In The Maze Runner:The Death Cure, on the night of the WCKD city attack by cranks, Teresa tests a captured Thomas's blood to see if his immunity to the Flare virus could heal...sure enough she found his natural serum didn't just stop the flare...but destroyed it. If Teresa found this this quickly, why didn't WCKD...with all that highly advanced technology...and so many scientists discover this serum in Thomas's blood before the maze trials?
Well the whole point of the mazes is to stimulate the immunes to produce more and stronger enzymes that defeat the flare virus. Before being put in the maze Thomas' enzyme wasn't as active.
Then from when he "escaped" the maze until when Teresa tests him WCKD never had an opportunity to check him, their original plan was to start harvesting from a couple of immunes at a time and his turn hadn't come yet.