Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron entry involves spike (S) glycoprotein-mediated fusion of viral and late endosomal membranes. Here, using single-molecule Förster resonance energy transfer (sm-FRET) imaging and biochemical measurements, we directly visualized conformational changes of individual spike trimers on the surface of SARS-CoV-2 Omicron pseudovirions during fusion activation. We observed that the S2 domain of the Omicron spike is a dynamic fusion machine. S2 reversibly interchanges between the pre-fusion conformation and two previously undescribed intermediate conformations. Acidic pH shifts the conformational equilibrium of S2 toward an intermediate conformation and promotes the membrane hemi-fusion reaction. Moreover, we captured conformational reversibility in the S2 domain, which suggests that spike can protect itself from pre-triggering. Furthermore, we determined that Ca2+ directly promotes the S2 conformational change from an intermediate conformation to post-fusion conformation. In the presence of a target membrane, low pH and Ca2+ stimulate the irreversible transition to S2 post-fusion state and promote membrane fusion.

中文翻译：

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SARS-CoV-2 Omicron 刺突三聚体在单分子分辨率融合激活过程中的构象动力学


严重急性呼吸系统综合症冠状病毒 2 （SARS-CoV-2） 奥密克戎进入涉及病毒和晚期内体膜的刺突 （S） 糖蛋白介导的融合。在这里，使用单分子 Förster 共振能量转移 （sm-FRET） 成像和生化测量，我们直接可视化了 SARS-CoV-2 Omicron 假病毒粒子在融合激活过程中单个刺突三聚体表面的构象变化。我们观察到 Omicron 尖峰的 S2 结构域是一个动态融合机器。S2 在融合前构象和两个先前未描述的中间构象之间可逆地互换。酸性 pH 值使 S2 的构象平衡向中间构象移动，并促进膜半融合反应。此外，我们在 S2 结构域中捕获了构象可逆性，这表明 spike 可以保护自身免受预触发。此外，我们确定 Ca2+ 直接促进 S2 构象从中间构象转变为融合后构象。在存在靶膜的情况下，低 pH 值和 Ca2+ 刺激融合后不可逆地过渡到 S2 状态并促进膜融合。