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.

For some, the future is now. More than 4 million people have had a shot of a vaccine, each jab sparking a little flash of hope. Social media and family WhatsApp groups ping with people keen to share the news that a parent, a grandparent, a great-aunt, anyone they know has had the vaccine. Each story is offered as proof that the light at the end of the national tunnel is drawing closer. Britain is cautiously optimistic, and that’s good for a government that hasn’t won much praise for managing the crisis so far. YouGov finds 61% think the government is handling the vaccine rollout quite well or very well.

Are we about to emerge from the darkest days and start putting the strains and pains of the pandemic behind us? Don’t bank on it. Britain and Boris are happy right now, but both should enjoy that tentative feeling of vaccine-driven optimism while they can, because a whole new set of problems is on the way. Indeed, if luck is against us — and it generally has been — then it’s ominously possible that vaccinating Britain against Covid-19 will bring about a greater test of faith in the state — in our coherence as a society and in our national character — than the virus itself was.

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The first act of the vaccine-tension drama is regional, with different bits of the country complaining that other bits are getting more jabs more quickly. Any metro-mayor or local political baron worth his or her salt has already jumped on this bandwagon of grievance already: Sadiq Khan says London is hard done-by; a cross-party group of pols in Birmingham say the same for their city. This will make for good local headlines but will fade away as long as the overall rollout continues well. And thankfully none of our sharp-eyed local leaders has yet decided to copy the health boss in Italy’s rich North who wants vaccine stocks allocated according to regional GDP.

Far more serious is how people behave — and see each other — once some of them have had the vaccine. Will the Covid rules survive the partial vaccination of Britain?

Despite the fretting of politicians and headline-writers, posterity will remark that the most notable aspect of Britain’s early pandemic experience was near-universal acceptance of restrictions meant to protect some of our society from harm. The UCL Covid Social Study found more than 97% compliance with Lockdown 1, with no reduction from March to May last year. Britain really did stick to the rules and, although most people with symptoms still don’t get tested, overall compliance in early 2021 is near the levels of May 2020.

Why? Far from being an atomised amalgamation of hyper-individual libertarians, Britain is, when the chips are down, still a coherent society where people feel themselves part of something bigger than themselves. We stay inside to “protect the NHS” not just because we want it to be there to look after us, but for other people too. We stay inside to “save lives” not just because we fear for our own and those of our family, but to avoid increasing the risk of the virus killing a complete stranger several links down the infection chain.

The uniformity of compliance is all the more noteworthy given that economic experiences of lockdown are anything but uniform: staying at home is an annoying way to save money for people with decent and secure incomes, but a financial disaster for many people in poverty. Even the young and healthy who have less to fear from the virus than others have, mostly, complied with restrictions that have disrupted their lives and damaged their life-chances. Far from being feckless and reckless, their compliance rates are not much different to those of older people, and they’re actually more likely than others to get themselves tested.

Young people haven’t turned their lives upside down just to prevent Covid killing their gran. They’ve done it to protect other people’s grans too. And this is where the vaccine, the lovely vaccine that will protect from the dreadful virus, could end up injecting real discord into British life.

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The fact is, people who are vaccinated might still be able to spread the virus — and therefore still pose a threat to people who aren’t, some of whom will end up in hospital and possibly dead. And then there’s the nightmare scenario where a virus circulating in an only partially-vaccinated population mutates into something resistant to that vaccine. In short, there are still good reasons to keep a lid on things even after a big chunk of the population is vaccinated. But will there be persuasive arguments for that? The idea that you might kill someone’s gran unless you stay at home loses its force when grannies are out to lunch because they’re all vaxxed up and raring to go.

Will vaccinated older Brits comply with the rules if the lockdown persists well into the spring? There are reasons to think that many will not. Among them, the evidence that older people aren’t very compliant with some of the key elements of Covid strategy. The Covid Social Study shows 75% of adults aged 60+ say they have never requested a test despite experiencing symptoms on one or more occasions since the pandemic started. Will those people step up their compliance once they’ve been given a shot? No wonder ministers are ramping up their messaging to the vaccinated to tell them that they need to keep playing by the rules.

On current progress, by early spring the vaccine should be cascading down to people in their 60s. Will it really be politically viable for any government — but especially a Conservative one dependent on older voters — to instruct millions of fit, healthy 60-somethings to accept ongoing restrictions to contain a disease to which they are now immune? Especially given that those 60-somethings might be keen to get out and spend money in bits of the economy that dearly need their custom.

