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Is New York City Ready for the Omicron Variant?

The increase, epidemiologists say, is likely caused by the changing of the seasons, with colder weather pushing people indoors and prompting them to close windows, raising the risk of transmission. Cold, drier air may also benefit the coronavirus by helping viral particles to survive and linger in the air for longer.

Holiday travel and gatherings could also accelerate transmission.

One disease model from a team at New York University Grossman School of Medicine, which predated Omicron, predicted about 10 deaths a day from Delta in the weeks ahead, according to a member of the team, Dr. Ronald Scott Braithwaite, a professor at N.Y.U. and an adviser to the city. At an earlier point this year, during the height of last winter’s wave, there were as many as 98 Covid-19 deaths in a single day.

In New York City, the Delta variant is expected to drive only a minor surge in cases. But it is creating a potentially dire situation in Western New York, where last week, the number of coronavirus patients admitted to hospitals on a single day — 120 on Nov. 26 — was the highest in the region since the start of the pandemic.

As new forms of the virus began to emerge across the globe early this year, New York City began cobbling together its own surveillance system. Turning to universities, hospitals and other laboratories, the city set out to analyze at least 10 percent of coronavirus cases in New York for mutations.

The Pandemic Response Lab, a private start-up that opened last year, quickly became a big player in this effort. By early this year, it was sequencing — examining genetic material for mutations — hundreds of coronavirus cases each week, and offering insights into how different variants were circulating across the city.

About 15 percent of confirmed Covid-19 cases in the city are sequenced, a number some epidemiologists hope will grow. In recent months, just about every virus sample run through genome sequencing machines has turned out to be the Delta variant, said Dr. Jon Laurent, who oversees the Pandemic Response Lab’s sequencing program.

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