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Are SF’s virus defenses strong enough for Omicron?

Omicron testing Covid-19

As COVID-19 case counts rise across the country and globally due to the Omicron COVID-19 variant, medical experts in San Francisco are optimistic the city can avoid further lockdowns—and residents can stay safe if they stay on top of the science.

Since the first U.S. Omicron infection was discovered in San Francisco at the beginning of December, a number of now-familiar dominos have fallen: major event cancellations (JP Morgan took its big healthcare conference online); blue chip companies delaying their return to office plans (see decisions by Uber Technologies and Google); and of course California’s decision to reimpose a statewide mask mandate (though not in San Francisco.)

But Dr. Peter Chin-Hong, an infectious disease expert at UCSF said the likelihood of more dramatic restrictions—at least in the Bay Area—is slim. 

“I think in the Bay Area I would be shocked if we go into a lockdown situation again because our hospitals are likely to be OK,” Chin-Hong said. With effective vaccines, therapeutic tools like monoclonal antibodies and an array of at-home testing measures, Chin-Hong said “we’re light years away from where we were last March.”

Dr. Jordan Shlain, founder and managing partner at primary care medicine practice Private Medical, said in the past 36 hours he has seen a number of his patients test positive for Omicron, many of whom didn’t know when or where they were exposed. But he said the new treatments—including paxlovid, a forthcoming antiviral pill from Pfizer—combined with vaccines preventing severe disease had drastically changed the risks.  

“I think everyone’s going to get this one. Even if you got by without getting the first version or delta, you’re probably pretty lucky if you don’t get omicron,” Shlain said. “We haven’t even seen the beginning of this surge. It’s almost inevitable.”

That expectation, Shlain said, should lead San Franciscans to “recalibrate our psychology” around the virus. 

“I think we need to start thinking about this like it’s part of our life, like it’s furniture. If people get it, nobody should feel bad,” Shlain said. “We’re at this moment where it’s OK to get it, but it's not okay to give to people who are vulnerable.”

Dr. Anthony Harris, CEO of occupational health company HFit Health, said a “viral blizzard” is in the cards for this winter and it’s still critical to take steps to limit the spread of disease,  including social distancing, strict masking policies and “testing, testing testing.”

Case in point: the San Francisco Unified School District has announced an effort to offer antigen rapid testing for staff, students and the larger community when students return from winter break.

Public health authorities are starting to make some changes in response to the different dynamics of the latest wave. For instance, Marin County health officials announced earlier this month that they would focus on COVID-19 hospitalization rates rather than daily case rates as a guide for pandemic response policies.

“I think that Marin was completely on the right track of how this is going to evolve in the future,” Chin-Hong said. “In the old days of COVID, there was a close gap between infections and seeing hospitalizations rise. In a highly vaccinated area, there's more asymmetry, so when you see infections rise, hospitalizations don't typically rise. That's probably what we'll end up seeing here.”

Even if a mass economic shutdowns like those seen at the front end of the pandemic don’t come to pass, individual restaurants and businesses may make the decision for themselves, particularly because of omicron’s ease of transmission.  

“But what will happen in the next few weeks will be very uncomfortable because people are going to see infections go up like crazy, people are going to have friends that have quote-unquote ‘COVID,’ but it’s not the same as being unvaccinated and hit with Delta,” Chin-Hong said. “We’re going to end up in the right place at the end, but there’s going to be a lot of heartache in the meantime.”

Dr. John Swartzberg, an infectious disease expert at UC Berkeley, was a bit less sanguine.

“I think the Bay Area is going to do better than the rest of the state and I think the state is going to do better than the rest of the country, but there’s an open question on whether that means doing well enough to avoid a shutdown,” Swartzberg said.

The Latest Data 

Whether the new variant causes more or less severe symptoms remains an open question. Early data from South Africa, where the strain was first identified, suggested it might cause less severe illness. But new research from Imperial College London found “no evidence” of Omicron having different severity from Delta, though researchers cautioned hospitalization data is still limited. 

A lab-based study from The University of Hong Kong found that while Omicron variant had a much higher presence in the upper respiratory tract, it had a correspondingly lower presence in areas like the bronchi and the lungs, which have generally been the cause of severe COVID-19 illness.

Locally, Omicron has barely arrived, though overall case numbers are ticking up. San Francisco has seen a roughly 43% increase in hospitalizations due to the virus in the past two weeks of data and a 7-day average daily case count of 104, according to data from the New York Times COVID-19 dashboard. For comparison, the average count is similar to those seen in mid-August and mid-November of 2021.

While there are higher overall COVID-19 case counts nationwide than the same time last year, that is not the case in San Francisco. Overall deaths and hospitalizations due to the disease have remained low for the time being, although both are generally considered lagging indicators. There have been five deaths in San Francisco over the past two weeks and the latest count of hospitalized patients is 45. 

In all, San Francisco has seen roughly 58,500 total COVID-19 cases and 679 deaths over the course of the pandemic.

Kaiser Permanente said that the delta variant continues to be the dominant strain in the country and the cause of most new infections and hospitalizations. 

“The omicron variant is more transmissible and we are concerned about the impact to hospitals as both delta and omicron variants are circulating,” the health system said in a statement. “We expect that impact to be felt most after the upcoming holidays, which is why exercising caution is so important when considering holiday gatherings (especially indoors) and travel at this time.”

Dignity Health, which operates a number of health facilities across the Bay Area, said their San Francisco hospitals currently only have one or two hospitalized patients and have yet to see a large increase in serious cases because of Omicron. 

Kevin Truong can be reached at