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In any other context, it wouldn’t have been remarkable: On Sunday, November 28, a San Francisco resident, feeling mildly ill, tested for Covid. It tested positive the next day.
But what set off the alarm bells was the resident’s recent return from South Africa, where the newly discovered variant of Omicron is common.
The passenger’s test specimen has been flagged for priority genomic sequencing, which will reveal the precise genetic code of the virus that infected the passenger and whether it has the defining mutations of Omicron.
To make the sequence, San Francisco microbiologist Dr. Chiu was commissioned. Until 18:00 on Tuesday, November 30, Dr. Just hours after Chiu first learned about the sample, it was hand-delivered to his lab, packaged in dry ice.
Dr. Chiu and his colleagues quickly got to work. Although it took hours to create the full array, the scientists chose to use a technique known as nanopore sequencing, which allows them to analyze the results in real time as the process continues.
Dr. “As the data accumulated, we were able to detect more and more mutations,” Chiu recalls.
Before dawn he was sure: it was Omicron, first case found in the United States. Less than a week has passed since South Africa first publicly announced the existence of the variant.
We can’t fight what we can’t see, and preventing the next pandemic starts with detecting and tracking down the pathogens that threaten us. In this regard, at least, “we’re in extraordinarily good shape compared to this time last year,” said genomic epidemiologist Joseph Fauver of the University of Nebraska Medical Center in Omaha.
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