The Bloody Deluge — Adrian Tchaikovsky

A year ago, civilisation died, drowning and choking on its own blood in the brutal scourge of the Cull.
Eking out a living on the newly primitive land, British-born biochemist Katy Lewkowitz finds a new life as a doctor among the small communities springing up in Eastern Germany... until a terrible new cult, calling itself the 'New Teutonic Order,' begins purging all 'undesirables.'
Katy and her friend and old tutor Dr. Emil Weber, fleeing the depredations of the fanatical Order, escape into Poland, eventually taking refuge among the strangely anachronistic survivors at the monastery of Jasna Góra.
A battle of faith ensues, that could decide the future of humankind...