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There’s another reason the political climate will make it harder still to keep the vaccinated at home and masked up. They don’t boast about it, but newspapers in the UK are largely read by people who will get vaccinated by the time the tulips are up. Most also rely on advertisers and sales that have been hammered by Covid restrictions. Don’t expect Fleet Street to argue that 60-somethings with an armful of vaccine and a wallet full of cash should stay at home until the whole population is jabbed in the autumn.

The prospect of lots of people once again circulating freely while the virus is still active is troubling scientists and health officials, and for good reason. The risks that arise from older people cutting loose once vaccinated include a domino effect on the behaviour of others. We’re social animals and group norms affect all of us: a powerful force behind Covid compliance is the sense that everyone else is doing it so we should too. If we think other people aren’t playing by the rules, why should we?

More specifically, why should 20-somethings who face no significant risk from Covid, and who have put their lives in the bin for a year to protect their grandparents’ generation, continue to do so when that generation has been very visibly (and expensively) vaccinated — and is out and about making up for lost time?

In the dry verdict of the Government’s SPI-B behavioural analysis experts: “Adherence might decline if people feel less of a need for protection, or the rules and guidance seem less salient to them as attention focuses more on the vaccine.” Crucially, SPI-B notes: “These factors might vary across different sectors of society.” In other words, a vaccination plan that only covers some of the country may well mean that when it comes to Covid compliance, we no longer stand together. Whatever national unity we maintained during the earlier phases of the pandemic will be tested as never before.

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Will ministers try to hold the ring and urge ongoing restraint, more social distancing and curbs on gatherings? Already, this week’s attempts to curb Britain’s enthusiasm are looking rather underpowered. As the vaccine rollout continues, emotive arguments for ongoing restrictions and compliance will only get harder. By the time the vaccine reaches the 60+ group, the best reason to go on restricting movement and curbing viral spread will be that among those still unprotected are the group who are among the most likely to end up in intensive care with Covid, with all the attendant burdens on the NHS: overweight middle-aged men.

“Don’t kill gran” had moral force and emotive power. “Stay at home because Fat Uncle Barry could end up in ICU” seems unlikely to sway the British population in quite the same way. Maybe the vaccination journey will see some realignment in Britain’s intergenerational relations, the young and the old uniting to demand the restoration of their freedom, at a public health cost to the generation in between.

Then there’s race. One study reckons 72% of black Britons are reluctant to be vaccinated, and 42% of those of Pakistani or Bangladeshi heritage; conspiracy theories about the vaccine are said to spread widely in some British Asian communities.

This isn’t just awful because of the ongoing risk to those who decline the vaccine. There’s also a nasty risk to social coherence. Significant numbers of Covid-vulnerable BAME Brits going without the vaccine bolsters the need to maintain Covid restrictions for longer. Public health policy and basic humanity both dictate that they must be protected even if they’ve chosen not to take up the vaccine.

But I fear that point could be taken badly in some corners of the emotive, social media-driven debate about the virus. A country where a small number of people are willing to accuse NHS staff of lying about hospital occupancy is capable of unpleasant conversations about whether a majority group should have to make compromises to ensure the welfare of a minority group.

Sometimes, wartime unity is replaced by peacetime tensions. When the pandemic raged with no sign of an ending, Britain was all in it together. But we won’t get out of it together, and that could be our toughest test yet.

Today, though, the presence of some level of prior resistance and immunity to Covid-19 is fast becoming accepted scientific fact. Results have just been published of a study suggesting that 40%-60% of people who have not been exposed to coronavirus have resistance at the T-cell level from other similar coronaviruses like the common cold.

Now, from the unlikely source of a prominent member of the “Independent SAGE committee”, the group set up by Sir David King to challenge government scientific advice and accused by some of being populated with Left-wing activists, comes a claim that the true portion of people who are not even susceptible to Covid-19 may be as high as 80%.

Professor Karl Friston, like Michael Levitt, is a statistician not a virologist; his expertise is in understanding complex and dynamic biological processes by representing them in mathematical models. Within the neuroscience field he was ranked by Science magazine as the most influential in the world, having invented the now standard “statistical parametric mapping” technique for understanding brain imaging — and for the past months he has been applying his particular method of Bayesian analysis, which he calls “dynamic causal modelling”, to the available Covid-19 data.

