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

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

In a closet-sized 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 strain. Hours later, Dr. Baha Abdalhamid 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 immediately screened the 64 samples, and sure enough, six of them were Omicron.” Nebraska officials announced the six cases, the state’s first, Friday.

Scientists around the world are rushing to understand how widespread Omicron is and how serious its danger can be. That has labs like Dr. Abdalhamid placed on the front lines in the fight against the coronavirus pandemic.

To underscore growing concerns about Omicron, scientists in South Africa said on Friday that the variant appeared to be spreading more than twice as fast as Delta, the most contagious version of the virus to date. It is still unclear whether and to what extent Omicron can circumvent the protection of current vaccines.

In the United States, a hunt for the variant began last week when South African researchers announced Omicron’s series of worrying mutations. The search has intensified in recent days, with at least 10 states identifying cases. Researchers comb wastewater samples for signs of the variant. Contact tracers are ramping up their efforts in places where cases have occurred.

And at sequencing labs like the one in Nebraska, a state where the number of cases is already high and hospitals are already under pressure, scientists have accelerated the screening of samples from international travelers to see if Omicron has arrived.

Local health officials in rural southeastern Nebraska said that of the cases Dr. Abdalhamid, 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 had severe symptoms; only one had been vaccinated.

“The concern is what might show up if it gets in here,” Peter Iwen, the director of the Nebraska Public Health Laboratory, said Thursday before the localized cases were found. “Are we going to see the same wave? Or where this one drops out and this other one begins to take off?”

When word spread on Thanksgiving about the discovery of Omicron in Africa, scientists in the United States turned their backs on holiday weekends and began looking for clues as to whether the variant was here, too. They looked back in old virus samples to see if Omicron had been quietly spreading. They’ve taken a close look at recent positive tests. They started studying Omicron’s mutations so they could manually detect it in the genetic code if their sequencing software didn’t.

Experts say knowing where and how extensively Omicron circulates is the best way to understand and respond to the level of threat it poses. Scientists have expressed concern about Omicron’s mutations and the impact they may have on transmissibility, disease severity and ability to evade previous immunity.

There is limited real-world data so far to confirm those concerns, but it is becoming increasingly clear that Omicron is already present in much of the United States. Scientists in California announced a case on Wednesday. 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, one in Colorado and one in Hawaii.

More cases came to light on Friday, including one in Pennsylvania, another in Missouri, another in Utah and three in Maryland. Many, but not all, cases were related to travel.

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

They focus on the highest-risk cases: those with major outbreaks or children or international travelers. The results, which are uploaded to a global database, show which variants exist in the state and whether individual cases are linked together. When a New York Times reporter and photographer visited the lab on Thursday, the scientists had just finished sequencing the samples containing the six Omicron cases, but hadn’t yet examined the results.

“If we have a cluster of people, like 10, 15, 20 people, one of them is detected with Omicron. The others, do they have Omicron or not? If they have Omicron, how related are those Omicron viruses to each other? Are they the same?” said Dr. Abdalhamid, while explaining some of the questions he would try to answer if the variant showed up in his lab. “Are they one clone, one cluster? Or more than one cluster?”

That level of detail, which was largely unavailable before this pandemic, may subsequently inform public health officials’ response.

“It’s amazing we can do that because in the old days all you had to do was ask questions,” says Dr. Lindsay Huse, director of health in Douglas County, Neb., which includes Omaha. She added, “It just helps us be much more focused in the recommendations and mitigation efforts we’re making.”

At the beginning of this year, American researchers published the sequences of several thousand virus samples every week, leaving the United States far behind other countries in their ability to identify and respond to variants. Since then, sequencing capacity has increased significantly, to approximately 80,000 virus samples per week and 14 percent of all positive PCR tests.

In the past few months, nearly every sample researchers have examined has shown the highly transmissible Delta variant, which spiked cases in the South during the summer and fueled continued increases across much of the Midwest and Northeast.

“It started to get a little boring, honestly, because it was 100 percent Delta,” said Richard Michelmore, a researcher at the University of California, Davis, who studies the lineage of coronavirus samples in his area.

In recent days, as news about Omicron spread, Dr. Michelmore that his lab revived a program to obtain and examine samples from underserved populations. While it’s too early to know how dangerous Omicron is, Dr. Michelmore doesn’t care that it will appear in his lab anytime soon.

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

The introduction of Omicron comes at a precarious time in the country’s virus fight. Although infection and hospitalization rates nationally are much lower than they were a year ago before vaccines were available, some states in the Upper Midwest and Northeast are inundated with the Delta variant and are experiencing their worst peaks from the pandemic.

Federal medical teams have been dispatched to bolster staff at hospitals in Minnesota and Michigan. Case numbers have risen to record levels in Vermont and New Hampshire. And in Nebraska, hospital officials held press conferences this week to warn of limited capacity and pleas to get vaccinated.

“It’s serious: Our hospitals are currently out of resources in terms of beds,” said Dr. Huse, the district health director.

It’s been nearly two years since the virus started showing up in the United States — including among overseas travelers quarantined on the same Omaha campus where the six Omicron cases were discovered this week. Unlike then, Omicron has so far exerted no pressure to impose lockdowns or drastic restrictions on everyday life. Instead, as Nebraska Governor Pete Ricketts put it in a statement 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 death rates from coronavirus and protected our hospital capacity, all with no lockdowns, no mask mandates, and no vaccine mandates,” said Mr. Ricketts, a Republican, in a statement.

He promised that this policy would continue.

Noah Weiland and Apoorva Mandavilli reporting contributed.

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