When Chequers was donated to the nation, the accompanying Act of Parliament was explicit about the intended effect. ‘The better the health of our rulers, the more sanely will they rule,’ it said. Prime ministers need time to think, as well as recuperate, and as Boris Johnson continues his convalescence there, he will be in need of that help. Not only is he still recovering from several days in intensive care, he is also facing a policy problem without precedent — and without good answers. Whatever solution he opts for will determine his premiership, the public’s faith in the British state and this country’s future standing in the world.

In the absence of the optimist-in-chief, an air of depression has settled on the government. ‘We are living in a world of bad options,’ says one of those at the heart of the policy-making process. This is exacerbating tensions between departments. Every-one is better at pointing out the flaws in others’ ideas than proposing ideas of their own.

The Prime Minister might not be back in Downing Street but he is engaging in more and more issues from Chequers. When the government makes the big decisions on corona-virus, they will be his. Those in cabinet who want an easing of restrictions like to believe the return of their Tiggerish leader will speed a return to normality. But those who know Boris Johnson will think that his brush with death means that he is now much more cautious about when and how the lockdown should be lifted.

There are, of course, only three lasting solutions to coronavirus. A cure, a vaccine or herd immunity. All remain out of reach, although as Matt Ridley explains in this issue, there are reasons to hope for a cure. The phrase ‘herd immunity’ has caused much political agony but it is not some form of ‘social Darwinism’, simply a pooling of resources. The normal trajectory of a viral infection is that it keeps spreading until enough people catch it, recover and develop antibodies. Once those responsible for around 60 per cent of social interactions have immunity, the virus doesn’t find anywhere to go. It then peters out and the rest of the population is protected. Many had hoped that the virus had spread widely before the lockdown, which might mean the UK was already close to that 60 per cent. But this does not appear to be the case. No studies have been released in Britain, but government sources say that most epidemiologists calculate that the percentage of people with immunity is very low. Even in London, where the outbreak has been most severe, it is estimated that the percentage with immunity is in the low double digits — nowhere near the percentage needed to remove the threat posed by Covid-19.

All over the world scientists are searching for a treatment but there is no clear answer yet. Huge amounts of work are going towards creating a vaccine. Researchers at Oxford University have spoken about having one by September, but many in government are sceptical. They point out that scientists have been trying to develop a vaccine for coronaviruses for years with little success. The research interest, funding and urgency have all increased dramatically — but a vaccine within months is still very ambitious. Even if a vaccine does become available, there would have to be a national immunisation programme. Everything takes time.

But meanwhile is it realistic to keep the economy in suspended animation until the country is immunised or a cure is found — given the impact of the lockdown on education, public health, and society more broadly? The answer has to be no.

Some cabinet ministers worry about continuing the lockdown even beyond the next three weeks. Covid has split the cabinet into two groups: the inner cabinet, those who are involved in the pandemic meetings, and the outer cabinet, those who are not. Those on the outside worry about the damage inflicted by lockdown. One warns that ‘businesses will hit a brick wall in the next month and then public opinion will flip very fast’. One minister estimates that two thirds of the cabinet favour a significant easing of the lockdown at the next review in just under three weeks’ time. These ministers are aware that the real decision to extend the lockdown had been taken before last week’s cabinet meeting. Several of them felt that with Michael Gove playing the role of intellectual enforcer, there was little point in debating the matter. They also believed that the real decision would have to wait for Johnson’s return. They had thought that he would decisively shift the debate in favour of a substantial easing of the lockdown.

Johnson is not back at his Downing Street desk yet but he is, in the words of one government source, ‘more and more in play’. No. 10 are keen to stress that the main concern at the moment is the danger of a second peak; and so the current restrictions should only be lifted very gradually.

Some are proposing a variable lockdown: loosening restrictions and then tightening them again if infections spike. But in Whitehall, there’s a fear that this approach would be ineffective. Once the virus gets going it’s extremely hard to contain, and it might be tricky to persuade people to accept curbs on their liberty for a second time. One influential figure likens it to ‘ripping off a plaster and then trying to stick the same plaster back on again’. Government insiders now expect only a mild easing of the lockdown restrictions at next month’s review.

