Of all the schools with positive cases, Lane Tech, Chicago's largest high school with 4,200 students, has the most students in isolation.
Two cases at the Roscoe Village high school have led to a staggering 408 identified as close contacts. All of them are now in quarantine.
CPS reported another two cases at Washington High School this week, and with 168 from the South East Side school who had close contact.
Students said part of the problem is that social distancing is hard sometimes.
"When we get out of class, we have to go to another class - everyone is close to each other. It's kind of hard to keep a distance in the hallways.," said Washington High school senior Dariana Quinteros.
The increase in the number of known infections at CPS comes as the district updated its dashboard for COVID metrics on Wednesday evening.
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That dashboard shows there are currently at least 160 confirmed cases district-wide, including 89 students and 71 staff, with nearly 3,000 people in isolation as a result. Most cases are cropping up in high schools, where social distancing poses a greater challenge, as students move every period.
However, the Chicago Teachers Union raised questions Thursday about the safety and transparency in the nation's third-largest school district, saying the online database is inaccurate.
CTU's President Jesse Sharkey sharply criticized Mayor Lightfoot Thursday.
"She is responsible for the deplorable lack of transparency and misinformation. And she is responsible for the frightening lack of safety and the numerous COVID outbreaks in schools across the city," he said in a statement.
The union said the data doesn't match reports from teachers and families while the Chicago Tribune showed lags in reporting. The claims come amid ongoing negotiations over pandemic safety protocols.
"Our school communities need trust, truth, transparency and leadership from the mayor and her team at CPS," Sharkey added. "Instead, they continue to stonewall educators, parents and the public about safety issues in a pandemic."
The district and Chicago Department of Public Health issued a joint statement earlier this week on reporting practices.
"The public tracker is not currently set up to report on dynamic numbers, meaning, how many people are quarantined at a given time. The tracker represents one point in time," the statement read. "Some who are quarantined initially are no longer in quarantine after the investigation is complete and they are found to be vaccinated. This is not reflected in the tracker."
The news comes less than two weeks since the first day back to school, and just a couple of days after the district called on unvaccinated students who traveled out of state over the holiday to quarantine for seven to 10 days.
"The mitigations that I thought were going to happen are not happening," Lane Tech parent Melanie Apel said. "It's just a sort of a ticking time bomb before they have to close the whole thing down again."
"We can't afford to take half-measures in this situation, we need to be as aggressive as possible," added 47th Ward Alderman Matthew Martin.
That guideline, however, is not being enforced. The district is leaving it up to parents to voluntarily self-report any travel.
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Chicago's top doctor has cautioned in the past that this increase in the number of cases was expected as students return to school, but many parents remain concerned, reporting overcrowding and poor social distancing inside their children's schools.
"The hallways are crazy crowded, and there's no -- it's just regular school with masks. There's nothing else going on as far as he can tell," Apel said.
Medical experts warn that all mitigations must be followed while children attend school.
"We can have children in school safely with masks, distancing, a[nd] with keeping kids out of school when they're sick, by getting them tested when they are sick, if they are positive, contact tracing and quarantine other children who are exposed," said Dr. Larry Kociolek, medical director of infection prevention and control at Lurie Children's Hospital of Chicago
Negotiations on that and other issues continue behind the scenes between CPS and the Chicago Teachers Union.
For more information about COVID cases in CPS, visit https://www.cps.edu/services-and-supports/health-and-wellness/covid-19-readiness-data/.
The Chicago Tribune and Associate Press contributed to this article.