The summer surge in coronavirus subvariants dubbed FLiRT has given way to increasingly contagious strains, a key reason behind the current high levels of COVID in California and across the country.
And doctors and scientists are keeping an eye on another subvariant, XEC, which could overtake the latest hyperinfectious subvariant, KP.3.1.1, which is now considered the most common across the country. XEC was first detected in Germany and has since captured the attention of doctors and scientists around the world.
XEC is “just starting to manifest itself around the world and here,” said Dr. Eric Topol, director of the Scripps Research Translational Institute in La Jolla. “And that will take many weeks, a couple of months, before it really takes hold and starts to cause a wave.”
“The XEC variant is definitely taking over… That appears to be the next variant,” Topol added. “But it is months away from reaching high levels.”
While XEC has emerged in the United States, its prevalence is low and it is not being tracked individually on the U.S. Centers for Disease Control and Prevention's variant tracking website. A lineage must be estimated to be circulating above 1% nationally over a two-week period to be trackable.
The long-awaited midyear wave began in May, when the dominant winter subvariant, JN.1, gave way to a series of subvariants dubbed FLiRT — a cheeky name based on the letters of two key mutations, F456L and R346T, Topol said. (Focus on just the letters and add an “i” as a connector, and you get FLiRT, which includes the subvariant officially named KP.2.)
Then, “FliRT eventually gave way to new variants that had even more growth advantages,” Topol said.
A successor subvariant, KP.3, had a different mutation (Q493E) and deleted R346T. It was nicknamed FLuQE, pronounced “fluke.” And an even more contagious subvariant (KP.3.1.1) had a mutation that was deleted, giving it the unofficial nickname FLuQE, or “de-fluke.”
The “S31 deletion,” Topol said, is “what has made it sort of a very pathogenic and very immune-evasive variant. That S31 deletion has been studied, in particular by the Sato lab in Japan, and it’s the culprit for this wave being prolonged and affecting a lot of people who otherwise might not have gotten sick.”
“KP.3.1.1 is definitely an exception in terms of the growth advantage,” he added. “Obviously, this is not over yet. And we are going to have new variants beyond KP.3.1.1.”
KP.3.1.1 is estimated to remain the most common subvariant in the country. During the two-week period beginning Aug. 18, KP.3.1.1 was estimated to account for 42.2% of coronavirus samples nationwide, up from 19.8% a month ago, according to the CDC.
The Moderna and Pfizer vaccines, which came to market just before Labor Day weekend, are designed against KP.2, a predecessor of KP.3.1.1, so they are relatively compatible with the major variants in circulation. However, XEC will not be as closely aligned.
The new vaccines are still much better for the current season compared with the vaccine launched a year ago, which targeted XBB.1.5, but the difference between what the latest vaccine is designed against and XEC is “pretty substantial … and we'll see how that plays out,” Topol said.
“It would be surprising if this wasn’t the next challenge,” Topol said. Still, “any booster will help induce a higher level of immunity.”
Dr. Elizabeth Hudson, regional chief of infectious diseases for Kaiser Permanente Southern California, said she thought the new vaccines would still offer some protection against XEC “because there is some overlap, as they are all sub, sub, subgrandchildren of the original Omicron. So there will still be some level of protection.”
“We’re not like a new Greek letter: It’s not that different; it’s not something completely new,” Hudson said.
XEC is a recombination of two different, little-discussed subvariants: KS.1.1 and KP.3.3, Hudson said. “It’s a variant I’m definitely keeping an eye on,” he said.
“But this is a little bit different and appears to be showing what we call a growth advantage over the JN.1, deFLuQE or FLiRT variants,” Hudson said.
“It’s going to be a little bit difficult to know where this is going to go, because right now, the predominant variant is still KP.3.1.1,” Hudson said. “So we have to be very attentive not only to what’s happening within the U.S., but also to what’s happening in Europe as we get into the colder seasons.”
In addition to Germany, XEC has been reported in other parts of Western Europe, including the Netherlands, and has spread relatively quickly, Hudson said.
“We'll really have to keep an eye on it, because the overall information on that is not very solid right now, but I imagine over the next few weeks, particularly if it starts to go up more and more, we'll hear a little bit more about it,” Hudson said.
COVID has proven to be much more cunning than the flu. Instead of one fall and winter wave, as flu usually does, COVID appears to generate two waves each year.
There are several reasons for that difference. “One is that the virus is still evolving and it takes a long time for a variant to really gain traction and become dominant,” Topol said.
The second is that our immunity, at least in terms of infection, is short-lived, allowing many who recover in the winter to get COVID again in the summer, Topol said. (Fortunately, protection against hospitalization and death has been longer-lasting, which explains why hospitals are no longer overburdened despite high levels of coronavirus circulating across the country.)
And finally, few people are taking precautionary measures that were much more common years ago, Topol said. Fewer people are wearing masks in crowded indoor spaces, keeping up with their vaccinations or even staying home when they're sick.
In the spring, 22.5% of U.S. adults and 29.1% of a subset of people 65 and older received a COVID-19 vaccine for the 2023-24 season. Vaccination rates were highest for influenza, with an estimated 48.5% of adults and 50.6% of older people vaccinated.
In California, as of July 31, 37% of seniors had received the updated COVID-19 vaccine for the 2023-24 season, as had 18.7% of people ages 50-64 and 10.1% of younger adults.
