In any other context, it would have been unremarkable: On Sunday, Nov. 28, a San Francisco resident who had been feeling mildly ill took a Covid test. The next day, it came back positive.

What set off alarm bells, however, was that the resident had recently returned from South Africa, where the newly discovered Omicron variant was widespread.

The traveler’s test sample was flagged for priority genomic sequencing, which would reveal the precise genetic code of the virus that had infected the traveler — and whether it had Omicron’s telltale mutations.

Dr. Chiu, the San Francisco microbiologist, was tapped to do the sequencing. By 6 p.m. on Tuesday, Nov. 30, just a few hours after Dr. Chiu first learned about the sample, it was hand-delivered to his lab, packed in dry ice.

Dr. Chiu and his colleagues quickly got to work. Although generating the full sequence takes hours, the scientists chose to use a technique known as nanopore sequencing, which allowed them to analyze the results in real-time, while the process was still underway.

“As the data accumulated, we were able to identify more and more mutations,” Dr. Chiu recalled.

Before dawn, he was certain: It was Omicron, the first case found in the United States. Less than a week had passed since South Africa first publicly announced the existence of the variant.

We cannot fight what we cannot see, and preventing the next pandemic begins with detecting and tracking the pathogens that threaten us. In that regard, at least, “we’re extraordinarily better off than we were this time last year,” said Joseph Fauver, a genomic epidemiologist at the University of Nebraska Medical Center in Omaha.

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