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Omicron variant identified in U.S.: First case of covid-19 linked to new variant found in California

On Dec. 1, top infectious-disease expert Anthony S. Fauci said the first case of the omicron coronavirus variant had been detected in California. (Video: The Washington Post)
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The omicron variant of the coronavirus — which has sparked concern across the world — has landed on U.S. shores, with the nation’s first case identified in a San Francisco resident who recently returned from South Africa. Amid uncertainty surrounding the potential threat of omicron, health officials said the discovery was both expected and a sign that precautions for travelers are working to keep tabs on the new variant.

The San Francisco resident, who arrived Nov. 22 from South Africa, began feeling ill around Nov. 25 and got tested for the coronavirus Nov. 28, California Gov. Gavin Newsom (D) said Wednesday at a news conference.

The previously healthy patient, who was fully vaccinated with the Moderna vaccine but had not received a booster shot, tested positive Nov. 29, officials said.

The person had received a second vaccine dose in August and had not yet reached the six-month mark to become eligible for a booster, according to a state health official briefed on the case. The individual — who is between the ages of 18 and 49, according to San Francisco’s health department — has mild symptoms that are improving and is in self-isolation. Genetic sequencing was performed by the University of California at San Francisco and confirmed by the Centers for Disease Control and Prevention.

There is no sign the omicron variant is spreading through community transmission within the United States.

“The individual is self-quarantining and all close contacts have been contacted and all close contacts thus far have tested negative,” Anthony S. Fauci, President Biden’s chief medical adviser and longtime director of the National Institute of Allergy and Infectious Diseases, said Wednesday.

Since the new variant was first reported in southern Africa last week, it has been identified in more than 20 countries spanning the globe, and officials had expected it to appear in the United States as international travelers passed through airports and returned from trips abroad.

“We knew that it was only a matter of time until the Omicron variant was detected in our city, and the work that we have done to this point has prepared us to handle this variant,” San Francisco Mayor London N. Breed (D) said in a statement.

In the Bay Area — which boasts high vaccination rates, with 77 percent of adults fully vaccinated in San Francisco — many residents took the news of omicron’s arrival in stride.

Sitting in the sun at a picnic table in front of Nick’s Pizza in Oakland, Heather Ball and Kristi Kenney, both 46, said they were on alert but still unsure how to think about the omicron variant.

“I’m going to wait a couple of weeks to start to worry,” Ball said, until more data is available about the variant’s risks. Ball, who works at a food pantry, recently received her booster shot, and her daughter Freyja, 10, who was enjoying an after-school slice, will soon be fully vaccinated.

They have tickets to travel to Chicago for Christmas, Ball said, but would consider canceling the trip if travel becomes riskier in coming weeks.

Kenney, whose family is also fully vaccinated and boosted, said she was alarmed but not surprised to hear the variant had arrived.

“I’m not that freaked out,” said Kenney, a stay-at-home mom working toward a master’s degree in library science. “It’s par for the course. This is the new normal. Our kids are vaccinated, and I got a booster. I feel okay.”

California public health officials credited the state’s “large-scale testing and early detection systems” for identifying the omicron variant and said in a statement that the state would be increasing testing at airports for arrivals from eight countries in southern Africa identified by the CDC. Effective Tuesday, the CDC was requiring airlines to share contact information about travelers to the United States who have been in those countries in the two weeks before their flight to the United States.

Health officials said they do not anticipate changing health orders or restrictions.

“Omicron is here; we knew it was here. I don’t want us to get overly focused on when’s the next case coming, when’s the next case going to be detected,” Grant Colfax, San Francisco’s health director, said in a news conference Wednesday.

He added: “We should all be focused on getting vaccinated and boosted, and get tested if you know you have been exposed. And continue to wear those masks.”

Fauci said Wednesday that people should get a booster now, if eligible, and not wait for an omicron-specific reformulated booster that, even if approved, would not be ready for months. He cited the tremendous spike in antibodies seen after boosting.

Experience with the vaccines has shown that even if they are not targeted to a variant, such as delta, they spark a sufficiently robust immune response, Fauci said, and “that’s the reason why we feel, even though we don’t have a lot of data on it, there’s every reason to believe that that kind of increase that you get with the boost would be helpful, at least in preventing severe disease of a variant like omicron.”

Officials praised the San Francisco resident who developed symptoms three days after returning and sought out testing and then self-quarantined.

The omicron variant has a swath of mutations that raised concerns that this version of the virus might be able to evade immunity and withstand existing treatments for those infected with covid-19.

Many questions about omicron remain unanswered — vaccine manufacturers are working to determine how effective existing shots and boosters will be against it, and public health experts are carefully watching to see if omicron will displace delta as the most prominent variant.

Health officials highlighted that the California patient had been vaccinated and appears to be recovering swiftly.

“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,” Mark Ghaly, California’s secretary of health and human services, said at a news conference Wednesday. “The evidence that an individual with omicron, identified by sequencing, actually has mild symptoms, is improving — I think is a testimony to the importance of the vaccinations.”

Even before officials in South Africa alerted the world to the existence of the troubling new strain of the coronavirus, omicron had spread. Dutch officials said this week that they detected the variant in the Netherlands at least a week before omicron’s worldwide debut.

Still, public health experts in the United States have tried to caution against panic while emphasizing the importance of continued mitigation efforts — including vaccinations, mask-wearing and social distancing — to prevent the spread of all covid variants amid fears of a possible winter surge of cases.

“There’s no reason to panic — but we should remain vigilant. That means get vaccinated. Get boosted. Wear a mask indoors,” Newsom said on Twitter.

California officials were able to move quickly to identify the arrival of the variant in their state.

Charles Chiu, who heads UCSF’s sequencing lab, said during the Wednesday news conference in San Francisco that he heard about the sample at 3 p.m. Tuesday, received it by 8 p.m. and administered a fast molecular test that detected a signal suggesting the specimen might be omicron.

But his team needed confirmation and was able to sequence almost the entire genome within the next few hours. By 4 a.m. Wednesday, he said, the team was able to demonstrate conclusively that the infection was indeed from the omicron variant.

Across the bay in Berkeley, at Cornerstone Craft Beer & Live Music, Justin Fox tended bar for a handful of daytime regulars in front of a sign requiring all customers to show their vaccination cards.

“Everybody is over being scared of everything,” said Fox, 33, who is fully vaccinated. “But then again, I don’t see the people who are going to be scared and stay home.”

All the employees at Cornerstone are vaccinated, and the bar and music venue plans to continue to require masking and proof of vaccination, he said. It’s also still booking bands to perform in the coming weeks. There’s plenty of demand.

“The college kids still come around,” he said. “They’re the ones who are less worried about it than anyone.”

Sun and Shepherd reported from Washington; Greenberg reported from Oakland, Calif. Joel Achenbach and Eugene Scott contributed to this report.

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