Omicron has been detected — and may have first arisen — in Gauteng province, South Africa. There have only been a few hundred cases detected, so it’s hard to say much about it with any real certainty. But it appears to be more transmissible and there are concerns that immunity, whether from vaccination or prior infection, will be less effective against it. There have been, as I write, three cases detected in the UK, and there are real (and justified) fears that we are heading once again into a lockdown Christmas. 

But nonetheless, we have been very lucky.

We mustn’t forget that the virus is constantly mutating. Every time it copies itself, there is a chance that it will make some minor error. Most of those mutations either have no effect or make it less effective at spreading. But every so often one will improve it: perhaps make it harder for the immune system to see, or make the virus quicker at copying itself.

The other new variants, notably Alpha and Delta, had several mutations, but Omicron has dozens: around 50. And 10 of them are on the bits of the “spike” protein on the virus’s surface which bind with our cells — the “receptor binding domains”. Sir Jeremy Farrar, the director of the Wellcome Trust and former member of SAGE, tells me that these are exactly the kind of mutations which virologists have been expecting and dreading: “It’s biologically plausible that they will drive higher transmission. They’ve been identified before as ones we should be really careful about.”

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So far, it doesn’t sound very lucky. But in one mutation, Omicron has been kind to us. Like Alpha before it, it has a particular mutation, 69-70del, two missing RNA letters in its genome — part of the “S gene” which codes for the spike protein. By happy chance, those missing letters are at one of three places that many PCR tests look at.

What it means is that if a PCR test comes back positive on two out of its three areas — if it has an “S-gene dropout” — then you can be pretty sure you’ve got one of the variants. It means that Alpha last year and now Omicron can be tracked pretty effectively, just with PCR testing: even without sequencing the genomes, you can see where these S-gene dropout results are happening and it’ll give you a good idea of how the variant is spreading.

“It’s a complete gift that the S-gene dropout hits this variant,” says Ewan Birney, the deputy director-general of the European Molecular Biology Laboratory. If it didn’t, we would have much less of an idea where Omicron is. (We’ve actually been lucky twice. If Delta hadn’t replaced Alpha, then the S-gene dropout wouldn’t have told us anything, because both the circulating variants would have had it.)

So far, so good. But is the new variant more transmissible and/or more able to bypass our immunity, whether from vaccines or infection? And is it more or less dangerous to people who catch it?

These are hard questions to answer, because at the moment, we only have data from South Africa, and South Africa’s population is tricky to compare with ours. It’s younger, for a start — the median South African is 26-years old, while the median Brit is 40. It’s also much less vaccinated: somewhere around 75% of Britons have been double-jabbed, while barely a quarter have in South Africa (which is, to my surprise, more to do with uptake than supply). It has also had far fewer confirmed cases per capita.

That said, we can make some guesses. When a new variant emerges, it’s difficult to tell whether it has spread because it is better at spreading, or because it happens to have arisen in a convenient place. Imagine a virus which happened to mutate into a new variant in someone who was about to go to a major conference. It might infect hundreds of people and show up all over the country, but it wouldn’t be because it was any more transmissible — it was just that it got lucky.

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With Omicron, this seems unlikely to be the case. Thanks to the S-gene dropout, we can see that it’s spreading faster than you’d expect. Farrar says that “there has been a clear upswing of transmission in Gauteng, which seems to be driven by the variant”. “It probably can outcompete Delta,” says Babak Javid, an immunology lab director at the University of California San Francisco, “although by how much is still up in the air.” 

Is that because it’s better at spreading in general, or because it can evade immunity? So far, we don’t have the data to say for sure. Soon, we’ll start to get results from laboratory studies, and later from epidemiological observations, but Rupert Beale, leader of the Cell Biology of Infection lab at the Crick Institute, thinks it’s “a few weeks before we get useful information, and the other side of Christmas before we know anything definitive”.

But on the plus side, antibodies aren’t the only part of our immune system. We also have T-cells, which are less easily fooled by mutations. To oversimplify, antibodies stop you getting infected in the first place, but T-cells stop you from getting very ill. So Javid and Birney think it is plausible that Omicron will spread quite easily among vaccinated and/or previously infected people, but will be less likely to kill them or make them severely ill.

There has also been speculation that Omicron is inherently less deadly to people with no pre-existing immunity. That’s not impossible, but everyone I spoke to said that any definitive conclusions are premature. “The speculation is extremely uninformed,” says Beale. “We just don’t know until it gets into a more vulnerable population, which sadly it seems it’s likely to. We can hope it’s less pathogenic, but it’s foolish to make that assumption.”

