Long-term Effects of SARS-CoV-2 on Ciliary Function and Ciliogenesis

Abstract

Introduction: Cilia are critically important in the mucociliary clearance of the airways. This study explored long-term effects of SARS-CoV-2 on ciliary regeneration and function.

Aim: We aimed to investigate respiratory epithelial recovery and ciliary function in individuals 3-12 months post SARS-CoV-2 infection.

Methods: Three post-COVID cohorts; the first of which (FOLLOW n=41) underwent nasal epithelial cell sampling 3-12 months after the first waves of SARS-CoV-2 infection in both hospitalised and community settings, and self reported Long-COVID symptoms were recorded. The second cohort, (ULTRON n=15) contained patients 3-12 months post-Omicron variant infection, all of whom were vaccinated; the third cohort (PROSAIC n=46) had RNA extracted from nasal brushings 6-12 months after recovery from severe infection with the pre-omicron variant of SARS-CoV-2. In the first two cohorts, ciliary function was assessed using high-speed-video-microscopy, with ultrastructural analysis assessed by Transmission Electron Microscopy. Expression of the ciliogenesis gene, FOXJ1, was measured by qRT-PCR in the third cohort. Additionally data of other virus and bacterial positive nasal brushings were analysed to ascertain the effect of a multitude of other infections on cilia function to contextualise post-COVID’s effect on cilia.

Results: There was significant ciliary dysfunction eithin early pandemic SARS-CoV-2 patients, persisting up to a year post-infection. 90% of individuals had ultrastructural defects, marked by mislocalised basal bodies and intracytoplasmic cilia up to 12 months post infection; without correlations with any long-term COVID-19 symptoms. With post-Omicron infected, vaccinated cohort, ciliogenesis was normal, and no mislocalised basal bodies nor intracytoplasmic cilia were seen. Across cohorts, defects in cilia function were present compared to pre-pandemic controls: Reduced cilia beat frequency (FOLLOW p<0.01), reduced amplitude per second: (FOLLOW p<0.01, ULTRON p<0.01). Foxj1 expression post-COVID was significantly reduced 6 months (p<0.001) and 12 months (p=0.002) within pre-omicron-variant infection, compared with healthy volunteers, with some recovery of Foxj1 mRNA at 12-months. A Clinical cohort investigated for primary ciliary dyskinesia and found to be PCD-Negative showed no ciliary defects from other viral/bacterial infections.

Conclusion: Persistent cilia loss, and ciliogenesis defects post COVID are explained by a reduction in FOXJ1 gene expression, affecting ciliogenesis and ciliary function. There are differences observed between early and Post-Omicron infections, with vaccinated individuals being less affected, although some cilia impairments persist. There is a long-term cilia movement restriction following SARS-CoV-2, and specific to infections 2020-2021, is a decreased cilia beat frequency. Exploring the virus’s long-term effects on gene expression is merited, and understanding the viral kinetics of FOXJ1 expression may shed light on how this is impaired, and provide insights into Long-COVID clinical manifestations.

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DOI

https://dx.doi.org/10.15132/20000550

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https://discovery.dundee.ac.uk/en/studentTheses/8265790b-1a05-4c73-a1df-aa4064306377