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3 Things to Know About FLiRT, the New Coronavirus Strains

BY KATHY KATELLA June 7, 2024

A Yale Medicine expert weighs in on the potential impact of the new strains on the spread of COVID.

[Originally published: May 21, 2024; Updated: June 7, 2024.]

Note: Information in this article was accurate at the time of original publication. Because information about COVID-19 changes rapidly, we encourage you to visit the websites of the Centers for Disease Control & Prevention (CDC), World Health Organization (WHO), and your state and local government for the latest information.

The good news is that in the early spring of 2024, COVID-19 cases were down, with far fewer infections and hospitalizations than were seen in the previous winter. But SARS-CoV-2, the coronavirus that causes COVID, is still mutating. In April, a group of new virus strains known as the FLiRT variants (based on the technical names of their two mutations) emerged.

The FLiRT strains are subvariants of Omicron, and they now account for more than 50% of COVID cases in the U.S. (up from less than 5% in March). One of them, KP.3, accounted for 25% of COVID infections in the United States by the end of the first week of June; KP.2 made up 22.5%, and KP.1.1 accounted for 7.5% of cases.

Some experts have suggested that the new variants could cause a summer surge in COVID cases. But the Centers for Disease Control and Prevention (CDC) also reports that COVID viral activity in wastewater (water containing waste from residential, commercial, and industrial processes) in the U.S. has been dropping since January and is currently “minimal.”

“Viruses mutate all the time, so I’m not surprised to see a new coronavirus variant taking over,” says Yale Medicine infectious diseases specialist Scott Roberts, MD. If anything, he says the new mutations are confirmation that the SARS-CoV-2 virus remains a bit of a wild card, where it’s always difficult to predict what it will do next. “And I’m guessing it will continue to mutate.”

Perhaps the biggest question, Dr. Roberts says, is whether the newly mutated virus will continue to evolve before the winter, when infections and hospitalizations usually rise, and whether the FLiRT strains will be included as a component of a fall COVID vaccine.

Below, Dr. Roberts answers three questions about the FLiRT variants.

1. Where did the FLiRT strains come from?

Nobody knows exactly where the FLiRT variants first emerged. They were first detected in the U.S. in wastewater by the CDC, which tests sewage to detect traces of SARS-CoV-2 circulating in a community, even if people don’t have symptoms. (The data can be used as an early warning that infection levels may be increasing or decreasing in a community.) The FLiRT strains have since been identified in several other countries, including Canada and the United Kingdom.

To better understand how the FLiRT strains emerged, it might help to see how the SARS-CoV-2 virus has changed over time, with new variants forming as mutations emerged in its genetic code. Omicron was a variant of SARS-CoV-2 that took hold in the U.S. in 2021 and began to spawn subvariants of its own. One of those was JN.1, which was identified in September 2023 and spread through the country during the winter months, leading to a spike in COVID hospitalizations. JN.1 also has descendants; the FLiRT subvariants are spinoffs of one called JN.1.11.1.

2. What do we know—and not know—about the FLiRT variants?

We know the FLiRT variants have two mutations on their spike proteins (the spike-shaped protrusions on the surface of the virus) that weren’t seen on JN.1 (the previously dominant strain in the U.S.). Some experts say these mutations could make it easier for the virus to evade people’s immunity—from the vaccine or a previous bout of COVID.

But, the fact that the FLiRT variants are otherwise genetically similar to JN.1 should be reassuring, Dr. Roberts says. "While JN.1 occurred during the winter months, when people gather indoors and the virus is more likely to spread, its symptoms were milder than those caused by variants in the early years of the pandemic," he says.

There is no news yet about whether a COVID illness will be more severe with the FLiRT variants or how symptoms might change. Because everyone is different, a person’s symptoms and the severity of their COVID disease usually depend less on which variant they are infected with and more on their immunity and overall health, the CDC says.

3. How can people protect themselves against the FLiRT strains?

Vaccination is still a key strategy, says Dr. Roberts, adding that everyone eligible for COVID vaccination should make sure they are up to date with the latest COVID vaccines. While vaccination may not prevent infection, it significantly lowers a person’s risk of severe illness, hospitalization, and death from COVID.

“We know that the updated monovalent vaccine, which was designed for the XBB.1.5 variant, worked against JN.1, and I strongly suspect it will have some degree of activity against the FLiRT mutations as well,” Dr. Roberts says.

“I would especially recommend anyone who qualifies for the vaccine because of advanced age get it if they haven’t already,” Dr. Roberts adds. “The reason is that the biggest risk factor for a bad outcome from COVID is advanced age.” Anyone over age 65 is eligible for both the first updated vaccine offered in the fall of 2023, and a second shot four months later.

He also says COVID tests should be able to detect the FLiRT strains, and antiviral treatments should remain effective against them. Paxlovid, the primary treatment for most people with COVID, acts on a “nonspiked part of the virus,” he says. “It's relatively variant-proof, so it should really act against many future COVID iterations.”

Other preventive efforts can help. You can avoid getting too close to people who are sick, mask strategically, wash hands properly, improve ventilation, and stay aware of COVID transmission levels where you live and work. Additional strategies are available on the CDC website.

Information provided in Yale Medicine articles is for general informational purposes only. No content in the articles should ever be used as a substitute for medical advice from your doctor or other qualified clinician. Always seek the individual advice of your health care provider with any questions you have regarding a medical condition.