How does infect step of epidemic interact with mutation?
This situation should never occur.  The mutation cards are put into the Infection Discard Pile at the beginning of the game.  So they aren't even in the deck until after the first Epidemic, and at that time they will be put on the top of the deck with the rest of the discard pile.  The only way for them to be on the bottom is to draw the entire Infection deck without hitting an Epidemic, which shouldn't be possible (at least without fan-based rules.