Omicron evolution drives increased ciliated cell tropism and dysfunction in nasal epithelia

SARS-CoV-2 Omicron variants demonstrate greater replication efficiency in the upper respiratory tract than both ancestral virus and Delta variant, potentially due to stronger interactions with motile cilia in human nasal epithelial cells. Despite the emergence of numerous Omicron variants, such as BA.1, BA.5, and XBB, there has been no comprehensive investigation comparing their specific interactions with ciliated cells. Here, we use differentiated primary human nasal epithelial cell (NEC) cultures to compare an ancestral isolate (QLD02) to Omicron variants BA.1, BA.5 and XBB. Transcriptomic analysis revealed that BA.5 and XBB infection, unlike BA.1 and QLD02, drives a distinct host response, defined by the profound downregulation of genes essential for cilium assembly and function at 48-hours post-infection. The BA.5 and XBB signature was also characterized by the strong upregulation of pro-apoptotic and inflammatory pathways. Immunofluorescence (IF) of nucleocapsid-positive cells in NECs showed a significant 13-fold increase for BA.5 and 9-fold increase for BA.1 relative to QLD02. Additionally, BA.1 and BA.5 exhibited greater tropism (7.6-fold for BA.1, 9-fold for BA.5) for ciliated cells compared to QLD02. Finally, while BA.5 and BA.1 infection was associated with widespread apoptosis in both infected and bystander cells, the total number of ciliated cells remained unchanged. Overall, we demonstrate a stepwise evolution at the nasal barrier: while enhanced ciliated cell tropism and widespread apoptosis is a conserved feature of Omicron infection, transcriptional ciliary dysfunction is a distinct phenotype emerging with BA.5 and preserved in the XBB variant.