Virgil is 'Red John'

He left CBI just after De Boscos team were wiped out and he gave an unconvincing speech to the press

Also, in season one, the episode 'red Johns shoes' Virgil is shown walking up a staircase in CBI with red shoes on. - but this scene was cut from the aired show and was a deleted scene

At the time of filming season 1 the writers had no idea of how sucessful the show would become and so wouod have needed somwone from the beginning to be Red John in case the show was pulled and a swift conclusion to the mystery was needed

Virgil also gives Patrick a list of suspects, a red john list made up by red john himself

Heres the clincher... in another deleted scene from season one, patrick is talking to virgil... virgil is drinking tea... and on the bottom of his cup.... is this symbol.... :)