Affective polarization is a defining feature of 21st century American politics—partisans harbor considerable dislike and distrust of those from the other party. Does this animus have consequences for citizens’ opinions? Such effects would highlight not only the consequences of polarization, but also shed new light onto how citizens form preferences more generally. Normally, this question is intractable, but the outbreak of the novel coronavirus allows us to answer it. We find that affective polarization powerfully shapes citizens’ attitudes about the pandemic, as well as the actions they have taken in response to it. However, these effects are conditional on the local severity of the outbreak, as the effects decline in areas with high caseloads—threat vitiates partisan reasoning. Our results clarify that closing the divide on important issues requires not just policy discourse but also attempts to reduce inter-partisan hostility.