Trooper Ernest Boatright was charged with child endangerment and harassment, WTAE-TV first reported Tuesday.
Boatright told investigators he had pepper sprayed two cats on an enclosed porch, according to court records, but the boy told investigators that Boatright sprayed the chemical into his room in April. The boy told police the trooper also had sprayed him with the substance before, police said.
The trooper didn't immediately return a message seeking comment, but his attorney, Matthew Zatko, told The Associated Press Boatright "categorically denies all of the allegations and welcomes the opportunity to defend himself and clear his name."
Boatright, 48, of Penn Hills, has been a trooper since 1989 and was assigned to the New Stanton barracks, which largely patrols a section of the Pennsylvania Turnpike, state police officials said.
The April 19 encounter that prompted the charges occurred at the home the boy shares with Boatright's girlfriend in Menallen Township, near Uniontown, about 40 miles south of Pittsburgh. That's where Boatright faces a preliminary hearing Jan. 22.
Fayette County child welfare workers had referred the case to law enforcement. The charges were filed in November, at which time the trooper was suspended, Zatko said.
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