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A troubling strain of the coronavirus has emerged, first in South Africa. It’s now spreading around the world, including in the US.
Potentially more troubling: A flurry of data released this week shows the virus has changed in ways that likely diminish the efficacy of leading vaccines.
“We can see that we are going to be challenged,” Dr. Anthony Fauci, the director of the National Institute of Allergy and Infectious Diseases, said Friday, calling the most recent findings “a wake-up call for us to be nimble and to be able to adjust.”
Vaccine developers are relatively confident the current shots will still fight the pandemic, including the troubling variants. But the latest results show the world has entered a new phase of the pandemic, one that may challenge people’s expectations of a smoothly gliding return to normalcy once most people are vaccinated.
“The glass is half-full, but let’s be careful,” John Wherry, an immunologist at the University of Pennsylvania, told Insider. “There are things trying to poke holes in the bottom of the glass.”
In particular, a strain widely circulating in South Africa is tapping against the glass. This variant appears able to re-infect some people who have recovered from COVID. And a handful of research suggests some of the mutations in this variant, shared by another prominent variation identified in Brazil, lower the efficacy of the leading vaccines.
“These new, more fit viruses are going to take over the population, and that’s going to happen in the US,” SVB Leerink biotech analyst Geoffrey Porges told Insider. “There’s nothing we can do, we don’t really have control on our pandemic.”
Vaccine makers Pfizer, Moderna, Johnson & Johnson, and Novavax are now developing shots tailored to fight certain strains. That work has been going on quietly in the background for several weeks, as the leaders are preparing for trouble to come, either from a circulating variant or a future mutation.
“A new variant will pop up and the vaccine is not that effective. This is not the case yet,” Pfizer CEO Albert Bourla said Friday at the Davos World Economic Forum. “It’s a very high likelihood that one day that will happen.”
To be prepared for that possibility, Pfizer is aiming to be able to craft a new version of its shot in 100 days or less, Bourla added.
All the leading vaccines target the spike protein, the viral protrusions that allow the coronaviruses to cling onto human cells and infect our bodies.
The approach unambiguously succeeded. The first vaccines, developed by Moderna and Pfizer, were stunningly effective, with late-stage clinical readouts in December showing 94% and 95% effectiveness at preventing symptomatic disease, respectively.
The vaccines were more effective than most scientists had expected. Most virologists and vaccine developers were hoping for the first shots to be between 70% and 80% effective.
But in the fight to survive, the coronavirus has done what all viruses do: mutate. And it’s kept vaccine developers busy.
A few variants have stacked up several mutations on the all-important spike protein. Most notably, a strain first found in South Africa called B.1.351 has racked up 10 mutations on the spike protein. Another variant, called P.1, is surging in Brazil with many of the same mutations as B.1.351.
Another version, called B.1.1.7 and first seen in the UK, has raised alarms with research suggesting it is more contagious.
The US has effectively been driving blind in the face of these threats. The nation ranks 38th in the world in sequencing efforts that identify variants. Instead of tracking these mutants every step of the way, the US public health system sees only fractions of what is going on with the pandemic.
The US confirmed its first cases from the P.1 and B.1.351 variants just in the last few days. Two South Carolinians were infected with the B.1.351 version, despite not having traveled to South Africa or to other countries where it is spreading.
“We should be treating every case as if it’s a variant,” Dr. Rochelle Walensky, director of the Centers for Disease Control and Prevention, said Friday.
B.1.1.7, the variant that first emerged in the UK, is expected to become the dominant strain of the virus in the US by late-March or early April, Fauci said.
There’s evidence to think vaccines will fare well against the strain. A vaccine candidate developed by Novavax proved to be 89% effective in a large UK-based trial while the variant was spreading there. And laboratory research using existing vaccines show the shots still provide a potent immune response.
Instead, the B.1.351 variant poses more of a risk because it appears to diminish the effectiveness of current vaccines.
While it remains to be seen whether the variant will become dominant in the US, data from four top vaccine programs released this week show the potential risk from this strain that is now widely circulating in South Africa.
Novavax said Thursday that its shot was about 49% effective at preventing symptomatic COVID-19 in a South Africa trial of about 4,000 volunteers, compared to being 89% effective in a UK-based study.
