Omicron Was Probably in N.Y.C. Well Before the First U.S. Case Was Detected, Wastewater Data Suggest

Midtown Manhattan on Christmas Day last year. The Omicron variant of coronavirus may have been present in the city for more than a month by then, even before the first U.S. case was detected.

Omicron was probably present in New York City’s wastewater more than a week before the first case of the new variant was detected in the United States, according to a new report from the Centers for Disease Control and Prevention and researchers across the country.

The samples suggest that someone in New York City may have had the Omicron variant as early as Nov. 21, four days before South African scientists first announced cases of the variant and ten days before the first U.S. case was reported. Researchers in California and Texas also found evidence of Omicron in wastewater samples from late November.

The findings suggest that at the time, the Omicron variant was more widespread in the United States than the case data alone would indicate, and provide more evidence that wastewater surveillance can serve as an early warning system about the spread of new variants.

“At first it was uncertain whether this variant was going to come to the United States,” said Alexandria Boehm, an environmental engineer at Stanford and an author of the paper. “The wastewater answered that question way before the clinical samples could, and the answer was yes.”

The research does not provide conclusive evidence that Omicron was present in these cities. The virus present in wastewater is fragmented, and while the researchers detected many of Omicron’s telltale mutations, the findings do not prove that they were all present on the same genome.

Still, the results are highly suggestive, and are consistent with what scientists have learned about how quickly Omicron spreads and where it was likely to pop up first, said Amy Kirby, the program lead for the C.D.C.’s National Wastewater Surveillance System and an author of the paper.

“I don’t think anyone is surprised to see a new variant show up in a major city like New York first,” she said.

A team of scientists from several institutions —  John Dennehy at Queens College, Monica Trujillo at Queensborough Community College, Davida Smyth at Texas A&M University and Marc Johnson at the University of Missouri — have been tracking the coronavirus in New York City’s wastewater since the summer of 2020. The team typically collects samples weekly and then sequences the virus they find.

The scientists collected one of their routine samples on Nov. 21 and sent it for sequencing two days later. By the time they got the results, in early December, the Omicron news had broken, and they “immediately recognized” the new variant’s distinct mutations, Dr. Dennehy said.

Dr. Boehm’s team took a different approach in California, using P.C.R. tests capable of detecting some of Omicron’s specific mutations. They got their first hit on Nov. 26, from a sample collected in Merced the previous day, Dr. Boehm said. They got another on a sample collected in Sacramento on Nov. 30.

The first confirmed case of Omicron in the U.S. was announced on Dec. 1.

“We have really rapid turnaround and really frequent sampling,” Dr. Boehm said. She added, “This just gives information way earlier than clinical sequencing can.”

— Emily Anthes