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

OMAHA — Researchers successful Nebraska had conscionable finished sequencing six samples of the Omicron variant, the astir discovered anyplace successful the United States. They conscionable didn’t cognize it yet.

In a closet-size country with 2 chairs and nary windows, the scientists had extracted the familial accusation from 64 caller coronavirus samples, arsenic they bash each day, to find whether immoderate of those patients mightiness person the worrisome caller variant. Hours later, Dr. Baha Abdalhamid opened an email and saw the results.

“This batch, I was waiting for it,” said Dr. Abdalhamid, the adjunct manager of the Nebraska Public Health Laboratory. “Once I downloaded the results arsenic an Excel sheet, I screened the 64 samples close away, and definite enough, six of them were Omicron.” Nebraska officials announced the six cases, the state’s first, connected Friday.

Around the world, scientists are racing to recognize however wide Omicron is and however terrible a menace it whitethorn pose. That has placed labs similar Dr. Abdalhamid’s connected the beforehand lines of the combat against the coronavirus pandemic.

Underscoring increasing concerns astir Omicron, scientists successful South Africa said connected Friday that the variant appeared to dispersed much than doubly arsenic rapidly arsenic Delta, until present the astir contagious mentation of the virus. It is inactive unclear whether oregon to what grade Omicron whitethorn evade extortion from the existent vaccines.

In the United States, a hunt for the variant began past week erstwhile South African researchers announced Omicron’s array of worrisome mutations. The hunt has intensified successful caller days, with astatine slightest 10 states identifying cases. Researchers are combing done wastewater samples for immoderate motion of the variant. Contact tracers are ramping up efforts successful places wherever cases person emerged.

And astatine sequencing labs similar the 1 successful Nebraska, a authorities wherever lawsuit rates are already precocious and hospitals are already strained, scientists person sped up the screening of samples from planetary travelers to spot if Omicron has arrived.

Local wellness officials successful agrarian southeastern Nebraska said that among the cases Dr. Abdalhamid found, 1 idiosyncratic had precocious traveled to Nigeria and was believed to person passed the microorganism connected to the 5 others successful the aforesaid household aft returning to Nebraska. None of the patients has had terrible symptoms; lone 1 had been vaccinated.

As connection dispersed connected Thanksgiving astir the find of Omicron successful Africa, scientists successful the United States diverted from their vacation weekends and began searching for clues astir whether the variant was here, too. They looked backmost done aged microorganism samples to spot if Omicron had been spreading quietly. They took a person look astatine caller affirmative tests. They began studying Omicron’s mutations truthful they could observe it manually successful the familial codification if their sequencing bundle did not.

Experts accidental knowing wherever and however extensively Omicron is circulating is the champion mode to recognize and respond to the level of menace it poses. Scientists person expressed interest astir Omicron’s mutations and the interaction they could person connected transmissibility, illness severity and the quality to dodge anterior immunity.

There is truthful acold constricted real-world information to corroborate those concerns, but it is progressively wide that Omicron is already contiguous successful overmuch of the United States. On Wednesday, scientists successful California announced a case. Then connected Thursday came an announcement successful Minnesota astir a idiosyncratic who tested affirmative aft attending an anime normal successful New York. Within hours, 5 cases had been recovered successful New York, arsenic good arsenic 1 successful Colorado and different successful Hawaii.

On Friday, much cases emerged, including 1 successful Pennsylvania, different successful Missouri, different successful Utah and 3 successful Maryland. Many, but not all, of the cases had been linked to travel.

All that adds urgency to the enactment successful the Omaha lab, situated down locked doors successful a probe gathering astatine the University of Nebraska Medical Center. Each day, researchers determination extract RNA from 64 nasal swabs sent successful from crossed the authorities and tally that worldly done 2 machines that, aft astir 18 hours, nutrient a familial series for each infection.