So it might be better at spreading, and able to escape our immunity to at least some degree; and while it’s theoretically possible it might be less deadly, that’s certainly not a proposition we want to put any weight on. The question is: what should we do, and are we facing a second bleak Covid winter?

The pandemic should have taught us that acting early is usually better than acting late, and that preparing for worst-case scenarios is important. It’s like chess, says Beale: “You play your moves in the most flexible order.” If we assume it’ll all be OK, we might be right, but if we’re wrong, we’ll end up with Omicron spreading all over the place. Whereas if we assume it’ll be pretty bad, we can always open up again later on.

I’ve seen a lot of people, some of them very sensible, suggesting that there’s no point closing borders to South Africa because variants will get through anyway, and that it’s just punishing countries for doing good surveillance. But I think they are wrong. 

Yes, the variant will get through, if it hasn’t already. Farrar points out that it was first identified on 11 November, and its sequence suggests that it had already been circulating for some time before then. “I think it may already be on every continent,” he says. But that doesn’t mean that there’s no point in trying to reduce its spread. “Border closures might buy you a little time.” Birney agrees: “Shutting the borders until we understand it, minimising the seeding events, is a good rational move.”

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It’s true that there’s a risk of punishing countries for responsible surveillance, but I don’t see what the alternative is — pretending that they don’t have lots of Omicron circulating? Perhaps the thing to do is also put restrictions on countries with poor surveillance.

Because “buying a little time” might be important. If nothing else, it gives us time to understand it: if Omicron is highly virulent and vaccine-resistant, then our best response will be rather different to what it would be if it isn’t. It also gives us a chance to get more boosters in arms and to stockpile antiviral drugs. 

All the same arguments apply to other non-pharmaceutical interventions, such as introducing vaccine passports or asking people to work from home if possible. But there are other things Britain can do, too. 

One thing is to hugely increase our vaccine manufacturing capacity — something which would be good for us and for the world. Rolling out children’s vaccines and booster jabs faster wouldn’t hurt. One scientist I spoke to suggested making antiviral meds available by post when people get a positive result: “They need to be given quickly to have a good effect, so you can’t rely on GP appointments. You need to link them to Track & Trace”. Cheaper, quicker PCR testing at airports would help.”

But while those measures are important, they’re not addressing the root of the issue. For Farrar, the emergence of Omicron is just another reminder that we need to vaccinate the world, not just the rich world. “There’s been political drift for months now, in terms of access to vaccines,” he said. “The rich world thought it was over, so they’ve been kicking it into the long grass.” Variants like Omicron will continue to arise until the world has a decent level of immunity.

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We’ve been lucky, with Omicron. But it may well still end up becoming the dominant strain, just as Delta did before it. If it doesn’t, then another one will come along. And it will be “incredibly disruptive”, says Farrar: “Everyone’s putting restrictions in.” Certainly, to avoid another lockdown Christmas, we need to act now.

But if we want to be sure we don’t have another one next year, we need to get this pandemic behind us — and that means billions more doses of vaccine, distributed around the world. We won’t always be so lucky.

Most of the vulnerable have been vaccinated, and weekly deaths are still below the five-year average. Over the past week, an average of 10 people died from Covid-19 every day in the UK, a drop of 9% on the week before’s toll. Although each death is a human tragedy, we would not normally reorganise society on this scale to prevent 3,560 deaths per year.

Numbers of cases (by positive tests) and admissions to hospital are rising, but from a very low point. The ONS estimates that in England and Scotland just under 1 in 500 people had Covid in the week ending 5 June. Prevalence in Wales and Northern Ireland is much lower.

“We have seen an increase in cases as lockdown measures have loosened, but this has not been the same across all age groups,” says Professor Jennifer Rogers, a member of the Royal Statistical Society Covid-19 Task Force. “The week ending 6 June saw an overall increase in Covid-19 cases compared to the week before, but this was an increase of 124% in the 20-29 age group compared to an increase of 27% among those aged 60+.” She doesn’t think this rise in cases among the young should in itself be cause for concern:

“The younger age groups are more likely to be unvaccinated (or have received only one dose) and arguably they are also more likely to be heading to the pubs socialising with their friends. We probably shouldn’t be too surprised that we have seen an increase in cases, but we know that this younger age group also has the lowest risk if they do catch Covid-19, so an increase in cases shouldn’t necessarily mean a subsequent increase in hospitalisations and deaths.”

