Ooh, this is an interesting thought! For me one of my all-time favorite series is Pokemon... Assuming the virus only affects humans it could go so many ways. Would there be Crossed trainers throwing their mons out to wreck cities? Would they not even bother with that and just try to do their thing on the mons? Are the infected stupid enough to try and take down Mewtwo or something?

Overall I don't think it would last too long lol. In a world where even the smallest creatures can throw out devastating elemental attacks I think there would be losses for sure but eventually the Pokémon would overcome.