“Most important,” she said, “is the ability to move rapidly to prevent transmission clusters.”

She said she would recommend to “stay the course, continue to monitor the situation carefully, and be ready to take a step back if this becomes necessary.”

Other school buildings affected included some operated by the 1,050 community-based organizations that contract with the city to provide free pre-K, including Beth Jacob Day Care Center in Borough Park and Divine Mercy Catholic Academy in Ozone Park, Queens. Each had one reported case but did not shut down.

Troubling delays in testing and tracing for schools were a key reason, along with staffing issues, that the city’s teachers’ union pushed for an additional week delay to in-person instruction for most students, said Michael Mulgrew, the president of the United Federation of Teachers.

But, he said, the city made improvements. Fast Track testing sites for teachers are now returning results quickly, often within 24 hours. Mayor de Blasio opened a Covid situation room that puts staff from the Department of Education, the Department of Health and the city’s Test and Trace Corps in the same room to speed up contact tracing.

A dedicated team of phone-based contact tracers has been assigned to handle schools.

“When they tried to handle it through their normal process, it wasn’t working,” Mr. Mulgrew said. “As the situation room seems to be humming, it is getting better and better.”

In a deal made earlier this month between the teachers’ union and the city to avoid a strike, between 10 and 20 percent of the individuals reporting for in-person class in every school will be tested each month, starting in October.

Brandon Perthuis, the chief commercial officer of Fulgent Genetics, which is handling much of the testing for the city’s public schools, said that while details were still being hashed out, it’s likely his company would send staff to a given school one day each month to test 10 to 20 percent of students.

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