Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events – e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.

自 SARS-CoV-2 大流行爆发以来，对纯化的病毒成分和灭活的病毒进行了深入的结构研究。然而，关于 SARS-CoV-2 感染如何在天然细胞环境中进展的结构和超微结构证据很少，并且缺乏对 SARS-CoV-2 复制周期的全面了解。为了将 SARS-CoV-2 诱导的细胞病变事件与冷冻水合细胞中的病毒复制过程相关联，我们建立了一个独特的多模式、多尺度低温相关平台来对 Vero 细胞中的 SARS-CoV-2 感染进行成像。该平台将串行 cryoFIB/SEM 体积成像和软 X 射线低温断层扫描与基于细胞薄片的低温电子断层扫描 (cryoET) 和子断层图平均相结合。在这里，我们报告了关键的 SARS-CoV-2 结构事件——例如病毒 RNA 运输门户，病毒组装中间体、病毒出口途径和天然病毒刺突结构，在全细胞体积的背景下显示出剧烈的细胞病变。这种综合方法可以全面了解 SARS-CoV-2 感染，从整个细胞到单个分子。