Hernandez allegedly targeted the girl because she had a speech impediment and would have a hard time telling anyone about the crime.
However, the victim was able to indicate to her mother that the driver touched her private parts.
Eyewitness News has learned investigators took eventually took a DNA vaginal swab. However, that failed to produce results, so they submitted a sample of saliva found on the child's underpants.
Hernandez recently agreed to a DNA swab and a match to the saliva found on the underpants was made Wednesday, the source said.
Hernandez was arrested Thursday at the Mid-Island's 122nd Precinct and is expected to be arraigned today in Stapleton Criminal Court.
Police say the 51-year-old bus driver is charged charged with sex abuse and endangering the welfare of a child.
