Scanning Transmission Electron Microscopy Tomography in Virology: 3D Imaging of High-pressure Frozen,...

Electron microscopy (EM) and especially three-dimensional (3D) EM techniques have become established methods in structural virology. Investigation of virus-induced alteration of the cellular ultrastructure, such as Zika virus (ZIKV)-induced replication factories or coronavirus replication organelles, demands 3D imaging. Transmission electron microscopy (TEM) tomography is a widely used method, despite its limitation to samples with a thickness of up to 200 nm. Focused ion beam-scanning electron microscopy (SEM)-tomography can produce 3D data of larger volumes with isotropic, albeit typically lower resolution. Alternative techniques, such as block face-scanning electron microscopy (BF-SEM), SEM array tomography, or TEM imaging of serial sections are used for imaging of larger volumes. However, compared to the previously mentioned techniques, these techniques come at the cost of much lower resolution along the Z-axis of the sample. A technique that provides 3D information of samples up to 1 µm thickness with isotropic resolution of a few nanometers is scanning transmission electron microscopy (STEM) tomography. Here, we present a protocol for the preparation of high-pressure frozen, freeze-substituted, and resin-embedded virological specimens and their analysis using STEM tomography. This protocol benefits from the advantages of room temperature imaging while preserving the biological ultrastructure in a near-native state. We show two representative examples for questions that can be answered using STEM tomography. First, we apply the protocol for studying virion morphogenesis of a recombinant vesicular stomatitis virus (VSV). The STEM tomograms offer information on recombinant VSV budding that is otherwise not accessible by 2D imaging. Second, we show correlative light and electron microscopy (CLEM) using Foerster resonance energy transfer (FRET) imaging and STEM tomography (FRET-3D-CLEM) of EF-C peptide nanofibrils. This recently published combination gives new insights into the uptake and disassembly of infection-enhancing peptide nanofibrils, especially profiting from the large volume that is accessible by STEM tomography.