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A swirl of Covid variants turns SF summer into one long surge

Nurse practitioner Mawayidna Tombegou self-tests for COVID-19 at the City Health mobile testing van, which parked at 16th and Mission streets on Wednesday, May 25, 2022, while waiting to test Mission residents in San Francisco, Calif. | Camille Cohen/The Standard

Earlier this year, the Omicron wave of the pandemic took the form of a sharp increase in cases followed by an equally steep decline down to lower background levels of local infection.

But San Franciscans holding out hope for that familiar pattern have instead seen the current wave, which started in late April, bucking that trend and seeming to last much longer than the initial Omicron wave. 

That’s because the emergence of variants notorious for evading immune protections is colliding with a prior Omicron wave —all while San Franciscans are primed for summer fun and travel, according to Dr. Peter Chin-Hong, an infectious disease specialist at UCSF. 

“During the last Omicron wave, we were like on the Matterhorn ride at Disneyland where we quickly went down and everyone celebrated,” Chin-Hong said. “Now it’s like we’re in Denver, a mile above sea level and we’re slowly making our way down.”

The 7-day average of new cases per day in the city has breached 400 for most of the past two months, greater than the peak of the Delta wave last year. And because of the ubiquity of at-home testing, those case counts likely don’t come close to capturing the full picture: Some experts estimate that recorded cases are only around 20% of the actual number of infections. 

Updated state projections suggest the wave could last well into the summer, with its forecast showing a continuing rise in Covid cases in San Francisco throughout July and into August.

Previous pandemic surges were driven by discrete strains, like Delta and the original Alpha variant, but the current wave is driven by multiple Omicron subvariants wreaking havoc at the same time. It’s also coinciding with a busy summer travel and festival season, with people eager to get out and armed with vaccines and the existence of new treatments like Paxlovid.   

In early June, a majority of cases were caused by the Omicron BA.2.12.1, with only 9% caused by the newer BA.5 strain. But BA.5—which is more transmissible due to mutations in its spike protein—has since grown dominant regionally, with the majority of cases in the Western U.S. now caused by BA.5 according to the CDC. The multiple active Omicron strains, plus the emergence of BA.5, mean that a recent Covid infection is not necessarily a guard against getting sick again.

“We’re in this weird situation where we have multiple different things circulating at the same time, and although they are all flavors of Omicron, they all act differently,” Chin-Hong said. “We have one pipe coming into the tank, while one is leaving. That means the baseline level is staying high.”

Chin-Hong used the example of a person who was infected three weeks ago with BA.2.12.1, the then-predominant strain. That person would still be at risk of getting infected with BA.5 today. 

“In the old days if you got the one thing, you’re not going to get the same thing again,” Chin-Hong said. “But in this new era, it’s like starting from scratch. If BA.5 stays dominant and it becomes the only game in town then we will end up eventually seeing a downturn.”

Last week, the Food and Drug Administration recommended that vaccine manufacturers update their booster formulations to address the BA.4 and BA.5 subvariants, which could help stem the tide of reinfections if the strains remain dominant.  

This confluence of Omicron waves means that hospitalizations are remaining consistent for now. According to city data, there are currently 118 Covid hospitalizations in San Francisco, similar to the levels seen during the peak of the Delta wave. However, there are only around half the number of patients in the ICU, indicating less severe illness. 

“The virus isn’t killing us, but it certainly is infecting us as well or better than any time in the pandemic,” said Dr. John Swartzberg, an infectious disease expert at UC Berkeley. “The reality is we’re in a sea of virus and if we’re not really careful it’s just about impossible to not get infected.”

He said that the virus’ level of transmissibility is approaching that of measles, which is the most transmissible known respiratory virus, and posited that Covid could be close to maxing out its level of infectiousness. 

Early research into the impacts of BA.5 and its related cousin, BA.4, have been mixed. While animal studies have shown a possibility for more severe illness with the new strains, real-world data from South Africa and Portugal, where BA.4 and BA.5 emerged earlier, did not show a significant increase in hospitalizations or deaths.

Even with the emergence of the new Omicron variants, Swartzberg said the “armory” of vaccines, antivirals and other treatments that have been built up over the past two years have given him a sense of confidence that the public will be protected from the worst of the virus. 

“The virus is always ahead of us and we’re always chasing it, but tucked into that is the observation that the race is getting a lot tighter than it once was,” Swartzberg said. “We’re not quite neck-and-neck, but we’re getting there.”

Kevin Truong can be reached at