United States: The relentless march of COVID-19 has unveiled an array of subvariants, each more adept at spreading than its predecessors. The most recent summer surge, fueled by the FLiRT subvariants, has now given way to even more contagious strains, significantly contributing to the elevated COVID-19 levels in California and across the nation.
Medical experts and scientists are now fixated on yet another emerging subvariant—XEC. This particular variant threatens to surpass the current frontrunner, KP.3.1.1, which has established itself as the predominant strain nationwide. First identified in Germany, XEC has swiftly captured the attention of the global medical community, according to the Los Angeles Times.
Dr. Eric Topol, the director of the Scripps Research Translational Institute in La Jolla, remarked, “XEC is just beginning to establish its presence globally and locally. However, it will take several weeks, perhaps months, for it to gain significant traction and instigate a new wave.”
“XEC is undeniably asserting itself… It appears poised to become the next dominant variant,” Topol continued, “though it remains months away from achieving widespread prevalence.”
Despite its detection in the United States, XEC’s current prevalence is minimal, and it has not yet warranted individual tracking on the U.S. Centers for Disease Control and Prevention’s variant tracker. For a lineage to be monitored, it must be estimated to circulate above 1% nationally over a two-week period.
The anticipated midyear wave began in May, when the winter’s dominant subvariant, JN.1, was supplanted by a series of subvariants colloquially dubbed FLiRT—a whimsical moniker derived from the letters of two pivotal mutations, F456L and R346T, according to Topol, as per Los Angeles Times.
Subsequently, “the FLiRT subvariants were eventually overtaken by newer variants with an even greater growth advantage,” Topol explained.
A successor subvariant, KP.3, introduced a different mutation—Q493E—while dropping R346T, earning it the nickname FLuQE, pronounced “fluke.” An even more contagious subvariant—KP.3.1.1—underwent a deletion mutation, leading to the unofficial designation deFLuQE, or “de-fluke.”
The “S31 deletion,” Topol noted, “has made this variant particularly pathogenic and highly immune evasive. The S31 deletion has been extensively studied—especially by the Sato lab in Japan—and it is this alteration that has prolonged the current wave and infected many who might have otherwise avoided illness.”
“KP.3.1.1 stands out as an outlier in terms of growth advantage,” he added. “This is far from over, and we can expect new variants to emerge beyond KP.3.1.1.”
KP.3.1.1 continues to be the most prevalent subvariant in the US. As of the two-week period beginning on August 18, KP.3.1.1 was estimated to constitute 42.2% of coronavirus samples nationwide, up from 19.8% just a month earlier, according to the CDC.
The recently released Moderna and Pfizer vaccines, which debuted just before the Labor Day weekend, were designed to target KP.2, a precursor of KP.3.1.1. As such, they remain a relatively close match for the primary circulating variants. However, XEC may present a challenge due to its divergence from these vaccines.
Nevertheless, the new vaccines are markedly superior to those released a year ago, which targeted XBB.1.5. The disparity between the current vaccines’ target and XEC is “substantial…and we’ll have to see how it unfolds,” Topol remarked.
“It would be surprising if this doesn’t emerge as the next significant challenge,” Topol said. “But any booster will undoubtedly elevate immunity levels,” according to reports by the Los Angeles Times.
Dr. Elizabeth Hudson, regional chief of infectious diseases for Kaiser Permanente Southern California, expressed optimism that the new vaccines would still offer considerable protection against XEC. “There is some overlap since these are all sub, sub, sub-descendants of the original Omicron. So, there will still be a degree of protection.”
“We’re not dealing with a new Greek letter; they’re not vastly different—it’s not as if something entirely new has emerged,” Hudson added.
Hudson explained that XEC is a recombinant of two relatively obscure subvariants: KS.1.1 and KP.3.3. “It’s definitely one to watch.”
“But this is somewhat distinct, and it does seem to exhibit what we refer to as a growth advantage over JN.1, deFLuQE, or the FLiRT variants,” Hudson said.
“It remains uncertain where this will lead, as KP.3.1.1 remains the predominant variant,” Hudson said. “We must closely monitor developments not only within the US but also in Europe as they approach their colder seasons.”
Beyond Germany, XEC has been reported in other parts of Western Europe, including the Netherlands, where it has spread with remarkable speed, Hudson noted.
“We’ll need to keep a vigilant watch—given the limited information currently available—but I expect we’ll learn more about XEC in the coming weeks, especially if it continues to rise in prominence,” Hudson said.
COVID-19 has proven to be far more cunning than the flu. Unlike the flu’s typical pattern of a single fall-and-winter wave, COVID-19 tends to produce two waves each year.
Several factors contribute to this divergence. “One is the virus’s constant evolution, which allows it to gather momentum and become dominant over time,” Topol said.
The second factor is our relatively short-lived immunity, at least in terms of infection, which enables many individuals who recovered in the winter to contract COVID-19 again in the summer, Topol explained.
Finally, adherence to precautionary measures has waned considerably compared to previous years, Topol said. Fewer people are wearing masks in crowded indoor settings, staying up to date on their vaccinations, or even staying home when they are ill.
As of spring, 22.5% of US adults and 29.1% of seniors aged 65 and older had received the COVID-19 vaccination for the 2023–24 season. In comparison, flu vaccination rates were higher, covering 48.5% of adults and 50.6% of seniors, as per the Los Angeles Times.
In California, as of July 31, 37% of seniors had received the updated COVID-19 vaccine for the 2023–24 season, along with 18.7% of those aged 50 to 64, and 10.1% of the youngest adults.