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

Abstract

The ongoing SARS-CoV-2 pandemic has brought an urgent need for animal models to study the pathogenicity of the virus. Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. Particularly, this model exhibits age and gender related skewed distribution of mortality akin to severe COVID-19, and the 50% lethal dose (LD50) of MASCp36 was ~100 PFU in aged, male BALB/c mice. Deep sequencing identified three amino acid mutations, N501Y, Q493H, and K417N, subsequently emerged at the receptor binding domain (RBD) of MASCp36, which significantly enhanced the binding affinity to its endogenous receptor, mouse ACE2 (mACE2). Cryo-electron microscopy (cryo-EM) analysis of mACE2 in complex with the RBD of MASCp36 at 3.7-angstrom resolution elucidates molecular basis for the receptor-binding switch driven by amino acid substitutions. Our study not only provides a robust platform for studying the pathogenesis of severe COVID-19 and rapid evaluation of coutermeasures against SARS-CoV-2, but also unveils the molecular mechanism for the rapid adaption and evolution of SARS-CoV-2 in mice.

Variants with the N501Y mutation extend SARS-CoV-2 host range to mice, with contact transmission

“…However, other changes among the constellations defining the VOC lineages might also play a role in the resulting in vivo phenotype. Indeed, the mouse-adapted variants reported by Gu et al 10 and later Sun et al 19 induced pathological and inflammation features that were not observed here, and were also associated with genetic changes outside of the spike. Further studies are needed to dissect the combinatory role of the mutations defining the SARS-CoV-2 VOCs.…”

SARS-CoV-2 variants resist antibody neutralization and broaden host ACE2 usage

“…4, the three variants UK501Y.V1, SA501Y.V2, and BR501Y.V3 gained substantial ability to infect HeLa mouse-ACE2, which correlated with those pseudoviruses bearing single (K417N, K417T, E484K, and N501Y) and triple (K417N-E484K-N501Y) mutations. This agrees well with the recent reports where either single N501Y or triple K417N-Q493H-N501Y mutations were found in the mouse-adapted SARS-CoV-2 strains, although the triple mutant causes more severe acute respiratory symptoms and mortality in standard laboratory mice ( 50, 51 ). Single N501Y mutation found in UK501Y.V1 and two of three (K417N and N501Y) found in SA501Y.V2 and BR501Y.V3 therefore likely enhanced the binding to mouse ACE2 thereby improved entry efficiency into HeLa mouse-ACE2.…”

“…S4). This finding indicates that N501Y plays a role in enhanced binding, which is consistent with earlier reports on both human and mouse ACE2 ( 39, 40, 50, 51 ). The single K417N mutation, however, decreased ACE2 binding by about 6.4-fold.…”

ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions

“…The N501Y mutation in the RBD is predicted to generate new interactions between Y501 with mACE2-H353, and new polar interactions between Y501 and hACE2-K353 (Figure 1F). Our modeling supports the observation that viruses with K417N and N501Y mutations have increased affinity for mACE2, with both appearing in mouse-adapted SARS-CoV-2 (41).…”