A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells
Leonid Andronov, Mengting Han, Ashwin Balaji, Yanyu Zhu, Lei S Qi, W E Moerner
doi:10.1101/2025.08.15.670620
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.
Confocal image analysis Image processing was performed in Fiji (ImageJ). Projections of adjacent Z planes showing maximum loci fluorescence were generated. For conditions 1 and 2 in Figure S4A , the number of infected cells and total cells were both manually counted using the "multi-point" function in Fiji. For condition 3, the number of infected cells was manually counted. Each field of view has several hundred cells in condition 3. To count the total number of cells, a Gaussian blur filter with sigma = 3.5 pixels was first applied to blur the fluorescence image of nsp4 and nsp5. The following functions in Fiji "Image->Adjust->Threshold", "Process->Binary->Fill Holes", "Analyze->Analyze particles" were sequentially performed to measure the cell number, with the size threshold set to greater than 30 µm 2 . The infection ratio was calculated using the number of infected cells divided by the total number of cells in each condition. Statistical analysis was performed using one-way ANOVA in GraphPad.
Optical setup for 2D 2-and 3-color SR microscopy 2D 2-and 3-color (d)STORM SR imaging was performed on a custom-built microscope 5 , using a Nikon Diaphot 200 inverted frame with an oil-immersion objective 60x/1.35 NA (Olympus UPLSAPO60XO) and a Si EMCCD camera (Andor iXon Ultra 897, 512×512 pixels). The sample was mounted on two stacked piezo stages (coarse U-780.DOS and fine P-545.3C8S, both Physik Instrumente). A 642 nm..
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"abstract": "<jats:title>Abstract</jats:title>\n <jats:p>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.</jats:p>",
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