Authorities say the man, identified as 39-year-old Haneef Cooper, was spotted around 8:30 p.m. Thursday at SEPTA's Frankford Transportation Center and was taken in for questioning.
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Cooper has been charged in connection with six incidents of vandalism, including two churches and other businesses.
Suspect in custody following Philadelphia vandalism spree
Saint John Neumann Shrine in Philadelphia's Northern Liberties was among the properties hit, police say. On Feb. 20, three stained-glass windows were broken by rocks and a brick.
The church estimates the damage to the stained glass, imported from Austria, is around $20,000.
National shrine in Northern Liberties targeted in vandalism spree; new video released of suspect
"The areas that were broken, it's going to take extensive work to try to repair it," said Father Micael Cunningham, the pastor at the Saint John Neumann Shrine.
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The shrine, dedicated to the first male saint in the United States whose body is kept on the altar, has been visited by the likes of Pope Francis.
READ MORE: 134-year-old historic church vandalized in Philadelphia's Society Hill
Police said Cooper also targeted another historic church: Mother Bethel AME on the 400 block of South 6th Street in Society Hill.
Police say the church's stained glass windows were shattered. The windows date back to the 1800s and will cost around $15,000 to repair, according to the church.
He is also accused of hitting the Science History Institute in Old City, Touraine Apartments on Spruce Street, an electronics repair shop on Walnut Street, and a Playa Bowls in Center City.
Another video captured by 1600 Spruce St. Interior Design & Home shows the suspect causing damage to another small business at 16th and Spruce streets.
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Police previously stated that Cooper has a history of vandalism and has previously been charged with criminal mischief.
He has been in and out of jail since 2011 for similar crimes.
Cooper has been charged with six counts each of criminal mischief and possession of an instrument of crime for the six incidents.
He has also been charged with institutional vandalism for the two incidents involving places of worship, police say.
Investigators are still working to determine if Cooper is tied to any other instances of vandalism.
Anyone with information is asked to call police at 215-686-TIPS.
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Vandal wanted for damaging historic church, small businesses in Philly