Integrative imaging reveals SARS-CoV-2 induced reshaping of subcellular morphologies. Cortese et al.

In this study we combined light and electron microscopy imaging to determine the morphological organelle alterations induced by SARS-CoV-2 infection in lung epithelial cells. SARS-CoV-2, similar to other positive-strand RNA virus, replicates its genome in specialized virus-induced compartments called viral "replication organelles" (ROs). Additionally, ROs allow for enrichment of metabolites, viral enzymes and cofactors, and protect the viral RNA from degradation and sensing by pattern recognition receptors of the innate immune system. Double-membrane vesicles (DMVs) are the most abundant structure constituting coronaviral ROs. Whole cell 3D analysis of infected cells, generated through focus-ion beam scanning electron microscopy, revealed a network of DMVs embedded in an ER matrix (MOVIE S1). High-throughput electron microscopy allowed defining the 3D architecture of SARS-CoV-2 ROs (MOVIE S2, S3, S4) and their association with cellular organelles, such as mitochondria, peroxisomes, the Golgi apparatus and the cytoskeleton (MOVIE S5). In addition, super-resolution microscopy and live cell imaging shows how the cytoskeleton network is remodeled during the course of infection, forming a cage-like structure that surrounds the ROs (MOVIE S6 and S7). Pharmacological inhibition of cytoskeleton dynamics strongly impairs SARS-CoV-2 replication and virus particle secretion.