First confirmed case of U.S. omicron in San Francisco traveler – Times-Herald

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

The traveler, a San Francisco resident who was vaccinated with the Moderna vaccine but was not given a booster, is suffering from mild symptoms and is recovering, health officials said. The person isolates himself and his contacts are sought. So far all close contacts have tested negative.

“It’s no surprise,” said Dr. Grant Colfax, director of the San Francisco Department of Public Health, at a press conference Wednesday. “We knew omicron was going to be here. We thought it would, it was already there. We just hadn’t detected it yet.

“It is a source of concern,” he said. But with 77% of the city’s residents fully vaccinated, “that’s certainly not a cause for panic for us either. We are prepared here in the city.

The traveler returned from South Africa on November 22 and was tested on November 29 after developing symptoms, Dr Anthony Fauci said during a White House press briefing on Wednesday morning.

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 said to be more transmissible than the delta variant, on Wednesday federal officials asked airlines to provide the US Centers for Disease Control and Prevention with the names and contact details of all passengers. who have boarded flights to 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 trying to understand an unexpected increase in infections.

This is concerning because it has many more mutations than any of its predecessors – including more than 30 mutations that encode the spike protein, used by the virus to infect cells. Some of these mutations influence the rate of transmission of the virus and its ability to escape protective antibodies.

The San Francisco case was detected by genomic sequencing in the laboratory of virologist Dr. Charles Chiu of UC San Francisco, who worked with the San Francisco Department of Public Health, the California Department of Public Health and the Biotech company Color, whose Burlingame testing facility can process tens of thousands of clinical samples per day.

The suspect sample was confirmed overnight, with astonishing speed. Chiu received the sample at 4 p.m. on Tuesday, then performed a very rapid molecular test that looks for one of the variant mutations for the spike protein, called spike “gene loss.” The result, obtained in just two hours, signaled the possible detection of omicron – but it was inconclusive.

The evidence was obtained after sequencing the viral genome with a pocket tool manufactured by Oxford Nanopore technologies.

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

“So by 4am last night we had actually assembled most of the genome, we were able to conclusively demonstrate that it was indeed an infection with the omicron variant,” Chiu said.

How fast does the virus spread? How easily can it be transmitted? Can omicron re-infect people who are cured? How far does it evade vaccine-induced immunity? How much of a vigorous response is needed to overthrow it? There are no answers to these questions yet.