FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist

The visualization of cellular ultrastructure over a wide range of volumes is becoming possible by increasingly powerful techniques grouped under the rubric volume electron microscopy or volume EM (vEM). Focused ion beam scanning electron microscopy (FIB-SEM) occupies a Goldilocks zone in vEM: iterative and automated cycles of milling and imaging allow the interrogation of microns-thick specimens in 3-D at resolutions of tens of nanometers or less. This bestows on FIB-SEM the unique ability to aid the accurate and precise study of architectures of virus-cell interactions. Here we give the virologist or cell biologist a primer on FIB-SEM imaging in the context of vEM and discuss practical aspects of a room temperature FIB-SEM experiment. In an in vitro study of SARS-CoV-2 infection, we show that accurate quantitation of viral densities and surface curvatures enabled by FIB-SEM imaging reveals SARS-CoV-2 viruses preferentially located at areas of plasma membrane that have positive mean curvatures.

Automated summary

Volume electron microscopy techniques make visualizing cellular ultrastructure across different volumes possible, with focused ion beam scanning electron microscopy (FIB-SEM) being a key method for studying virus-cell interactions due to its unique capabilities in high-resolution 3-D imaging. In a study on SARS-CoV-2 infection, FIB-SEM imaging enabled accurate quantification of viral densities and surface curvatures, showing the viruses' preference for areas of positive mean curvatures on the plasma membrane.