San Francisco detects first known U.S. omicron case

National and local health officials confirmed Wednesday that the first U.S. case of the omicron coronavirus variant was detected in San Francisco resident.

Local public health officials and Dr. Anthony Fauci, White House chief medical advisor, said the person returned to the U.S from South Africa on Nov. 22 and tested positive Nov. 29 after exhibiting mild symptoms.

Dr. Grant Colfax, San Francisco’s public health director, said the individual was fully vaccinated with Moderna but had not received a booster. Colfax said the individual’s symptoms have been mild, and Fauci said earlier that his symptoms are improving.

Colfax added:

“The person recently traveled to South Africa and developed symptoms upon their return and they did the right thing and got tested and reported their travel history.”

Officials said the person was self-isolating and the health department is continuing to speak with them about recent close contacts. Fauci said Wendesday that close contacts so far identified have tested negative.

Gov. Gavin Newsom said in a tweet:

“There’s no reason to panic–but we should remain vigilant. That means get vaccinated. Get boosted. Wear a mask indoors.”

UCSF was able to identify the variant through genome sequencing. Dr. Charles Chiu, of University of California, San Francisco, said his lab is working with local and state public health departments to sequence positive Covid-19 cases.

Chiu said he was notified about the omicron sample Tuesday at 3 p.m. and received it at the lab by 8 p.m.. He explained that they first ran a two-hour molecular test that showed a potential for omicron, though the test was inconclusive. 

For confirmation, Chiu said they then utilized a pocket-sized genome sequencer, adding:

“We were able to confirm the detection of omicron within five hours, and we have most of the genome within eight hours.”

The U.S. Centers for Disease Control and Prevention then further confirmed the sequencing as the omicron variant, officials said.

Colfax and Fauci said there are still many unknowns regarding the new variant, including transmissibility, illness severity and whether it can evade current vaccines. It may take two to three weeks of observation to answer those questions with any level of certainty. 

Colfax said The City is “well-positioned” to respond to new variants due to high vaccination rates.

He said:

“Our vaccine rate is high, more boosters are going to arms every day.”

The World Health Health Organization classified the new variant as B.1.1.529 on Nov 26, as a “variant of concern” and named it omicron just days later on Nov. 30.