In some other context, it will have been unremarkable: On Sunday, Nov. 28, a San Francisco resident who had been feeling mildly in poor health took a Covid check. The subsequent day, it got here again optimistic.

What set off alarm bells, nevertheless, was that the resident had not too long ago returned from South Africa, the place the newly found Omicron variant was widespread.

The traveler’s check pattern was flagged for precedence genomic sequencing, which might reveal the exact genetic code of the virus that had contaminated the traveler — and whether or not 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, simply a few hours after Dr. Chiu first realized about the pattern, it was hand-delivered to his lab, packed in dry ice.

Dr. Chiu and his colleagues rapidly set to work. Although producing the full sequence takes hours, the scientists selected to make use of a method often known as nanopore sequencing, which allowed them to research the leads to real-time, whereas the course of was nonetheless underway.

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

Before daybreak, he was sure: It was Omicron, the first case found in the United States. Less than a week had handed since South Africa first publicly introduced the existence of the variant.

We can’t combat what we can’t see, and stopping the subsequent pandemic begins with detecting and monitoring the pathogens that threaten us. In that regard, a minimum of, “we’re extraordinarily better off than we were this time last year,” mentioned Joseph Fauver, a genomic epidemiologist at the University of Nebraska Medical Center in Omaha.

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