For several months last spring, New York City was the U.S. epicenter of the coronavirus pandemic: Hospitals were overwhelmed by patients, a makeshift morgue was erected in Manhattan, and residents feared to leave the safety of their homes.

But after a months-long lockdown, New York gained the upper hand on the virus, and since then, the city’s number of COVID-19 cases has remained low, even as other states continue to grapple with troubling outbreaks.

As a result, America’s largest city opened schools for in-person classes on Sept. 21—but the phased reopening has been anything but smooth. By the end of the school day, more than 100 early childhood centers and school buildings across the city have each reported at least one case of COVID-19. The following day, 11 more schools and two pre-kindergartens reported cases, as well, The New York Times first reported.

In a matter of days, six school buildings had to close their doors temporarily.

“My fear, right now, is I’m going to make my students sick, and then I’m going to go home and make my daughter sick, and then she’s going to go to school and make her teacher sick,” Sarah Yorra, who works at Franklin Delano Roosevelt High School, told WCBS.

So far, there’s no indication New York City’s school system will return to full-time remote learning. According to the city’s guidelines, individual schools will close if there are at least two cases in different classrooms or if the percentage of positive tests in the city exceeds 3 percent.

The mayor’s office told The Daily Beast the vast majority of these positive cases were contracted before classrooms reopened for students, with the exception of a “handful,” and many of the individuals who tested positive did not end up going to school.

“Identifying and tracing positive cases are a sign our extensive safety and health protocols—ranked among the most rigorous in the world—are working to prevent the spread of the virus,” a spokesperson for the mayor’s office said. “With an infection rate that has been at or below 1 percent for months, we are able to safely reopen and welcome our kids back to classrooms—something no major school system in America is currently able to do. We moved heaven and earth to make this reopening possible and we’ll continue to do all we can to keep our school communities safe as we welcome students back to classrooms this fall.”

To date, at least 19,159 people have died and 236,841 individuals have been infected with the virus across the city of 8.6 million, according to the Health Department. The city’s daily death toll has dropped dramatically since the peak of the pandemic, with zero deaths being reported some days. While the positive rate in the city remains below 1 percent, the city is targeting six neighborhoods that have seen recent upticks in cases.

“We’re launching a targeted approach that applies more pressure where there is growth in COVID-19 rates,” Health Commissioner Dr. David Chokshi said this week. “We’re doing this to communicate the urgency we feel, and that we need everyone to feel about following guidance to prevent the spread of COVID, and to protect one another.”

But the uptick has implications for the New York City public school system, which teaches over 1.1 million students and employs 75,000 teachers across 2,500 school buildings and early childhood centers.

As of Monday, students in 3K (or school for three-year-olds), pre-K, and District 75 schools, which teach special education, are participating in in-person classes. The rest of the system’s students began school remotely and are expected to start in-person classes as part of a phased opening next week.

Data from the city’s Department of Education, analyzed by Gothamist/WNYC, shows that cases in school buildings were first reported between Sept. 8, when teachers and staff members first reported to school, and the first day of classes, when 90,000 students arrived for in-person learning.

The latest school to face a temporary closure is the Torah Academy for Girls in Far Rockaway, which was shuttered Thursday in a move that shocked officials. Torah is not affiliated with the New York City public school system.

“At 9:30 this evening (Sept. 23), we received a phone call from the NYC Department of Health ordering that the school be closed effective immediately,” the school’s dean, Rabbi Meter Weitman, wrote in a letter to the community. “We have not been provided with any specific details as relates to the reasons, causes, or duration of the closure. We anticipate a meeting with the DOH tomorrow morning at which we hope to receive additional information which we will share with you.”

The K-12 school said it would transition to virtual learning. In Brooklyn, Magen David Yeshiva told families on Tuesday evening that buildings would be closed through Oct. 12. The two schools are located in the six heavily Orthodox neighborhoods in Brooklyn and Queens that officials say have contributed to 20 percent of all new virus cases across New York City.

The Department of Health on Tuesday revealed Midwood, Borough Park, and Bensonhurst are reporting a 4.71 percent positive coronavirus rate, while Kew Gardens, Edgemere, Far Rockaway, Flatbush, and Williamsburg are seeing their own uptick. Those local increases could have citywide implications, as Mayor Bill de Blasio has said that he will shut down all schools if the citywide rate exceeds 3 percent.

Dr. Jessica Justman, an associate professor of medicine in epidemiology at Columbia University’s Mailman School of Public Health, says the rising number of cases was expected in the transition to in-person learning during the ongoing pandemic.

“It’s not a surprise that we are seeing some cases in the NYC schools as they reopen. It tells us that our detection systems are working,” Justman told The Daily Beast. “We have to be prepared for the numbers to go up more and for school closures to happen. It will be hard to have unpredictable schedules but I think New Yorkers will understand. No one wants to repeat the searing experience we had in NYC last April.”

Zakiyah Ansari, New York City director of the Alliance for Quality Education, told The Daily Beast that while some positive tests were expected given the amount of testing, the rate is still “concerning.”

“I don’t think I am necessarily surprised,” Ansari said, stressing that the non-profit is still worried about the implications of so many positive cases so soon. “We are concerned but we think it’s a result of the testing more than anything. Folks are getting tested and we are experiencing the results of those tests. We are getting numbers.”

Those numbers are likely to climb when the system begins its mandatory testing program for public schools in October. As part of that, students will be tested once a month.

In an effort to prevent a widespread outbreak, the city has crafted rules for how cases are handled at individual school buildings. For example, one confirmed case in a classroom could force the entire class to go remote for two weeks, and close contacts of the positive individual would have to quarantine. Two cases, however, means the entire school will close.

Ansari says that while the pandemic is one issue, the future of the city’s public school system is already in danger after statewide budget cuts. On top of a billion-dollar budget decrease, Gov. Andrew Cuomo—who has warned of a COVID spike when schools reopen in New York City—has controversially withheld a portion of the state education aid on which the city relies.

The lack of funds, Ansari said, could result in an economic snowball effect for parents who are already back at work—and don’t have the resources to guide their children through remote learning.

“If schools close down, what happens to the families whose parents have to go to work?” she said. “The same kids that were getting screwed before COVID ar getting screwed again. We need all hands on deck, which includes dollars.”

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