Why Omicron Was First Found in San Francisco

A San Franciscan who flew home from South Africa last week became the first U.S. case of the new coronavirus variant.


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Cyclists and pedestrians near San Francisco City Hall.Credit…Mike Kai Chen for The New York Times

As soon as the first U.S. case of the Omicron variant of the coronavirus was reported in San Francisco, California officials began sounding the same message: Don’t panic.

“We are not surprised by this. This was predictable. This was predicted,” Gov. Gavin Newsom said in a news conference yesterday. “We should assume that it’s in other states as well.”

Omicron, a highly mutated version of the coronavirus that was first identified in South Africa, has been detected in more than 25 countries. But that still raises the question: If Omicron is spreading far and wide, why was the first U.S. case discovered in San Francisco?

As with most things, there’s an element of randomness here. If we think back to the spring of 2020, an early coronavirus outbreak at a Seattle nursing home signaled terrible luck — not that the city was the most infected in the nation.

It’s most likely a similar situation in San Francisco. The city is one of the most vaccinated places in the country — with 77 percent of residents fully immunized against Covid-19 — so it’s not particularly susceptible to coronavirus outbreaks.

But its popularity with global travelers does make it vulnerable to contagion imported from elsewhere.

On Tuesday, before the Bay Area case was identified, Dr. Rochelle Walensky, head of the Centers for Disease Control and Prevention, announced expanded Omicron screening at San Francisco International Airport, calling it one “of the busiest international airports in the country.”

Indeed, the San Franciscan infected with Omicron had returned from a trip to South Africa on Nov. 22. The patient’s symptoms began three days later.

That set off a rapid chain of events. The infected person, who is between the ages of 18 and 49, was tested on Sunday and got a positive result on Monday. In less than 24 hours, scientists at the University of California, San Francisco, had determined that it was Omicron.

Newsom chalked up the diagnosis to California having “the most robust testing program and protocols in the nation” as well as strong collaborations with major academic centers such as U.C.S.F.

Compared with the nation overall, California does perform genetic sequencing on a higher percentage of coronavirus samples — roughly one in five. (Since August, those tests have shown that at least 98 percent of Californians with Covid-19 have been infected with the Delta variant.)

Dr. Mark Ghaly, the state’s secretary of health and human services, said that the San Francisco patient was self-isolating and had mild symptoms that were improving, and that no close contacts had tested positive — what he called “a testimony to the importance of vaccinations.” The patient had received two doses of the Moderna vaccine but no booster.

Though scientists must still determine how well the shots will ultimately protect against Omicron, many experts expect they will ward off severe illness and death, if not infections altogether. Answers about whether Omicron is more contagious or deadly remain elusive.

In light of Omicron’s arrival in the United States, Dr. Anthony S. Fauci, the president’s top medical adviser, said that Americans should not wait for pharmaceutical companies to develop a booster shot designed for the new variant and that the available doses would provide extra protection.

“Get boosted now,” he said. “We may not need a variant-specific boost.”

For more:

What we know about Omicron so far.

Omicron prompts swift reconsideration of boosters among scientists.

President Biden projects normalcy and optimism amid new threat.

More than 50 percent of San Diegans who died of Covid-19 in the first year of the pandemic were immigrants, Voice of San Diego reports.


Protesters addressed the Torrance City Council after Christopher De’Andre Mitchell was killed by the police in 2019. A prosecutor is reopening an investigation into whether the shooting was justified.Credit…Axel Koester

If you read one story today

Prosecutors are reopening old cases against police officers.


Players for the Overtime Elite league warming up before their first game.Credit…Victor Llorente for The New York Times

The rest of the news

A better path to the N.B.A.?: These teenagers are getting six figures to leave their high schools for basketball.

Severe drought: State officials say that major water agencies won’t get any of the water they’ve requested and that mandatory restrictions could be coming, The Associated Press reports.

Poor abortion access: About 40 percent of California counties have no clinics that provide abortions, KQED reports.

Prosecuting shoplifters: Gov. Gavin Newsom said that shoplifters should be prosecuted under existing state laws, The Associated Press reports.


“Ghost gun” ban: The Los Angeles City Council unanimously passed a ban on untraceable guns made from build-it-yourself kits, The Associated Press reports.

Jacqueline Avant: The philanthropist and wife of the music producer Clarence Avant was fatally shot in her Beverly Hills home.


High-speed rail: An appeals court ruled that building high-speed rail in the San Joaquin Valley was permitted under the State Constitution, The Fresno Bee reports.


Record high temperatures: Several Bay Area cities, including San Francisco, recorded their warmest start to December yet, The San Francisco Chronicle reports.

Student vaccine mandate: Most students in the Sacramento City Unified School District failed to meet the district’s Nov. 30 vaccination deadline, The Sacramento Bee reports.


Credit…Julia Gartland for The New York Times

What we’re eating

Pasta with caramelized peppers, anchovies and ricotta.

Where we’re traveling

Today’s travel tip comes from Barry Naiditch:

“A four- or five-day trip from San Diego to the Central Coast is a favorite for this household. The beaches are clean and uncrowded, with wine tasting venues nearby.”

Tell us about your favorite places to visit in California. Email your suggestions to CAtoday@nytimes.com. We’ll be sharing more in upcoming editions of the newsletter.

Tell us

Has your child been vaccinated against Covid-19?

Share stories of your children receiving their coronavirus shots and how it has affected your holiday plans. Please include your child’s name, age and city of residence — and even a photograph, if you’d like.

Email me at CAtoday@nytimes.com and your submission may be included in a future newsletter.

And before you go, some good news

“The Hare With Amber Eyes.” “The Dangerous Book for Boys.” “Heart of Darkness.”

Those books and others are prized possessions for Tiffany Bey, but she doesn’t have a safe place to store them. So Bey, who lives in a tent in downtown Los Angeles, signed up for the Bin, a storage facility for homeless people in the city.

Each bin is a repurposed 60-gallon trash can where individuals can keep whatever they treasure most.

“I’m happy I found it because it really helped me out when I needed it,” she told Spectrum News 1 as she unloaded her books. “I store the items that are most valuable to me in here.”

Thanks for reading. I’ll be back tomorrow. — Soumya

P.S. Here’s today’s Mini Crossword, and a clue: “___ of You” (Spotify’s most-streamed song) (5 letters).

Steven Moity and Mariel Wamsley contributed to California Today. You can reach the team at CAtoday@nytimes.com.

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