How San Francisco scientists were 1st in U.S. to ID omicron case

SAN FRANCISCO, Calif. (KRON) — When it comes to containing COVID-19’s variants, public health officials have a need for speed.

Earlier this week, top scientists at the University of California San Francisco confirmed the first-ever case of omicron in the U.S. after pulling an all-nighter in their lab.

Dr. Charles Chiu, director of the UCSF Abbott Viral Diagnostics and Discovery Center, is one of the leading COVID genetic sequencing experts in the country.

Chiu and his team have worked throughout the pandemic on developing technology that can genetically sequence COVID-19 and its variant with speed.

Since 2020, a genetic sequencing machine has been running 24-hours a day inside Chiu’s laboratory sequencing genomes of viruses that infected COVID-19 patients around the Bay Area. 

To help track and slow down the spread of COVID in California, the lab uses a process called “high-throughput sequencing,” or sequencing massive amounts of DNA at once.

Their hard work paid off when they became the first scientists to confirm a case of the omicron variant in America.

Venice Servellita, left, clinical laboratory scientist, works with Dr. Charles Chiu in their China Basin lab that is now dedicated to stopping the spread of COVID-19 by researching the virus’ genome in a process called “high-throughput sequencing” or sequencing massive amounts of DNA at once. (UCSF)

The variant entered the U.S. in an infected traveler who flew from South Africa to San Francisco on Nov. 22. The traveler developed COVID-like symptoms on Nov. 28, received a positive COVID test result on Nov. 29, and alerted the San Francisco Department of Public Health the same day about his test and recent travel history.

Chiu’s lab received the patient’s nose swab sample at 10 p.m. on Nov. 30 with the task of confirming whether or not it contained the omicron variant.

“To confirm this finding, we needed to sequence the viral genome,” Chiu said.

Chiu’s team sequenced the variant’s genome in less than eight hours. On the morning of Dec. 1, the team alerted the Centers for Disease Control and Prevention that omicron had officially entered the U.S.

San Francisco Mayor London Breed said health officials knew it was “only a matter of time” until omicron surfaced in the city.

“The work that we have done to this point has prepared us to handle this variant,” Breed said at a recent press conference. “We continue to encourage everyone to get vaccinated, get boosted, and take steps to keep each other safe.”

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