How the UK lost control of the mutant strain of Covid-19

In July, scientific advisers warned of the potential for a significant coronavirus variant to occur in the winter. But instead of preparing for the worst, the government created the ideal conditions for the virus to mutate – and thrive.

By Phil Whitaker

The United Kingdom is recording well over 50,000 new cases of Covid each day, figures that would have been unimaginable even a few weeks ago. Fifty-thousand cases equate to roughly 3,000 hospital admissions per day. On 5 January, the country recorded more than 60,000 daily cases for the first time since the pandemic began. We now have more than 26,000 inpatients with Covid – at least 30 per cent higher than at the peak of the first wave in April 2020 – and, once discharges are taken into account, the hospital Covid patient population is growing by around 33 per cent each week. Even with improved treatments, daily death rates are hovering around the 500 mark. And worrying data that has emerged in previous days suggests far worse is to come as January progresses.

Anecdotal reports testify to the parlous conditions in many NHS trusts caused by this relentless onslaught. In London and the south-east, currently the epicentre of the surge, overloaded hospitals are having to divert patients across long distances to where vacant beds are to be found. Elective operations such as joint replacements are being suspended, and NHS managers are reportedly considering delaying cancer surgery for all but emergency cases. Exhausted nurses and doctors are stretched unsustainably thinly, reportedly to the point where care has sometimes become unsafe – a problem exacerbated by staff absences through Covid illness or self-isolation. And Covid is far more than admissions and death rates. With up to 10 per cent of infected individuals developing Long Covid, a form of the disease that persists for months on end, the burden of chronic, debilitating ill health – “invisible” to the public because of the lack of official data collection – is also mounting inexorably.

The principal cause of the surge is a new Covid variant, B117, which was first identified in the UK in October. At that time, there was nothing to distinguish it from the numerous harmlessly altered versions that regularly arise through the process of genetic mutation, which occurs randomly as the virus replicates inside human cells. Even as recently as mid-December, when it became apparent that B117 was associated with a regional surge in the south-east of England, there was still much debate as to whether this represented a genuinely problematic shift in the pandemic. As with every aspect of the global scientific effort on coronavirus, however, the speed with which information is being gathered and disseminated is astounding. On 31 December, a team at Imperial College published its preliminary analysis of data about B117, just ten days after it had been designated a variant of concern (VOC) by Public Health England.

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The Imperial report quantifies what was widely suspected: the VOC is up to 75 per cent more transmissible than the strain that had previously dominated the UK pandemic. It is not yet certain what mechanism underlies this, but it is already clear that the VOC doesn’t replicate any more swiftly once it infects someone. More likely, the mutations that have altered its spike protein – the “key” with which it gains entry into a human cell – have rendered it substantially more effective, so increasing the efficiency with which the VOC can establish footholds when it encounters fresh hosts.

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The Imperial analysis, taken alongside data released simultaneously by the London School of Hygiene and Tropical Medicine (LSHTM), makes for sobering reading. Together, they strongly suggest the present situation, already alarming enough, is fast going to deteriorate further. The English national lockdown in November suppressed the original Covid strain, and its numbers began to dwindle. But while the four weeks of heightened social control measures did somewhat slow the growth of the VOC, it still continued to flourish, soon becoming the dominant strain in the south-east, where it already had a presence. The VOC has subsequently spread to all areas of the country, where it has been accelerating under the four-tier system, which, like the November lockdown, has only been assisting its continued rise to ascendancy. Where London and the south-east have gone, the rest of the country is soon to follow.

In evolutionary terms, “tier” or “lockdown” restrictions are termed a “selection pressure”. By making it harder for viruses to spread between people, any mutated strain that has a greater infectivity gains an advantage and becomes “selected” by dint of being able to reproduce itself more often. Ironically, the November lockdown, intended to allow Boris Johnson to keep his promise of a five-day Christmas social spree, was like pouring petrol on the flames of the VOC.

The Imperial and LSHTM reports offer clues as to what needs to be done. The VOC originally took off in children and teenagers. There are several possible explanations for this, but it seems likely that schools staying open throughout the November lockdown was highly relevant. The reservoir of VOC infections in the young has then spread up through the age groups and, as of the end of December, it has become the dominant strain in all but the most elderly. Stringent social restrictions on the adult population alone were not going to suppress the VOC; they were inevitably going to have to be reinforced by increased restrictions among the young. The pressure on Johnson to close schools became irresistible. But there is a depressing sense of déjà vu. Interviewed on the BBC’s Andrew Marr Show on 3 January, Johnson repeatedly insisted children should be sent into class the next day. By the evening of the 4 January, he had shut schools nationwide. The one-day return will have enabled further viral transmission. The sense of chaotic mismanagement is overpowering.

