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.