Dangerous new strains of the novel coronavirus are spreading fast across the United States. And they all have at least one thing in common: a mutation scientists call “N501Y” that makes the virus more likely to infect our cells.
It gets worse. Indications are that at least two of the three major new strains—the ones from the United Kingdom and South Africa—evolved their N501Y mutations independently. In other words, there’s a good chance the U.K. and South African strains aren’t directly related. One didn’t evolve into the other.
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It’s unclear yet whether the new strain from Brazil also mutated N501Y on its own. But the separate appearance of even two similar strains is cause for concern. “There is substantial convergent evolution happening,” tweeted Trevor Bedford, a professor of vaccines and infectious diseases at Fred Hutchinson Cancer Research Center in Seattle.
While it’s too soon to say for sure, that might mean we’re going to see more new strains appear that also exhibit either N501Y or some similar mutation that could make the novel coronavirus more transmissible. “The fact that we’ve observed three variants of concern emerge since September suggests that there are likely more to come,” Bedford tweeted.
N501Y affects the spike protein that’s a distinctive feature of the novel coronavirus. The spike protein helps the virus grab onto and enter our cells. It seems N501Y makes the spike protein “grabbier.” Given roughly equal exposure to the older strain of SARS-CoV-2 and one of the new strains, the new strains could be more likely to make you sick.
Bedford theorized that mutations to the spike protein arise in chronic cases of COVID “during which the immune system places great pressure on the virus to escape immunity and the virus does so by getting really good at getting into cells.”
Niema Moshiri, a geneticist at the University of California, San Diego, told The Daily Beast the theory makes sense. “If three separate lineages gave rise to the N501Y variant independently... then it does indeed seem likely that it’s being positively selected for in some way.”
That’s an ominous possibility, although Bedford stressed that it’s “highly speculative at this point.” As we race to build population-level immunity via vaccination, the virus seems to be fighting back with new mutations that could help it spread even faster than before.
Identifying these mutations is tricky. Devising strategies against them could pose new challenges, too. “It seems important to remember that we have only known about this virus for about a year and there is still more to learn,” Jennifer Reich, a sociologist at the University of Colorado Denver specializing in vaccination, told The Daily Beast.
For most of that year, SARS-CoV-2 mutated without actually producing significant new strains. That began to change in September with the emergence of the B.1.1.7 strain in the United Kingdom and, a few weeks later, the first appearance of B.1.351 in South Africa. Several weeks after that, the P.1 strain was detected for the first time, in Brazil.
There are signs that B.1.1.7, B.1.351, and P.1 are more transmissible than the baseline novel coronavirus—and might also partially resist the immunity-inducing effects of the new COVID-19 vaccines.
B.1.1.7 reached the U.S. in December and has since spread to around half of states. P.1 and B.1.351 were first documented in the United States last month. Scientists have been scrutinizing samples of the new strains to understand how they evolved and what impact they might have on therapies, vaccines, and public-health policies.
A growing number of studies indicate that both the vaccines the U.S. Food and Drug Administration has OK’ed for use in the United States—and one new vaccine that’s on the cusp of FDA authorization—are less effective against the new strains. Meanwhile, South African officials were so dismayed by early signs that the AstraZeneca vaccine—which has not been authorized in the U.S.—was not effective against mild or moderate cases of the strain devastating that country that they halted the rollout of those shots on Sunday, as the New York Times reported.
Don’t panic. “Bottom line is that the vaccine efficacy may be somewhat diminished, but it still probably offers good protection,” James Lawler, an infectious disease expert at the University of Nebraska Medical Center, previously told The Daily Beast of the U.S. vaccines.
But owing to N501Y and other mutations, the new strains do appear to be more transmissible—potentially twice as transmissible, according to some experts.
As we learn more about N501Y and similar mutations, it’s important to detect new strains with the same or related mutations as quickly as we can and track their spread as accurately as possible.
In other words, surveillance. “Our best defense against any variant is to support science that can be proactive in genetically sequencing viruses,” Reich said.
That’s easier said than done, however. Experts told The Daily Beast that the U.S. Centers for Disease Control and state health authorities aren’t sequencing nearly enough COVID samples.
It’s a problem. “Without continual surveillance efforts, we are effectively flying blind in terms of the risk from emerging variations of this and other pathogens,” Christopher Mason, a biophysicist at Weill Cornell Medicine in New York, previously told The Daily Beast.
Ramping up monitoring requires more technicians in more labs getting wider access to bigger sets of samples from doctor’s officers, pharmacies, hospitals, and other testing sites.
And then there’s all the computing. “The files are large, the data transfers are slow, and the computational pipeline can take hours or days to run depending on data volume,” Rob Knight, the head of a genetic-computation lab at the University of California, San Diego, told The Daily Beast.
But gathering more samples, staffing more labs, and booting up more computers alone won’t solve the surveillance problem. “The technologies that can sequence the whole genome at once have high error rates—in other words, a lot of the ‘mutations’ you see are errors in sequencing—and the accurate technologies only read a small part of the genome,” Knight said.
The harder we look for N501Y or some other potentially dangerous mutation, the more false alarms we’re likely to trigger.
Health officials are already struggling to keep people in their masks, out of restaurants, and six feet apart as the pandemic enters its second year in the United States and “COVID fatigue” deepens.
Now add touch-and-go efforts to detect significant mutations like N501Y and the prospect of having to convince people to take extra precautions to halt the resulting new strains. The proliferation of N501Y and similar mutations could compel authorities to extend social-distancing measures and restrictions on businesses. Double-masking could become the new standard.
Expect resistance. “Everyone wants to get back to the ‘normal’ life we had before SARS-CoV-2 surfaced,” Aimee Bernard, a University of Colorado immunologist, told The Daily Beast.
But the novel coronavirus doesn’t care what we want. “Sadly, it doesn’t matter how fatigued we are, if we don’t continue to follow the necessary precautions to stop the spread of the virus and all get vaccinated, the virus will continue to do what it does best—survive, mutate, and spread to more people,” Bernard added. “The longer the virus is in circulation, the more opportunity to mutate.”
