Corey's twin sister, Brandi, and their brother, Mason, 4, remained in critical condition at the hospital Monday night, a spokeswoman there said.
The children's father, Michael Howard, was at work in Frederick, Md., at the time of the fire, Martinsburg Fire Department officials said.
Sara Howard, 37, was charged with child neglect on June 1 after Brandi Howard, then 2, was found playing near the street in the 800 block of Winchester Avenue around 9 a.m., according to records in Berkeley County Magistrate Court. At the time, the family lived at 735 Winchester Ave., court records state.
The child, dirty and wearing only a diaper, had been without supervision for at least 30 minutes, court records allege.
According to court records, Sara Howard told police her then 16-year-old daughter had failed to wake her before going to school that morning and that was why she didn't know where Brandi was.
The child neglect case was transferred to Berkeley County Circuit Court on Aug. 24 after probable cause was found to support the charge, court records state.
Games-Neely said she and Martinsburg City Police Cpl. Carl Franklin asked the West Virginia Department of Health and Human Resources to remove the children from their mother's custody for their own protection, but the request was denied.
That phone at that office was answered Monday evening by a machine with a message giving office hours.
Games-Neely said the West Virginia Legislature states that department has jurisdiction over cases alleging abuse and neglect against children.
Another state agency, the Children's Fatality Team, will investigate the death of Corey Howard, Games-Neely said.
Fire Capt. David Brining said a smoke detector on the second floor of the house contained no batteries.
The federal Bureau of Alcohol, Tobacco and Firearms also is investigating the fire, said Martinsburg Fire Chief Phil Martin.
The bureau is helping because the investigation crosses state lines since the father works in Maryland and two children are in a Washington hospital, Martin said.