COVID-19 cases have inched up in California since early April, and the greater San Francisco Bay Area is reporting more new cases per day than any other region in the state. Experts are reassuring people that amid the uptick, hospitalizations and the burden of severe disease remain low due to the region’s high vaccination rates and infection-acquired immunity from the surge of the omicron variant in winter.
Four of the region’s nine counties — Marin, San Francisco, San Mateo, Santa Clara — slid up from the green tier to the more severe yellow tier last week on the Centers for Disease Control and Prevention’s COVID Data Tracker for community transmission. Santa Cruz County is also yellow. A county moves to the yellow level when it reports more than 200 new cases per 100,000 people in the past week. All five of the other Bay Area counties and the rest of the state are green, with fewer than 200 new cases per 100,000.
The uptick is pronounced, and many people who avoided the coronavirus for more than two years are becoming infected, but it’s not nearly as severe as the winter surge. At UCSF’s four hospitals, 13 people were hospitalized with COVID on Monday. During the recent peak in January, 151 people were hospitalized on Jan. 20.
“There has been a decoupling of case rates from hospitalization rates,” said Dr. George Rutherford, director of UCSF’s Prevention and Public Health Group. “We’re not seeing nearly the high rates in hospitalizations that we’ve seen in past surges, especially compared to delta — which is indication the vaccine is working.”
Experts at UCSF said a handful of factors are likely contributing to the Bay Area increase, and the new omicron subvariant BA.2.12.1 is among them. The CDC has said early research indicates that it does not cause more serious disease, but it is more transmissible than its predecessors.
“BA.2.12.1 is thought to be 25% more transmissible than BA.2, which is itself 30% to 80% more transmissible than BA.1, which is itself 200% more transmissible than delta,” UCSF infectious diseases expert Dr. Peter Chin-Hong said.
BA.2.12.1 is on track to become the dominant variant in the United States and Chin-Hong said the Bay Area could be seeing faster spread than other parts of the state due to an influx of visitors from outside the region.
While the CDC estimates about 17% of cases are BA.2.12.1 in California, Chin-Hong said this number could be much higher as the data often lags what’s happening on the ground.
“BA.2.12.1 was first seen in the U.S. in central New York City, and at the end of late February, it accounted for less than 1% of cases,” Chin-Hong said. “Now it’s more than 90% of cases. We’re not seeing those numbers in the Bay Area yet, but gene-sequencing lags.”
UCSF infectious diseases expert Dr. Monica Gandhi explained that while the vaccines provide protection against severe disease from the omicron variants and subvariants, their effectiveness against infection wanes.
“During the omicron variant surge this winter, we did see a greater chance of reinfection compared with previous variants — but not in severe disease across the general population,” Gandhi wrote in an email. “A boost or a temporary increase in antibodies might be necessary for certain groups to maintain protection against severe disease, including the immunocompromised, older people and those with multiple risk factors.
Another hypothesis that might explain the increase in cases: Bay Area residents who were cautious for more than two years and stayed home are re-entering society and getting infected for the first time. Chin-Hong pointed out that the Central Valley had some of the state’s highest COVID rates during past surges and the region now has some of the state’s lowest COVID rates. That could be because many of those people were already infected and are benefiting from immunity from both vaccines and prior infection.
“Vaccines alone are spectacular at preventing serious disease, hospitalization and death but previous omicron exposure is better at preventing BA.2 infection,” Chin-Hong said. “That is why the current rates are higher in the wealthiest ZIP codes in San Francisco but lowest in the Central Valley. But the best insurance for the future still lies in being vaccinated and boosted.”
Chin-Hong said another hypothesis experts are considering is that Bay Area residents could be testing at clinics more than people in other regions who may not be testing or may be using at-home tests that don’t get recorded by the state.
“The Bay Area has a tradition of being very responsible about protecting the community and may not dismiss symptoms that may be mild or dismissed/not tested in other areas,” Chin-Hong said. “However, the fact that test positivity rate is also increasing suggests that the increase in official cases is not primarily due to more testing in general. If more ‘worried well’ were coming forward to get tested at the slightest drop in the bucket, we would expect a lower test positivity rate as more might be negative.”
