Just as vaccines are beginning to offer hope for a way out of the pandemic, officials in Britain raised an urgent alarm last weekend over what they called a highly contagious new variant of the coronavirus circulating in England.
Citing the rapid spread of the virus through London and surrounding areas, Prime Minister Boris Johnson has imposed the country’s toughest lockdown since March.
“If the virus changes its attack method, we have to change our defense method,” he said.
London train stations are filled with crowds scrambling to get out of the city when the restrictions took effect. On Sunday, European countries began closing their borders to travelers from the United Kingdom, hoping to shut out the new iteration of the pathogen.
A similar version of the virus has surfaced in South Africa, sharing one of the mutations seen in the British variant, according to scientists who discovered it. That virus has been found in up to 90% of samples whose genetic sequences have been analyzed in South Africa since mid-November.
Scientists are concerned about these variants, but are not surprised. Researchers have recorded thousands of minor changes in the genetic material of the coronavirus as it has spread around the world.
Some variants are more common in a population simply because of luck, not because the changes boost the virus in some way. But as it becomes more difficult for the pathogen to survive – due to vaccinations and increasing immunity in human populations – researchers also expect the virus to develop beneficial mutations that allow it to spread more easily or escape detection by the immune system.
Read: European countries ban UK flights as UK says new coronavirus strain is ‘out of control’
“It’s a real warning that we need to pay more attention,” said Jesse Bloom, an evolutionary biologist at Fred Hutchinson Cancer Research Center in Seattle. “Certainly these mutations will spread, and sure, the scientific community, we have to monitor these mutations, and we have to characterize what effects have.”
The British variant has about 20 mutations, including some that affect how the virus attaches to and infects human cells. These mutations may allow the variant to replicate and transmit more efficiently, said Muge Cevik, infectious disease expert at the University of St Andrews in Scotland and scientific adviser to the UK government.
But the estimate of greater portability – UK officials said the variant was as much as 70% more transferable – is based on models and has not been confirmed in laboratory experiments, Cevik added.
“Overall, I think we need a little more experimental data,” she said. “We cannot entirely rule out that some of this portability data may be related to human behavior.”
In South Africa, too, scientists soon noted that human behavior was causing the epidemic, not necessarily new mutations whose effect on transmissibility had yet to be quantified.
The UK announcement also raised concerns that the virus could evolve to become resistant to the vaccines just rolled out. The concerns center on a few changes in the viral genetic code that may make it less vulnerable to certain antibodies.
But several experts urged caution, saying it would take years – not months – for the virus to evolve enough to make current vaccines impotent.
“No one has to worry that there will be a single catastrophic mutation that will suddenly render all immunity and antibodies inoperable,” said Bloom. “It will be a process that takes place over a time scale of several years and requires the accumulation of multiple viral mutations. It’s not going to be an on / off switch. “
The scientific nuance mattered little to Britain’s neighbors. The Netherlands is concerned about the potential influx of travelers transporting the variant, saying it would suspend flights from Britain from Sunday to January 1.
Italy also suspended air travel and Belgian officials on Sunday issued a 24-hour ban on arrivals from the United Kingdom by air or train. Germany imposes regulations restricting travelers from Great Britain and South Africa.
According to local media, other countries are also considering a ban, including France, Austria and Ireland. Spain has asked the European Union for a coordinated response to the flight ban. New York government Andrew Cuomo asked the Trump administration to consider banning flights from Britain.
In England, transportation officials said they would increase the number of police officers checking interchanges such as train stations to ensure only essential journeys were made. Matt Hancock, the country’s health minister, called those who packed the train Sunday “ clearly irresponsible. ”
He also said the restrictions imposed by Johnson could last for months.
Like all viruses, the coronavirus is a shape-shifter. Some genetic changes are insignificant, but some may give it a head start.
Scientists are especially afraid of the latter possibility. The vaccination of millions of people can force the virus into new adaptations, mutations that help it evade or resist the immune response. There are already small changes in the virus that have emerged independently multiple times around the world, suggesting that the mutations are beneficial to the pathogen.
