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Mitchell Wiener died on Sunday evening, Flushing Hospital Medical Centre spokesman Andrew Rubin told AP news agency.
A woman and child wear masks while waiting in the subway system in New York Masks on NY subway Intermediate School 238 in Queens, where Mr Wiener worked, is one of 11 closed in New York City over swine flu fears.
By the time the school shut on Thursday, Mr Wiener, 55, had already been sick for nearly a week.