Unlike last autumn, when there wasn’t much we could do in the face of rising cases, other than staying away from each other, the continuing vaccination programme means we can now expect things to get better, not worse. Over half the adult population has double-dose protection, including over 95% of the over 70s, for whom Covid-19 bears the highest risk of causing death or acute illness.

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So why has the Government decided to defer freeing us from measures that are, at best, annoying and, at worst, devastating to whole sectors of the economy and society? There are two answers to this, a scientific one and a political one, though in practice it’s hard to separate them.

The scientific one is that, although the current figures for deaths and hospitalisations look better than the predictions upon which the roadmap was based, the near future is still very uncertain. All the models used to plan the roadmap are full of caveats about assumptions, as they should be. Among the things that they foresaw changing were new variants (which might be more transmissible and/or evade immunity), seasonal factors, and human behaviour.

All viruses mutate into new variants. That’s a fact of life. But it makes models of their future behaviour provisional. If the current variant spreads fast enough, and evades enough immune systems — either the previously infected or the vaccinated — models drawn up in February could look optimistic.

Then again, vaccine uptake and effectiveness (especially against death and severe illness) look better than the conservative assumptions made at the end of 2020. By March, Sage advisors were revising their predictions downwards. It was always expected that there would be a third wave of infections this summer, putting more people in hospital and sending some to their deaths. But still, we can’t know how bad the third wave will be.

Three separate institutions drew up new models for Sage in early June, all giving a range of predicted outcomes depending on variants, vaccines and policy options. At best, they foresee a rise in infections similar to January, but mainly among the young, with hospital beds occupied on a similar scale to November 2020, and deaths kept to a few hundred per day. At worst, they predict a repeat of January’s peak death rate. That outcome may not be the most likely, but the scientists modelling possible outcomes have put it into their reports.

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This is where the question becomes a political one. A decision taken now could lead to tens of thousands of deaths in the next few months — or inflict pointless damage to tens of thousands of lives in order to save a small number of them. The continuance of restrictions may not bother those happy working from home and socialising outdoors; but for many who work in hospitality, the arts and entertainment, it could be a fatal hammer blow to their working lives. Social distancing rules make many businesses unviable.

Too long a delay to the final Step 4 of unlocking could even result in more deaths in the medium term, as some infections are pushed into autumn and winter. As the LSHTM Interim Roadmap Assessment comments, “even the 2 or 5 week delay to Step 4 can result in modest increases in morbidity and mortality when measured until the end of the year as more cases are pushed back into the autumn”.

If you are in government, faced with massive uncertainty from your scientific advisors, and potentially massive impacts whichever course you decide, what are you supposed to do? You could take a principled decision to do what you reasonably think will have the best outcome, accepting that you can’t control the actual outcome — but will be held accountable in any case. Or you could consider what policy will minimise the chance of your being blamed for a very bad outcome. You could look at what the public thinks you should do.

Every time the Government announces new restrictive measures, or decides to extend existing restrictions, some of us object, on the grounds that the measures are disproportionate to the real dangers of Covid, or are more harmful to the fabric of society than alternative measures (supporting people to self-isolate, for example). Tens of thousands have taken to the streets to object.

But the truth is that the majority of Britons have supported the lockdown measures. Yes, that expressed support may go along with a certain amount of common-sense rule-bending, but in-principle objection is a minority position. A snap survey by YouGov, following the Liberation Day announcement, showed that 70% of the English population supported the extended restrictions. Older people were the most supportive, but it was a majority across all age groups.

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Given that public sentiment, what government would dare go ahead with a policy that might be seen to lead to another wave of Covid deaths?

The trouble is, we haven’t done nearly enough rational assessment of the harms and benefits of anti-Covid strategies. Invoking the idea of existential risk to push us all into complying with behavioural rules got the Government a free pass for policies that, in normal times, would have been unthinkable. Critics of specific measures were easily lumped in with conspiracy theorists who said the whole thing was a hoax, or “just the flu”. Suggesting that baton-charging sunbathers in parks was counter-productive provoked cries of “How many people do you want to die!?”

But there is also a danger that we’ll come to see the world only through the prism of risk, whether quantifiable or existential. If no level of risk is acceptable, why not surrender our everyday freedoms forever? When will we ever reach the point of it being safe to take off the masks and sit next to a stranger? When they first announced a lockdown in March 2020, the UK government turned on the tap of fear, but I don’t think they realised how hard it would be to turn off.

