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Inside a Sequencing Lab on the Front Lines of America’s Search for Omicron

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OMAHA — Researchers in Nebraska had just finished sequencing six samples of the Omicron variant, the most discovered anywhere in the United States. They just didn’t know it yet.

In a closet-size room with two chairs and no windows, the scientists had extracted the genetic information from 64 new coronavirus samples, as they do every day, to determine whether any of those patients might have the worrisome new variant. Hours later, Dr. Baha Abdalhamid opened an email and saw the results.

“This batch, I was waiting for it,” said Dr. Abdalhamid, the assistant director of the Nebraska Public Health Laboratory. “Once I downloaded the results as an Excel sheet, I screened the 64 samples right away, and sure enough, six of them were Omicron.” Nebraska officials announced the six cases, the state’s first, on Friday.

Around the world, scientists are racing to understand how widespread Omicron is and how severe a threat it may pose. That has placed labs like Dr. Abdalhamid’s on the front lines of the fight against the coronavirus pandemic.

said that among the cases Dr. Abdalhamid found, one person had recently traveled to Nigeria and was believed to have passed the virus on to the five others in the same household after returning to Nebraska. None of the patients has had severe symptoms; only one had been vaccinated.

announced a case. Then on Thursday came an announcement in Minnesota about a person who tested positive after attending an anime convention in New York. Within hours, five cases had been found in New York, as well as one in Colorado and another in Hawaii.

On Friday, more cases emerged, including one each in Louisiana, Missouri, New Jersey, Pennsylvania and Utah and three in Maryland. Many, but not all, of the cases had been linked to travel.

All that adds urgency to the work in the Omaha lab, situated behind locked doors in a research building at the University of Nebraska Medical Center. Each day, researchers there extract RNA from 64 nasal swabs sent in from across the state and run that material through two machines that, after about 18 hours, produce a genetic sequence for each infection.

They focus on the highest-risk cases: Those involving large outbreaks or children or international travelers. The results, which are uploaded into a global database, show them which variants are present in the state and whether individual cases are linked to one another. When a New York Times reporter and photographer visited the lab on Thursday, the scientists had just finished sequencing the samples that included the six Omicron cases but had not yet examined the results.

about 80,000 virus samples a week and 14 percent of all positive P.C.R. tests.

For the past few months, almost every sample researchers have examined has shown the highly transmissible Delta variant, which drove up case totals in the South over the summer and is fueling ongoing surges in much of the Midwest and Northeast.

“It was kind of getting boring, quite honestly, because it was 100 percent Delta,” said Richard Michelmore, a researcher at the University of California, Davis, who examines the lineage of coronavirus samples in his area.

In recent days, as word of Omicron spread, Dr. Michelmore said his lab revived a program to acquire and examine samples from underserved populations. Though it is too early to know just how dangerous Omicron is, Dr. Michelmore has little doubt that it will soon turn up in his lab.

“It’s a matter of when,” Dr. Michelmore said. “My prediction, we will have seen it probably by Christmas.”

The introduction of Omicron comes at a precarious moment in the country’s virus fight. Though infection and hospitalization levels remain far lower nationally than they were a year ago, before vaccines were available, some states in the Upper Midwest and Northeast are overrun with the Delta variant and are enduring their worst case surges of the pandemic.

Federal medical teams have been sent to bolster staffing at hospitals in Minnesota and Michigan. Case rates have soared to record levels in Vermont and New Hampshire. And in Nebraska, hospital officials have held news conferences this week to issue warnings about limited capacity and pleas to get vaccinated.

“It’s serious: Our hospitals, they’re out of resources at this point in terms of beds,” said Dr. Huse, the county health director.

It has been almost two years since the virus began to emerge in the United States — including in overseas travelers who quarantined on the same Omaha campus where the six Omicron cases were detected this week. Unlike back then, Omicron has so far not brought a push to impose lockdowns or sweeping restrictions on everyday life. Instead, as Gov. Pete Ricketts of Nebraska put it in a statement on Friday after the state’s new cases were announced, there is a sense that “coronavirus will be with us forever.”

“Nebraska has maintained one of the lowest coronavirus death rates and protected our hospital capacity all without lockdowns, without mask mandates and without vaccine mandates,” Mr. Ricketts, a Republican, said in a statement.

He pledged that those policies would continue.

Noah Weiland and Apoorva Mandavilli contributed reporting.

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