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Salon
Salon
Science
Troy Farah

"Variant soup" could drive COVID surge

Conceptual paper illustration of coronavirus in a lab (Getty Images/Eugene Mymrin)

If the last two winters are any indication, North America and Europe will likely experience a surge in COVID infections by the end of this year, driven by cold weather, students in close quarters in classrooms and holiday travel. Public health officials are closely watching the situation by monitoring wastewater, sequencing the genetics of the virus and tracing positive cases.

But an increasing number of experts are worried that this wave could be markedly different from years previous. The emergence of multiple variants with the ability to evade immunity could surge simultaneously, which is something we haven't seen previously.

"We haven't had one like this before. This is different."

"We anticipate continued circulation of the virus that causes COVID-19 and the potential for surges in virus circulation over the next several months," Jasmine Reed, a spokesperson for the Centers for Disease Control and Prevention (CDC), told Salon in an email. The CDC is urging anyone age five years and older who is eligible for an updated vaccine booster to get one. "Importantly, we know updated COVID-19 vaccines provide additional protection against the currently circulating variants," Reed added, referring to newly-available bivalent vaccines that have been found in studies to protect well against the BA.5 omicron variant.

The question remains how bad the wave will be this time around, but several factors — including low booster uptake and fewer people wearing masks in public — may add complications to the potential surge. The data on COVID infections is also somewhat muddled because positive tests are going uncounted while the CDC and many state agencies have switched to updating their data weekly instead of daily.

To make matters worse, a cluster of COVID variants is slowly starting to dominate simultaneously — what many experts are calling a "variant soup" — with many strains showing surprising immunity to certain COVID drugs. While the latest vaccines have still been demonstrated to work against these variants, it means we could have a few less tools at our disposal this winter. If this will translate into overwhelmed hospitals, supply chain disruptions or an uptick in deaths is yet to be seen.

"We haven't had one like this before. This is different," Dr. T. Ryan Gregory, an evolutionary and genome biologist at the University of Guelph in Canada, told Salon. "You hear cloud or swarm or cluster or variant soup. All these things at once that are all immune-escaping."

Last winter in the U.S., the omicron BA.1 variant smashed records for daily cases. But unlike with delta, it didn't disappear after a while; rather, it kept mutating. Omicron's subvariants or children stuck around, like BA.5, which has been largely responsible for infections, hospitalizations and death in the U.S. for most of this year. While cases have yet to spike severely again as they did in January 2022, the pandemic instead morphed into "a long, never-ending plateau" as The Atlantic put it.

Gryphon is a recombinant strain, which means it has the genetic code of two different omicron subvariants. It's also been described by the WHO as "the most antibody-evasive variant yet."

At last, BA.5's supremacy is finally starting to wane, emerging data shows. Unfortunately, this time, it could be replaced by multiple variants at once.

"I suspect we're set up for a lot of cases," Gregory said. "How serious are they individually remains to be seen."

This variant soup includes viruses like XBB, BQ.1 and BF.7. Understandably, these random mishmashes of letters can be quite confusing to keep track of, so Gregory has proposed a list of nicknames for certain variants based on monsters from Greek mythology. So BF.7 is Minotaur and BQ.1 is Typhon, for example.

These variants are emerging in different ways across the globe. Earlier this month, the Gryphon variant (XBB) began rising sharply in Singapore, but the World Health Organization (WHO) has now reported it in 25 other countries, according to Fortune. Gryphon is a recombinant strain, which means it has the genetic code of two different omicron subvariants. It's also been described by the WHO as "the most antibody-evasive variant yet."

Luckily, there are other tools against Gryphon, including the drug Paxlovid, which attacks the virus differently than antibodies. So humanity is not completely unarmed against this version of the virus.

Meanwhile, New York is seeing a stark rise in Typhon (BQ.1) and Cerberus (BQ.1.1) cases, making up 16.6 percent of cases in total as of October 21, a jump from 5.1 percent two weeks ago. They also seem able to evade antibody drugs like Evusheld and Bebtelovimab.

"BA.5 continues to be responsible for most infections. BQ.1 and BQ.1.1 represent a small but fast-growing group of BA.5-related viruses in the United States," Reed said, emphasizing that the mRNA vaccines from Pfizer and Moderna include components that target earlier lineages of the virus, so they will still help prevent hospitalization and death.

The CDC is closely monitoring all of these variants, but as they are still just emerging, there is limited data on them. We don't know how much immunity one variant will provide against another, so some folks could become sick again immediately following an infection. Or they may contract multiple variants at once.

"I am worried about the fall, that there will be a peak, but we wouldn't even know that there is a peak."

So far there's no evidence to suggest these variants cause more severe disease. But as anyone with long COVID will tell you, it doesn't make sense to call any of these omicron offshoots "mild."

"We don't know a lot of things about the variants. We don't know, are any of them more severe than others?" Gregory said. "Do they attack different tissues? Is one more likely to have brain fog than another or heart problems? We don't know. Those are really hard to predict, much more difficult to predict than if it is going to escape immunity. That you can look at the structure of the protein and make a good guess. With what's it going to do in the body is, we have to wait and see."

The good news is the newer vaccines seem to work against all of these variants, but relying on vaccines alone is shortsighted. We need more testing and surveillance of the virus, as well as more masking and improved indoor ventilation.

Dr. Rajendram Rajnarayanan, an assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Arkansas, says that store-bought antigen tests should still be able to detect these variants — but because the results aren't reported to health agencies, it could leave people in the dark.

"I am worried about the fall, that there will be a peak, but we wouldn't even know that there is a peak. That's what I'm more worried about," Rajnarayanan told Salon. He emphasized that the public should not panic, but stay informed and monitor the situation to take steps to protect one another.

"Booster uptake is low, masking is pretty low," Rajnarayanan said. "And whether liberal or not, it's really not about the politics anymore. It's really about looking out for each other. That kind of camaraderie is what we have to promote."

Even though this soup of variants can seem scary, and some of our tools against them have been blunted, we still have plenty of resources at our disposal, especially masks and social distancing. The question is: Will we use them in time? As Time Magazine recently posited, it doesn't seem like America is ready for a winter wave. But there's still time to adjust course.

"The less we try to stop viruses from replicating, the more we're going to see new variants," Gregory said. "The situation is different in many ways. There's multiple variants, they all escape immunity quite well. They're rising simultaneously, which we haven't seen before. But my reaction to that is the same as it was with delta. And the same with the first omicron. We should strive to stop transmission as much as we can."

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