With at least 30 cases of the highly mutated omicron variant now identified in the United States — including two new cases reported in Los Angeles County on Monday — health experts can’t yet say whether it will pose a bigger threat than the delta strain, which is still driving the national coronavirus pandemic.
So far six coronavirus cases have been identified as omicron in the Bay Area: one reported on Tuesday in San Francisco, which was the first in the U.S., and a cluster of five in Alameda County that were reported on Friday. Alameda County officials characterized those five as being in an outbreak of 12 coronavirus cases, but have not yet said if the other seven were identified as omicron.
California has reported nine omicron cases in all, though public health officials said they expect to find many more in the coming weeks.
Dr. Charles Chiu, the UCSF scientist who led the team that identified the San Francisco omicron case, said Monday that his team is actively screening for such cases and working with some other Bay Area counties to do more “systematic surveillance for omicron” with other labs. The idea is to “create a coordinated effort across the state to be able to do sequencing,” he said.
Marin County is expediting its sequencing of samples from people who have traveled to areas where omicron is known to be spreading, county Public Health Officer Dr. Matt Willis said Monday. The county routinely sends a quarter of its samples for sequencing, and all in the past two months have been the delta variant, with no omicron detected, he said.
Federal health officials say early signs indicate omicron may cause less severe disease than the dominant delta variant, though much more study is needed. Scientists also are trying to determine if omicron’s dozens of mutations make it more infectious and better able to evade vaccines.
“Thus far, it does not look like there’s a great degree of severity to it,” Dr. Anthony Fauci, the top U.S. infectious disease expert, told CNN on Sunday. “But we have really got to be careful before we make any determinations that it is less severe or it really doesn’t cause any severe illness, comparable to delta.”
As of Monday, the United States had submitted genomic sequences from 30 omicron cases to GISAID, an international database. The variant has been detected in at least 17 U.S. states, and Centers for Disease Control and Prevention Director Rochelle Walensky said in an interview with ABC News on Sunday that they continue to receive reports of new omicron cases.
One Los Angeles County case reported Monday was in a fully vaccinated college student who had traveled to the East Coast, and reported mild symptoms. The other was in a fully vaccinated person who recently traveled from West Africa. That second person also had mild symptoms, and their close contacts are fully vaccinated and have tested negative, L.A. health officials said.
In a sweeping move aimed at stemming further coronavirus spread over the winter months, New York City Mayor Bill de Blasio announced Monday that all private employers in the city must require employee vaccinations starting Dec. 27. There were no hints of any similar Bay Area mandates in the offing, business leaders said Monday.
Also on Monday, new travel rules imposed by the Biden administration took effect: All inbound international travelers now are required to test for COVID-19 within one day of departure for the United States.
Across California, delta still makes up more than 99% of coronavirus cases and is driving the coronavirus pandemic in all counties.
California is reporting on average about 16 cases per 100,000 residents — up from about 9 cases per 100,000 a week ago, but less than half the rate reported last year at the start of the winter surge. The Bay Area is reporting an uptick also, with about 10 cases per 100,000 residents, up from about 6 cases per 100,000 last week.
Hospitalizations are seeing a slight increase statewide, with 3,200 people hospitalized with COVID as of Sunday, about 100 more than the previous week. The numbers are still trending down in the Bay Area, with 271 people hospitalized as of Sunday, compared with 288 a week ago.
“Delta is all over everywhere. That’s the thing to pay attention to,” said Dr. George Rutherford, an infectious disease expert with UCSF. “We can figure out what’s going on with omicron over time, but delta is causing all the disease right now.”
Since Sept. 27, 98.3% of sequenced specimens from Alameda County residents came from delta or its subvariants. The county has seen a slight uptick in recent days, but case rates are generally steady.
The Alameda County outbreak reported on Friday included one infected person who had traveled internationally before attending a wedding in Wisconsin on Nov. 27. The five cases that were sequenced and identified as omicron — with the infected individuals described as “mildly symptomatic” by public health officials — emerged from an outbreak of 12 coronavirus infection cases in people ranging in age from 18 to 49, according to a press release. Health officials on Monday declined to answer further questions on the outbreak.
San Francisco’s omicron case was detected in an individual who had returned from South Africa on Nov. 22, developing symptoms three days later and testing positive on Nov. 29. The person was fully vaccinated but not yet boosted, and experienced mild symptoms. No additional omicron cases had been identified by the health department as of Monday.
Other than Alameda County and San Francisco, no other Bay Area counties have yet reported omicron cases and they continue to monitor for the variant.
“A key goal is to learn what we can about this variant, from data emerging internationally,” Marin County’s Willis wrote in an email. “We are expecting to see omicron in the coming days or weeks, and will not be surprised when this occurs.”
Willis said the county’s overall coronavirus cases have “increased significantly over the past week” but the hospitalization rate continues to decrease, withno COVID patients in county hospitals on Sunday.
Contra Costa County officials said 97% of its sequenced samples reveal infections caused by the delta variant, and they are seeing a small uptick in cases but declining hospitalizations.
Santa Clara County’s health department, which reviews 20% to 40% of reported coronavirus cases — including by examining wastewater — also said Monday that no omicron has yet been found.
San Francisco Chronicle staff writer Chase DiFeliciantonio contributed to this report.
Kellie Hwang and Erin Allday are San Francisco Chronicle staff writers. Email: kellie.hwang@sfchronicle.com, eallday@sfchronicle.com Twitter: @KellieHwang, @erinallday