A Secret of Birds and Bone - Kiran Millwood Hargrave

In an Italian city ravaged by plague, Sofia's mother carves beautiful mementoes from the bones of loved ones. But one day, she doesn't return home. Did her work lead her into danger? Sofia and her little brother Ermin are sent to the convent orphanage but soon escape, led by an enigmatic new friend and their pet crow, Corvith.

Together they cross the city underground, following clues in bones up to the towers of Siena, where - circled by magpies - the children find the terrible truth…