The injunction would have prevented the city from requiring public school employees to be vaccinated while the court heard other arguments for religious exemptions.
Public school employees claimed to have religious objections to the vaccine and sought the injunction after their first appeal was denied.
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Most of the plaintiffs were denied a second time and sought the injunction to prevent their termination.
District Judge Valerie Caproni found the vaccine mandate to be rational.
"The Court has no facts before it on which it could conclude that the Citywide Panel's process was irrational in any way or infected with hostility to religion," Caproni said.
Caproni's decision comes almost one week after the U.S. Supreme Court declined a petition from New York state healthcare workers who also opposed the vaccine mandate for religious reasons.
So far, as long as mandates are generally applied and do not single out a particular religion the courts, courts at all levels have allowed them to stand.
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