A new COVID variant is dominant in the US: What are its symptoms?

A new COVID variant is dominant in the US: What are its symptoms?
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In recent weeks, a new COVID-19 variant called KP.3 has gained dominance in the United States. KP.3 is part of a family of mutated strains nicknamed "FLiRT," which are driving an increasing proportion of cases across the country. As KP.3 spreads, some are concerned about potential summer wave.

The FLiRT strains — which include KP.3, KP.2, and KP.1.1 — now account for more than half of all COVID-19 infections nationwide, according to the latest data from the U.S. Centers for Disease Control and Prevention.

These new variants, which scientists dubbed "FLiRT" after the locations of their spike protein mutations, have been circulating in the U.S. since the early spring. In April, KP.2 quickly overtook JN.1, the omicron subvariant that drove a surge in COVID cases this past winter.

In a matter of weeks, the KP.3 variant overtook KP.2 to become the most prevalent strain in the U.S., per the CDC.

During a two-week period ending on June 8, KP.3 made up an estimated 25% of cases in the U.S., up from about 9% in early May. After KP.3, the next most common variant is KP.2, another FLiRT variant that gained dominance in May and now accounts for about 22% of cases. It's followed by LB.1, a JN.1 subvariant, and another FLiRT variant, KP.1.1.

Together, the FLiRT variants make up an estimated 55% of cases in the U.S.

Although hospitalizations are down and COVID-19 numbers are relatively low, there has been a small uptick in test positivity and emergency room visits, per the latest CDC data. These trends, along with previous summer waves, have stoked fears about a surge of infections this summer.

Scientists are warning that the FLiRT variants may be better at evading the immune system due to their spike protein mutations, and that waning immunity and poor uptake of the latest COVID-19 vaccine have created a more susceptible population.

Will there be another COVID-19 wave? What are the symptoms of the FLiRT variants? Are vaccines still effective? We spoke to experts to learn more.

What is KP.3?

KP.3 is one of the FLiRT variants — along with KP.2 and KP.1.1 — which are spinoffs of JN.1.11.1, a direct descendant of JN.1. They were initially detected in wastewater samples from across the country.

KP.3 and the other new variants have additional mutations that set them apart from JN.1 and appear to give them an advantage over previous variants, Dr. Albert Ko, infectious disease physician and professor of public health, epidemiology and medicine at Yale School of Public Health, tells TODAY.com.

The nickname "FLiRT" is based on the technical names for their mutations, according to the Infectious Disease Society of America.

Just like other COVID-19 strains that have gained dominance in the U.S. over the last year — JN.1, HV.1, EG.5 aka Eris, and XBB.1.16 or Arcturus — the FLiRT variants part of the omicron family.

The emergence of KP.3 and other FLiRT variants is the "same old story," Andrew Pekosz, Ph.D., virologist at Johns Hopkins University, tells TODAY.com. The SARS-CoV-2 virus mutates and gives rise to a new, highly contagious variant, which becomes the dominant strain. "The timeline that it happens in, three to six months, is much faster than we see with other viruses like influenza," says Pekosz.

Is KP.3 more transmissible?

“It’s still early days, but the initial impression is that this variant is rather transmissible,” Dr. William Schaffner, professor of infectious diseases at Vanderbilt University Medical Center, tells TODAY.com.

The proportion of cases caused by KP.3 is increasing, while the proportion caused by other variants is decreasing, which suggests the FLiRT variants have features that give it an advantage, the experts note.

Over 97% of people in the U.S. have natural or vaccine-induced antibodies against the the SARS-CoV-2 virus, per the CDC, but this immune protection fades over time.

Low vaccination rates and waning immunity create a vulnerable population, which may allow the FLiRT variants to take hold. Only time and more data will tell, the experts note.

Laboratory studies suggest that the FLiRT variants are mutated enough such that current vaccines and immunity from prior infection will only provide partial protection, says Schaffner. "We'll have to see how true that is, but it appears, over time to be becoming a more prominent variant," he adds.

“It’s still really early ... but I don’t think we need to sound the alarm bells as of yet,” says Ko.

The state of COVID in the U.S.

It's too soon to tell whether KP.3 and the FLiRT variants will cause a summer wave or surge, the experts note. However, it is clear that COVID-19 is still circulating and won't be taking any time off.

"We're seeing these infections year-round, at modulating levels. ... We’re probably not at the stage yet where we’ll see COVID go away completely at any time of the year,” says Pekosz.

Test positivity, which is an early indicator of case levels, was 5.4% as of June 8, up 0.8% from the previous week but a sharp decline from a peak of about 12% in mid-January, per the CDC. (The CDC no longer tracks the total number of cases in the U.S.)

