Police say Christopher Davila, the father of King Jay Davila, confessed and led investigators to the field to show them where he buried his son.
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Investigators dug up a black backpack with what appeared to be a baby's body wrapped in a blanket, an arrest affidavit says.
At a Thursday night news conference, San Antonio Police Department Chief William McManus said Davila is believed to have injured the child severely, then told police the boy was in a car that was stolen.
McManus says Beatrice Sampayo, the child's grandmother, is suspected of disposing of the child's car seat and dropping off Angie Torres, the child's cousin, who was seen on surveillance video as participating in a staged kidnapping.
Now all three family members have been charged with tampering with evidence in the case. Sampayo and Torres are in custody.
After Davila was arrested for tampering with evidence, officials say he led them to his son's body. Davila initially denied involvement in his child's disappearance.
Police had suspected him of faking the kidnapping to cover up foul play.
"Christopher has said that King Jay's death was an accident. He panicked and did not call 911," said Chief McManus.
McManus says that based on that information, Davila is charged with felony injury to a child causing serious bodily injury - omission, felony possession of a firearm and possession with the intent to deliver a controlled substance.
Authorities say Davila had drugs on him at the time of his arrest. The felony possession of a firearm stems from his long criminal history.
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His bond is set at $1,000,000.
McManus says that an autopsy is expected to be performed on the baby Friday to determine exactly how he died.
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The Associated Press contributed to this report.