The Omicron variant of SARS-CoV-2 — it’s like a line from some science fiction movie. Probably within minutes of the news breaking you knew about the new variant, given how we are obsessively checking the news on Covid-19. Certainly, the headlines grabbed you, screaming “scientists are very concerned”.
ere’s an update. The bottom line is there’s a lot we don’t know, so you might as well stop thinking about it and go back to thinking about the admittedly slightly less terrifying prospect of another Christmas in a pandemic.
More than 5.6 million different SARS-CoV-2 genomes (meaning the RNA recipe that makes the virus) have been documented so far. In those there are 23 related groups. Delta is the most transmissible variant so far, but thankfully the vaccines help prevent it from causing severe disease and death. If they didn’t, we would be in full lockdown.
From November 15 (just under three weeks ago) South African scientists noticed that case numbers jumped from 400 a day to over 2,000. This kind of jump has happened in many countries now that winter is here. But it’s summer in South Africa so the scientists wondered why. They examined the virus and to their dismay saw that it was a new variant, now known as Omicron.
One scientist has called Omicron “weird” as it is very unlike any other variant, including Delta. It has 35 differences in a key part of SARS-CoV-2, the spike protein, and 10 of those are new to science. That’s a lot.
It’s still not clear where Omicron came from. It might have grown in someone who was immunosuppressed, producing offspring for months and months, changing all the time and finally ending up as Omicron. Or it might have been in a community rarely tested where it could grow and spread and change, especially if that community had a low level of vaccination — hence the need for widespread vaccination. There is even a possibility that it developed in an animal. The Wuhan variant might have jumped back into an animal, and then grew over time into Omicron, jumping back into a human.
The changes in Omicron are mainly in the spike protein, which the virus uses to get inside your lungs. The spike is a bit like a key going into a lock on cells in your lungs which is called ACE2. Scientists used an Artificial Intelligence programme called DeepMind to figure out the shape of the Omicron spike. Yet again that reads like a line from a science fiction movie. The change in the spike key means it might be able to slip into the ACE2 lock more easily and open the door into your lung cells. That would make Omicron more transmissible because it would enter your lungs much more readily, but this is still a prediction.
The second thing that is important about the spike is it gets swamped by antibodies made by your immune system. This is clever because the bunging up of the spike key stops it getting into the ACE2 lock, preventing the lock from opening and allowing entry into your lungs.
Do the changes in the spike on Omicron make antibodies less able to mask it? That would mean your immunity against Omicron would be lessened if you’d been exposed to a previous variant, increasing the chance of you becoming very sick. Equally it might make the vaccine you’ve had less able to protect you. In both cases the antibodies you have against a previous version of the spike key would be less able to stick to it. The Omicron key might have become slippier for antibodies.
It is these issues that have made scientists concerned. Scientists are often concerned. It’s what makes them do experiments to find stuff out. But the truth is on November 25 when Omicron was announced we just didn’t know enough about what the changes in the spike might mean. Stock markets fell around the world, and all because of speculation about a protein on a virus. Unprecedented times yet again.
The rise in cases in South Africa is being watched closely. We have just heard that Omicron does seem to be better able to infect people who have been previously infected, although so far that infection doesn’t appear to be causing severe disease, which is good.
Many countries banned travel from affected countries. The country that reported Omicron, South Africa, a country where only 24pc are fully vaccinated, was rewarded by being cut off. Surely a disincentive for other countries to report variants?
The travel bans are designed to buy time in case Omicron is really bad. But the cat is already out of the bag when it comes to Omicron, as it has been detected in over 30 countries including Ireland.
The UK has ramped up its booster campaign: everyone over 18, and a shortened gap of three months between the second and third shots. It is essential that Ireland does the same.
This is sensible anyway, because of waning vaccine effectiveness against Delta. But it’s more urgent, because if the antibodies you make are less able to stick to Omicron’s spike, quantity of antibodies will trump quality, so let’s get on with boosting. This is important in the run-up to Christmas, and more so because of Omicron.
Ugur Sahin, who made the Pfizer vaccine, is hopeful that it will still offer protection. The strong antibody response will work somewhat but also the other key arm of your immune system, the T cells, can recognise parts of the spike outside the parts that are different in Omicron and should offer protection against severe disease. If the army of antibodies is weakened slightly, the airforce of the T cells is still powerful enough to bomb Omicron. Also, the antiviral drugs Paxlovid and Molnupiravir are likely to work as they are hitting parts that haven’t changed substantially.
But we still need more data. Hopeful signs are coming from Israel. Health minister Nitzan Horowitz has said there is initial data that the booster shot, or indeed recent vaccination, is offering almost as good protection against Omicron as against Delta. We’ll need to see the data, but we can be hopeful.
A trying week where every news bulletin began with Omicron comes to an end. How much more can our nerves take? There is talk of vaccine mandates, working from home mandates and even lockdowns. We may be about to limit household mixing and restrict hospitality again. And all because of fears over a different spike protein which are yet to be realised, in the face of a hospital situation that has stabilised.
We can be more certain of using booster shots and widespread antigen testing to fight Omicron, and surely the focus should be on them rather than more restrictions — at least until we find out a bit more in the coming week or so.
There will of course be more challenges ahead. Yet again we must use the best science has to offer to provide us with some cheer in the run-up to Christmas, our second of the Covid-19 pandemic.
Luke O’Neill is professor of biochemistry in the school of biochemistry and immunology at Trinity College Dublin