Omicron likely in NYC sooner than detected, wastewater data suggest

Omicron was likely present in New York City wastewater more than a week before the first case of the new variant was discovered 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 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 US case was reported. Researchers in California and Texas also found evidence of Omicron in wastewater samples as of late November.

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

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

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

Still, the results are highly suggestive and in line with what scientists have learned about how quickly Omicron is spreading and where it’s likely to show up first, said Amy Kirby, the program leader for the CDC’s National Wastewater Surveillance System and an author of the paper. .

“I don’t think anyone would be surprised to be the first to see a new variant appear in a big city like New York,” she said.

A team of scientists from several institutions — John Dennehy of Queens College, Monica Trujillo of Queensborough Community College, Davida Smyth of Texas A&M University and Marc Johnson of the University of Missouri — has been monitoring the coronavirus in New York City’s wastewater since the summer of 2020. The team typically collects samples on a weekly basis and then analyzes 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 come out, and they “instantly recognized” the different mutations of the new variant, said Dr. dennehy.

The team of dr. Boehm took a different approach in California, using PCR 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, said Dr. boo. They got another one from a sample collected in Sacramento on Nov. 30.

The first confirmed case of Omicron in the US was announced on December 1.

“We have a very fast turnaround time and very frequent sampling,” said Dr. boo. She added, “This just provides information much sooner than clinical sequencing can.”

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