Just as the vaccine offers hope for a way out of the outbreak, British officials issued an urgent warning over the weekend that a new, highly contagious variant of the new coronavirus is spreading in Britain.
Prime Minister Boris Johnson ordered the UK’s tightest lockdown since March in light of the rapid spread of the virus in and around London. “When the virus changes its means of attack, we must also change our means of defense,” he said.
A woman walks down a rainy Oxford Street on the first day of London’s three-tier prevention and control controls. The city has adopted stricter restrictions.
A woman walks down Oxford Street in the rain on the first day of London’s three levels of control. The city has adopted stricter restrictions. ANDREW TESTA FOR THE NEW YORK TIMES
London’s train stations are packed with people rushing to get out of town as restrictions take effect. On Sunday, European countries began closing their borders to travelers from Britain, hoping to keep out new iterations of the pathogen.
A similar version of the virus has emerged in South Africa, which is identical to a mutation seen in the British variant, according to the scientists who discovered it. Since mid-November, South Africa has analyzed the genetic sequences of samples and found the virus in 90 percent of them.
Scientists are concerned about these variants, but not surprised. As the new coronavirus spread around the world, researchers documented thousands of subtle variants in the virus’ genetic material.
Some variants became more common in the population simply by luck, not because the variants somehow enhanced the virus. But as the pathogen becomes more difficult to survive – because of human vaccinations and growing immunity – the researchers also expect the virus to acquire useful mutations that would make it easier to spread or avoid detection by the immune system.
“This is a real alarm that we have to pay more attention to,” said Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle. “These mutations certainly spread, and there’s no question that the scientific community – that’s us – needs to monitor these mutations and characterize which ones have an impact.”
There are about 20 mutations in the U.K. variant of the virus, several of which affect the way the virus targets human cells and infects them. Muge Cevik, an infectious disease expert at the University of St. Andrews (Scotland) and a scientific adviser to the U.K. government, said the mutations could make the variant more efficient at replicating and spreading.
But estimates of wider infectiousness – British officials say the variant is 70 percent more contagious – are based on modeling and have not been confirmed in laboratory experiments, Dr. Cevik added.
“All in all, I think we need a little bit more experimental data,” she said. “We can’t completely rule out the fact that some of the infectious aspects of the data may be related to human behavior.”
In South Africa, scientists were also quick to point out that human behavior was driving the spread of the outbreak, not necessarily new mutations, the latter of which have not been quantified in terms of their impact on infectiousness.
The U.K. announcement also raised concerns that the virus may have evolved resistance to the just-introduced vaccine. The concern centers on a pair of changes in the virus’ genetic code that could make it less susceptible to attack by certain antibodies.
But some experts urge caution, saying it would take years, not months, for the virus to evolve to the point where it would render existing vaccines ineffective.
“There is no need to worry about some single catastrophic mutation that would suddenly render all immunizations and antibodies ineffective,” Dr. Bloom said.
“This would be a process that occurs over a multi-year span and requires the accumulation of multiple viral mutations,” he added. “It’s not the same as flicking a switch.”
For Britain’s neighbors, the scientific nuances don’t matter. Fearing a possible influx of travelers carrying the mutated virus, the Netherlands said it would suspend flights from Britain from Sunday until Jan. 1 next year.
Italy has also suspended air travel, and Belgian officials issued a 24-hour ban Sunday on flights or trains from Britain. Germany is drafting rules to restrict travelers from Britain and South Africa.
Other countries such as France, Austria and Ireland are also considering enacting bans, according to local media reports. Spain has asked the European Union to come up with a coordinated response to the flight ban. New York Gov. Andrew Cuomo has asked the Trump administration to consider banning flights from the United Kingdom.
In the U.K., transportation officials say they will increase police presence to monitor hubs such as train stations to ensure people make only essential trips. Matt Hancock, the U.K. health minister, said Sunday that people who crowd into trains are “clearly irresponsible.
He also said the restrictions imposed by Johnson could last for months.
Like all viruses, the new coronavirus is variable. Some genetic changes are inconsequential, but others may give it an edge.
Scientists are particularly worried about the latter possibility: that vaccination of millions of people could force the virus to develop new adaptations and mutations that would help it avoid or resist an immune response. The virus has already shown subtle changes that have emerged independently many times around the world, suggesting that these mutations can be helpful to the pathogen.
Such mutations affecting antibody susceptibility – terminologically known as 69-70 deletions, meaning there are missing letters in the genetic code – have been found at least three times: in Danish mink, in English people, and in an immunocompromised patient whose susceptibility to recovering plasma was greatly reduced.
“This stuff keeps spreading, developing, adapting,” says Ravindra Gupta, a virologist at the University of Cambridge. He described in detail last week the recurrence and spread of the deficiency. “But people don’t want to hear what we’re saying, which is: this virus mutates.”
The new genetic deletion alters the stinger protein on the surface of the new coronavirus used to infect human cells. Variants of the virus with this deletion appeared independently in Thailand and Germany in early 2020 and became endemic in Denmark and the United Kingdom in August.
Several recent papers have shown that neo-coronaviruses can evolve to avoid being recognized by a single monoclonal antibody, a mixture of two antibodies, or even a recovery serum given to a specific individual.
Fortunately, the body’s overall immune system is a much stronger opponent.
The Pfizer-BioNTech and Modena vaccines induce an immune response only to the stinger protein carried on the surface of the new coronavirus. But each infected person produces a large, unique and complex library of antibodies against this protein.
“The truth is, you have a thousand machine guns pointed at this virus,” says Kartik Chandran, a virologist at the Albert Einstein College of Medicine in New York. “No matter how twisted and intertwined the viruses are, it’s not easy to find a genetic solution that actually resists all these different antibody specificities, let alone the other weapons of the immune response.”
In short: Although a new coronavirus may take on multiple variants, it will have a hard time escaping the body’s defenses.
To escape the immune system, a virus must accumulate a series of mutations, each of which causes the pathogen to erode the effectiveness of the body’s defenses. Some viruses, such as influenza viruses, accumulate these changes relatively quickly. But other viruses, such as the measles virus, accumulate almost no changes.
Bloom noted that even influenza viruses take five to seven years to collect enough mutations to completely escape immune recognition. A new report from his lab, published Friday, shows that the coronavirus of the common cold can also evolve to escape immune detection – but it takes many years.
In this pandemic, the sheer scale of infection could cause new coronaviruses to quickly become diverse. Nevertheless, the vast majority of the world’s population has not yet been infected, which gives scientists hope.
I would be a little surprised if we were seeing active selection for viral immune escape,” said Emma Hodcroft, a molecular epidemiologist at the University of Bern in Switzerland.
“In a population where most people are not infected, the virus doesn’t need to do that yet,” she says. “But in the long run, it’s something we need to be wary of, especially as we start vaccinating more people.”
Immunizing about 60 percent of the population in about a year and reducing the number of cases in the meantime would help minimize the chances of a mutation of the virus, Holdcroft said.
Still, scientists need to closely track evolving viruses to find mutations that could give them a head start on vaccines.
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