Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress

Luiza Mendonça, Andrew Howe, James B. Gilchrist, Yuewen Sheng, Dapeng Sun, Michael L. Knight, Laura C. Zanetti-Domingues, Benji Bateman, Anna-Sophia Krebs, Long Chen, Julika Radecke, Vivian D. Li, Tao Ni, Ilias Kounatidis, Mohamed A. Koronfel, Marta Szynkiewicz, Maria Harkiolaki, Marisa L. Martin-Fernandez, William James and Peijun Zhang ()
Additional contact information
Luiza Mendonça: University of Oxford
Andrew Howe: Diamond Light Source, Harwell Science and Innovation Campus
James B. Gilchrist: Diamond Light Source, Harwell Science and Innovation Campus
Yuewen Sheng: Diamond Light Source, Harwell Science and Innovation Campus
Dapeng Sun: University of Pittsburgh, Pittsburgh
Michael L. Knight: University of Oxford
Laura C. Zanetti-Domingues: Rutherford Appleton Laboratory
Benji Bateman: Rutherford Appleton Laboratory
Anna-Sophia Krebs: University of Oxford
Long Chen: University of Oxford
Julika Radecke: Diamond Light Source, Harwell Science and Innovation Campus
Vivian D. Li: University of Cambridge
Tao Ni: University of Oxford
Ilias Kounatidis: Diamond Light Source, Harwell Science and Innovation Campus
Mohamed A. Koronfel: Diamond Light Source, Harwell Science and Innovation Campus
Marta Szynkiewicz: Rutherford Appleton Laboratory
Maria Harkiolaki: Diamond Light Source, Harwell Science and Innovation Campus
Marisa L. Martin-Fernandez: Rutherford Appleton Laboratory
William James: University of Oxford
Peijun Zhang: University of Oxford

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-021-24887-y

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