Comparison of SARS-CoV-2 evolution in paediatric primary airway epithelial cell cultures compared with Vero-derived cell lines

Connor Bamford*, Lindsay Broadbent, Elihu Aranday-Cortes, Mary McCabe, James McKenna, David Courtney, Olivier Touzelet, Ahlam Ali, Grace C Roberts, Guillermo Lopez Campos, David Simpson, Conall McCaughey, Derek Fairley, Ken Mills, Breathing Together Investigators, Ultan Power*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

SARS-CoV-2 can efficiently infect both children and adults albeit with morbidity and mortality positively associated with increasing host age and presence of co-morbidities. SARS-CoV-2 continues to adapt to the human population, resulting in several ‘variants of concern’ (VOC) with novel properties, such as ‘Alpha’ and ‘Delta’. However, factors driving SARS-CoV-2 fitness and evolution in paediatric cohorts remain poorly explored. Here, we provide evidence that both viral and host factors co-operate to shape SARS-CoV-2 genotypic and phenotypic change in primary airway cell cultures derived from children. Through viral whole genome sequencing, we explored changes in genetic diversity over time of two pre-VOC clinical isolates of SARS CoV-2 during passage in paediatric well-differentiated primary nasal epithelial cell (WD-PNEC) cultures and in parallel, in unmodified Vero-derived cell lines. We identified a consistent, rich genetic diversity arising in vitro, variants of which could rapidly rise to near fixation within 2 passages Within isolates, SARS-CoV-2 evolution was dependent on host cells, with paediatric WD-PNECs showing a reduced diversity compared to Vero cells. However, mutations were not shared between strains. Furthermore, comparison of both Vero-grown isolates on WD-PNECs disclosed marked growth attenuation mapping to the loss of the polybasic cleavage site (PBCS) in Spike, while the strain with mutations in Nsp12 (T293I), Spike (P812R) and a truncation of Orf7a remained viable in WD-PNECs. Altogether, our work demonstrates that pre-VOC SARS-CoV-2 efficiently infects paediatric respiratory epithelial cells, and its evolution is restrained compared to Vero cells, similar to the case of adult cells. We highlight the significant genetic plasticity of SARS-CoV-2 while uncovering an influential role for collaboration between viral and host cell factors in shaping viral evolution and ultimately fitness in human respiratory epithelium.
Original languageEnglish
JournalViruses
Early online date05 Feb 2022
DOIs
Publication statusEarly online date - 05 Feb 2022

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