First you should check at what stage of turn resolution sequence does message about decease appear.
If it comes at spellcasting stage with message like: "Suddenly cloud of death appeared bla bla bla" - it's Leprocy Spell, D5, Thau6 in CBM.
If message: "deadly disease is spreading in province bla bla bla" appears after all actions are taken - it's an enemy stealthy commander with reaper ability or bane venom charm item in your province or magic site which spreads disease.
You can learn about magic sites spreading decease in Edi's Database
here.