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Is New York City Ready for the Omicron Variant?

As reports of the new Omicron variant began to circulate the world late last week, scientists in Queens who search for mutations in coronavirus samples drawn from infected New York City residents double-checked their work to see if they had missed any cases. They hadn’t.

But even if the new variant, which has been detected in California, has not reached the city yet, health officials say it remains just a matter of time before it does. “We do anticipate detecting Omicron in New York in the coming days,” the city’s health commissioner, Dr. Dave Chokshi, said on Monday.

The question now is whether Omicron could plunge the city back into a period of spiking case counts and hospitalizations, lockdowns and isolation. Or will it be much like the Delta variant, which provoked anxiety when it arrived six months ago, but did not significantly change daily life in the city?

The answer will depend mainly on whether the new variant proves to be more contagious, more deadly or more resistant to vaccines than Delta and previous mutations — questions scientists may take weeks to answer.

Here are some things to know about New York and the Omicron variant:

This could be the fourth variant to hit the city in 2021

New York City has already weathered rising caseloads from three coronavirus variants this year. First there was a homegrown variant, called B.1.526 or Iota, which spread rapidly from January to March. That was followed this spring by the highly transmissible Alpha variant, first identified in Britain. Then by summer came the even more highly transmissible Delta variant, which caused a small wave of infections and then subsided in October before rising again in November.

Each new variant provoked worry. But so far, the coronavirus has been diminishing as a threat, after the devastating first wave last year. The long second wave that stretched from the autumn of 2020 to this spring saw far fewer infections and deaths than the first, even as several strains of Covid-19 spread.

The pattern of diminishing waves is different than what has been seen in much of the country and owes something to New York’s relatively high rate of vaccination — about 77 percent of residents have received at least one shot.

There are other factors: Considerable levels of natural immunity from the devastation of the first wave in spring 2020. A willingness to wear masks. Widely available testing and a robust public health apparatus.

“I think we are potentially more prepared than most,” said Dr. Bernard Camins, an infectious diseases specialist and medical director of infection prevention for the Mount Sinai Health System. “The question is whether at this point people are more fatigued from all those mitigation strategies, and they may not listen.”

Mayor Bill de Blasio says that a mask mandate could prove a distraction from the city’s main goal: getting vaccines and booster shots into more people.Credit…Stephanie Keith for The New York Times

What happens next turns mainly on the variant

Initial reports suggest this variant might be especially contagious. But little is known about Omicron’s virulence, or what protection existing coronavirus vaccines offer.

“We do expect the vaccines to retain some degree of effectiveness, but precisely how much will take a few weeks to clarify,” Dr. Chokshi said on Monday. “We’re counseling, you know, a bit of patience as the science sorts itself out.”

But Dr. Denis Nash, an epidemiology professor at CUNY School of Public Health, warns that “if this is more transmissible than Delta or more virulent, or more evasive of the immune protection that the vaccine provides,” then the city “could be susceptible to a surge.”

Amid these unknowns, Mayor Bill de Blasio had some blunt advice: Get vaccinated, or get a booster shot, and “get those masks back on now,” he said on Monday. Fewer than 20 percent of adult residents have gotten their booster shot.

In particular, he urged parents to get their children vaccinated. Just 17 percent of 5- to 11-year-olds have received a first dose since they became eligible a month ago. “It’s time,” he said.

Even without Omicron, cases have been rising

Since Nov. 1, daily case counts have risen more than 75 percent, reaching 1,500 newly identified cases a day last week. The rise, driven by the Delta variant, has been steepest in Queens, a borough with vaccination rates well above the citywide average.

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.

Surveillance and testing systems are strong

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.

The Coronavirus Pandemic: Key Things to Know

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The Omicron variant. The latest Covid-19 variant was identified on Nov. 25 by scientists in South Africa and has since been detected in more than 20 countries, including the U.S., which reported its first case on Dec. 1. Should you be concerned? Here are answers to common questions about this variant.

Travel restrictions and lockdowns. As more Omicron cases emerge globally, countries are responding in varied ways. Japan joined Israel and Morocco in barring all foreign travelers, and Australia delayed reopening its borders for two weeks. The C.D.C plans to increase testing and screening of international fliers to the U.S.

A patchwork of regulations. As the new Omicron variant spread around the world, two KLM flights from South Africa became emblematic of the scattershot and lax global approach to coronavirus containment. Of the more than 60 people who tested positive for the virus, at least 14 had Omicron.

A new type of treatment. An expert panel voted to recommend that the F.D.A. authorize a Covid pill from Merck for high-risk adults, the first in a new class of antiviral drugs that could work against a wide range of variants, including Omicron. The pill could be authorized within days, and available by year’s end.

Vaccine hesitancy in Africa. The detection of the Omicron variant in Africa signals the next stage of the battle against Covid-19: getting more people inoculated in poorer nations. But though vaccine supplies are becoming sufficient, the new hurdle is overcoming local skepticism or outright hostility.

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.

A person showing proof of vaccination to get into a venue in Ridgewood, Queens. The city raised the vaccination rate through mandates for municipal employees and by imposing restrictions on people who are not vaccinated. Credit…Stephanie Keith for The New York Times

New York City is focusing on vaccines and boosters

When the coronavirus reached New York early last year, New York’s officials, including then-Gov. Andrew M. Cuomo and Mr. de Blasio, were slow to act.

Citing this history, a reporter asked Mr. de Blasio on Monday why he was merely recommending mask wearing, rather than imposing interventions like a mask mandate until more about Omicron was understood.

Mr. de Blasio said that he worried that a mask mandate would prove a distraction from the city’s main goal: getting vaccines and booster shots into more people.

“What we do not want to do is mix messages about what’s the thing that actually has the most profound impact,” Mr. de Blasio said. “The thing that we need to do with urgency is get people vaccinated.”

Dr. Jay Varma, an epidemiologist who has helped guide New York City’s pandemic response as a mayoral adviser, says that like Delta, Omicron could take months to spread widely in New York, giving the city time to nudge more residents to get vaccinations or boosters, and convince more companies to impose vaccine requirements.

Nearly 89 percent of adults in New York City have gotten at least one dose — six percentage points higher than the national average. In recent months, the city raised the vaccination rate through mandates for municipal employees and by imposing restrictions on people who are not vaccinated.

Yet the rate is uneven. Though the gap has shrunk, Black residents are less likely to be vaccinated than other groups, particularly among younger people; just 57 percent of Black New Yorkers between 18 and 44 have gotten at least one dose of a vaccine. And children younger than 5 still remain ineligible for vaccination.

Public health experts also worry that nursing homes are underprotected.

As of last week, only 51.4 percent of the nearly 92,000 nursing home residents statewide had received a booster shot, according to the state Department of Health. Across the city, there are more than 30 nursing homes where fewer than 25 percent of residents have received booster shots.

“I find it highly, highly distressing,” said Dr. Nash, the epidemiology professor. “I’m afraid it will be a travesty with a lot of avoidable deaths.”

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