First U.S. omicron case confirmed in San Francisco traveler

San Francisco on Wednesday confirmed the nation’s first case of the new omicron coronavirus variant in a vaccinated person who recently returned from South Africa.

The traveler, a San Francisco resident who was inoculated with the Moderna vaccine but was not boosted, suffered from mild symptoms and has recovered, health officials said. The person is isolating at home and their contacts are being traced. So far, all close contacts have tested negative.

“This is not a surprise,” said Dr. Grant Colfax, director of the San Francisco Department of Public Health, in a Wednesday press conference. “We knew that omicron was going to be here. We thought it was already here. We just hadn’t detected it yet.”

“This is cause for concern,” he added. But with 77% of the city’s residents fully vaccinated, “it is also certainly not a cause for us to panic. We are prepared here in the city.”

The traveler returned from South Africa on Nov. 22 and was tested on Nov. 29 after developing symptoms, said Dr. Anthony Fauci, President Biden’s top COVID-19 advisor, during a White House press briefing Wednesday morning.

The traveler had tested negative for COVID-19 within 72 hours of boarding a flight, as required.

San Francisco Health Officer Dr. Susan Phillip commended the traveler for a quick response.

“They did the right thing,” she said. “They recognized that they had recently traveled. They recognized that they had symptoms. And they did what we should all be doing — which is to go and get tested, with symptoms. And then they reached out to our team. We were able to speak with them.”

At least 23 other countries have reported omicron infections, according to the World Health Organization. To reduce the spread of the new variant, which is believed to be more transmissible than the delta variant, federal officials on Wednesday directed airlines to provide the U.S. Centers for Disease Control and Prevention with the names and contact information of all passengers who boarded flights bound for the United States since Nov. 29 after spending time in South Africa, Botswana, the Kingdoms of Eswatini and Lesotho, Malawi, Mozambique and Namibia.

The omicron variant was discovered in November by South African scientists who were trying to understand the nation’s unexpected surge in infections.

It is worrisome because it has far more mutations than any of its predecessors — including more than 30 mutations that encode for spike protein, used by the virus to infect cells. Some of these mutations influence the virus’s rate of transmission and its ability to evade protective antibodies.

The San Francisco case was detected through genomic sequencing in the lab of virologist Dr. Charles Chiu of UC San Francisco, which has been working with the San Francisco Department of Public Health, the California Department of Public Health and the biotech company Color, whose San Francisco-based testing facility can process tens of thousands of clinical samples a day.

The suspect sample was confirmed overnight, with stunning speed. Chiu received the sample at 8 p.m. on Tuesday, then ran a very fast molecular test that looks for one of the variant’s mutations for the spike protein, called a spike “gene dropout.” The result, obtained in only two hours, signaled the possible detection of omicron — but it wasn’t conclusive.

Proof was obtained after sequencing of the viral genome with a pocket-sized tool made by Oxford Nanopore Technologies.

The lab was able to confirm the sample was omicron within five hours, and the entire genome was assembled within eight hours, Chiu said.

“So at 4 a.m. last night, we actually had assembled most of the genome, and we were able to conclusively demonstrate that this was, indeed, infection from the omicron variant,” Chiu said.

How quickly does the virus spread? How easily can it be transmitted? Can omicron reinfect recovered people? How well does it evade vaccine-induced immunity? How vigorous a response is needed to knock it down? There are not yet answers to those questions.

But Chiu’s detection and isolation of the virus will accelerate U.S. research. Once the variant is successfully grown in a lab, it will be quickly and freely shared with labs around the nation — shipped by FedEx, with a special federal permit.

Now, with the virus in hand, scientists can create cell cultures to grow it, then study its behavior. They’ll watch how quickly it infects healthy cells. They’ll also test how many antibodies — either from the vaccine or infection — are needed to knock it down.

The variant is unlikely to completely eliminate our protection from vaccines based on older versions of the virus, noted Chiu. Instead, it may reduce protection.

“Immunity is not a ‘black-or-white’ situation, where you either have all protection or no protection,” said Chiu.

But to stay healthy, we may need a higher number of protective antibodies. That’s a challenge, because 70% to 80% of antibodies wane within six months of initial vaccination. Boosters restore the antibody levels above a critical threshold, he said.

If the variant slips past antibodies, other parts of the immune system — such as T-cells — may catch it. You’ll get sick, but not too sick.

The arrival of omicron suggests that there may be larger numbers of breakthrough infections to come among the vaccinated — and more reinfections among those who were infected and recovered. But this isn’t all bad news: Harvard research published in Wednesday’s New England Journal of Medicine found that vaccinated people with breakthrough infections are less likely to spread the virus than people who are infected but unvaccinated.

It is not yet known if we’ll need a redesigned vaccine. Pfizer and Moderna say a variant-specific boost could be ready in about three months.

But Fauci said Wednesday that might not be necessary. He said there are reasons to believe ”that current versions of vaccines will protect against severe disease from omicron.”

He added, “Get boosted now.”

Wire services contributed to this report.