During the encounter Barnes became infected by a plague that the Priors had quietly unleashed to pressure human civilizations to turn to the Ori for salvation. After returning to Earth Barnes went to the medical ward complaining of fatigue. Roughly an hour later he could barely stand. He soon had symptoms of high fever, chest pain, and respiratory distress (identical to the symptoms experienced by the people of P8X-412).
The Fourth Horseman, Part 1 - Hours after returning to Earth from a long-term undercover mission, Colonel Barnes begins to display symptoms of a Prior plague.