The mutation affecting antibody sensitivity – technically called the 69-70 deletion, meaning letters missing from the genetic code – has been seen at least three times: in Danish mink, in humans in Great Britain, and in an immunosuppressed patient which is much less sensitive to restorative plasma.
‘This thing is shipping. It is acquiring. It is constantly adapting, ”said Dr. Ravindra Gupta, a virologist at the University of Cambridge, who detailed the repeated emergence and spread of the deletion last week. “But people don’t want to hear what we’re saying, which means this virus will mutate.”
The new genetic deletion changes the spike protein on the surface of the coronavirus, which it needs to infect human cells. Variants of the virus with this deletion emerged independently in Thailand and Germany in early 2020 and were common in Denmark and England by August.
Scientists initially thought the new coronavirus was stable and unlikely to escape the vaccine-induced immune response, said Dr. Deepti Gurdasani, a public health clinical researcher at Queen Mary University of London.
“But it has become very clear in recent months that mutations can occur,” she said. “As selection pressures increase with mass vaccination, I think these mutants will become more common.”
Several recent articles have shown that the coronavirus can evolve to avoid recognition by a single monoclonal antibody, a mixture of two antibodies, or even restorative serum given to a specific individual.
Fortunately, the body’s entire immune system is a much more formidable opponent.
The Pfizer BioNTech and Moderna vaccines only elicit an immune response against the spike protein carried on the surface by the coronavirus. But every infected person produces a large, unique and complex repertoire of antibodies to this protein.
“The fact is, you’ve targeted a thousand great guns on the virus,” said Kartik Chandran, a virus expert at Albert Einstein College of Medicine in New York. “Regardless of how the virus twists and turns, it’s not that easy to find a genetic solution that can really combat all of these different antibody specificities, not to mention the other branches of the immune response.”
In short, it will be very difficult for the coronavirus to escape the body’s defenses, despite the many variations it can take.
In order to escape immunity, a virus must accumulate a series of mutations that allow the pathogen to affect the effectiveness of the body’s defenses. Some viruses, such as influenza, bring about these changes relatively quickly. But others, such as the measles virus, barely collect changes.
Even the influenza virus takes five to seven years to collect enough mutations to escape immune recognition completely, Bloom noted. His lab released a new report Friday showing that common cold coronaviruses are also evolving to escape immune detection – but for many years.
The scale of the infections in this pandemic may quickly create diversity in the new coronavirus. Still, a vast majority of people worldwide have yet to be infected, and that has made scientists hopeful.
“It would be a bit surprising to me if we saw active selection for immune escape,” said Emma Hodcroft, molecular public health researcher at the University of Bern in Switzerland.
“In a population that is still largely naive, the virus just doesn’t have to do that just yet,” she said. “But it is something we want to pay attention to in the long term, especially now that we are getting more people vaccinated.”
Immunizing about 60% of a population within about a year and keeping the number of cases low while that happens will reduce the chances of the virus mutating significantly, Hodcroft said.
Still, scientists will have to closely monitor the evolving virus to spot mutations that could give it an edge over vaccines.
Scientists routinely track mutations in flu viruses to update vaccines and should do the same for the coronavirus, said Trevor Bedford, an evolutionary biologist at Fred Hutchinson Cancer Research Center in Seattle.
“You can imagine a process like that for the flu vaccine, where you exchange these variants and everyone gets their annual Covid-19 shot,” he said. “I think that will generally be necessary.”
The good news is that the technology used in the Pfizer-BioNTech and Moderna vaccines is much easier to adapt and update than conventional vaccines. The new vaccines also generate a massive immune response, so the coronavirus may need many mutations over years before the vaccines need to be modified, Bedford said.
In the meantime, he and other experts said, the Centers for Disease Control and Prevention and other government agencies should establish a national system to link viral sequence databases with real-life data, such as whether an infection occurred despite vaccination.
“These are useful little bags for scientists and governments to get systems in place – now before we need them, especially as we begin to vaccinate people,” Hodcroft said. “But the public doesn’t necessarily have to panic.”