The baby's 19-year-old mother was lured to a home on the Southwest Side, where police said she was killed and had her baby cut from her womb on April 23.
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The baby, Yovanny, had been hospitalized in intensive care before dying Friday.
In a statement, the spokesperson said, "It is with great sadness that we inform you of the passing of baby Yovanny Jadiel Lopez. He passed away this morning Friday June 14, 2019 from his severe brain injury.
"Please keep his family in your thoughts & prayers as they go through this difficult time."
Ochoa Lopez's family has been by her baby's side for weeks praying for his recovery. The baby initially couldn't breathe or eat on his own.
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Three people have been charged in Marlen Ochoa Lopez's death. Prosecutors said Clarisa Figueroa lured 19-year-old Marlen Ochoa-Lopez to her home with the promise of free baby clothes, then allegedly killed the young woman with the help of her daughter Desiree.
Police said Clarisa Figueroa showed up to the hospital with the infant after she killed Ochoa-Lopez and removed the child from the womb.
According to the Department of Children and Family Services, the hospital contacted the agency on May 9, more than two weeks after Figueroa first checked into the hospital.
Three weeks after Marlen's disappearance, police said her remains were found in the Southwest Side home where police said she was murdered.
Clarisa Figueroa and Desiree Figueroa have been charged with first-degree murder. Clarisa's boyfriend, Piotr Bobak, has been charged with concealing a homicide.