ABSTRACT

SARS-CoV-2 B.1.1.529.1 (Omicron BA.1) emerged in November 2021 and quickly became the predominant circulating SARS-CoV-2 variant globally. Omicron BA.1 contains more than 30 mutations in the spike protein, which contribute to its altered virological features when compared to the ancestral SARS-CoV-2 or previous SARS-CoV-2 variants. Recent studies by us and others demonstrated that Omicron BA.1 is less dependent on transmembrane serine protease 2 (TMPRSS2), less efficient in spike cleavage, less fusogenic, and adopts an altered propensity to utilize the plasma membrane and endosomal pathways for virus entry. Ongoing studies suggest that these virological features of Omicron BA.1 are in part retained by the subsequent Omicron sublineages. However, the exact spike determinants that contribute to these altered features of Omicron remain incompletely understood. In this study, we investigated the spike determinants for the observed virological characteristics of Omicron. By screening for the individual changes on Omicron BA.1 and BA.2 spike, we identify that 69–70 deletion, E484A, and H655Y contribute to the reduced TMPRSS2 usage while 25–27 deletion, S375F, and T376A result in less efficient spike cleavage. Among the shared spike mutations of BA.1 and BA.2, S375F and H655Y reduce spike-mediated fusogenicity. Interestingly, the H655Y change consistently reduces serine protease usage while increases the use of endosomal proteases. In keeping with these findings, the H655Y substitution alone reduces plasma membrane entry and facilitates endosomal entry when compared to SARS-CoV-2 WT. Overall, our study identifies key changes in Omicron spike that contributes to our understanding on the virological determinant and pathogenicity of Omicron.

 抽象的

SARS-CoV-2 B.1.1.529.1 (Omicron BA.1) 于 2021 年 11 月出现，并迅速成为全球主要传播的 SARS-CoV-2 变种。 Omicron BA.1 的刺突蛋白含有 30 多个突变，与祖先 SARS-CoV-2 或之前的 SARS-CoV-2 变体相比，这导致其病毒学特征发生改变。我们和其他人最近的研究表明，Omicron BA.1 对跨膜丝氨酸蛋白酶 2 (TMPRSS2) 的依赖性较低，刺突裂解效率较低，融合性较低，并且采用改变的利用质膜和内体途径进行病毒进入的倾向。正在进行的研究表明，Omicron BA.1 的这些病毒学特征部分被随后的 Omicron 亚系保留。然而，导致 Omicron 这些特征改变的确切尖峰决定因素仍未完全了解。在这项研究中，我们研究了观察到的 Omicron 病毒学特征的尖峰决定因素。通过筛选 Omicron BA.1 和 BA.2 尖峰的个体变化，我们发现 69-70 缺失、E484A 和 H655Y 导致 TMPRSS2 使用量减少，而 25-27 缺失、S375F 和 T376A 导致尖峰效率降低分裂。在 BA.1 和 BA.2 共有的刺突突变中，S375F 和 H655Y 降低了刺突介导的融合性。有趣的是，H655Y 的变化持续减少了丝氨酸蛋白酶的使用，同时增加了内体蛋白酶的使用。与这些发现一致，与 SARS-CoV-2 WT 相比，单独的 H655Y 取代可减少质膜进入并促进内体进入。总体而言，我们的研究确定了 Omicron 尖峰的关键变化，这有助于我们了解 Omicron 的病毒学决定因素和致病性。