Didnt they already explain that in the previous chapters?Unmentioned detail: Timothy's order to step up the finding/killing of suspected witches are because he believes his father's behavior is a result of witches doing something to him. Obviously enough, not all the people executed are really witches.
Fairly important spoiler about that - However his father is still alive (for now), in an underground cell in Hermes (The capitol of the church). A fanatic was made to be a fake king got sent back in his place, ordered the succession games, and eventually killed himself. All to guarantee civil war in the world's strongest nation.
It is the church. Remember what that shitty pope said to archbishop mayne new chemical weapon? This it. Crazy bastatd I tell ya.My prediction: disease is actually experimental poison developed by the church and the nobles decided it was time to get rid of some refugees
Or fuck it all just blame a witch lol