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New ‘FLiRT’ COVID Variants Could Be Driving an Uptick in Cases. Here’s How to Avoid Them

COVID numbers are low, but some evidence suggests they could be rising. Here’s how to protect yourself this summer, according to experts

silhouette of a person wearing a face mask stands at an airport, with an airplane visible in the background.

Allen J. Schaben/Los Angeles Times via Getty Images

Editor’s Note (6/5/24): Today the Food and Drug Administration’s Vaccines and Related Biological Products Advisory Committee unanimously voted in favor of an updated 2024–2025 monovalent COVID vaccine to target the JN.1 lineage. Data from vaccine manufacturers Pfizer, Moderna and Novavax showed that formulas based on JN.1 provided cross protection against subvariants in the lineage, including FLiRT variants. Pfizer and Moderna, which produce mRNA vaccines, and Novavax, which produces protein-based vaccines, are prepared to produce vaccines based on the JN.1 variant for the fall season.

COVID infections in the U.S. have declined since this past winter. But as seasonal travel picks up and heat waves bring more people indoors in the Northern Hemisphere, public health experts are on the alert for signs of yet another summer spike in cases.

The Centers for Disease Control and Prevention’s wastewater surveillance program currently reports low levels of viral activity—a combined measurement of the presence of the COVID-causing virus SARS-CoV-2 in samples from sewage collection sites nationwide. (A higher measurement at a wastewater site can suggest a potential increased risk of infection in the community, which would be reflected in clinical cases approximately four to six days later.) But that may be changing: national levels reported on May 25 increased approximately 7 percent from the previous week’s data collection period. Meanwhile WastewaterSCAN, a separate wastewater dataset that is monitored by researchers at Stanford University and Emory University, indicates that SARS-CoV-2 levels have been high and continuing to rise in the past 21 days. Some states, particularly in the West, have been reporting even greater increases in COVID wastewater concentrations. California has been seeing levels creep up since early May.

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Peter Chin-Hong, infectious disease physician and a professor of medicine at the University of California, San Francisco, says he had been treating people with COVID in the hospital in May. “It’s not gone away,” he says. National infection, hospitalization and death rates have been low, but they’re “not zero.”

Summers with COVID have typically been less severe than winter surges. Cases have peaked during summer in the Northern Hemisphere, however. These peaks have been associated with the emergence of new variants, the waning of immunity from vaccines, increased travel and less social distancing. This week public health experts in the U.S. are expected to decide on a new fall vaccine that could help protect against novel variants. “The writing is kind of on the wall to see a summer increase in cases this year,” Chin-Hong says. Whether or not there’s a full-blown COVID wave, “some people are going to get sick, unfortunately, and that is preventable.”

Scientific American spoke with public health experts about the outlook for COVID spread this summer, as well as the status of viral variants and vaccines.

“FLiRT” Variants

A new group of Omicron variants dubbed “FLiRT” has rapidly begun to circulate in the U.S. The name refers to amino acids involved in two new mutations on the virus’s spike protein: phenylalanine (F), leucine (L), arginine (R) and threonine (T). In December 2023 a different Omicron variant, JN.1, became dominant in the U.S. And as of May 25, JN.1 remains the most abundant variant detected in wastewater, appearing in 74 percent of samples. Despite JN.1 being more prevalent, the Omicron descendants in the new FLiRT group, including KP.2, KP.3 and KP.1.1, are causing more infections. In March the FLiRT variants made up less than 5 percent of infections. As of May 25, these variants have come to represent more than 50 percent of infections, with KP.2 alone causing 28.5 percent of them. The FLiRT variants are “coming up pretty quickly,” Chin-Hong says.

The name FLiRT derives from mutations in specific sites of the virus’s spike protein. These spike protein mutations may make it better at evading the immune system than previous variants, which may explain KP.2’s increasing prevalence, says Ziyad Al-Aly, a long COVID researcher and a clinical epidemiologist at the Washington University School of Medicine in St. Louis. On May 20 researchers in Japan published a paper in the Lancet Infectious Diseases that suggests KP.2 may be more transmissible, too. The study also showed the current vaccine based on the Omicron XBB.1.5 variant was less effective against KP.2 than it was against JN.1. Still, it’s unclear whether KP.2 is causing more or less severe disease than previous variants, Al-Aly says. “Anecdotally, at least in the U.S., I’m not seeing much of a rise in hospitalizations and emergency room visits, so maybe it’s not more pathogenic than the variant that preceded it,” he says. “But the data doesn’t exist yet. It’s very new still.”