Until Covid came along, that falling appetite for taking risks was a soft cultural slide. Parents worried about letting their children play outside unsupervised (as they probably did at the same age) and then worried about their child’s mental health when their social lives moved online. Intimacy was something that the young, especially, liked to postpone, preferring more casual relationships, and mediation though technology. Why risk the awkwardness of telephone conversations, when you can text instead? Culture, from comedy to Young Adult literature, was trying to be less edgy and more inclusive, by avoiding material that might make somebody uncomfortable.

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By Freddie Sayers

Covid is a real danger. It has killed millions worldwide, and it is far from over. It is reasonable to be afraid, and reasonable to take measures against it. But it’s not reasonable to expect a government to save every single person from it. It’s not reasonable to sacrifice every other social value to save every possible life.

Unfortunately, the Government’s authoritarian response to this deadly disease has been welcomed by a population that values protection above all. And having once offered itself as the strong, paternalistic shield against Covid, the Government will find it hard to back away.

Is there any hope for a citizenry so fearful, so averse to taking risks, so willing to give up liberty in return for safety?

There is one counter-example in recent history. A narrow majority of us willingly chose the riskier path in voting to take Britain into an unknown future, against expert advice and government warnings of financial loss and social chaos. Back in 2016, there was an appetite for taking a risk in the name of higher values — democracy, sovereignty, a sense of agency in an unpredictable world.

A country that voted for Brexit surely can’t be completely ready to give up all control over everyday life for ever.

And the existing vaccines were designed to mimic the original strain of Covid. We’ve been broadly lucky so far – the vaccines all still work against the variants we’re aware of. But they work less well against the new Delta variant; a Lancet paper last month found that people who had had the Pfizer vaccine had a reduced immune response to the new variant, and a recent Public Health England report says that a single dose of either Pfizer or AstraZeneca only reduces the likelihood of infection by about 33%. 

I don’t want to be too downhearted. It is worth remembering that even though we don’t have data from this vaccine, on the whole the immune system has an excellent memory, and vaccine protection usually lasts for years. And a double dose of either vaccine is much more effective, even against Delta: PHE says 60% in the AZ case, 88% with Pfizer. And they are much more protective than those headline figures against severe disease and death: another PHE paper finds that people who have had both jabs, of either vaccine, are more than 90% less likely to end up in hospital.

But Delta is a warning shot. We might well see a new variant – I was going to say Epsilon, but apparently we’re already up to Kappa – which escapes the vaccines even more effectively.

That’s why we need to start talking about third jabs.

If we want to maintain the freedoms we currently have, and certainly if we ever want to get rid of the disease, we are going to have to have a third innoculation. “The virus is very likely to remain endemic, for the next year at least,” says Dr Rupert Beale of the Crick Institute. Even with everyone double-jabbed, Delta is transmissible enough and vaccine-resistant enough to keep circulating. 

The latest SPI-M-O modelling suggests that it has an R0 of seven. (R0 is the number of people the average infected person spreads the disease to, in a population that has no immunity and no countermeasures against the disease.) If that’s true, then somewhere around 85% of people would need to be fully immune to reach herd immunity. With two jabs in every arm, we still wouldn’t reach that. In that situation it may not kill all that many people, but it will not go away, either. 

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And it may still kill quite a few. Vaccinated people are protected from severe disease, but not perfectly: another Lancet paper suggests that the risk of hospitalisation, if you get the disease, is about a quarter what it would be if you weren’t. SPI-M-O suggests that an uncontrolled third wave could cause hundreds of deaths a day by autumn, even though almost everyone would be double-jabbed, hence Monday’s announcement of the delay to the roadmap.

So we need to talk about what the strategy should be.

So for starters, should we wait for variant-specific vaccine updates? The pharma companies aren’t idiots: they’ve already started creating vaccines for the Alpha to Delta variants. The mRNA vaccines, such as Pfizer and Moderna, are especially quick to turn around, since you can code a new one almost like computer software. 

Amin Khan, head of vaccines at the biotech firm GreenLight[1. Full disclosure: I’ve done some paid work with GreenLight during the pandemic], says that you can get a new variant-specific mRNA vaccine ready to go in a few weeks. And if the new version simply targets a slightly modified version of the spike protein, as the existing vaccines do, it won’t need much in the way of testing and regulatory approval. Changing your manufacturing system is more complicated, “but within two or three months, you can get a new variant to the market”.

Playing whack-a-mole with new variants isn’t a long-term solution, though. The hope is that “third-generation” vaccines will be capable of covering all the existing variants and most foreseeable future ones. But, says Khan, that’s a bit more complicated. A more complete version might target other parts of the virus than the spike protein; that would mean a much more rigorous testing and approval regime, and it may take months longer to get such a vaccine to market. 

