Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
SARS-CoV-2 continues to evolve, resulting in several ‘variants of concern’ with novel properties. The factors driving SARS-CoV-2 fitness and evolution in the human respiratory tract remain poorly defined. Here, we provide evidence that both viral and host factors co-operate to shape SARS-CoV-2 genotypic and phenotypic change. Through viral whole-genome sequencing, we explored the evolution of two clinical isolates of SARS-CoV-2 during passage in unmodified Vero-derived cell lines and in parallel, in well-differentiated primary nasal epithelial cell (WD-PNEC) cultures. We identify a consistent, rich genetic diversity arising in vitro, variants of which could rapidly rise to near-fixation with 2 passages. Within isolates, SARS-CoV-2 evolution was dependent on host cells, with Vero-derived cells facilitating more profound genetic changes. However, most 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. Our work highlights 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 fitness in human respiratory epithelium.
Article activity feed
-
SciScore for 10.1101/2021.07.16.452629: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: All SARS-CoV-2 work was carried out under BSL3 conditions in a dedicated facility in QUB. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Contamination: Cell lines were routinely tested for mycoplasma contamination and no evidence of contamination was detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Stocks were prepared in Vero or VeroE6 cells in DMEM containing 2.5% FCS (v/v) infected at a low MOI (~0.001). VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Near confluent monolayers of Vero cells in 24 or 6 well plates were infected. Verosuggested: None… SciScore for 10.1101/2021.07.16.452629: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: All SARS-CoV-2 work was carried out under BSL3 conditions in a dedicated facility in QUB. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Contamination: Cell lines were routinely tested for mycoplasma contamination and no evidence of contamination was detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Stocks were prepared in Vero or VeroE6 cells in DMEM containing 2.5% FCS (v/v) infected at a low MOI (~0.001). VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Near confluent monolayers of Vero cells in 24 or 6 well plates were infected. Verosuggested: NoneExperimental Models: Organisms/Strains Sentences Resources Continuous cell line culture: In this study, 3 continuous cell lines were used: Vero wildtype (number), Vero E6, and Vero E6 expressing human ACE2 and TMPRSS2 (VAT) (Rihn et al., 2021). Verosuggested: NoneSoftware and Algorithms Sentences Resources Following PCR, the amplicons from pools A & B were combined, and the resulting pooled amplicons (98 x 450 bp overlapping tiled amplicons, spanning the SARS-CoV-2 genome) were purified using Kapa HyperPure beads (Roche Molecular Systems Inc) and quantified using a Qubit fluorometer and dsDNA HS Assay Kit (Thermo Fisher Inc, Manchester, UK) Thermo Fisher Incsuggested: NoneSequence analysis: The FASTQ files were uploaded into the Galaxy web platform, and we used the public server at usegalaxy.eu to analyse the data (Afgan et al., 2018). Galaxysuggested: (Galaxy, RRID:SCR_006281)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
