How a Lab in Nebraska Is Tracking the Spread of Omicron

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.

Underscoring growing concerns about Omicron, scientists in South Africa said on Friday that the variant appeared to spread more than twice as quickly as Delta, until now the most contagious version of the virus. It is still unclear whether or to what degree Omicron may evade protection from the current vaccines.

In the United States, a hunt for the variant began last week when South African researchers announced Omicron’s array of worrisome mutations. The search has intensified in recent days, with at least 11 states identifying cases. Researchers are combing through wastewater samples for any sign of the variant. Contact tracers are ramping up efforts in places where cases have emerged.

And at sequencing labs like the one in Nebraska, a state where case rates are already high and hospitals are already strained, scientists have sped up the screening of samples from international travelers to see if Omicron has arrived.

Local health officials in rural southeastern Nebraska 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.

“The concern is what might start showing up if it starts coming in here,” Peter Iwen, the director of the Nebraska Public Health Laboratory, said on Thursday before the local cases had been found. “Are we going to see the same wave? Or where this one falls out and this other one starts to take off?”

As word spread on Thanksgiving about the discovery of Omicron in Africa, scientists in the United States diverted from their holiday weekends and began searching for clues about whether the variant was here, too. They looked back through old virus samples to see if Omicron had been spreading quietly. They took a closer look at recent positive tests. They began studying Omicron’s mutations so they could detect it manually in the genetic code if their sequencing software did not.

Experts say knowing where and how extensively Omicron is circulating is the…