"FLiRT" COVID variants are now more than a third of U.S. cases. Scientists share what we know about them so far.

More than a third of COVID-19 cases in the U.S. are now estimated to be from a new, fast-growing member of a group of so-called "FLiRT" variants, nicknamed for their small but distinctive changes relative to the JN.1 strain. JN.1 was the variant behind this past winter wave of infections.

The largest among them, called KP.2 by scientists, has quickly multiplied in recent weeks to become the now-dominant new COVID-19 strain. 

According to the Centers for Disease Control and Prevention's every-other-week variant estimates, KP.2 and another strain with the same FLiRT mutations, called KP.1.1, together make up a projected 35.3% of infections this week. This is up from 7.1% a month ago.

"That means that while KP.2 is proportionally the most predominant variant, it is not causing an increase in infections as transmission of SARS-CoV-2 is low," a CDC spokesperson told CBS News in a statement.

The strain also does not have large amounts of worrying changes, unlike some previously highly-mutated variants that have raised alarm in years past. 

However, the swift change in circulating variants has resulted in the Food and Drug Administration this week delaying a key step in its process for picking out the strain to target with this fall's COVID-19 vaccines, citing the need for more "up-to-date" data.

While federal requirements for hospitals to report COVID-19 data to authorities lapsed this month, the CDC says it still has reliable figures from sources like wastewater testing and emergency rooms to continue tracking activity from the virus. 

Here's the latest of what we know about COVID-19 variants in the U.S.

What is the current new variant of COVID-19?

According to the latest projections published by the CDC, around 28.2% of COVID-19 cases nationwide are now being caused by a sublineage of the virus called the KP.2 variant. 

The next largest variant on the rise is another JN.1 descendant called JN.1.16. That strain has not grown as quickly, only inching up to an estimated 10% of cases this week.

That projection is based on genetic sequences of the virus reported by mostly public health labs, which have dropped significantly in recent weeks alongside the slowdown in cases overall. Other CDC data from wastewater and traveler testing still does not separate out KP.2 from its JN.1 parent.

KP.2 is a closely related descendant of the JN.1 variant from this past winter, which turned out not to be significantly more severe than the variants that were dominant before it, despite its large number of mutations.

"So it's one that we are watching. It's one that we are monitoring. And again, reiterate the need for continued surveillance of SARS-CoV-2 in people around the world, so that we can monitor this evolution," the World Health Organization's Maria Van Kerkhove told reporters Wednesday.

Why are these COVID-19 variants called FLiRT?

The nickname FLiRT comes from two distinctive mutations seen in several descendants of the JN.1 variant that have sprung up around the world after its sweep over the winter. Some of the largest strains with FLiRT mutations in the U.S. right now are KP.2 and KP.1.1.

"It is essentially just making a word out of the specific amino acid changes in the spike protein F456L + R346T, or phenylalanine (F) to leucine (L) at position 456 and arginine [R] to threonine [T] at position 346," Canadian biologist Ryan Gregory, a professor at the University of Guelph, told CBS News in an email. 

Gregory coined this nickname in March, and it gained traction among the variant trackers who have spotted and nicknamed many distinctive changes to the virus during the pandemic. Though unofficial, these nicknames have become commonly used names for a number of variants.

FLiRT won out over another nickname — "tiLT" variants — which had been coined by Australian consultant Mike Honey. FLiRT refers to a collection of faster-growing JN.1 offshoots the trackers are keeping an eye on, KP.2 among them.

"Basically, pretty much everything right now is a descendant of BA.2.86.1.1 (JN.1) and things are evolving rapidly, so it makes more sense to focus on mutations of interest rather than individual variants for the time being," wrote Gregory.

Do FLiRT variants lead to different COVID-19 symptoms?

Unlike some previous highly mutated variants that had raised concerns over potential changes to symptoms in recent years, the JN.1 variant many Americans already likely caught over the winter is closely related to the KP.2 strain now on the rise. 

"Based on current data there are no indicators that KP.2 would cause more severe illness than other strains," a CDC spokesperson told CBS News. 

KP.2's two distinctive so-called FLiRT mutations have also been seen before, in XBB.1.5 variants that were circulating throughout 2023, the spokesperson said. 

A draft study from scientists in Japan, released as a preprint that has yet to be peer-reviewed, found that the variant did appear to dodge antibodies better than the JN.1 variant. This "increased immune resistance" likely explains its rise, the scientists said.

In general, health authorities and experts have downplayed claims that variants were causing different symptoms. Changes to a person's immunity from vaccines and prior infections often play a role in different symptoms, rather than specific mutations.

"Mutations happen frequently, but only sometimes change the characteristics of the virus," the CDC says.

Will vaccines work against FLiRT variants?

The CDC has not made any changes to its current vaccine recommendations, which were last updated in April. But the emergence of these new JN.1 variant descendants like KP.2 might affect what vaccine the FDA picks out for this coming fall and winter.

Most Americans remain eligible to get at least one dose of this past season's updated COVID-19 vaccine, which CDC data so far suggests was up to 51% effective against emergency room or urgent care visits during a time when JN.1 was on the rise.

"CDC will continue to monitor community transmission of the virus and how vaccines perform against this strain," the agency said of KP.2.

Last month, the World Health Organization's experts recommended that vaccine manufacturers produce shots targeted at the JN.1 variant for next season. A panel of the FDA's own vaccine experts were scheduled to weigh that approach for the American vaccine market next week. 

However, the agency recently announced it had decided to delay the meeting until June in hopes of buying more time to ensure it picks out a vaccine target that is "most appropriate to be used for the strain(s) anticipated to be circulating" in the fall.

"The FDA, along with its public health partners, carefully monitors trends in the circulating strains of SARS-CoV-2. As has happened since the emergence of COVID-19, we have recently observed shifts in the dominant circulating strains of SARS-CoV-2," an FDA spokesperson told CBS News in a statement.

Pfizer has generated data from research of its vaccines against KP.2, but a company spokesperson said they were currently unable to share the results. A Moderna spokesperson did not respond to a request for comment.

A Novavax spokesperson said they had data showing their vaccine candidate for the fall aimed at JN.1 has "good cross-reactivity" for KP.2. While Novavax's vaccine takes longer to make than the mRNA shots from Pfizer and Moderna, the spokesperson said FDA's delay to the meeting "will not affect" their ability to deliver a shot this fall.

"We have manufactured JN.1 consistent with the recommendations and are on track to deliver an updated vaccine this fall," the Novavax spokesperson said.

In:
• COVID-19 Vaccine
• COVID-19
• COVID-19 Pandemic
• Coronavirus

Alexander Tin

Alexander Tin is a digital reporter for CBS News based in the Washington, D.C. bureau. He covers the Biden administration's public health agencies, including the federal response to infectious disease outbreaks like COVID-19.

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