A new COVID-19 strain is now driving the majority of infections in the Bay Area as disease levels remain high at the start of the school year, according to Stanford research.
The XFG "Stratus" strain now dominates in parts of San Francisco, Sacramento and San Jose, according to the Stanford WastewaterSCAN program, which tracks COVID-19 through sewage samples at four sites across those three cities. The new strain makes up more than half of all variants detected at three of the four locations.
"We have routinely seen XFG as the predominant variant since July 2025," Amanda Bidwell, the scientific program manager for WastewaterSCAN, told SFGATE in a statement.
Data from the week of Aug. 16 shows the strain firmly outpacing other variants: "We are seeing the XFG variant ... make up approximately 82% of variants followed by NB.1.8.1 [Nimbus] at approximately 5.2%," Bidwell explained.
Dr. Peter Chin-Hong, an infectious disease expert at UCSF, told SFGATE that Stratus is behaving "very similar" to earlier COVID lineages like Nimbus, which spread during summer and, in some cases, caused severe "razor-blade" sore throat symptoms.
"There's a little bit more sore throats with some people," Chin Hong said. "Particularly in those who are older, who didn't get vaccinated last year." He added that Stratus has shown "a wider range of symptoms," including congestion and gastrointestinal issues, though most cases remain mild.
The variant is also more contagious.
"It's more transmissible, so we expect that a lot of people will get it," he said, referring to Stratus. "Particularly with kids going back to school, a sniffle is likely going to be COVID."
Dr. Eric Ball, a pediatrician in Orange County, said the timing of the new surge collides with a confusing and restrictive vaccine rollout.
"I literally just got off of an emergency call with my practice, because we're trying to figure this out because it is incredibly confusing," he told SFGATE. "We're getting different messages from different government agencies and insurance companies ... the guidance is really unclear."
U.S. Health and Human Services Secretary Robert F. Kennedy Jr. announced Wednesday on X that the Food and Drug Administration has approved updated COVID-19 vaccines, with new restrictions. The vaccines from Moderna are approved for children as young as 6 months, Pfizer for ages 5 years and up, and Novavax for those 12 years and older -- but only for patients considered to be at higher risk. Parents are being told to consult with their doctors to determine eligibility, adding another layer of complexity.
Adults over 65 will be able to get the vaccines without restrictions.
A key Centers for Disease Control and Prevention advisory panel is expected to meet in the coming weeks to decide whether to recommend the updated COVID-19 shots.
This approach reflects a policy shift announced in a May video, when Kennedy said the CDC would no longer recommend COVID-19 shots for healthy children or pregnant people. The American College of Obstetricians and Gynecologists broke from that guidance, recommending individuals get a COVID-19 vaccine during pregnancy. The American Academy of Pediatrics also continues to recommend that infants over 6 months and children be vaccinated against COVID-19.
Ball warned that children under 2 years old could be at risk for severe COVID-19 symptoms if they are not vaccinated.
"Kids from 6 months old to 2 years old have the highest rate of hospitalization of any Americans, equivalent to that of people who are 65 and older," he said. "They are not included in this guidance."
He also flagged a potential "two-tiered system" of access, which may deepen inequities in care. He pointed to the federally funded Vaccines for Children program that provides routine vaccinations for children on Medicaid. The program generally follows CDC guidance on what is considered a routine vaccine.
"In California, over 50% of kids are on Medicaid, and they get their vaccines this way, and they might not be able to get them this year," Ball said. "We already have a socioeconomic disparity ... and now we're going to put even more barriers on a lot of people."
Despite the hurdles, both doctors urged parents to turn to trusted health providers for guidance.
"Any family who wants to vaccinate their kid after conversations with their doctor should have the opportunity," Ball said.
Chin-Hong added that while the rollout has been chaotic, there is still some reassurance: "We will have a new vaccine this year, and the people who need it the most are going to get it."