In a big setback for the city’s recovery, the schools chancellor, Richard Carranza, said the nation’s largest district would return to all-remote learning.

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New York City’s entire public school system will shutter on Thursday, the schools chancellor Richard A. Carranza wrote in an email to principals, in a worrisome signal that a second wave of the coronavirus has arrived. Schools have been open for in-person instruction for just under eight weeks.

“As of this morning, November 18, the City has now reached this threshold of test positivity citywide and, as a result, the DOE will temporarily close down all public school buildings for in-person learning, Thursday, November 19,” Mr. Carranza wrote shortly after 2 p.m. on Wednesday, about four hours after Mayor Bill de Blasio was scheduled to give a news conference. Mr. de Blasio confirmed the news in a tweet.

The shutdown — which was prompted by the city reaching a 3 percent test positivity rate over a seven-day rolling average — is perhaps the most significant setback for New York’s recovery since the spring, when the city was a global epicenter of the outbreak.

It was also a major disappointment for Mr. Blasio, who was the first big-city mayor in the country to reopen school buildings. Moving to all-remote instruction will disrupt the education of many of the roughly 300,000 children who have been attending in-person classes and create major child care problems for parents who count on their children being at school for at least part of the week.

Virus transmission in city schools had remained very low since classrooms reopened at the end of September, and the spike in cases does not appear to be caused by the reopening of school buildings.

Still, the city is choosing to end in-person learning while allowing indoor dining and gyms to remain open at reduced capacity. Nonessential workers are also continuing to use public transportation to commute to offices. Read more at NY Times