Here’s what’s happening with COVID in the Bay Area right now

Right now, BA.5, the most infectious subvariant of the coronavirus yet, is driving a surge of cases in California, including the San Francisco Bay Area.

Many people who had avoided the virus for more than two years are getting COVID for the first time. Others are getting infected for a second or even third time. This is particularly likely thanks to the new subvariant of omicron, known as BA.5, which is harder for the body’s first line of defense – called neutralizing antibodies – to recognize and block from infecting cells.

The good news is, people with prior immunity are still significantly protected from severe cases of the virus, according to data from countries like South Africa, where BA.5 has already swept through. Mortality rates remain low, and while hospitalizations have inched up slightly, they aren’t anywhere near the level they were at in previous surges.

“More so than in previous waves, there are a significant number of hospital intakes admitted for reasons other than COVID-19, but who test positive for COVID-19 when screened,” wrote a Santa Clara County Public Health Department spokesperson in an email to SFGATE. “We are fortunately seeing that current cases admitted for COVID-19 tend to be less serious than in the past.”

Nonetheless, the uptick in cases is still putting some in the hospital, leading to long COVID for some and upending many people’s summer plans.


Every county in the San Francisco Bay Area, except Santa Clara, is in the red level on the Centers for Disease Control and Prevention’s COVID Data Tracker for community transmission. At this level, the CDC recommends that people mask in indoor public places and on public transit. Does this mean mask mandates are coming back to the Bay Area?

SFGATE reached out to all nine counties in the Bay Area and eight of them responded – Alameda, Marin, Napa, San Francisco, San Mateo, Santa Clara, Solano and Sonoma – and said they are not considering a countywide mask mandate at this time. (Contra Costa County did not respond as of 2:30 pm on Friday.) This messaging differs from that released on Thursday by Los Angeles County’s Health Director Barbara Ferrer, who said she will reinstate the mask mandate if the county enters into the CDC’s high COVID-19 community transmission level.

That said, counties urged people to use a mask to prevent spread. They also asked that residents keep up with vaccinations.

The San Francisco Department of Public Health said it is “strongly recommending that people wear masks in indoor, public settings” and that people “stay up-to-date on vaccinations to prevent severe illness and hospitalization.”

BA.5 is the dominant variant in the San Francisco Bay Area

Recent data from the Centers for Disease Control and Prevention shows that, in region 9, which includes California, the BA.5 sublineage made up 51.9% of confirmed omicron cases sequences June 25 to July 2 and those cases were up from 40.5% the week before.

In other words, as Dr. Bob Wachter, the chair of the department of medicine at UCSF, wrote in his most recent Twitter update: “The die is now cast: BA.5 is destined to be our dominant virus.”

That’s likely because the new subvariant is the best yet at evading our bodies’ first lines of defense, the so-called neutralizing antibodies which glom onto the spike protein and block the virus from infecting cells.

“BA.5 appears to be more transmissible than prior omicron variants BA.1 and BA.2, which were already more transmissible than delta and earlier variants,” Dr. Anne Liu, a professor of infectious diseases at Stanford, told SFGATE. “The antibodies we have from vaccination or prior infections are less protective against BA.5 than they were against prior variants.”

The new subvariant’s most significant genetic adaptations have cropped up in the spike protein, the key the coronavirus uses to enter your cells. The vaccines available in America teach your body to recognize the spike protein, triggering several layers of protection. That includes neutralizing antibodies, which circulate in your body for several months after infection or vaccination. Because of the changes to BA.5’s spike protein, those frontline antibodies are now struggling to grab on tightly enough to do their jobs, making it more likely the virus will get into cells and start reproducing.

However, thanks to the body’s secondary lines of defense, people with previous exposure to vaccines or COVID-19 can still recognize and kill off their own cells that have been infected, clearing the virus from the body, according to Dr. Monica Gandhi, a professor of medicine at UCSF who specializes in infectious diseases. (Indeed, most symptoms of the coronavirus, including fever, chills, headache and cough, are triggered by that immune cascade, not by damage from the virus itself.)

“South Africa has excellent genomic surveillance and data output and has shown us that BA5 is likely to cause rises in cases (as it already is in the US) but not major increases in severe disease with the degree of population immunity we now have in this country, ”Gandhi wrote by email.

Still, to help protect people from catching the virus in the future, an FDA advisory committee recently asked vaccine manufacturers to begin testing booster vaccines containing genetic code for both the original spike protein and for the genetically adapted version seen in BA.5 and its close relative, BA.4.

Who should be cautious amid the San Francisco Bay Area surge?

The experts that SFGATE talked to said that people who are unvaccinated should be especially cautious whenever the virus is surging, as it is now.

“Even an infection with BA.5 that may be mild in someone who is vaccinated, may send an unvaccinated person to the hospital and even kill them,” UCSF infectious diseases expert Dr. Peter Chin-Hong wrote in an email. “The US is still averaging about 300 deaths a day even in the Omicron era.”

Liu told SFGATE that anyone who is at a high risk for disease, or who has a job that can not be done if you have COVID, may want to avoid this highly transmissible strain.

Can anyone let their guard down?

“I think if you are up-to-date with vaccines and know how to access Paxlovid (if you are at risk of getting serious disease), you can navigate the world more confidently,” said Chin-Hong. “Even though there is less risk in a vaccinated person, the specter of ‘long COVID’ is always looming. As a vaccinated and boosted person I am not worried about getting seriously ill. I still dine indoors, go to the gym and hang out with friends – but I always carry around a good mask and put it on when I feel it is a risky indoor area with poor ventilation, and I am there for some time. “

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