Omicron COVID variant detected in San Francisco: First U.S. case

The person had traveled to The City from South Africa

The first U.S. case of the Omicron variant was confirmed Wednesday in San Francisco.

“This is not a surprise. We knew that Omicron was going to be here and we thought it was already here. This is cause for concern but not for panic,” said San Francisco Health Director Grant Colfax. “We are prepared for this.”

The case was found in an individual who traveled to the United States from South Africa on Nov. 22 and tested positive for COVID-19 on Monday, Colfax said.

The individual was fully vaccinated and experienced mild symptoms, Dr. Anthony Fauci said Wednesday in a briefing with reporters. The person is now self-isolating.

City health officials said the individual had not received a booster shot.

“We don’t know how infectious it is, but (there is a) likelihood it could be stronger than Delta,” said Colfax. “And we don’t know yet how fully protective the vaccines are for the new variant. Most experts I have spoken to believe the vaccines will be critical in protecting ourselves and our community.”

The detection makes San Francisco the first U.S. city to find a case with the variant. Omicron also has been detected in nearly two dozen countries, including Canada, the United Kingdom and South Africa, where it was first reported.

“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,” said Mayor London Breed. “We continue to encourage everyone to get vaccinated, get boosted and take steps to keep each other safe.”

San Francisco officials said The City was a likely spot for detection given its high volume of international travelers.

The variant was discovered through genomic sequencing at UCSF after the individual came forward.

Dr. Charles Chiu at UCSF confirmed the case sample was received Tuesday at 8 p.m. Within hours the lab had test results showing potential for an Omicron variant. The crew then sequenced the viral genome and by 4 a.m. Wednesday had determined it was an Omicron infection.

S.F. Health Officer Dr. Susan Philip said Tuesday no close contacts have tested positive for the virus and the health department is continuing to speak with the individual who was infected to see if the person may have come into contact with anyone else. “It is possible,” Philip said when asked whether the person could have exposed others to the virus.

“Get vaccinated for goodness sake if you aren’t already,” Colfax said.

Compared with other variants, Omicron has more mutations, and it contains the highly infectious Delta mutation that is still the most prevalent in California. That’s led some scientists to fear that the latest variant could pose a dangerous new threat as the Delta wave subsides.

“We see the same mutants in Delta that we are now seeing in Omicron,” said Nevan Krogan, director of the QBI Coronavirus Research Group at UCSF. “These mutants in Omicron have combined with potent spike mutations. If there was a greatest hits album, this virus has it all.”

Some experts worry the large collection of mutations — including many that have been associated with other variants of concern — could make Omicron a problematic new threat in a pandemic that many hoped was winding down.

At this time, San Francisco’s Department of Health does not anticipate changing any health orders or restrictions in The City, Colfax said.

“Some people are worried this could mean a new lockdown. But I don’t think so,” said Philip. “Nothing we are seeing now from a public health standpoint tells me we need to change our approach.”

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