The mantra, throughout this crisis, is that the government is being led by the science. But in private, there is an admission that there was, perhaps, a belief early on that the science was more definitive than it actually is. One Johnson ally accepts that the inquiry will criticise them for not interrogating the evidence enough in the early months of the year, of accepting the expert advice too readily. Inside government, they admit that they didn’t realise quickly enough that epidemiology was more like economics than physics: lots of variables, lots of assumptions, and no one right answer.

Cabinet members have been taken aback by the disagreements among those now advising the government. One minister remarks, with a note of shock, that ‘scientists are as bitchy a bunch as lawyers’ and that ‘there are a lot of people who want Whitty’s job’, a reference to the chief medical officer Chris Whitty. Another notes: ‘The Sage [Scientific Advisory Group for Emergencies] committee members don’t even agree with each other, they bicker. And we talk about following “the science” as if there’s one opinion and not at least seven.’

The science will continue to dominate in the coming weeks. There are three big questions that must be answered. First, once restrictions are relaxed, how quickly would the virus spread? This is the oft-cited ‘R number’: whether an infected person infects one other (R=1) or a bit more (R=1.2). The difference between these two numbers could, according to those familiar with the models, determine whether or not the NHS is overwhelmed or not. The natural rate of infection for Covid-19, left to its own devices, is about 2.2.

The second question relates to the effect of the lockdown. How many mental health problems are developing? How many children are not being immunised against other diseases? Is there reason to believe that more people will die from the degradation of cancer care than from the virus itself, as some oncologists say? There is no bar on people going to the doctor or to hospital, but the current environment means that many don’t want to take the risk. The government has run its public health messaging like an election campaign. ‘Stay home, protect the NHS, save lives’ has been repeated as endlessly and as effectively as ‘Get Brexit done’. This discipline has undoubtedly contributed to the remarkably high levels of public compliance with the restrictions and helped slow the spread of the virus. But as long as this message is being driven home every day, people will be reluctant to risk making a journey that they think they can delay — even if that journey is to see a GP.

The third question is what the economic impact will be of trying to crush the disease — as opposed to seeing it as a manage-able risk. This isn’t just an issue of money. One of those inside government who have changed their minds and now want more rather than less easing at the next review argues that the Tories have spent the past two election campaigns saying that a strong NHS requires a strong economy and the government can’t suddenly forget that.

A further complication is that Boris Johnson is determined that the UK must act as one as it heads out of the lockdown. But the devolved administrations (which are not responsible for the economy in the same way that central government is) are almost certain to want to be more cautious than London. Persuading the public it is safe to go back to work will be even more difficult if Nicola Sturgeon is still urging Scots to stay at home. Ministers are worried that this could slow the process still further.

And then there’s the problem of PPE: personal protective equipment. Asking healthcare workers to treat patients without giving them the right kit is like sending out troops in Snatch Land Rovers when the enemy is using roadside bombs. Any significant easing of the lockdown will require the government to procure more PPE at a time when nearly every country in the world is trying to do the same. Teachers and other public servants who come into close contact with people will, for understandable reasons, want to be supplied with their own protective gear. In a sign of where policy will go in future, the Prime Minister has taken to talking to colleagues about the importance of ‘national self-sufficiency’ in medical matters.

When all this is done, he will face the question of how to cover the debts incurred in this pandemic. One cabinet minister who is very familiar with the mood on the back-benches says that ‘austerity might have been right in 2010 and cemented a reputation for good government and fiscal control, but we couldn’t get away with it now. It is just not politically possible’. Combine this with Johnson’s own criticisms of austerity in his interview with this magazine during the election campaign and it is clear this is not the route he will take. Indeed, when he became Mayor of London straight after the financial crisis of 2008, his economic action plan was all about going for growth. We should expect him to take the same approach once the economy is reopened.

The government and the NHS can claim one remarkable and undisputed success in this pandemic: they have expanded hospital capacity at great speed and prevented the system from being overwhelmed. At the start of this crisis, few would have thought that the UK could have 800 deaths a day at the peak without the health service collapsing.

So the question now for Boris Johnson is how to get the balance right — how to ease the lockdown while not overwhelming the expanded NHS. And how to limit the economic and social damage that the virus and these restrictions are causing. The decisions he makes at Chequers in the days ahead will define him and his government.