For the past several weeks, a dizzying array of gastrointestinal and respiratory viruses have been circulating throughout the Bay Area, and San Francisco appears to be experiencing the worst of it.

According to recent data from WastewaterSCAN, an organization that monitors viral traces in municipal wastewater, while rates of COVID-19 are low, rates of rotavirus, norovirus, human metapneumovirus (HMPV), influenza A and B, and RSV remain high (influenza A, however, is moderate in southeast San Francisco).

Though it’s still unclear why these viruses are so prevalent in San Francisco, health experts say changing vaccine recommendations could be partly to blame.

Rotavirus in particular, a gastrointestinal illness that can cause fatal diarrhea in small children, is much higher in 2026 compared with 2025, wastewater data reveals. Dr. Monica Gandhi, an infectious disease specialist at UC San Francisco, said that it could be due to a variety of reasons ranging from better wastewater surveillance in San Francisco to lower vaccine rates, but it’s difficult to tell.

“We’ve been worried about rotavirus” because vaccination against it is no longer recommended by the Centers for Disease Control and Prevention, “which is insane,” she told SFGATE on Monday. While rotavirus used to be part of routine childhood vaccination, the Department of Health and Human Services, now led by noted vaccine skeptic Robert F. Kennedy Jr., has changed that recommendation. Now the rotavirus vaccine is only recommended based on “shared clinical” decision-making between a doctor and patient or their guardian.

Much like norovirus, or “the stomach flu,” which often ravages cruise ships and other crowded indoor spaces, rotavirus is extremely contagious and spreads via the fecal-oral route. UCSF says that about 50,000 children are hospitalized with the illness each year, experiencing symptoms ranging from fever and nausea to “intense vomiting” and watery diarrhea.

In addition to seeing a rise of lesser-known viruses like rotavirus and HMPV, Northern California rang in the new year with flu hospitalizations and emergency visits.

Seasonal flu typically peaks in cold winter months from December to February, the CDC says. While flu cases are down from their peak in February, the virus remains at high levels in the wastewater. Kaiser Permanente health experts in Northern California said that the introduction of a new flu strain paired with lower vaccination rates have led to an increase in hospitalizations after the holidays this year. Nationally, the CDC estimates that 23,000 people have died and 380,000 people have been hospitalized from the flu this season.

Similarly, Gandhi believes lower public immunity means viruses typically seen in winter months are now lingering into spring in the Bay Area, she said.

To prevent illness, experts advise sticking with basics like hand-washing to stop norovirus and staying up to date on your vaccinations, including those for the seasonal flu and rotavirus. More information about the illness can be found here.

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This article originally published at San Francisco is getting ravaged by multiple viruses. Experts aren’t sure why..