"We're not seeing a lot of hospitalizations, and we're certainly much lower than we were in the winter, so I'd say right now we're at a low point, which is reassuring," says Ko.

Wastewater data published by the CDC show that the viral activity level for COVID-19 is currently “low” — it was considered high or very high for most of January and February.

"It seems like transmission is pretty low right now, and that makes sense because usually the big peaks are in the winter, when people are inside and in more contact," says Ko.

COVID-19 has caused summer waves in the past, the experts note, which are often smaller than the winter surges. “I don’t think that we’ll see any kind of massive surge in cases,” says Pekosz.

The seasonality of COVID-19 is something scientists are still trying to understand. But one thing is obvious: “This virus is now integrating itself into our population and our way of life,” says Schaffner.

Adds Ko: “I’m not expecting a large surge in the summer, but again, we have to be cautious and we have to follow the data. ... We always have to be humble because SARS-CoV-2 has taught us a lot of new things.”

What are the symptoms of KP.3?

It is still too early to tell whether the symptoms of KP.3, KP.2 and other FLiRT variants are different from previous strains.

“The FLiRT variants are probably not going to create very distinctive symptoms. It looks at the moment to follow the other subvariants,” says Schaffner.

The symptoms of the FLiRT variants are similar to those caused by JN.1, which include:

  • Sore throat

  • Cough

  • Fatigue

  • Congestion

  • Runny nose

  • Headache

  • Muscle aches

  • Fever or chills

  • New loss of sense of taste or smell

  • Shortness of breath or difficulty breathing

  • Nausea or vomiting

  • Diarrhea

According to the CDC, the type and severity of symptoms a person experiences usually depend more on a person’s underlying health and immunity rather than the variant that caused the infection.

Similar to JN.1 and other omicron subvariants, the FLiRT variants seem to be causing milder infections, says Schaffer.

Do vaccines protect against KP.3?

Early laboratory studies indicate that the vaccines will continue to provide protection the FLiRT variants — "a little less protection, but not zero by any means," says Schaffner.

As the virus mutates, it is becoming progressively different from the omicron strain targeted in the latest updated booster released in the fall of 2023. "We would expect that to happen, and we anticipate the plan is to have an updated vaccine in the fall available to everyone," says Schaffner.

Advisers to the U.S. Food and Drug Administration met on Tuesday, June 5, to decide which strains to include in the updated COVID-19 vaccines for 2024–2025. The committee unanimously voted to recommend a monovalent vaccine targeting the JN.1 variant for this fall, the agency said in a press release.

Even if vaccines do not prevent infection, they can still offer some protection by preventing severe disease, hospitalization, and COVID-19 complications, TODAY.com previously reported.

“It’s still clear that the more severe cases that come into the emergency room predominate in people who either are not up to date on their vaccines or haven’t gotten a vaccine in a really long period of time,” says Pekosz.

Vaccination is especially important for the elderly, says Pekosz, which is why the CDC recently recommended adults ages 65 and older get an additional dose of the 2023-2024 updated COVID-19 vaccine.

Unfortunately, vaccination uptake is still poor, the experts note. "The vaccines are still showing signatures of effectiveness, but they're not being utilized anywhere close to the level that they should be," says Pekosz.

As of April 2024, only about 22% of adults and 14% of children have reported receiving the updated COVID-19 vaccine released in September 2023, according to the CDC.

All current PCR and at-home tests are recognizing KP.3 and other FLiRT variants, the experts note. (Though if you have symptoms of COVID and test negative, it's a good idea to stay home to avoid potentially exposing other people, TODAY.com previously reported.

If you are using an at-home antigen test, always remember to check the expiration date and whether it’s been extended by the FDA.

“Antivirals (such as Paxlovid) are also working well. ... There’s not any major signals of antiviral resistance in the population, which is a positive sign,” says Pekosz.

How to protect against KP.3 and FLiRT variants

While it's too early to tell how the FLiRT variants will pan out this summer, people can always take steps to protect themselves and others against COVID-19.

The CDC recommends the following prevention strategies:

  • Stay up to date with COVID-19 vaccines.

  • Test for COVID-19 if you have symptoms or an exposure.

  • Stay home when you are sick.

  • Return to normal activities only after you have been fever-free and symptoms have been improving for at least 24 hours.

  • Practice good hand hygiene.

  • Improve ventilation.

  • Wear a mask in crowded, indoor spaces.

  • Practice social distancing.

This article was originally published on TODAY.com