Authorities say the man, who has since been identified as 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, 39, has been charged in connection with four incidents of vandalism, including two churches and other businesses.
Suspect in custody following Philadelphia vandalism spree
Police said there are six other incidents of vandalism they are looking at that may be connected to Cooper.
Saint John Neumann Shrine in Philadelphia's Northern Liberties was among the properties hit. Three 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 iconic historic church: 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.
He is also accused of hitting the Science History Institute in Old City 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 said 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.
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