A new strain of the novel coronavirus that first appeared in South Africa has been detected in the United States for the first time.
On Wednesday, geneticists at the U.S. Centers for Disease Control and Prevention told South Carolina health officials they had found a case of the B.1.351 variant of SARS-CoV-2 in samples from the Palmetto State. The same day, testers with the South Carolina Department of Health and Environmental Control found a second case of B.1.351 in state samples.
The two cases could signal a new chapter in the ongoing COVID-19 pandemic, which has killed nearly 2.2 million people—including more than 432,000 in the United States—since it first took hold in China in December 2019.
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For almost a 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 variant in the United Kingdom and, a few weeks later, the first appearance of B.1.351. A few weeks after that, the P.1 strain was detected for the first time, in Brazil.
There are tentative signs that B.1.1.7, B.1.351 and P.1 are more transmissible than the baseline novel coronavirus—and might also resist the immunity-inducing effects of the new COVID-19 vaccines.
P.1 hasn’t been confirmed in the United States yet, but B.1.1.7 reached the U.S. in December and has since shown up in around half of states. If B.1.351 is anything like its British cousin—and there are reasons to believe it is—it could spread quickly, too.
What is it?
B.1.351 is a strain of the basic SARS-CoV-2 virus that includes, among others, a mutation scientists call “N501Y.” That mutation alters the spike proteins that are a defining feature of the novel-coronavirus.
The virus uses its spike proteins to grab onto, and enter, the receptors in human cells. The N501Y mutation could help the spike proteins grab more tightly to receptors. That might make the B.1.351 strain more transmissible.
Another mutation called “E484K” that’s also present in B.1.351 could function as a sort of disguise that confuses the infection-fighting antibodies that would normally recognize and attack SARS-CoV-2. If that’s the case, it’s possible B.1.351 could resist some COVID therapies and—perhaps more worryingly—certain vaccines, as well.
But don’t panic. The plausible worst-case scenario, so far, is that some vaccines might work slightly less well against B.1.351. “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, told The Daily Beast.
Where is it?
B.1.351 first appeared in South Africa in October. It soon spread beyond that country’s borders. While the CDC and DHEC detected the strain in samples from South Carolina COVID patients just this week, it’s possible—likely, even—that the strain has been in South Carolina and other states for weeks or longer.
That’s because the United States lacks a comprehensive surveillance system that’s capable of quickly detecting and tracking new strains of the novel coronavirus.
That kind of surveillance system takes a lot of money and effort. Health officials need to cut deals with major testing sites—chain pharmacies, for example—in order to tap a steady stream of samples. Next, geneticists need to quickly sequence those samples. That requires special equipment and lots of computing power.
The CDC began expanding its National SARS-CoV-2 Strain Surveillance system last fall, but critics say the expansion is too little and too late. Last week, the administration of President Joe Biden pledged to “expand surveillance and genomic sequencing to monitor for COVID-19 hotspots, variants of concern and emerging infectious disease threats.”
But geneticists are playing catch-up. “There are many challenges remaining, everything from data and metadata curation to user interface for lab automation to phylogenetic and statistical analysis to numerical computing issues to ports of slow steps in the code,” Rob Knight, the head of a genetic-computation lab at the University of California, San Diego, told The Daily Beast.
If testers with limited resources found two cases of B.1.351, it’s highly likely there are actually many, many more cases of the new strain that no one has identified. And if B.1.351 is in South Carolina, a state that’s not exactly a major hub for international travel, it’s safe to say the strain is putting down roots in other states, as well.
All that is to say—B.1.351 is here. It’s undoubtedly spreading. And if it isn’t already in your community, it’s probably coming soon.
Just how much more dangerous is it?
Depends on how you define “dangerous.”
The science is clear: The B.1.351 strain includes mutations that could, in theory, make the strain more transmissible and somewhat more resistant to vaccines and therapies.
