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Prosecutors say Derek Vaughn Rayo, 27, and Kelly Gene Richardson, 28, had fentanyl and other opioids in their systems at the time of their 18-month-old daughter's death.
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If convicted, they face at least 15 years to life in prison.
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Rayo's arraignment was scheduled for 1:30 p.m. Wednesday at the Hall of Justice in San Jose while Richardson is not yet in custody.
It is the first time the Santa Clara County District Attorney's Office has charged parents for the murder of their own child in a fentanyl-related death, according to prosecutors.
At about 11 p.m. on Aug. 12, San Jose police officers went to the 1500 block of Huddersfield Court in response to Rayo's call that his daughter was not conscious and not breathing.
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She was later found to have been dead for hours, according to prosecutors.
"During a search of the home, investigators located fentanyl on the nightstand of the master bedroom, a scraping tool with fentanyl residue on the desk, and another scraping tool with fentanyl on a rug located underneath the baby's body," prosecutors said in a news release Wednesday.