In situ structures of membrane-assisted assembly and selective autophagy of enteroviruses

Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome replication. New virions are thought to be assembled near the genome replication sites and are released in vesicles through secretory autophagy. Here, we use cryo-electron tomography to show that poliovirus assembles directly on replication membranes. Assembly progression beyond a membrane-bound half-capsid intermediate requires the host lipid kinase VPS34, whereas inhibition of ULK1, the initiator of canonical autophagy, leads to accumulation of virions in vast intracellular arrays followed by an increased release at later time points. We further identify multiple layers of selectivity in virus-induced autophagy, with a strong selection for RNA-loaded virions over empty capsids and the segregation of virions from a second class of autophagic membranes containing protein filaments bundles. These findings provide an integrated structural framework for multiple stages of the poliovirus life cycle.