Bay Area Health Officials Brace for Arrival of Omicron Variant

Update, 11:45 a.m. Wednesday: The first identified case of the omicron COVID-19 variant in the U.S. has been detected in California, according to the Centers for Disease Control and Prevention.

The University of California San Francisco performed the genomic sequencing that identified the strain, found in a traveler — and San Francisco resident — returning from South Africa on Nov. 22. They are experiencing mild symptoms and are in quarantine, according to the CDC. All of their close contacts have been identified and tested negative.

Original post, 1:15 p.m. Tuesday: Local and state health officials in California are closely monitoring for any signs of the new omicron COVID-19 variant, and bracing for its likely arrival.

Although little is so far known about the new variant, which researchers in South Africa first identified last week, the World Health Organization on Monday cautioned that "the overall global risk ... is assessed as very high." That's due in part to the variant's "unprecedented" number of mutations, the agency said.

No cases of the omicron variant have yet been detected in the U.S., but most experts agree that it is probably already here — a consensus that prompted President Biden on Monday to announce that "this variant is a cause for concern — not a cause for panic."

"I think it's quite possible, even likely, that there are small numbers of individuals that have already been infected with this variant in the United States and in the Bay Area," Dr. Benjamin Pinsky, who heads the Clinical Virology Laboratory at Stanford, told KQED on Monday.

Dr. Peter Chin-Hong, UCSF professor of medicine, explained to KQED that additional studies are necessary to determine whether omicron — named after the 15th letter of the Greek alphabet — is more transmissible than the delta variant, whether it will cause more serious symptoms, and how it will affect people who are already vaccinated.

"We thought delta was the only game in town for a long time," he said. "This is not the end of the story, and we have to be on guard and encourage our communities to be vaccinated, because at the end of the day, that's what's going to kick us out of this current quagmire."

Speaking with Alexis Madrigal on KQED's Forum on Monday, Kirsten Bibbins-Domingo, the chair of UCSF's Department of Epidemiology and Biostatistics, said it may take weeks before experts know more about the omicron strain.

"Unfortunately, in this pandemic, we need varying strands of science to tell us not just what they do in the laboratory, but what we see in the populations," Bibbins-Domingo said.

As to whether the new variant can evade vaccines and cause more breakthrough infections, Bibbins-Domingo expects answers in a few weeks. Labs are currently testing whether antibodies can neutralize it, she said.

Additionally, she said, researchers will be closely tracking hospitalization rates where outbreaks occur to see how patients diagnosed with the new variant fare, and will also analyze population data to determine whether omicron is more transmissible than previous strains.

"The science will come in bits and pieces from various lines of evidence from various parts of the world," Bibbins-Domingo said. "And luckily, we have a head start and these great tools with the mRNA vaccine."

In the meantime, Bibbins-Domingo encourages people to get booster shots to improve the protection the vaccines offer.

"I keep hearing people say things like, 'Well, I'm not going to get [it] now because I'm going to wait and see what we need to do with omicron.' That's really not a good strategy right now. The winter surge is the biggest threat to people right now, and that threat is best combatted by getting boosted," she said.

With little new information on hand, the California Department of Public Health (CDPH) said it is currently focusing on strongly encouraging more residents to get the COVID-19 vaccines and booster shots, and preparing to increase testing at airports across the state for people returning from countries in Southern Africa, including South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi — all places where the variant has been detected.

"We are doubling down on our vaccination and booster efforts to ensure that all Californians have access to safe, effective, and free vaccines that can prevent serious illness and death," Dr. Tomás Aragón, the agency's director, said in a statement Sunday.

As of Monday, 71.6% of all Californians have had at least one shot of the vaccine, with 63.8% — about 25 million residents — being fully vaccinated, according to the CDPH.

State health officials have also established a public-private partnership through an initiative called COVIDNet, which is aimed at ramping up genomic sequencing to better detect the new form of the virus. Notably, the United States has lagged behind many other wealthy countries during the pandemic in its reporting of genomic sequencing — a crucial method for tracking new variants.

"The surveillance systems in this country, although they've improved greatly, are not as advanced and not as comprehensive as they are in the U.K. and Israel and South Africa," San Francisco Public Health Officer Susan Philip said Monday.

Philip says it's too early to know how the omicron variant could affect the Bay Area, but notes she's encouraged by early reports from South Africa, which suggest mild symptoms for people who are fully vaccinated.

The Bay Area has some of the highest vaccination rates in the state and the country, with San Francisco near the top of the list: To date, more than 77% of the city's total population is fully vaccinated, with 5,000 residents receiving booster shots every day, health officials said. The rate in Santa Clara County is similarly robust, and is even higher in Marin County, where more than 79% of residents are fully vaccinated.

While Philip is urging residents not to panic, she said hospitals in the city are prepared for any uptick in COVID-19 patients.

"We have the plans that we put in place in preparation for the delta surge and for any additional winter surge that would occur now," she said. "So we're not having to roll out those plans just yet, but it is very good that we have them in place and ready to go."

Bibbins-Domingo, the UCSF professor, said concerns over the new variant should prompt people to be more careful during the upcoming holidays — and to make sure everyone they're gathering with is vaccinated.

"We're about to now start traveling and mingling and doing more together," Bibbins-Domingo said. And, she said, we may have to look out for when we're "at that level that we really have to start saying, if we're in a higher-risk category, we're not going to engage in certain types of activities — that we do need to double down a little bit more to ensure more people in the environment we're gathering in are in fact vaccinated."

KQED's Holly McDede, Alexis Madrigal, Natalia Navarro, Raquel Maria Dillon and Joe Fitzgerald Rodriguez contributed to this report.