At least one coronavirus case had been reported in more than 100 school buildings and early childhood centers in the New York City school system by the first day of in-person instruction on Monday, according to the Department of Education.
Nearly all the buildings remained open, though six were closed temporarily, in accordance with city guidelines that only those schools that report at least two cases in different classrooms will be shut.
The cases occurred between Sept. 8, when teachers and staff reported to schools, and Monday, when the first students entered classrooms. In dozens of cases, the infected individuals got the positive test results and did not report to work, the department said. Others did report to school, and their close contacts in the buildings had to quarantine for two weeks.
Avery Cohen, a spokeswoman for Mayor Bill de Blasio, said the cases included a “handful” of students, but that “the vast majority” were among staff before schools reopened for students.
Cases were reported at 11 additional schools and two community-based prekindergartens on Tuesday.
Some public health experts said the statistics reflect a new reality of in-person learning during a pandemic in a system of 1.1 million schoolchildren, 75,000 teachers and 2,500 school buildings and early childhood centers. Daily positive cases will be inevitable, and individual building closings will be a common occurrence, they said.
Dr. Michael Mina, an assistant professor of epidemiology at Harvard T.H. Chan School of Public Health, said the city’s families should be prepared for a constant game of “Whac-a-Mole.” The virus is likely to re-emerge repeatedly in school buildings until there is either a vaccine or very frequent testing, he said. Ideally, 50 percent of all students and staff should be tested three times a week, Dr. Mina said.
“I think the vast majority of schools will have outbreaks, and then bring people back,” said Dr. Mina, whom the teachers’ union consulted about the city’s school testing plan. “Test people, and trace them and bring them back after a week or two. But that is such a disruptive process for K-to-12 schools, and for working adults.”
The city’s mandatory testing program for public schools does not begin until October, but some 19,400 teachers were tested voluntarily before Monday. So far, 65 of them — about 1 in 300 — tested positive, the city said.
That rate, of about .34 percent, is a third of the overall positivity rate for the city, which has been about 1 percent for weeks, but is still “a pretty high number to be virus positive,” said Dr. Mina, and indicates that there may be dozens of undiscovered cases among teachers who have not yet been tested.
“What this testing shows is that the virus is there; it is going to be brought into school buildings,” said Dr. Jeffrey Shaman, a professor of environmental health sciences at Columbia University and a leading modeler of infectious diseases. “Then the question is, will it transmit there?”
How city schools manage cases and prevent outbreaks will be key to keeping the district, the largest in the nation, open for at least some in-person instruction. Up to 90,000 students in pre-K and with advanced disabilities arrived in classrooms this week, with the rest of the city’s students slated to start in-person instruction next week. Parents can opt their children out of in-person classes at any point, and as of Monday, 46 percent have already done so.
Mayor de Blasio has said he will shut the entire school system down and move to remote instruction if the positivity rate in the city as a whole rises above 3 percent.
In neighborhoods where infections rates are above 3 percent — including a cluster in Midwood, Borough Park and Bensonhurst in Brooklyn, which have reported a 4.71 percent positive coronavirus rate, the Health Department said Tuesday — schools with fewer than two cases will remain open but the city will deploy additional testing efforts.
The buildings with at least one positive case between Sept. 8 and Sept. 21 spanned the city, from P.S. 165 on Manhattan’s Upper West Side to Albert Einstein Junior High School in the South Bronx and P.S. 139 in Ditmas Park, Brooklyn.
“People were scared and angry, that we are being put in this situation without all of the systems we were promised in place,” said Megan Jonynas, the union chapter leader and music teacher at P. S. 139, who said school employees were frustrated that it took about two and a half days for the city’s contact tracers to call staff after the positive result had been reported.
Wafaa El-Sadr, a professor of epidemiology at the Columbia Mailman School of Public Health, said that positive cases were to be expected, given that the virus is still circulating in the city, albeit at a low level. But they underscored how reopening schools was always going to be a balancing act.
“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.
At that rate, with about 1,600 city schools, Fulgent Genetics expects to have to visit more than 90 schools each school day. Parents must consent to have their children tested, or the children will be transitioned to remote learning. The test is a “a very simple, painless nasal swab” — not the deeper nasopharyngeal swab, Mr. Perthuis said.
Testing students just once a month will be helpful in determining the prevalence of the virus within a student body, but it is probably not frequent enough to contain most outbreaks, experts said.
“Testing like that isn’t going to be something you’re using to help control the virus,” said Dr. Shaman. “Essentially you’re taking the temperature and finding out what’s going on in the school, how much virus is here, and you can react to that,” he added.
Mr. Mulgrew said that health experts had told the union that random sample surveillance testing was the most important type of testing they could do.
“Testing everyone at the beginning of school, you will have peace of mind for four days,” he said. “If you have a surveillance program, you will be able to identify issues beforehand, and if you find anything, you can put in massive testing.”
Joseph Goldstein and Eliza Shapiro contributed reporting.
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