SAN FRANCISCO (CBS SF) — When word of a possible COVID omicron case reached UC San Francisco infectious disease specialist Dr. Charles Chiu, he knew that his team would have to work quickly.
Like all of us, he had heard the predictions and dire forecasts. Omicron was on its way. It would be here in the United States any day. That day arrived at 4 a.m. Wednesday morning.
“We have worked very closely with the San Francisco Department of Public Health, the California Department of Public Health and Color Genomics on genome surveillance of the virus,” Chiu said. “When we identify positive cases, COVID-19 cases in this city and county, we make an attempt to sequence all the cases.”
The UCSF lab received the suspicious positive test from the Color Lab Tuesday evening. The San Francisco resident had fallen ill after returning to San Francisco International Airport after a trip to South Africa — a hotbed of the new strain — on Nov. 23. A sample taken from the patient had tested positive for COVID, but what strain was it?
“This particular sample, I heard about it yesterday at about 3 p.m.,” Chiu said at a morning news conference. “We were able to receive the sample in the laboratory by 8 p.m. We ran a very fast molecular test which looks for spike gene dropout. What this test can tell you that you may have detected omicron, but it’s not conclusive.”
The team then worked well into the early hours of Wednesday morning further testing the sample. They had to sequence the viral genome using a high-tech device known as a nanopore sequencer, a device just slightly larger than a USB stick.
“It’s powered by the USB port in your laptop. It enables us to do very rapid sequencing,” said Chiu. “That’s how we were able to get a result and identify this variant within a few hours. If we had to run this on a traditional instrument, typically it takes at least a day.”
“We were able to confirm the detection of omicron in five hours and had nearly the entire genome in eight hours. At 4 a.m. last night we were able to conclusively demonstrate that this was an infection of the omicron variant.”
In a news release, San Francisco officials confirmed the individual was a traveler who returned from South Africa on November 22.
“The individual, who is a San Francisco resident, is self-isolating and is experiencing mild symptoms,” the officials said. “We are continuing to speak with the individual about any persons with whom they have been in contact.”
The individual, who was not named, fell ill and sought medical treatment that led to the discovery on Monday.
“The patient themselves reached out to San Francisco Department of Public Health as soon as they found out they were positive, because they were concerned themselves,” said Scott Topper, Vice President of Clinical Operations for Color Health.
The World Health Organization designates omicron a “variant of concern.” In a technical brief released this week, WHO noted that the variant poses a “very high” global risk. The variant was first identified by scientists in South Africa and has since been detected in several countries.
Scientists are working to determine how transmissible the variant is, how sick it makes people and how well current vaccines work against it. Until more information is learned about the variant, the United States restricted travel from South Africa and seven other countries.
Chiu believes this is not the only case of the omicron variant in the U.S., just the only detected one.
“I’m almost certain that this finding is only the tip of the iceberg and that we will continue to see cases in the United States.”
Andria Borba contributed to this report.