New COVID-19 variants, collectively named “FLiRT,” continue to gain dominance across the U.S., leading to increased case numbers in Los Angeles County and elevated concentrations of coronavirus in California’s wastewater.
Taken together, the data points to a resurgence of coronavirus in California, not entirely unexpected given trends seen in past pandemic-era summers, but driven by earlier-arriving and more contagious strains.
But it’s unclear how bad the COVID-19 situation will be this summer, and doctors have said they may have a better idea by the Fourth of July about what the remainder of the season will look like.
The U.S. Centers for Disease Control and Prevention estimates that FLiRT variants — formally known as KP.3, KP.2 and KP.1.1 — accounted for 62.9% of specimens nationwide in the two weeks ending Saturday, up from 45.3% a month ago.
Experts say the new subvariant is more contagious than the JN.1 subvariant that was dominant during the winter.
According to the CDC, California is currently one of 15 states with high or very high levels of coronavirus in their wastewater. These states are primarily in the West and South, and in New England. In addition to California, these states include Alaska, Colorado, Connecticut, Florida, Hawaii, Idaho, Missouri, Nevada, New Hampshire, New Mexico, Tennessee, Texas, Utah, and Wyoming.
Concentrations of coronavirus in wastewater across California have risen sharply since early May, contrasting with a national trend of more gradual increases. California’s latest levels of virus activity in wastewater are near the peak seen last summer.
In Santa Clara County, Northern California’s most populous county, wastewater levels are considered high across a wide swath of Silicon Valley, stretching from San Jose to Palo Alto.
Coronavirus levels in Los Angeles County’s wastewater have generally stabilized after rising last month. For the week ending June 8, the most recent data available, levels in wastewater were 15% of the winter 2022-23 peak, up from 13% the previous week but down slightly from 16% the week before that. Last summer, when levels peaked near the end of the season, levels in wastewater reached 38% of the winter 2022-23 peak.
But COVID-19 cases continue to rise. In the seven days ending June 16, an average of 154 cases were reported per day in Los Angeles County, up from 121 the previous week. The reported number of cases is an undercount because it only represents tests done in health care facilities and does not include at-home tests. It also does not reflect that far fewer people get tested for COVID when they are sick.
The average number of COVID-19 patients admitted to Los Angeles County hospitals each day is also trending up. In the week ending June 15, the average number of hospitalized patients was 138 per day, up from 126 the week before.
In the week ending May 28, COVID deaths remained steady at an average of less than one per day.
The percentage of positive COVID-19 tests administered in California health care facilities continues to rise. In the week ending June 17, 7.5% of COVID-19 tests statewide came back positive, up from 3.1% a month earlier. The peak last summer was 13.1%, recorded in late August.
In June, the California Department of Public Health updated its guidelines for older adults, especially those with weakened immune systems. Officials urged seniors to consider additional precautions, such as staying up to date on vaccinations and getting medication if they are exposed to COVID, wearing masks in crowded indoor spaces, opening windows and doors to improve ventilation, staying away from sick people, washing hands frequently and covering your mouth when coughing or sneezing.
The increase in COVID-19 tracking data comes after the U.S. Food and Drug Administration issued new advice to vaccine manufacturers in mid-June. In a June 13 statement, the agency urged manufacturers to design vaccine formulations this fall, if possible, to target one of the FLiRT variants, KP.2, rather than the parent strain, JN.1.
The new recommendation overrides guidance from just a week ago, when authorities recommended that vaccines be designed to counter JN.1.
“This change is intended to ensure that the COVID-19 Vaccine (2024-2025 Formulation) is more consistent with circulating strains of SARS-CoV-2,” the FDA said in a statement, referring to the official name of the COVID-19 virus.
Dr. Peter Marks, director of the FDA’s Center for Biologics Evaluation and Research, said at a press conference Friday that circulating COVID subvariants by this fall “will probably be closer to KP.2 than to JN.1.”
The mRNA-based vaccines made by Pfizer and Moderna will be ready to produce the vaccine for KP.2 as soon as this fall, but the protein-based vaccine made by Novavax will still be designed for JN.1 because mRNA vaccines can be manufactured more quickly, Marks said.
“Making a protein-based vaccine versus an mRNA vaccine allows you to do different things in terms of the agility to react to what’s next,” Marks said. Still, the difference between a vaccine designed against the new KP.2 variant and the slightly older JN.1 variant probably won’t be “that big of a difference.”
“I’m not going to pick sides,” Marks said about recommending the Pfizer or Moderna vaccines over Novavax, “The best vaccine for this fall season is the one you get in your arm.”
Marks said the vaccine against KP.2 is “probably a little bit more effective” than the vaccine against JN.1. “We’re hopeful that by using essentially the latest updates, we can provide longer-lasting protective immunity into the late fall and winter,” Marks said.
“It’s like trying to give people the biggest advantage, you know? Hundredths of a second can make the difference between winning and losing. [a race] “But I think the most important thing for people to know is that it’s totally fine to get one of these anyway,” Marks said.
Federal officials have said they hope a COVID vaccine will be available sooner this year than in 2023. The rollout last year was complicated, with updated COVID vaccines coming out slightly later than seasonal flu shots, making it more difficult for people to get both shots in one visit even if they wanted to.
Doctors say COVID-19 remains a disease to be wary of. Nearly 45,000 COVID-19 deaths have been reported nationwide since Oct. 1, and doctors say those most at risk are the elderly and immunocompromised who have not received up-to-date vaccinations.
“This isn’t something that just goes away into the night. It’s still here,” Marks said.