet friends or before I travel. If I’m positive, I will stay home and follow the procedures for getting PCR tested.

Will hospitals be overwhelmed?

We are not out of the woods yet I’m afraid, and it will just take a long time. But at the moment 40,000 cases a week means at any one time means around 900 Covid-19 patients in critical care beds in hospital. If the variant is more infectious and we end up with even twice as many people ending up in critical care, we will be in trouble because we do not have that many unoccupied critical care beds. I don’t think it is possible to get everyone vaccinated before Christmas.

How safe are those who have had three jabs?

I would say safer than we would otherwise be, which is why I absolutely agree that we need to get into everyone we can to be jabbed. I hope they do the students before they come back. I do know some people who have had the virus twice, including some of the students, which is very interesting. You do wonder if there is something about their immune system that gives them a predisposition to it. We know that some conditions like diabetes can mean you’ve got more of the receptors that the virus likes and therefore you are more susceptible to having bad disease. Maybe you’re also more susceptible to reinfection. It will take a long, long time before we’ve got all that data together.

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