How scientists in San Francisco found the first case of the omicron COVID-19 variant in the United States

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SAN FRANCISCO – The first case of the omicron variant of the coronavirus in the United States was confirmed at 4 a.m. Wednesday after an all-night session by scientists here.

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The city’s tightly connected network of researchers from the Center for Public Health and University Medicine teamed up to confirm the infections reported six days earlierIt was actually Omicron. As soon as the results came, they were immediately reported to the Centers for Disease Control and Prevention.

The case began on November 22, when a passenger took off from South Africa at San Francisco International Airport, California Gov. Gavin Newsom said at a news conference.


The San Francisco resident, who was not identified, did not develop COVID-19 symptoms until Thanksgiving Day. Two days later, on 28 November, he was tested and the results came back the next day. Positive.

Despite feeling ill, he went out of his way to contact the San Francisco Department of Public Health to alert officials about testing positive, and that he had recently been in South Africa.

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“He did the right thing and got tested and reported his travel history,” said the city’s director of public health, Dr. Grant Colfax said at the news conference.

The person had received the full two-dose course of Moderna Vaccine but no booster. He had mild symptoms and had recovered but is still self-quarantining. The CDC said public health officials have reached close contacts, all of whom have tested negative so far.

because the patient came from South Africa, which has a large number of well-known omicron Among the cases, the city’s medical community was on high alert for recent arrivals from that country.

“I heard about it yesterday at about 3 pm,” Dr. Charles Chiu said on Wednesday. His laboratory at the University of California, San Francisco, conducted the analysis. Chiu is an infectious disease specialist and director of the UCSF-Abbott Viral Diagnostics and Discovery Center.

The patient’s nasal swab sample arrived at 10 p.m. on Tuesday, and Chiu’s lab ran a very rapid molecular test, known as S gene dropout, where the spike gene is not detected on the test.

The test came back within two hours and it was found that the person had been infected with the drop-out version. s geneThe dropout is found with both Alpha and Omicron coronavirus variants, so testing only indicated that it could be Omicron, but that didn’t prove it.

“To confirm this finding, we need to sequence the viral genome,” Chiu said. Using a pocket-size gene sequencer, his lab assembled the entire genome of the variants within eight hours.

At 4 a.m. in San Francisco, results came out and Omicron’s first casein the United States. The CDC was alerted within two hours.

Officials cautioned that it is unlikely that the case was the country’s actual first, just the first one identified.

“We knew it was only a matter of time,” said the US government’s top infectious disease expert, Dr. Anthony Fauci.

Contact Elizabeth Weiss at [email protected]

USA Today

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