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San Francisco poised to jump into higher CDC Covid risk tier this week

SF is poised to join Marin, San Mateo and Santa Cruz counties in the CDC's medium Covid risk category this week | Getty Images

San Francisco is likely to join three other Bay Area counties in the Centers for Disease Control and Prevention’s medium risk tier for community Covid risk this week as local case counts and hospitalizations continue their general increase over the past few weeks. 

The CDC’s Community Levels are meant to help residents understand the state of the virus in their own local environments. Counties are only categorized as being in the green “low” tier if they are seeing fewer than 200 new Covid cases per 100,000 people for the preceding week, less than 10 new Covid hospital admissions per 100,000 people in a week and less than 10% of staffed inpatient beds occupied by Covid patients. 

Last week, the Bay Area’s Marin, San Mateo and Santa Cruz counties were placed on CDC’s yellow “medium” tier because they breached the 200 new Covid cases benchmark laid out by the agency. If current patterns continue, San Francisco is poised to join them when the data is updated Thursday.

“We’re going through another wave, there’s no question about that, we’ve been seeing the rise over the past couple weeks. But is it a foothill facing a peak or is this a foothill that drops off soon after?” said Dr. John Swartzberg, a UC Berkeley infectious disease expert. “Nobody knows the answer to that yet.”

According to Swartzberg, what makes this uptick different is that it’s “first time he can recall” a larger increase in cases in the San Francisco Bay Area than in Southern California. The trendline is continuing as a legal decision vacated the federal transit mask mandate, and Bay Area agencies are weighing whether to impose their own requirements. 

San Francisco’s 7-day daily average of 27 cases per 100,000 people ranks among the highest of any county in the state, according to the CDC. Overall average case counts in the city are at their highest level since mid-February, and are continuing to rise. 

At last count, San Francisco recorded 198.63 cases per 100,000 people, just under the benchmark level for the yellow tier. The increasing numbers of daily reported local infections, as well as other indicators such as wastewater surveillance data, appear likely to tip the city into a higher risk category.

Moving into the yellow tier doesn't automatically trigger any enhanced restrictions or mandates. However, those at high risk of illness are advised to have rapid testing available and to talk to their doctors about masking or other preventative measures and treatments. If someone in your household or social circle are at high risk, the CDC says to consider self-testing prior to contact and masking indoors.  

On a community level, the CDC recommends that local health officials implement enhanced measures at high-risk congregate settings, and consider boosting access to testing and vaccination.

Swartzberg said it’s possible that the higher Bay Area case counts could be a reflection of more robust local testing infrastructure than in other parts of the state. But noted that the official numbers are also an undercount due to the prevalence of at-home antigen tests, which must be confirmed by a lab test to be reflected in official records. 

Research from the University of Washington’s Institute for Health Metrics and Evaluation estimates that only around 7% of positive Covid cases in the country are being detected.

“Case counts alone don’t tell us how much virus is circulating in the population, but we can trust the fact that the numbers are continuing to go up even though they’re grossly underestimated,” Swartzberg said. 

Hospitalizations—usually a lagging indicator of community spread—have also started to tick up in San Francisco, although they remain far below the surges seen during the peak of the Delta and Omicron waves. 

One positive signal, according to Swartzberg, is that deaths from Covid have continued their fall even in the face of the rising cases.

“That decrease in deaths reflects a few positive things. One is that most people have some degree of immunity either from previous infection or vaccination, the second is that the current versions of Omicron don’t cause as serious illness as [the Delta variant], and the third is we’re getting better at treating people when they are infected,” Swartzberg said. 

Part of what could be driving the rise in cases, according to some experts, is the emergence of a new subvariant of the virus. Dubbed BA.2.12.1, the strain is an extension of the lineage of the BA.2 offshoot of the Omicron variant that currently makes up the majority of the cases in the nation. 

According to the CDC, the new variant is expected to be around 25% more infectious than BA.2 strain, which was already marked at 30% more infectious than the original Omicron variant. The new BA.2.12.1 variant makes up around 28.7% of cases nationally and 14.7% for the region of the country including California. There has been no evidence to this point that the strain leads to more severe illness than prior versions of the Omicron variant. 

“The virus is doing exactly what it’s expected to do, it’s trying to find a way to survive and in that process it is finding out how it can invade immunity in the host,” Swartzberg said.

Kevin Truong can be reached at