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

Bamford, C. G.G. et al. (2022) Comparison of SARS-CoV-2 evolution in paediatric primary airway epithelial cell cultures compared with vero-derived cell lines. Viruses, 14(2), e325. (doi: 10.3390/v14020325) (PMID:35215919) (PMCID:PMC8877208)

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 two passages. Within isolates, SARS-CoV-2 evolution was dependent on host cells, with paediatric WD-PNECs showing a reduced diversity compared to Vero (E6) 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 (E6) 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.

• Item Type: Articles
• Additional Information: Funding from UKRI/NIHR (MC_PC_19057) to U.F.P. and K.M.; PHA HSCNI R&D Division (COM/5613/20) to U.F.P., K.M., L.B., C.G.G.B. and G.L.C.; Wellcome Trust (108818/Z/15/B) to the Breathing Together consortium; and generous donations from the public to the Queen’s University of Belfast Foundation were used for the study.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Aranday-Cortes, Dr Elihu and Bamford, Dr Connor

Creator Roles

Bamford, C.: Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing
Aranday-Cortes, E.: Formal analysis, Writing – review and editing

• Authors: Bamford, C. G.G., Broadbent, L., Aranday-Cortes, E., McCabe, M., McKenna, J., Courtney, D. G., Touzelet, O., Ali, A., Roberts, G., Lopez Campos, G., Simpson, D., McCaughey, C., Fairley, D., Mills, K., and Power, U. F.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Viruses
• Publisher: MDPI
• ISSN: 1999-4915
• ISSN (Online): 1999-4915
• First Published: First published in Viruses 14(2):e325