UCSF doctor detects 1st U.S. omicron case in 8 hours

Doctors at a UCSF lab worked fast to confirm the first COVID omicron case in the country, pinpointing the virus to a person in San Francisco. 

They were able to get results within just eight hours – through genomic sequencing.

Most counties rely on the state lab for these types of tests, which can take weeks to return results.

But doctors at the University of California at San Francisco worked throughout the night Tuesday to make this confirmation, because they are among a few labs in the Bay Area with these capabilities.

Dr. Charlies Chiu – who runs the lab – said they first received a sample of a suspicious COVID test at 8 p.m. Tuesday. 

They got the positive omicron test by 11 p.m. – and were able to confirm it by 4 a.m. Wednesday.

Chiu said they sequenced the genome of the virus.

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"We used a pocket-sized sequencer called the nanopore sequencer made by Oxford Nanopore Technologies," he said Wednesday at a news conference. "This is a sequencing technology in which we can go from detecting the virus to being able to assemble the entire genome within a few hours."

Dr. Grant Colfax, the director of health for the city and county of San Francisco said the key component of gene sequencing is timeliness. It often takes too long to wait for state lab results, he said.  "So that's why we really wanted to run this locally as quickly as possible."

The patient in San Francisco was showing mild symptoms and was proactive in alerting health officials after getting a positive COVID test.

That person had recently returned to San Francisco from South Africa and was feeling sick. The person also tested positive despite being vaccinated, but hadn't received the booster shot. The patient is isolating at home and all of their close contacts have been notified and tested. So far, there are no other positive cases linked to this patient.

But health officials say there are likely more cases undetected.