Charges were upgraded Monday against Edward Weiher,49, and Alexa Balen, 28. They are accused of killing two-year-old Trinity, last November, the sheriff's office said.
Police said the couple's house on West Thorn Apple Drive was filled with drugs, garbage, and medical waste.
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The couple was in court Monday and released on pre-trial conditions. They also have a six-year-old child who is in protective custody.