Supporting data for Investigation on the Virological Characteristics of SARS-CoV-2 Omicron

Since the emergence of Omicron subvariants, the BA.1, BA.2, and BA.5 lineages and their related sublineages have been implicated in most infections. Although there is evidence that all Omicron sublineages can significantly evade the neutralizing antibody response, it is still unknown if these subvariants share evolutionary patterns with regard to their replication fitness and pathogenicity.In this work, we examined Omicron's virological characteristics by assessing TMPRSS2 usage, spike cleavage, cell-cell fusion, and virus replication and pathogenicity in virto and in vivo. We found that Omicron BA.1 is attenuated compared to ancestral WT and Delta strains in lung tissues of K18-hACE2 mice, and BA.2 is similarly attenuated compared to BA.1. Our data also indicates that BA.5 has replication advantages in the human nasal epithelium and followed by the BA.1 and BA.2.Consistently, BA.5 infected K18-hACE2 mice produce more infectious viral particles in the nasal turbinate. In sharp contrast, omicron sublineages continue to be less pathogenic than the lungs of K18-hACE2 and C57BL/6 mice.To investigate viral determinants of increased fitness of Omicron in the human nasal epithelium,we constructed infectious clones of WT and BA.1 by reverse genetics and found that spike defines the replication advantages of Omicron BA.1 in the nasal epithelium;RBD and SD domains are the minimal factors to contribute to this phenotype. Our study suggested that the Omicron subvariant has gained intrinsic replication fitness in the upper respiratory tract; however, the pathogenicity of Omciron is less severe in the lower respiratory tract. Immunocompromised individuals should be vaccinated and receive other treatments to prohibit serious illness caused by SARS-CoV-2 infection.My dataset contains the raw data of three chapters, each of which is in a separate folder. Within each folder, there are additional subfolders containing the Prism data and images from immunofluorescence. The Prism data and immunofluorescence data correspond directly to the figures in the paper.

自奥密克戎亚变种的问世以来，BA.1、BA.2及BA.5谱系及其相关亚谱系已与大多数感染事件关联。尽管有证据表明所有奥密克戎亚谱系均能显著逃避免疫中和抗体反应，但关于这些亚变体在复制适应性和致病性方面的进化模式是否具有共性，尚未有明确结论。在本研究中，我们通过对TMPRSS2利用、刺突蛋白裂解、细胞间融合以及病毒在体外和体内的复制与致病性进行评估，探究了奥密克戎的病毒学特征。我们发现，与野生型WT和Delta株相比，奥密克戎BA.1在K18-hACE2小鼠肺组织中表现出减弱的致病性，而BA.2与BA.1类似。我们的数据还显示，BA.5在人类鼻腔上皮细胞中具有复制优势，紧随其后的是BA.1和BA.2。与此一致的是，BA.5感染K18-hACE2小鼠的鼻甲部位产生了更多的传染性病毒颗粒。然而，与K18-hACE2和C57BL/6小鼠的肺部相比，奥密克戎亚谱系仍显示出较低的致病性。为探究导致奥密克戎在人类鼻腔上皮细胞中适应性增强的病毒决定因素，我们通过反向遗传学构建了WT和BA.1的感染性克隆，并发现刺突蛋白定义了奥密克戎BA.1在鼻腔上皮细胞中的复制优势；RBD和SD结构域是该表型的最小贡献因素。我们的研究提出，奥密克戎亚变体在呼吸道上段获得了内在的复制适应性；然而，奥密克戎在呼吸道下段的致病性相对较轻。免疫抑制者应接种疫苗并接受其他治疗，以预防由SARS-CoV-2感染引起的严重疾病。我的数据集包含三个章节的原始数据，每个章节的数据存放在独立的文件夹中。在每个文件夹内，还有包含Prism数据和免疫荧光图像的子文件夹。Prism数据和免疫荧光数据直接对应于论文中的图表。