At present, nothing suggests the VOC is more virulent – capable of causing more serious disease – than the original strain, although there is ongoing work to get hard data on this question. But even if the VOC proves no more virulent than the original strain, its impact will be felt through sheer weight of numbers, causing ever more hospital admissions and death, and condemning many more to the misery of Long Covid.

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The great hope, of course, is vaccination. The UK programme has attracted controversy following the abrupt extension of the interval between primary and booster doses of the Pfizer jab to match the 12-week gap licensed for the Oxford/Astra-Zeneca vaccine. The data from the Oxford/AstraZeneca trials showed one dose was sufficient to prevent severe disease, and hence hospitalisation and death. There is no data to prove the Pfizer jab does the same (though there is reason enough to hope it will), but the licensing conditions have effectively been thrown away in the anxious drive to protect as many vulnerable people as possible in the shortest period of time.

There is no reason to suppose the VOC will prove resistant to vaccine-induced immunity, given the changes in its spike protein have been evolutionarily selected solely for their enhanced infectivity (though it remains possible they will confer, by coincidence, some vaccine resistance). However, the same process of random mutation that gave rise to the VOC’s vigorous transmissibility will continue to throw up new variants as the virus replicates in the hundreds of thousands of UK individuals infected at any one time. Just as random mutation generated a strain capable of thriving despite – or, indeed, because of – the selection pressure exerted by lockdown, there is a distinct concern that the vaccination programme could exert its own selection pressure.

All our vaccines are targeted against the spike protein as configured in the original Covid strain. Were mutations to change the shape of the spike protein in ways that preserve infectivity but evade antibodies raised against the old Covid strain, then the presence of increasing numbers of vaccinated individuals in the population would select for a newly resistant strain, rendering our jabs decreasingly effective. BioNTech, Pfizer’s German biotech partner, has indicated that, in this eventuality, it would be able to readily adapt its vaccine, and there is no reason to think the Oxford/AstraZeneca jab would be any less agile. But we would lose precious time in the process of re-engineering, and potentially in conducting clinical trials to prove efficacy once again.

As the VOC begins to spread around the world – despite the restrictions hastily placed on UK travellers by more than 40 countries – an urgent question remains. Was its appearance in the UK simply bad luck? Or has the Johnson administration’s handling of the pandemic played a part in the VOC’s genesis and ascendancy?

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Since mid-March 2020, the government’s policies have primarily targeted hospital admissions. As long as the NHS seemed able to cope with the daily influx of Covid patients, further measures to suppress case numbers have been prevented by agitation to reopen the economy. Added to this was an incomprehensible failure to radically reform what should have been our most valuable public health weapon. The UK’s dysfunctional system for testing, tracing and isolating (TTI) infected patients and contacts kept background case rates up during the lull between the first and second waves.

In July, the government’s scientific advisory group Sage warned of the potential for a clinically significant mutation to occur during the winter. At the same time, the shadow group Independent Sage repeatedly urged the Johnson administration to take advantage of the summer hiatus to change its policy to a “zero Covid” strategy. This could have driven infection rates into the ground. Instead, we got “Eat Out to Help Out” and the progressive easing of restrictions that allowed daily case numbers to continue in four figures right into the autumn, pump priming the inevitable second wave. With countless billions of viral replications now occurring every day, the chance of advantageous mutations arising is high – far higher than in countries such as Taiwan, South Korea, Australia and New Zealand, where “zero Covid” policies have kept case numbers, and hence viral replications, at tiny levels. And our ailing TTI system, incapable of aggressive suppression of outbreaks, helped create conditions in which any new strain could start to flourish.

It was certainly bad luck that the VOC arose in the UK; there are many other countries with similarly compromised approaches to the pandemic. South Africa appears to have incubated an even more infectious variant, 501.V2, with a greater degree of structural change to the spike protein targeted by extant vaccines. But, like all “accidents”, the VOC wasn’t purely a freak occurrence. With its failure to heed warnings about quite how rapidly and seriously the Covid pandemic could change, the Johnson government has been caught playing with fire. As a consequence, we, and now the rest of the world, are going to get burned.