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First U.S. Case of Omicron Variant Found in San Francisco Resident

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The Pfizer COVID-19 vaccine is administered at a pop-up clinic offering vaccines and booster shots in Rosemead, California, on Nov. 29, 2021.  (Frederic J. Brown/AFP via Getty Images)

Updated 3:10 p.m. Wednesday

California and San Francisco health officials have detected the first U.S. case of the omicron variant in a San Francisco resident.

The individual “was a traveler who returned from South Africa on November 22, 2021,” the Centers for Disease Control and Prevention wrote in a statement. The individual, who was fully vaccinated with Moderna’s shot, has mild symptoms that are improving and is “self-quarantining and has been since testing positive,” the CDC wrote, adding that “all close contacts have been contacted and have tested negative.”

Grant Colfax, San Francisco’s director of health, urged caution and said in a statement the city is “relatively well positioned to handle COVID-19 and its variants because of our high vaccination rates, our high booster uptake, and other local health measures such as masking and testing.”

“We will stay alert and vigilant and do what we need to do to protect ourselves,” he said. “This means getting vaccinated, getting your booster, wearing a mask indoors, and taking the other steps we know help slow the spread.”

California’s robust surveillance system

Gov. Gavin Newsom said in a Wednesday press conference that on Nov. 28 the infected individual took a COVID-19 test, which returned positive the following day.

The testing company sent the sample to a UCSF lab, which quickly detected the omicron variant using genomic sequencing. Scientists working with the CDC later confirmed their work.

Newsom applauded California’s aggressive approach to testing.

“We have the most robust testing program and protocols in the nation,” he said.

Earlier this year, the U.S. struggled to keep pace with the need for genomic sequencing to track mutant variants of COVID-19, spurring President Joe Biden to spend roughly $1 billion to ramp up federal testing capability.

In January, the U.S. sequenced just 8,000 COVID-19 samples per week, but last month the country sequenced 10 times that many — roughly 1 in 7 positive cases, according to the CDC.

California, which last May received $17 million of Biden’s nationwide investment, sequenced 16% of its positive cases in August 2021, the latest numbers posted publicly by the state health department.

“I’ll remind people it’s not surprising in many respects that California is announcing the first case,” Newsom said. “This state is the birthplace of, after all, of the biotech [industry]. UCSF is one of the leading genomic sequencing institutions in the world, and we are blessed to have their partnership and have their expertise.”

Peter Chin-Hong, a professor at UCSF’s medical school, told KQED that California has a robust surveillance system for tracking COVID-19 variants. That system is more advanced than the nation’s, he said.

The U.S. “has not been at the forefront of genomic sequencing for variants in general,” he said.

“California Department of Public Health is doing better,” he said. “It’s easier in California, because of a close partnership between politicians, academics and private labs, and a really strong public health department.”

State and city health departments say they’re continuing to monitor for the variant using the genomic sequence surveillance system.

Aggressive testing underway

Newsom said officials cannot reveal too much information about the person’s private situation, but in broad strokes: They are not hospitalized, and no one they’ve come into contact with has tested positive “yet to our knowledge,” he said.

“To help detect and prevent the spread of this new variant, the State of California is increasing COVID-19 testing at our airports for arrivals from countries identified by the Centers for Disease Control and Prevention (CDC),” state health officials said in a statement.

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“CDC has been actively monitoring and preparing for this variant, and we will continue to work diligently with other U.S. and global public health and industry partners to learn more. Despite the detection of Omicron, Delta remains the predominant strain in the United States.”

California COVID cases inch upward

California’s test positivity rate ticked up a percentage point this past week, from 1.9% to 3%, according to state health statistics. Officials are still evaluating new data for signs of Thanksgiving-related coronavirus spread.

“The next few days, we’ll have a sense of what that Thanksgiving spread may have looked like,” Newsom said.

But the governor pointed out that the state’s test positivity rate is far lower now compared to last year at this time, when cases were spiking at the beginning of a winter surge.

The upcoming holiday season is another reason, among many, to ensure that people are vaccinated and boosted, said Mark Ghaly, California’s health secretary.

“This one individual, indeed, I want to highlight — fully vaccinated,” Ghaly said. “And some people might say, well, is that of concern? Does that mean the vaccines aren’t working? We have been talking for months about the fact that vaccinations do one really, really important thing: protect against severe disease, against hospitalization and death.”

The fact that the person who tested positive for omicron has mild symptoms “is a testament to the importance of vaccinations,” Ghaly said.

That also was the message from the White House, Wednesday.

Federal COVID-19 Response Coordinator Jeff Zients said, in a statement, that “it was only a matter of time” before omicron was detected here.

“This new variant is cause for continued vigilance, not panic,” he said.

KQED’s Natalia Navarro contributed reporting. 

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