Characterizing host–virus associations is critical due to the rising frequency of emerging infectious diseases originating from wildlife. Past analyses have evaluated zoonotic risk as binary, but virulence and transmissibility can vary dramatically. Recent work suggests bats harbor more viruses with high virulence in humans than other taxa. However, it remains unknown whether all bats harbor viruses of equal zoonotic potential. We used phylogenetic factorization to flexibly identify clades of mammals (at any taxonomic level) associated with low or high viral epidemic potential, and found virulence and transmissibility only cluster within bat subclades, often among cosmopolitan families. Mapping the geographic distributions of these bat clades with spatial data on anthropogenic footprint suggests high zoonotic risk in coastal South America, Southeast Asia, and equatorial Africa. Our results deepen understanding of the host– virus network and identify clades to prioritize for viral surveillance, risk mitigation, and future studies characterizing mechanisms of viral tolerance.