On Thursday, the Maryland-based company shared its plans to immediately start developing a version of its shot tailored to B.1.351, recognizing the decline in efficacy as a real challenge.
Less than 12 hours later, Johnson & Johnson released results from a 44,000-person trial that recruited people across the US, Latin America, and South Africa. J&J was testing a one-dose vaccine, which would simplify distribution and administration.
J&J’s shot was 72% effective in the US, but 57% effective in South Africa. In South Africa, the B.1.351 variant was responsible for 95% of reported cases.
Realizing the threat of the variant, J&J has been quietly researching it in the lab for weeks and preparing for the possibility of developing a new version of its vaccine for that strain, Mathai Mammen, J&J’s global head of R&D, told Insider on Friday.
But Mammen emphasized the single-dose shot was about 85% effective in South Africa at preventing severe COVID-19. No one in South Africa who got J&J’s vaccine died or was hospitalized from COVID-19, he added. He did not specify how many placebo recipients had such outcomes.
“This one does not seem to be warranting at all of coming up with a new vaccine, but it teaches us what to look for,” Mammen said, referring to B.1.351.
Even if variants cause vaccines to give less protection against symptomatic disease of any severity, partial protection is still quite valuable in the pandemic, experts said.
“60% efficacy is still really fairly good,” Deborah Fuller, a microbiologist and vaccine developer at the University of Washington, told Insider. Fuller has also helped develop a coronavirus vaccine candidate licensed to HDT Bio, which is now in early stages of research. “Remember, when we started this entire endeavor, we were hoping to have vaccines that were at least 50%. So 60% is still not something to just discard here.”
Dr. Larry Corey, a virologist at Fred Hutchinson Cancer Research Center who leads the COVID-19 Prevention Network, told Insider the Novavax and J&J results should both be seen as good, reassuring pieces of news “with respect to the issue that vaccines will reduce the health crisis and the epidemic crisis that we are having with COVID-19.”
“We need to get them into people’s arms,” he added.
Moderna and Pfizer have done lab testing using blood samples from vaccinated people and exposing them to an artificially made version of the virus. Moderna’s study found a six-fold drop in neutralizing antibodies, the virus-fighting proteins that play a central role in our immune response.
Pfizer’s vaccine also declined, although not as dramatically, in antibody levels. That study only tested against three of the mutations found on the B.1.351 variant, however.
Both companies are now developing new variant-specific versions of their vaccine, although Moderna seems more intent on progressing that into human testing as quickly as possible. A Pfizer research leader said the goal here is to be more prepared in responding to future strains overall.
“Just because people and companies are doing this work doesn’t mean we think these viruses are going to evade our current vaccines, but we think if we wait until we have definitive evidence, we will have waited too long,” Philip Dormitzer, Pfizer’s chief scientific officer of viral vaccines, told Insider on Thursday. “We don’t want to alarm people that we’re doing this. We just want to be prepared.”
While experts varied on just how big of a deal the current variants will be, all agreed that the coronavirus is around for the long term.
The virus will be endemic for years, the University of Washington’s Fuller said, with a realistic near-term goal of being able to bring down the devastation caused by this virus more in line with the flu — or even better.
The lack of genomic surveillance, widespread testing, and aggressive contact tracing will also undermine vaccination efforts, expert said.
“We still have no testing and tracing capacity in the US to speak of. That’s a monumental failure in the pandemic response,” Wherry, the Penn immunologist, said. “If we knew who to vaccinate to stop spread, we’d be able to vaccinate some small fraction of the population and limit spread by some huge factor. But we don’t even know where to go to do that, and that’s pandemic 101.”
And a critical unknown going forward will be if there is a more pernicious variant either lurking around the corner or already out there. Overall, the variant risk only increases the need to immunize and protect people as quickly as possible.
“The less replication there is in the world, the less chance that any of this happens,” J&J’s Mammen said. “So the faster that everyone gets vaccinated, the less chance we have a variant to worry about.”
Allison DeAngelis, Patricia Kelly Yeo, and Aylin Woodward contributed reporting.