When the coronavirus pandemic was in its infancy, one of the common silver linings scientists mentioned was the virus’s slow rate of mutation. It raised the hope that the virus lacked the agility to rapidly evolve around human immunity – whether from previous infection or vaccine. The virus is certainly slow to mutate by some standards. Sars-CoV-2 typically acquires two single letter changes in its genetic code a month, about half the rate seen in influenza.
So why are so many new variants emerging? At the heart of the problem is the fact the global pandemic is raging. Every new case is a chance for mutations to arise, spread and build up. In the simple arithmetic of evolution, when a virus mutates and gains an advantage it can rise above the others.
A particular feature of the Kent variant, named B117, is that rather than emerging gradually, mutation by mutation, it appeared out of the blue with 17 mutations. One theory is that it arose in a single patient who, perhaps because of an impaired immune system, harboured the infection for months – long enough for the more transmissible variant to evolve inside them. Other variants spotted first in South Africa and Brazil may have similar histories, but patchy genomic surveillance makes their origins hard to confirm.
“It’s fair to say that the degree of mutation has surprised many virologists,” said Deenan Pillay, a professor of virology at University College London and a member of the Independent Sage group. “If these variants were emerging almost mutation by mutation, we would see a certain pattern in the surveillance; however what seems to be happening is that a collection of mutations emerge almost as one.”
The scramble to contain the so-called South African variant makes sense, but the effort may slow its spread rather than eliminate it. Like the Kent variant, the South African one is more transmissible and contains multiple mutations. One of the most concerning genetic changes is known as E484K. This helps the virus dodge – to some extent at least – antibodies that are circulating in people’s blood, either because they had Covid in the past or had a shot of vaccine. The danger is that the variant, or one like it, spreads widely and puts a dent in vaccine protection.
Many scientists back the attempt to close down the spread of the South African variant in the UK by going door-to-door through neighbourhoods where cases have cropped up. But unless the outbreaks are limited to a workplace here and a household there, containment is a big ask.
The UK’s genomic surveillance network first detected the South African variant on 22 December and despite travel curbs and quarantine, known cases have risen to more than 100 since. Because sequencing takes time, the number reflects how widespread the variant was several weeks ago, so the real-time situation could be much worse.
Pillay believes the true number of cases, and the geographical spread, could be substantially greater. “We know there are probably 10 to 20 times as many cases in the UK, because we don’t sequence every case. It is naive to expect those 100 or so cases in those particular postcodes to be the only places where this variant is found,” he said.
Another problem public health officials face is that clamping down on the South African variant leaves more moles unwhacked. Even though lockdown has sent the national epidemic into decline, the number of new infections each day is still worryingly high. Beyond the immediate impact they have in causing illness and death, the spread encourages the emergence of further new variants.
As if to reinforce the point, a report from Public Health England on Monday revealed the worrying discovery of 11 cases of the Kent variant that had acquired the E484K immunity-reducing mutation, potentially making the UK’s most dominant variant more dangerous still.
“It’s a worrying development,” Pillay said. “I welcome the public health measures around the South Africa variant but they should be used in a more widespread way. All infections are bad news and new variants are going to emerge. It would be far better if we pre-empted that, rather than responding after the event.”