Unpredictable Patterns

The fact that the virus continues to spawn variants “somewhat unpredictably” makes it harder for scientists to determine if or when COVID might settle into a seasonal pattern similar to that of other respiratory illnesses, Al-Aly says. The flu, for example, has a relatively predictable seasonality in the Northern Hemisphere, with increased infections in the winter and lower rates in the summer. Researchers are also able to predict upcoming dominant strains to develop vaccines that help boost people’s immunity before flu season hits. Al-Aly and Chin-Hong say it’s still too early to tell if COVID has the same cadence, however.

The emergence of KP.2 further indicates that “COVID has not really figured out what it wants to be yet,” Al-Aly says. “Does it want to settle on being a seasonal winter virus? It keeps changing on us, so I definitely think that we’re not there yet.”

COVID also continues to be more deadly than the flu, he says. Al-Aly and his team published a paper in JAMA on May 15 that compared the risk of death in people hospitalized with COVID with the risk in those hospitalized with the flu between October 2023 and March 2024. The study found that COVID deaths were down from the previous fall-winter season in 2022 to 2023 but were still worse than flu: those hospitalized with COVID had an approximately 35 percent higher risk of death. “We were hoping we would see that finally COVID is on par with the flu, that it’s as deadly as the flu—not more, not less,” Al-Aly says. Yet “COVID is still a much more serious threat to human health than the flu, and it’s very, very clear in the data.”

In April the CDC reported almost 2,000 COVID deaths in the U.S. “It’s nothing to celebrate,” Chin-Hong says. “I think deaths should be close to zero.”

Current and Upcoming Vaccines

Versions of the COVID vaccines that target the XBB.1.5 variant are available, and those who are age 65 and older or immunocompromised are eligible to receive an additional shot if they already received one in the fall of 2023. (Immunocompromised people should wait to receive the additional dose for at least two months after their previous shot. People aged 65 or older who are not immunocompromised should wait at least four months.) As of May 11, CDC surveys found that just 22.5 percent of adults in the U.S. reported receiving the most recent vaccine. This vaccine might be less effective against the newer FLiRT variants, but it likely still offers protection against severe disease.

“People's immunities are wearing off around now if they got [the vaccine] over the winter,” Chin-Hong says. A study published in the New England Journal of Medicine on May 29 showed the XBB.1.5 vaccine reached 52 percent effectiveness against infection after four weeks. Then immunity began to wane, decreasing to 33 percent after 10 weeks and to 20 percent after 20 weeks. The study also showed the vaccine was 67 percent effective at preventing hospitalizations at four weeks and 57 percent effective after 10 weeks.

Chin-Hong adds that going into last summer, population immunity was much higher. “More people were vaccinated in addition to getting infected, so [there] was more hybrid immunity. Now we’re relying more on just [immunity from] infection,” he says. On top of that, people who had gotten sick with COVID in the winter likely built immunity for JN.1, but those same defenses might not work against KP.2. “Given the new variant looks a little bit different from the one that people might have been exposed [to] and infected with in the winter, you’re not going to escape it as easily,” he says.

Al-Aly says focusing on improving vaccination uptake is going to be important, particularly in getting the public onboard with annual updated COVID vaccinations. The U.S. Food and Drug Administration’s advisory committee for vaccines is expected to decide on a new formula—including the strain it may cover—for this fall at a meeting on June 5.

Most people are able to receive vaccines through private and government health insurance. The federally supported Bridge Access Program supplies free vaccines to those without insurance. It is ending in August, however. Local or state programs might continue to offer the vaccines for free or at low cost. But Chin-Hong encourages people who are eligible for an additional dose or who have not yet received one at all to get the current vaccine now.

Treatments, including the antiviral drug Paxlovid, are also available and are effective tools for preventing severe COVID, especially among adults aged 65 or older and other individuals who are at high risk of hospitalization from the disease. (Paxlovid can be prescribed at low or no cost through the federally supported PAXCESS program.)

Chin-Hong also recommends wearing masks and packing COVID rapid tests during summer traveling and vacations. And vaccination is still crucial for prevention. “Everybody I saw in the hospital,” he says, “the common feature when they were very sick right now with COVID is that they didn’t get a vaccine in the last year.”

Lauren J. Young is an associate editor for health and medicine at Scientific American. She has edited and written stories that tackle a wide range of subjects, including the COVID pandemic, emerging diseases, evolutionary biology and health inequities. Young has nearly a decade of newsroom and science journalism experience. Before joining Scientific American in 2023, she was an associate editor at Popular Science and a digital producer at public radio’s Science Friday. She has appeared as a guest on radio shows, podcasts and stage events. Young has also spoken on panels for the Asian American Journalists Association, American Library Association, NOVA Science Studio and the New York Botanical Garden. Her work has appeared in Scholastic MATH, School Library Journal, IEEE Spectrum, Atlas Obscura and Smithsonian Magazine. Young studied biology at California Polytechnic State University, San Luis Obispo, before pursuing a master’s at New York University’s Science, Health & Environmental Reporting Program.

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