UCSF lab worked quickly to confirm San Francisco Omicron case – CBS San Francisco

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SAN FRANCISCO (CBS SF) – When news of a possible omicron COVID case reached UC San Francisco infectious disease specialist Dr Charles Chiu, he knew his team would have to work quickly.

Like all of us, he had heard dire predictions and forecasts. Omicron was on his way. It would be here in the United States any day. That day arrived at 4 a.m. Wednesday morning.

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“We have worked closely with the San Francisco Department of Public Health, California Department of Public Health and Color Genomics on virus genome surveillance,” Chiu said. “When we identify positive cases, cases of COVID-19 in this city and county, we try to sequence all the cases. “

The UCSF lab received the suspect positive test from Color Lab on Tuesday evening. The San Francisco resident fell ill after returning to San Francisco International Airport after a trip to South Africa – a hotbed of the new strain – on November 23. A sample taken from the patient had tested positive for COVID, but what strain was it? ?

“This particular sample I heard about yesterday around 3 pm,” Chiu said at a morning press conference. “We were able to receive the sample at the lab at 8:00 pm We did a very rapid molecular test that looks for the breakthrough gene. What this test can tell you is that you may have detected omicron, but it is inconclusive.

The team then worked until the early hours of Wednesday morning to further test the sample. They had to sequence the viral genome using a high-tech device called a nanopore sequencer.

“We were able to get the results of this test in two hours, showing that it was potentially an omicron variant sample, but to confirm this finding we had to sequence the genome,” he said.

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“We were able to confirm the detection of the omicron in five hours and had almost the entire genome in eight hours. At 4 a.m. last night, we were able to show conclusively that it was an infection of the omicron variant. “

In a press release, officials in San Francisco confirmed the individual was a traveler who returned from South Africa on November 22.

“The individual, who is a resident of San Francisco, is self-isolating and exhibiting mild symptoms,” officials said. “We continue to speak with the individual about all of the people they have been in contact with.”

The individual, who has not been named, fell ill and sought medical treatment which led to the discovery on November 29.

The World Health Organization designates omicron as a “variant of concern”. In a technical note released this week, the 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.

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Scientists are working to find out how transmissible the variant is, how badly it makes people sick, and how well current vaccines work against it. Until more information is available on the variant, the United States has restricted travel from South Africa and seven other countries.

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