Latest COVID worry, FLiRT variants, sparks concern about vaccination rates

A new family of COVID variants nicknamed “FLiRT” is spreading across the country, as vaccination rates remain concerningly low for some public health experts.

While symptoms and severity seem to be about the same as previous COVID strains, the new FLiRT variants appear to be more transmissible, said infectious disease expert Dr. Robert Murphy.

FLiRT is not one specific strain. It is a nickname given to a series of mutations — S:F456L and S:R346T — culled from the letters in the technical mutation names.

“A new, more contagious variant is out there,” said Murphy, executive director of Northwestern University’s Institute for Global Health and a professor of infectious diseases at the Feinberg School of Medicine. “COVID-19 is still with us, and compared to flu and RSV, COVID-19 can cause significant problems off-season.”

Murphy urged the public to get up to date on COVID shots, particularly individuals who are at higher risk for severe complications from the virus. While much of the population has some immunity from vaccination or previous COVID infections, Murphy noted that “with COVID-19, immunity wanes over time.”

One FLiRT variant, KP.2, is estimated to account for roughly a quarter of recent COVID cases, according to Centers for Disease Control and Prevention data from late April.

The JN.1 variant is estimated to account for about 22% of recent COVID cases across the country, according to CDC data from late April.

Another FLiRT variant, KP.1.1, comprises over 7% of COVID cases nationwide, the CDC data shows. The name “FLiRT” is an acronym using the technical names for the mutations that caused the family of variants.

Nationwide, about 23% of adults and 14% of children were reported to be up to date on COVID vaccines as of late April, according to the CDC, based on data from the National Immunization Survey.

FLiRT has made itself known in Los Angeles County, but hasn’t made a lot of noise just yet. But officials expect to see the numbers grow.

“We are seeing these two mutations on the rise in various JN.1 strains,” said a statement from the Los Angeles Department of Public Health on Wednesday. “JN.1 is the Omicron variant that caused the surge this past winter.”

These two mutations are skilled at eluding the body’s immunity than other currently circulating lineages, the statement said. County health officials confirm the arrival of the variants here and expect to see growth in the next two weeks.

KP.2 is the currently dominant lineage with this set of FLiRT mutations, accountable for about 28% of new U.S. cases during the two weeks ending May 11.

In the latest complete data from L.A. County, KP.2 made up 5% of reported cases between March 31 and April 13.

No significant changes in symptoms or severity have been observed in strains with FLiRT mutations as of now, officials said.

“We have not seen an increase in infections and transmission of SARS-CoV-2 is still low,” county health officials added.

Pasadena and Long Beach operate their own health departments, and both had the FLiRT mutations on their collective radars, but have logged few reported cases.

The Long Beach Health Department has identified two COVID-19 cases as KP.2 variant strains with the first reported on April 16.

“Due to limited sequencing or genetic testing, this is likely an undercount of the total number of KP.2 variants,” said Jennifer Rice Epstein, a spokeswoman from Long Beach Department of Health and Human Services. “Fortunately, the Long Beach Health Department has not seen an increase in COVID-19 cases compared to recent months and will continue to monitor.”

Epstein also said COVID-19-related hospitalization remained low.

The Pasadena Public Health Department has continued to conduct case investigations and outbreak investigation for COVID-19 cases. Such efforts include monitoring results from wastewater surveillance.

Health Director Dr. Ying-Ying Goh said this week that reported levels of COVID-19 in the community remained low, with less than one confirmed case reported to the Pasadena Health Department on average per day.

Of those, Goh said the department estimates that of total cases sequenced in April, 28.1% were JN.1 (BA.2.86.1.1), 15.6% were JN.1.16, and 15.6% were JN.1.7.

But, like Long Beach, a more full-fledged count is difficult. The April counts were “state-level” data.

“Because of significantly reduced PCR testing, it is generally unreliable to draw conclusions about proportions of variants accurately at a city or county level,” said Goh in a statement.

Nonetheless, as with all new COVID variants, officials urged caution.

“For people who have fragile immune systems, they should take precautions around large crowds and places where they can be exposed,” said Dr. Elizabeth McNally, director of the Northwestern University Feinberg School of Medicine Center for Genetic Medicine. “For older people, it’s generally a good idea to stay up to date on vaccinations since immunity does wane with age.”

In February, the CDC recommended that Americans 65 and up get another dose of the updated vaccine that became available in September, if at least four months had passed since their most recent shot.

McNally said it’s hard to know the impact of new variants since “there is not a great deal of testing going on these days.”

But she noted that there doesn’t appear to be an increase in COVID hospitalizations, nor has she seen uptick in infections in her patients, who “tend to be quite sick at baseline and contact me when they are exposed or sick.”

COVID hospitalizations and deaths are on the decline in Chicago and nationwide, according to the city health department and CDC. The Chicago region’s current COVID-19 hospital admission level is low, as is most of the United States, according to the CDC.

While vaccination rates have tapered off, McNally noted that this “is on the backdrop of a great deal more immunity from repeated exposures from natural infection and vaccination,” compared with the early stages of the COVID pandemic.

“This translates to quicker recoveries and less prolonged illness when people do get COVID,” she said. “In 2020, we were dealing a virus for which humanity had little immunity. That is, thankfully, very different now.”

SCNG Staff Writers Kristy Hutchings and Teresa Liu contributed to this report. Jill Stewart of the L.A. Daily News and Angie Leventis Lourgos of the Chicago Tribune also contributed to this report.