A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells

The spatial organization of viral and host components dictates the course of infection, yet the nanoscale architecture of the SARS-CoV-2 life cycle remains largely uncharted. Here, we present a comprehensive super-resolution Atlas of SARS-CoV-2 infection, systematically mapping the localization of nearly all viral proteins and RNAs in human cells. This resource reveals that the viral main protease, nsp5, localizes to the interior of double-membrane vesicles (DMVs), challenging existing models and suggesting that polyprotein processing is a terminal step in replication organelle maturation. We identify previously undescribed features of the infection landscape, including thin dsRNA “connectors” that physically link DMVs, and large, membrane-less dsRNA granules decorated with replicase components, reminiscent of viroplasms. Finally, we show that the antiviral drug nirmatrelvir induces the formation of persistent, multi-layered bodies of uncleaved polyproteins. This spatial Atlas provides a foundational resource for understanding coronavirus biology and offers crucial insights into viral replication, assembly, and antiviral mechanisms.