We needn’t necessarily wait for a third-generation vaccine to start giving boosters, though. There is good reason to think that a third jab of an existing vaccine will provide a boost to protection, and there’s an ongoing trial at the University of Southampton to see whether that’s true — but it is true for other vaccines, so it’s probably true for Covid.

Assuming that it does offer greater protection, the next question is whether the booster jab should be the same vaccine you’ve already had, or a new one. Again, there are theoretical reasons to think that a different (“heterologous”) booster from the one you’ve already had might provide greater protection. But “there’s no substitute for large amounts of data”, says Beale. 

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At the moment there isn’t much data. A Lancet paper came out recently which found that a heterologous boost had greater “reactogenicity” – that is, it caused more of the mild, expected side effects (feverishness, headache, joint pains) that tell you a vaccine is probably working – than a same-vaccine jab, while also finding no severe adverse reactions. So that’s promising, as are a few other studies. 

And the Southampton trial will be assigning people one of seven different vaccines at random, so it should naturally show if there’s a significant difference between using the same jab and using a different one. That said, it has a relatively small sample size (about 3,000 people, divided between seven Covid vaccines and a control), so it may not be powerful enough to detect small differences. 

One thing that might be worth trying is letting people say that they’re happy to take a heterologous third dose at their own risk; I (for instance) would be quite happy to take a Pfizer or Moderna jab on top of my two AZ doses, and accept the risk of any negative consequences, because I’m extremely confident that there wouldn’t be any. And if a few hundred thousand people did that, then we would soon get some good data on the effectiveness of the strategy.

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Most likely, it will turn out that it’s best to do heterologous boosting. Not only might it be more effective, but it reduces the logistical difficulties of finding the right dose for the right person. A really crucial thing should be that we drop the restrictions on using the AstraZeneca vaccine in the under-40s; if we’re going to accelerate second jabs, let alone consider doing thirds, we’re going to need it.

The third question is who we should be giving it to. There is, as I understand it, good evidence that, insofar as vaccine-induced immunity gets weaker over time, it gets weaker fastest in the old; and since the old are the most vulnerable, it makes sense to boost from the eldest to the youngest again. I might add one detail, though, which is that since there is a clear difference in protection against Delta — at least according to the PHE data — between the Pfizer and the AstraZeneca vaccines, it may be worth preferentially giving boosters to people who had Ox/AZ. 

And the last question is: when? 

This is complicated; we need data. But assuming there is a real boost in protection from a third jab in people whose first jab was six months ago or more, then we probably need to start thinking about giving those elderly and vulnerable people the boost in the next couple of months. Professor Saul Faust, who heads the Southampton trial, says that the JCVI will make decisions in August or September, by which time the first vaccines will have been in people’s arms for nine or 10 months. 

If the UK hits its target of giving every adult a first dose by the end of July, then every adult should have had a second dose by the end of September or early October. Whether we ought to start giving third doses to the elderly before we give second doses to younger groups – or even whether we vaccinate children beforehand – is a question that can only be answered with a cost-benefit analysis, looking at how many lives (or rather years of life) we can expect to save with each. Until some actual data is in from the Southampton trial and others, we can’t reasonably do that analysis.

There’s another question, of course. Can we reasonably justify giving third doses to British citizens when billions of people around the world haven’t had a first dose? From a global perspective, the answer is obvious: a life in Malawi or Sri Lanka is worth no less than a life in the UK and should be given equal value. I instinctively want to say that we should throw huge amounts of money and all our spare vaccines into GAVI and Covax.

But from a UK government perspective, it’s not so clear. “The first duty of the Government is to afford protection to its citizens,” goes the axiom. If you hire a babysitter, you are paying that babysitter to look after your child, rather than every child in the world.

This doesn’t extend to a complete disregard for lives in other nations. If a babysitter saw a child drowning across the street, I think most of us would think it was justified for them to rush out and save it even if it meant leaving your child unattended for a few minutes; at some point, a large chance to save a life in the developing world outweighs a small risk to a life in your own country. But it is at least not obvious that, from a national government’s point of view, the right thing to do is share vaccines equitably. 

Most likely, I’m still well protected against Covid, including the Delta variant. But whether that will still be true by the time the Lambda, Upsilon, Pi and Omega variants arrive is not clear; each new variant that arrives is a new chance for it to escape the vaccines more effectively. 

This is still uncharted water. We need to chart them, as quickly as possible, and to get third jabs into people who need them, so that we can keep on opening up and not slide back into the dark days. I’ve put my name down for the Southampton trial.