NEW YORK — A resurgence of the coronavirus in New York City is threatening to halt the nation’s biggest experiment with in-person learning.

The city’s public school system this fall became one of just a few large, urban districts in the U.S. to welcome students back into classrooms. A little more than a quarter of the city’s 1.1 million pupils have been attending classes in person between one and three days a week.

Just a few weeks ago, the return was going well enough that officials decided to give a little shove to the majority of parents who had opted to stick with all-remote learning: Send your kids back now, parents were told, or forfeit the option of having them return later this academic year.

But as the Sunday deadline to make the switch loomed, the city also approached a threshold the mayor set to suspend in-person learning.

Mayor Bill de Blasio has said he will close all school buildings if 3% of the COVID-19 tests performed in the city over a seven-day period came back positive. That mark was set over the summer as the city was trying to avoid a teachers’ strike.

De Blasio said Friday that the citywide positivity rate has risen to 2.8% after climbing for several weeks. The city is preparing to close all school buildings as soon as Monday if the rate crosses the threshold over the weekend, he said.

“I want to urge parents to have a plan ready that they can put into effect as early as Monday,” de Blasio said during his weekly talk on WNYC radio. “Parents should have a plan for the rest of the month of November.”

Some parents expressed frustration that they were being asked to make a decision about sending children back into classrooms, when the city itself is not even sure what will happen next.

“The information that we have seems to indicate that these next few months are not going to be so great,” said Jared Rich, who has kept his son out of pre-kindergarten so far but would consider sending him in the spring when teachers can open windows and take students outside.

The mayor, Rich said, is “forcing us to make the decision to put our kids in person at a time when it’s not just a surge; this is out of control what’s going on.”

“It’s so upsetting,” the Brooklyn attorney said.

Over the summer, city officials gave parents a choice: They could do hybrid instruction, where students would be in classrooms some days, but learning online others. Or, they could go all-remote.

About 280,000 students signed up for classroom instruction, far fewer than officials expected.

The city initially said parents would have a chance each quarter to switch from remote to blended learning. The decision to end that system of quarterly choices was made “for the sake of stability,” Education Chancellor Richard Carranza said.

The teachers’ union said the single opt-in period undermines parents’ trust.

“The timing couldn’t be worse,” said Michael Mulgrew, president of the United Federation of Teachers.

Until now, the city has relied on targeted closures, rather than citywide shutdowns, to keep schools from fueling the pandemic.

Since the start of the school year, 1,800 students or staff in the system have tested positive for the virus. As a result, nearly 1,100 classrooms have gone through temporary closures. At least 115 school buildings have been closed for 24 hours because of positive tests; 62 have been closed for 14 days or more.

De Blasio, a Democrat, has been asked repeatedly whether he would consider changing the threshold for a citywide closure, given that some schools in Europe have remained open even as businesses have been ordered closed. Germany began a four-week period of restrictions Nov. 2, closing restaurants, bars, sports and leisure facilities, but keeping schools and shops open.

Children in neighboring France continue to go to school while most adults are confined to their homes for all but one hour a day.

Several states have kept schools open for in-person learning in areas where there are far more infections per capita than in New York City. While the city has seen an increase in cases lately, it now ranks far better than most other places in the country.

De Blasio said it was “crucial” to adhere to the standard he set over the summer.

If a shutdown does happen, the city will work to reopen as quickly as it can once infection rates decline, he said.

Urban school districts across the country are altering in-person plans as virus caseloads continue to rise.

Detroit Public Schools on Thursday joined a growing list of districts shifting to remote learning, telling students to stay home until Jan. 11. Philadelphia administrators on Tuesday scrapped plans to start bringing students back November 30. Minneapolis Public Schools on Monday put an indefinite hold on efforts to bring more children back to school. Boston public schools switched back to all-remote learning Oct. 22.

Some New York parents said they were content to stick with remote learning.

Sabretta Pryce said her 6-year-old son, Gavon, is doing well with all-remote learning at Public School 47 in the Bronx. Pryce chose online-only schooling in part to protect older family members from a possible coronavirus infection.

“We just tried to avoid anything that could be detrimental,” she said. “I just didn’t want to bring anything in.”

Manhattan parent Jess Allen said that while her 6-year-old son, Wolf, has benefited from in-person learning, she wouldn’t be angry if the city called it off.

“I certainly don’t want to feel like, you know, people are dying so my kid can be in school,” she said.