Thomas was arrested after a tip from Prince George's County, Md., where he is a suspect in at least four sexual assaults.
In late February, billboards went up across seven states with the mug shot of the suspect and a website was launched with information on the crimes.
Thomas is believed to be responsible for rapes and other attacks on 17 women since 1997. The most recent occurred in Virginia in 2009, where he was almost caught when a victim was able to send a text message for help to her mother. In that incident, two 17-year-olds and a 16-year-old were approached by a masked gunman in the 4300 block of Dale Boulevard on Halloween and ordered into the woods. He raped the 17-year-olds, but the 16-year-old was able to contact her mother.
DNA has linked 12 of the attacks.
The three charges in Louduon County are punishable by up to three life sentences.