Labeling and Localization Strategies for In Situ Cryo-Electron Tomography Across the Viral Life Cycle

Cryo-electron tomography (Cryo-ET) has emerged as a transformative tool for visualizing viral components within their native cellular environment, enabling structural interrogation of viral life cycle events at nanometer resolution without chemical fixation or heavy metal staining. However, a persistent challenge in applying Cryo-ET to virus research is the unambiguous identification of specific viral components within densely crowded tomographic volumes. Electron density encodes mass and shape but not molecular identity, and as the cellular environment grows more complex, the assumption that a given density has no plausible alternative assignment becomes increasingly difficult to defend. This review surveys labeling and localization strategies for in situ Cryo-ET of viral components, encompassing label-free exploitation of native electron density, Cryo-immunogold labeling, genetically encoded and synthetic molecular tags, and correlative Cryo-light/electron microscopy (Cryo-CLEM) combined with Cryo-focused ion beam (Cryo-FIB) milling. We first summarize the landmark structural discoveries that in situ Cryo-ET has delivered across virus families, and then evaluate each labeling strategy against the structural and functional constraints that viral proteins impose, providing a practical framework for matching a labeling approach to a specific viral component and life-cycle stage.