Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2

Shihui Sun,Rui-Ting Li,Xiangxi Wang,Guan Yang,Xiaopeng Song,Min Li,Rui Feng,Chao Zhou,Yuehong Chen,Xiao Yang,Si Qin,Yifei Zhang ,Xinquan Wang,Hui Wang,Lei Wang,Jun Lei ,Hang Fan,Yu‐Jun Cui ,Yini Qi,Lingna Zhao,Lei Cao,Huiying Gu ,Qing Ye,Na Zhu,Qi Chen,Meng‐Ru Shen ,Wenjie Tan,Yong‐Qiang Deng ,Yan Guo,Cheng‐Feng Qin

doi:10.1038/s41467-021-25903-x

Abstract

There is an urgent need for animal models to study SARS-CoV-2 pathogenicity. Here, we generate and characterize a novel mouse-adapted SARS-CoV-2 strain, MASCp36, that causes severe respiratory symptoms, and mortality. Our model exhibits age- and gender-related mortality akin to severe COVID-19. Deep sequencing identified three amino acid substitutions, N501Y, Q493H, and K417N, at the receptor binding domain (RBD) of MASCp36, during in vivo passaging. All three RBD mutations significantly enhance binding affinity to its endogenous receptor, ACE2. Cryo-electron microscopy analysis of human ACE2 (hACE2), or mouse ACE2 (mACE2), in complex with the RBD of MASCp36, at 3.1 to 3.7 Å resolution, reveals the molecular basis for the receptor-binding switch. N501Y and Q493H enhance the binding affinity to hACE2, whereas triple mutations at N501Y/Q493H/K417N decrease affinity and reduce infectivity of MASCp36. Our study provides a platform for studying SARS-CoV-2 pathogenesis, and unveils the molecular mechanism for its rapid adaptation and evolution.

Highlights

There is an urgent need for animal models to study SARS-CoV-2 pathogenicity
Clinically, the severe COVID-19 disease onset might result in death due to massive alveolar damage and progressive respiratory failure[23,24]
The MASCp36-based mouse model described here recapitulated most spectrums of seriously ill COVID-19 patients caused by SARS-CoV-2 infection, such as pulmonary oedema, fibrin plugs in alveolar, hyaline membrane, and scattered hemorrhage[25,26]

Summary

Introduction

We generate and characterize a novel mouse-adapted SARS-CoV-2 strain, MASCp36, that causes severe respiratory symptoms, and mortality. The symptoms of COVID-19 are similar to those of SARS-CoV and MERS-CoV infections, ranging from fever, fatigue, dry cough and dyspnea, and mild pneumonia to acute lung injury (ALI) and the acute respiratory distress syndrome in severe cases. Mouse-adapted strains of SARS-CoV-2 have been developed via either in vivo passaging or reverse genetics[13,14,15]. Most these models cause only mild to moderate lung damage in mice. Viral genome sequencing, and cryo-EM analysis clearly demonstrated the critical role of the progressively emerged amino acid mutations in the RBD of the mouse-adapted strains at different passages

Methods

Results

Conclusion