But viruses live in the real world, just like we do. They don’t behave the same way in big, messy populations the same way they do in sterile, tightly controlled labs. Sometimes they’re less dangerous in the real world. Sometimes they’re more dangerous.
South African researchers told The Wall Street Journal they believe B.1.351 is around 50 percent more transmissible than the main novel coronavirus. If that’s true and no other variables weigh on population-level vulnerability, the spread of B.1.351 could result in a spike in deaths as more people come down with COVID-19.
But that doesn’t necessarily mean that B.1.351 is any deadlier to any one infected person. “There is no evidence that these recently identified SARS-CoV-2 variants cause more severe disease than earlier ones,” the CDC stated.
Nor does elevated transmissibility necessarily change the way we prevent and, in many cases, treat COVID. Social distancing and masks work against all strains of the virus. Steroids and other repurposed drugs still seem to work on COVID infections, regardless of the strain that caused the infection.
And most of the data points to most of the vaccines working just fine. The messenger-RNA COVID vaccine from Massachusetts-based Moderna produces somewhat fewer antibodies when it makes contact with B.1.351 than it does with the baseline SARS-CoV-2, the company told investors this week.
But there are still enough antibodies to defeat the virus, the company insisted. “Neutralizing titer levels with B.1.351 remain above levels that are expected to be protective.”
Pfizer in New York said pretty much the same thing about its own mRNA vaccine. Scientists studying B.1.1.7 and B.1.351 on behalf of the company found “small effects of these mutations on neutralization.”
On the other hand, a baculovirus-based vaccine that Maryland biotech firm Novavax is developing— and which has yet to win FDA approval—appeared to be less effective in South Africa than other countries. Some experts read that data to mean the Novavax vaccine is less protective against B.1.351 than it is against other strains.
And the CDC is worried that B.1.351 might reduce the effectiveness of some COVID therapies. The agency warned about the strain’s “decreased susceptibility to therapeutic agents such as monoclonal antibodies.”
That doesn’t spell doom, but it could compel the pharmaceutical industry to shift focus. “If reports about the lack of responsiveness to existing treatment strategies— such as monoclonal antibodies— are validated, then new treatment modalities will need to be investigated,” Anthony Alberg, a University of South Carolina epidemiologist, told The Daily Beast.
What happens next?
How B.1.351’s spread might play out in the real world is difficult to predict. But that’s not stopping Edwin Michael, an epidemiologist at the Center for Global Health Infectious Disease Research at the University of South Florida, from trying. His team has run computer simulations depicting the spreads of both the U.K. and South African strains.
Michael cautioned that his computer models are only as good as his data— and data are limited. Still, he said he’s cautiously optimistic. After a post-Christmas spike, COVID-transmission rates appear to be slowly dropping in much of the United States. And Michael’s simulations indicate the pandemic could continue to cool down in coming months, even with the spread of new strains.
“With roll-out of vaccinations along with continued social measures... our model shows that the recent decline in transmission could become sustained over the longer term, leading to resolution of the pandemic between May to July, in most settings,” Michael told The Daily Beast.
But the appearance of B.1.351 and other major strains could point to future mutations producing even more unpredictable new strains.
SARS-CoV-2 actually mutates relatively slowly compared to other viruses, Niema Moshiri, a geneticist at the University of California, San Diego, told The Daily Beast. However, with so many active COVID infections—around 26 million, globally—the sheer volume of mutations means new strains are likely to appear in coming months.
Each individual infection tends to produce two mutations every two weeks, Moshiri explained. It adds up fast.
“What if we had 50 million people pull slot-machine levers simultaneously at the same time?” Moshiri asked. “We would expect at least one person would hit the jackpot pretty quickly. Now, replace the slot machine with ‘clinically meaningful SARS-CoV-2 mutation,’ and that’s the situation we’re in.”
But even those possible future strains seem unlikely to change the basic measures we all can take to protect ourselves from every known and projected form of the novel-coronavirus.
Wear your mask. Stay home when you can. Get vaccinated as soon as possible.
