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bioRxiv · 10.1101/2025.11.19.689397

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

Parry, R.·Mostafavi, H.·McCallum, G.·Sng, J. D. J.·Joensuu, M.·Short, K. R.·Slonchak, A.·Khromykh, A.
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Abstract

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, there has been no comprehensive investigation comparing their 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/XBB signature was also characterized by the strong upregulation of pro-apoptotic and inflammatory pathways. Immunofluorescence of nucleocapsid-positive cells in NECs showed a significant 13-fold increase for BA.5 relative to QLD02. Additionally, BA.1 and BA.5 exhibited greater tropism for ciliated cells (7.6-fold for BA.1, 9-fold for BA.5) than QLD02. BA.5 and BA.1 infection were associated with elevated apoptosis in both infected and bystander cells, however, the total number of ciliated cells remained unchanged. Consistent with this, BA.5 infection significantly reduced DNAH5 outer dynein arm protein in the cilia, indicating dysfunction of cilia motility rather than overt cilia loss. Overall, we demonstrate a stepwise evolution at the nasal barrier: while enhanced ciliated cell tropism and elevated apoptosis are conserved features of Omicron infection, ciliary dysfunction, evident at both the transcriptional and protein level, is a more pronounced phenotype emerging with BA.5 and preserved in the XBB variant. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/689397v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@11b1b60org.highwire.dtl.DTLVardef@a25e0borg.highwire.dtl.DTLVardef@1cc3904org.highwire.dtl.DTLVardef@b35447_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Parry, R., Mostafavi, H., McCallum, G., Sng, J. D. J., Joensuu, M., Short, K. R., Slonchak, A., Khromykh, A.. 2025-11-20. Omicron evolution drives increased ciliated cell tropism and dysfunction in nasal epithelia.. https://doi.org/10.1101/2025.11.19.689397

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