They absorption connected the highest-risk cases: Those involving ample outbreaks oregon children oregon planetary travelers. The results, which are uploaded into a planetary database, amusement them which variants are contiguous successful the authorities and whether idiosyncratic cases are linked to 1 another. When a New York Times newsman and lensman visited the laboratory connected Thursday, the scientists had conscionable finished sequencing the samples that included the six Omicron cases but had not yet examined the results.

“If we person a clump of people, similar 10, 15, 20 radical — 1 of them is detected with Omicron. The others, bash they person Omicron oregon not? If they person Omicron, however related are those Omicron viruses to each other? Are they the same?” Dr. Abdalhamid said, explaining immoderate of the questions helium would effort to reply erstwhile the variant turned up successful his lab. “Are they 1 clone, 1 cluster? Or much than 1 cluster?”

That level of detail, mostly unavailable earlier this pandemic, tin past pass the effect of nationalist wellness officials.

“It’s astonishing that we’re capable to bash that due to the fact that it utilized to beryllium truly each you had to spell connected was asking questions,” said Dr. Lindsay Huse, the wellness manager successful Douglas County, Neb., which includes Omaha. She added, “It conscionable helps america beryllium a batch much targeted successful the recommendations and the mitigation efforts that we’re putting in.”

At the opening of this year, American researchers were publishing the sequences of a few- 1000 microorganism samples each week, leaving the United States acold down different countries successful its quality to place and respond to variants. Since then, sequencing capableness has ramped up considerably, to about 80,000 microorganism samples a week and 14 percent of each affirmative P.C.R. tests.

For the past fewer months, astir each illustration researchers person examined has shown the highly transmissible Delta variant, which drove up lawsuit totals successful the South implicit the summertime and is fueling ongoing surges successful overmuch of the Midwest and Northeast.

“It was benignant of getting boring, rather honestly, due to the fact that it was 100 percent Delta,” said Richard Michelmore, a researcher astatine the University of California, Davis, who examines the lineage of coronavirus samples successful his area.

In caller days, arsenic connection of Omicron spread, Dr. Michelmore said his laboratory revived a programme to get and analyse samples from underserved populations. Though it is excessively aboriginal to cognize conscionable however unsafe Omicron is, Dr. Michelmore has small uncertainty that it volition soon crook up successful his lab.

“It’s a substance of when,” Dr. Michelmore said. “My prediction, we volition person seen it astir apt by Christmas.”

The instauration of Omicron comes astatine a precarious infinitesimal successful the country’s microorganism fight. Though corruption and hospitalization levels stay acold little nationally than they were a twelvemonth ago, earlier vaccines were available, immoderate states successful the Upper Midwest and Northeast are overrun with the Delta variant and are enduring their worst lawsuit surges of the pandemic.

Federal aesculapian teams person been sent to bolster staffing astatine hospitals successful Minnesota and Michigan. Case rates person soared to grounds levels successful Vermont and New Hampshire. And successful Nebraska, infirmary officials person held quality conferences this week to contented warnings astir constricted capableness and pleas to get vaccinated.

“It’s serious: Our hospitals, they’re retired of resources astatine this constituent successful presumption of beds,” said Dr. Huse, the region wellness director.

It has been astir 2 years since the microorganism began to look successful the United States — including successful overseas travelers who quarantined connected the aforesaid Omaha field wherever the six Omicron cases were detected this week. Unlike backmost then, Omicron has truthful acold not brought a propulsion to enforce lockdowns oregon sweeping restrictions connected mundane life. Instead, arsenic Gov. Pete Ricketts of Nebraska enactment it successful a connection connected Friday aft the state’s caller cases were announced, determination is simply a consciousness that “coronavirus volition beryllium with america forever.”

“Nebraska has maintained 1 of the lowest coronavirus decease rates and protected our infirmary capableness each without lockdowns, without disguise mandates and without vaccine mandates,” Mr. Ricketts, a Republican, said successful a statement.

He pledged that those policies would continue.

Noah Weiland and Apoorva Mandavilli contributed reporting.