Friston referred to some kind of “immunological dark matter” as the only plausible explanation for the huge disparity in results between countries in an interview with the Guardian last weekend. The eye-catching phrase attracted a lot of attention on social media, with some commentators keen to dismiss it as rubbish, but he meant it in a quite precise way: like dark matter, the undetectable substance that makes up approximately 85% of the universe, it is provably there by its effects. We just don’t know anything about it.

His models suggest that the stark difference between outcomes in the UK and Germany, for example, is not primarily an effect of different government actions (such as better testing and earlier lockdowns) but is better explained by intrinsic differences between the populations that make the “susceptible population” in Germany — the group that is vulnerable to Covid-19 — much smaller than in the UK.

As he told me in our interview, even within the UK, the numbers point to the same thing: that the “effective susceptible population” was never 100%, and was at most 50% and probably more like only 20% of the population. He emphasises that the analysis is not yet complete, but “I suspect, once this has been done, it will look like the effective non-susceptible portion of the population will be about 80%. I think that’s what’s going to happen.”

Theories abound as to which factors best explain the huge disparities between countries in the portion of the population that seems resistant or immune — everything from levels of vitamin D to ethnic-genetic and social and geographical differences may come into play — but Professor Friston makes clear that it does not primarily seem to be a function of government coronavirus policy. “Solving that — understanding that source of variation in terms of this non-susceptibility — is going to be the key to understanding the enormous variation between countries,” he said.

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Professor Friston is ultra-cautious in his choice of words, and understandably so: the impact of this realisation, if proven correct, is hard to overstate.

Immediately it would change how we should think about lifting lockdown: a tube carriage in London might in theory have to be restricted to 15% capacity to maintain social distancing of 2 metres, but if, as Professor Friston believes, the susceptible population in London was only ever 26% and 80% or more of that group is now provably immune via antibody testing, you can put a lot more people in a tube carriage without increasing the level of risk. Ditto restaurants, pubs, theatres and most recently, MPs in parliament. It would question the whole idea of social distancing being a feature of any “new normal”.

It would take the heat out of the political argument around the pandemic, and give the lie to the idea that it was ever primarily government actions (however incompetent or incompetently executed) that explain differing death rates. As Professor Friston puts it, once you put into the model sensible behaviours that people do anyway such as staying in bed when they are sick, the effect of legal lockdown “literally goes away”.

His explanation for the remarkably similar mortality outcomes in Sweden (no lockdown) and the UK (lockdown) is that “they weren’t actually any different. Because at the end of the day the actual processes that get into the epidemiological dynamics — the actual behaviours, the distancing, was evolutionarily specified by the way we behave when we have an infection.”

Most significantly, it would mean that the principal underlying assumption behind the global shutdowns, typified by the famous Imperial College forecasts — namely, that left unchecked this disease would rapidly pass through the entire population of every country and kill around 1% of those infected, leading to untold millions of deaths worldwide without draconian action — was wrong, out by a large factor. The largest co-ordinated government action in history, forcibly closing down most of the world’s societies with consequences that may last for generations, would have been based on faulty science.

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When I put this to Professor Friston, he was the model of collegiate discretion. He said that the presumptions of Neil Ferguson’s models were all correct, “under the qualification that the population they were talking about is much smaller than you might imagine”. In other words, Ferguson was right that around 80% of susceptible people would rapidly become infected, and was right that of those between 0.5% and 1% would die — he just missed the fact that the relevant “susceptible population” was only ever a small portion of people in the UK, and an even smaller portion in countries like Germany and elsewhere. Which rather changes everything.

With such elegant formulations are scientific reputations saved. Practically, it makes not much difference whether, as per Sunetra Gupta, the 40,000 officially-counted coronavirus deaths in the UK are 0.1% of 40 million people infected, or, as per Karl Friston’s theory implies, they are more like 0.5% of 8 million people infected with the remaining 32 million shielded from infection by mysterious “immunological dark material”. If you are exposed to the virus and it is destroyed in your body by mucosal antibodies or T-cells or clever genes so that you never become fully infected and don’t even notice it, should that count as an infection? The effect is the same: 40,000 deaths, not 400,000.

This wouldn’t mean that most of the population is technically immune to Covid-19 — scenarios with a very high viral load, such as doctors treating Covid-19 patients in hospitals may still overpower these defences — but it would mean under normal circumstances, most people would never have contracted the disease.

The atmosphere in the UK continues to change irrespective of Government policy, and if people ever were afraid they are becoming less so, having intuited that, for now at least, the coronavirus threat seems to be in retreat. Gradually, the scientists are providing explanations for why that might be.