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

doi:10.3390/v14020325

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

School of Medicine, Dentistry and Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

85 Downloads (Pure)

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 language	English
Journal	Viruses
Early online date	05 Feb 2022
DOIs	https://doi.org/10.3390/v14020325
Publication status	Early online date - 05 Feb 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.3390/v14020325Licence: CC BY

Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
Copyright 2022 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Final published version, 1.67 MBLicence: CC BY

Cite this

Bamford, C., Broadbent, L., Aranday-Cortes, E., McCabe, M., McKenna, J., Courtney, D., Touzelet, O., Ali, A., Roberts, G. C., Lopez Campos, G., Simpson, D., McCaughey, C., Fairley, D., Mills, K., Investigators, B. T., & Power, U. (2022). Comparison of SARS-CoV-2 evolution in paediatric primary airway epithelial cell cultures compared with Vero-derived cell lines. Viruses. https://doi.org/10.3390/v14020325

@article{94fc7dd8d09848c08a1447890eb3163f,

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

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 {\textquoteleft}variants of concern{\textquoteright} (VOC) with novel properties, such as {\textquoteleft}Alpha{\textquoteright} and {\textquoteleft}Delta{\textquoteright}. 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.",

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

year = "2022",

month = feb,

day = "5",

doi = "10.3390/v14020325",

language = "English",

journal = "Viruses",

issn = "1999-4915",

publisher = "Multidisciplinary Digital Publishing Institute",

}

Bamford, C, Broadbent, L, Aranday-Cortes, E, McCabe, M, McKenna, J, Courtney, D , Touzelet, O , Ali, A, Roberts, GC, Lopez Campos, G , Simpson, D, McCaughey, C, Fairley, D, Mills, K, Investigators, BT & Power, U 2022, 'Comparison of SARS-CoV-2 evolution in paediatric primary airway epithelial cell cultures compared with Vero-derived cell lines', Viruses. https://doi.org/10.3390/v14020325

TY - JOUR

T1 - Comparison of SARS-CoV-2 evolution in paediatric primary airway epithelial cell cultures compared with Vero-derived cell lines

AU - Bamford, Connor

AU - Broadbent, Lindsay

AU - Aranday-Cortes, Elihu

AU - McCabe, Mary

AU - McKenna, James

AU - Courtney, David

AU - Touzelet, Olivier

AU - Ali, Ahlam

AU - Roberts, Grace C

AU - Lopez Campos, Guillermo

AU - Simpson, David

AU - McCaughey, Conall

AU - Fairley, Derek

AU - Mills, Ken

AU - Investigators, Breathing Together

AU - Power, Ultan

PY - 2022/2/5

Y1 - 2022/2/5

N2 - 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.

AB - 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.

U2 - 10.3390/v14020325

DO - 10.3390/v14020325

M3 - Article

JO - Viruses

JF - Viruses

SN - 1999-4915

ER -

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

Abstract

UN SDGs

Access to Document

Fingerprint

Cite this