Inside a sequencing lab on the front lines of America’s search for Omicron

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 Abdalhamid, 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 such as Abdalhamid’s on the front lines of the fight against the coronavirus pandemic.

Underscoring growing concerns about omicron, scientists in South Africa said 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 12 states identifying cases. Researchers are combing through wastewater samples for any sign of the variant.

At sequencing labs such as 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.

It is increasingly clear that omicron is already present in much of the United States. On Wednesday, scientists in California 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.