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.