Police say Davis was raped and strangled. Mario McNeill, 29, is charged with the crime. He allegedly admitted kidnapping the girl.
The case has been tough for veteran investigators.
"And it's still pretty emotional -- still up and down," Captain Mark Bidgeman said. "You know it's one of those things, it's the hardest thing I've ever had to do in my career."
Davis disappeared from her home last Tuesday and her body was found in a wooded area just south of Sanford. Police announced Thursday that Cumberland County will have jurisdiction in the case.
According to court documents McNeill kidnapped, raped and killed the five-year old the same day she was reported missing from her mother's mobile home in Fayetteville.
Shaniya's mother, Antoinette Davis, is charged with trafficking and child abuse involving prostitution.
McNeill previously was charged with kidnapping. The newest charges against him include first-degree rape of a child and first-degree murder. Police say the 5-year-old was strangled.
McNeill made a court appearance for the new charges on Friday, where he learned he could face the death penalty if he's convicted.
"You're charged with first degree murder," District Court Judge George Franks said. "In the state of North Carolina that's punishable by the death penalty or life imprisonment without parole."
Attorney Allen Rogers has been hired by McNeill's family to represent him.
"You know, (McNeill's mother) is in shock that her son could be charged with such a serious crime," Rogers said. "And she stands by her son and she's remorseful for the family for the loss this young child."
McNeill is currently being held in Raleigh's central prison for what authorities call suicide watch and for his own safe keeping.
Police say there's still more work to be done in the case. They have to decide whether the child's mother will face any additional charges.
Meanwhile, Shaniya's father and his sister were on The Oprah Winfrey show via satellite from Fayetteville talking about their loss.
Carey Lockhart-Davis, Shaniya's aunt who often cared for her while her father was away a work, reflected on the last time she saw Shaniya alive -it was on October 9, when her mother called and asked to see her.
"Shaniya loved her mother very much, and she did want to be with her mother," Lockhart-Davis said. "I took Shaniya over there and gave her a kiss goodbye and told her to be a good girl for Aunt Carey, and as she ran off to her mom. She turned back and looked at me and said I love you Aunt Carey. I'll see you later."
Brad Lockhart says he never looked at Antoinette Davis as a bad parent.
"Antoinette never lived in the best neighborhoods and of course there was always that concern," he said. "But I never was concerned about her caring for her as a mother for the weekends she would keep her."
Lockhart told Oprah there was no formal custody agreement between the parents. Shaniya lived with her father and would often visit her mother.
Shaniya's funeral will be Sunday at 3 p.m. at the Manna Church off Cliffdale Road in Fayetteville.