California’s relentless FLiRT-fueled COVID surge continues to drive infections at a dizzying pace, with coronavirus levels in wastewater reaching some of the highest levels seen since 2022.
Sewage levels are now higher than all but one COVID spike in the past two years, and have far exceeded those seen during the typical summer seasonal spikes of the vaccine era.
“We’re seeing a very large increase right now. It’s starting to rival, really, what we saw last winter,” said Dr. Elizabeth Hudson, regional infectious disease chief at Kaiser Permanente Southern California.
For the week ending Aug. 10, coronavirus levels in wastewater were 84% of last winter’s peak in California, according to estimates released Friday by the U.S. Centers for Disease Control and Prevention. Coronavirus levels in wastewater have already surpassed peaks from the previous two summers, as well as the winter of 2022 to 2023.
“I’m really surprised that the number of cases hasn’t gone down yet,” said Dr. Peter Chin-Hong, an infectious disease specialist at the University of California, San Francisco. “The season is a little bit longer in California.”
There are few signs that the wave is slowing.
The COVID-19 test positivity rate continues to rise. In California, 14.7% of tests conducted at medical facilities were positive during the week ending August 12, a rate higher than any seen last winter and summer. A month ago, the test positivity rate was 10.6%.
During the 10-day period that ended Aug. 3, coronavirus levels in Los Angeles County wastewater climbed to 76% of last winter’s peak, up from 54% in the 10-day period that ended July 27.
And in Santa Clara County, the most populous in the San Francisco Bay Area, coronavirus levels in wastewater were considered high in three heavily populated sewer basins serving San Jose, Palo Alto and Sunnyvale.
FLiRT subvariants have been the primary culprits of this summer’s COVID surge, with one in particular starting to flex its hyper-infectious muscles. KP.3.1.1 is now the most common coronavirus strain circulating nationwide, making up about 36.8% of samples for the two-week period that ended Saturday, up from 12.7% a month ago, according to CDC data.
“It’s the confluence of a much more contagious variant and weakened overall immunity, whether it’s natural immunity or the vaccine,” Hudson said. “It’s kind of a perfect storm.”
This summer’s surge is shaping up to be particularly long. California has recorded “high” or “very high” levels of coronavirus in its wastewater for the past 10 weeks. In the summer of 2022, California spent 16 weeks in one or the other of those categories, and in the summer of 2023, the state recorded eight weeks with “high” virus levels in its wastewater.
Cases, while undercounted because they don’t account for people getting tested at home or not at all, are nonetheless rising. Los Angeles County averaged 484 COVID-19 cases per day during the week ending Aug. 11, a 35% increase from last month. The peak last summer was 571 cases per day.
COVID-19 is driving more people to emergency rooms. In the week ending Aug. 11, 4.3% of emergency room visits countywide were coronavirus-related, up from 4% the week before. The peak last summer was 5.1%.
Hospitalizations are up, but they remain very low compared to previous summers. Even in times of rampant infection, severe forms of COVID-19 are less frequent, thanks to acquired immunity and the widespread availability of anti-COVID drugs like Paxlovid.
In the week ending Aug. 10, there were an average of 462 people infected with the coronavirus in hospitals in Los Angeles County, up from 407 the week before. The peak last summer was 620, last winter was 825, and summer 2022 was more than 1,100.
At Kaiser Permanente Southern California, which serves more than 4.8 million members, the COVID surge has primarily driven an increase in visits to clinics and doctors’ offices.
“We’re not seeing a lot of people being admitted to the hospital with COVID,” Hudson said.
COVID-19 deaths in Los Angeles County remain relatively stable, averaging one to two per day, though it may take time for an increase in cases to appear in mortality data.
Still, while the early years of the pandemic were devastating, the overall burden of COVID-19 remains significant. Since October, more than 49,000 COVID-19 deaths have been reported nationally, compared with at least 25,000 influenza deaths estimated during the same period. An updated estimate of influenza deaths is expected later this year.
“COVID-19 remains a more important cause of severe illness and death than other respiratory viruses, but the differences in these rates are much smaller than they were early in the pandemic,” the CDC said in March.
People most at risk are those who are older or immunocompromised and who have not received an updated COVID-19 vaccine in the past year.
At some point, this summer spike will peak and the pace of new infections will begin to decline. But that won’t be clear until a few weeks after COVID indicators start to decline.
It remains an open question whether COVID-19 cases will continue to rise as children return to school. Doctors are urging people to stay home if they are sick and asking parents to keep sick children out of school to limit the spread of the disease.
Early estimates suggest that virus levels in California wastewater in the most recent week are about 3% lower than the previous week. But that figure is likely to change as more data becomes available.
California is one of 25 states where COVID-19 is estimated to be “increasing” or “likely to increase,” according to the CDC. COVID-19 is considered “likely to be declining” in five states: Alaska, Florida, Hawaii, Louisiana and New York. COVID-19 is stable or uncertain in 16 states and the District of Columbia. No estimates were available for Indiana, Missouri, Wisconsin and Wyoming.
Doctors have urged people, as well as health care providers, to get tested or request testing for their patients when they are experiencing symptoms of respiratory illness. An initial negative test does not mean you do not have COVID-19; doctors suggest testing up to five days after symptoms appear to see if a test becomes positive.
Dr. Abraar Karan, an infectious disease expert and epidemiologist at Stanford University, said confirming a COVID-19 diagnosis would help a patient get a prescription for Paxlovid to help treat the disease, while confirming another illness, such as the flu, could help a patient get a more targeted drug for that disease.
More regular testing in medical facilities could also help detect unusual strains that epidemiologists want to watch for, such as bird flu. Bird flu has recently gained attention due to outbreaks in U.S. poultry and dairy cows, and several human cases have recently been reported among U.S. dairy and poultry farm workers, according to the CDC.
Recent cases of H5N1 bird flu in humans have mostly caused mild symptoms, including conjunctivitis, Karan said. But one reason doctors are keeping a close eye on the situation is that in the decades we’ve known about bird flu in humans, some H5N1 strains have caused significant mortality rates. Human infections with H5N1, which have been reported in 23 countries since 1997, have resulted in severe pneumonia and death in about 50% of cases, according to the CDC.
Now that we know that bird flu has infected cows and that there is transmission from cows to humans, this poses a potential problem.
“Cow udders have receptors in common with birds, and they also have receptors in common with humans, where these viruses bind,” Karan said.
“With the human flu season coming up, you have the risk of what’s called viral reassortment, where a host can be infected with both avian flu and human flu, and then these flus start exchanging genetic material,” Karan said. “That’s kind of how the swine flu happened (in 2009). So that’s where we’re really concerned. It’s like a ticking time bomb of the human flu season coming up, and yet we still have this uncontrolled spread of avian flu in cows.”
Avian influenza has not resulted in sustained human-to-human transmission or caused a human pandemic in recent times.
“But this is one of those pathogens that has a high risk of mutating to the point of increasing its transmissibility. And the pathogen has a high virulence based on historical cases. … That’s the risk of where it could go,” Karan said.
This shows why it may be important for patients to get tested. If a test shows that a person has the flu, further screening – including genetic subtyping – could eventually determine whether a person has bird flu. This could help epidemiologists understand how bird flu may have spread and help doctors determine the best treatment.
Even if a case of bird flu causes mild symptoms, it’s important to diagnose it, Karan said, so the virus sample can be genetically analyzed and scientists can try to determine where it jumped from an animal to a human, and potentially treat the patient more aggressively with antivirals.
“But imagine – that will only happen if I test this patient for influenza,” Karan said.
