The present invention provides recombinant poxviruses, such as vaccinia virus, that contain an integrated exogenous sequence, such as a foreign gene, encoding a prodrug converting polypeptide that can convert a prodrug to a drug that prevents virus replication or is otherwise toxic to the virus. The recombinant poxviruses can be suitable for use as vaccines. The invention also provides, among other things, methods of inhibiting virus replication, methods of vaccination and methods of treating vaccinated subjects showing signs or otherwise at risk for of vaccination-induced disease.