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SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-Modal Multi-Scale Cryo-Imaging

44 Pages Posted: 8 Dec 2020 Publication Status: Review Complete

See all articles by Luiza Mendonça

Luiza Mendonça

University of Oxford - Division of Structural Biology

Andrew Howe

Diamond Light Source, Harwell Science and Innovation Campus

James B. Gilchrist

Diamond Light Source, Harwell Science and Innovation Campus

Dapeng Sun

University of Oxford - Division of Structural Biology

Michael L. Knight

University of Oxford - Sir William Dunn School of Pathology

Laura C. Zanetti-Domingues

Rutherford Appleton Laboratory - Central Laser Facility

Benji Bateman

Rutherford Appleton Laboratory - Central Laser Facility

Anna-Sophia Krebs

University of Oxford - Division of Structural Biology

Long Chen

University of Oxford - Division of Structural Biology

Julika Radecke

Diamond Light Source, Harwell Science and Innovation Campus

Yuewen Sheng

Diamond Light Source, Harwell Science and Innovation Campus

Vivian D. Li

University of Cambridge - Murray Edwards College

Tao Ni

University of Oxford - Division of Structural Biology

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 - Central Laser Facility

Maria Harkiolaki

Diamond Light Source, Harwell Science and Innovation Campus

Marisa L. Martin-Fernandez

Rutherford Appleton Laboratory - Central Laser Facility

William James

University of Oxford - Sir William Dunn School of Pathology

Peijun Zhang

University of Oxford - Division of Structural Biology

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Abstract

Understanding the genome replication, assembly and egress of SARS-CoV-2, a multistage process that involves different cellular compartments and the activity of many viral and cellular proteins, is critically important as it bears the means of medical intervention to stop infection. However, there is a lack of comprehensive knowledge on SARS-CoV-2 replicative cycle. Here, we investigated SARS-CoV-2 replication in the native cellular context using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging with cryo-electron tomography (cryoET) and subtomogram averaging. Our results reveal not only profound cytopathic effects of SARS-CoV-2 infection at the whole cell level, exemplified by the formation of membrane tunnels through which viruses exit and drastic cytoplasm invasion into nucleus, but also novel processes of SASR-CoV-2 assembly, budding and egress. The integration of multi-scale cryo-imaging data has led us to propose a model for SARS-CoV-2 replication pathway.

Funding Statement: This research was supported by the National Institutes of Health grant P50AI150481, the UK Wellcome Trust Investigator Award 206422/Z/17/Z, the UK Biotechnology and Biological Sciences Research Council grant BB/S003339/1, and the grant from the Chinese Academy of Medical Sciences Oxford Institute. Containment level 3 experiments were funded through the generous support of philanthropic donors to the University of Oxford’s COVID-19 Research Response Fund. M.L.K. is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/M011224/1).

Declaration of Interests: The authors declare no competing interests.

Keywords: SARS-CoV-2, COVID-19, CryoEM, cryoET, subtomogram averaging, cryoFIB/SEM, soft X-ray cryo-tomography, virus assembly, viral egress, spike

Suggested Citation

Mendonça, Luiza and Howe, Andrew and Gilchrist, James B. and Sun, Dapeng and Knight, Michael L. and Zanetti-Domingues, Laura C. and Bateman, Benji and Krebs, Anna-Sophia and Chen, Long and Radecke, Julika and Sheng, Yuewen and Li, Vivian D. and Ni, Tao and Kounatidis, Ilias and Koronfel, Mohamed A. and Szynkiewicz, Marta and Harkiolaki, Maria and Martin-Fernandez, Marisa L. and James, William and Zhang, Peijun, SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-Modal Multi-Scale Cryo-Imaging. Available at SSRN: https://ssrn.com/abstract=3733984 or http://dx.doi.org/10.2139/ssrn.3733984
This version of the paper has not been formally peer reviewed.

Luiza Mendonça

University of Oxford - Division of Structural Biology ( email )

United Kingdom

Andrew Howe

Diamond Light Source, Harwell Science and Innovation Campus

Oxfordshire
United Kingdom

James B. Gilchrist

Diamond Light Source, Harwell Science and Innovation Campus ( email )

United Kingdom

Dapeng Sun

University of Oxford - Division of Structural Biology

United Kingdom

Michael L. Knight

University of Oxford - Sir William Dunn School of Pathology

South Parks Road
Oxford, OX1 3RE
United Kingdom

Laura C. Zanetti-Domingues

Rutherford Appleton Laboratory - Central Laser Facility ( email )

Chilton, Didcot, Oxfordshire
England, England OX11 OQX
United Kingdom

Benji Bateman

Rutherford Appleton Laboratory - Central Laser Facility ( email )

Chilton, Didcot, Oxfordshire
England, England OX11 OQX
United Kingdom

Anna-Sophia Krebs

University of Oxford - Division of Structural Biology ( email )

United Kingdom

Long Chen

University of Oxford - Division of Structural Biology

United Kingdom

Julika Radecke

Diamond Light Source, Harwell Science and Innovation Campus

United Kingdom

Yuewen Sheng

Diamond Light Source, Harwell Science and Innovation Campus ( email )

United Kingdom

Vivian D. Li

University of Cambridge - Murray Edwards College

Cambridge
United Kingdom

Tao Ni

University of Oxford - Division of Structural Biology

United Kingdom

Ilias Kounatidis

Diamond Light Source, Harwell Science and Innovation Campus ( email )

United Kingdom

Mohamed A. Koronfel

Diamond Light Source, Harwell Science and Innovation Campus ( email )

United Kingdom

Marta Szynkiewicz

Rutherford Appleton Laboratory - Central Laser Facility ( email )

Chilton, Didcot, Oxfordshire
England, England OX11 OQX
United Kingdom

Maria Harkiolaki

Diamond Light Source, Harwell Science and Innovation Campus ( email )

United Kingdom

Marisa L. Martin-Fernandez

Rutherford Appleton Laboratory - Central Laser Facility ( email )

Chilton, Didcot, Oxfordshire
England, England OX11 OQX
United Kingdom

William James

University of Oxford - Sir William Dunn School of Pathology

South Parks Road
Oxford, OX1 3RE
United Kingdom

Peijun Zhang (Contact Author)

University of Oxford - Division of Structural Biology ( email )

United Kingdom

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