Delayed induction of type I and III interferons mediates nasal epithelial cell permissiveness to SARS-CoV-2

  1. Catherine F. Hatton
  2. Rachel A. Botting
  3. Maria Emilia Dueñas
  4. Iram J. Haq
  5. Bernard Verdon
  6. Benjamin J. Thompson
  7. Jarmila Stremenova Spegarova
  8. Florian Gothe
  9. Emily Stephenson
  10. Aaron I. Gardner
  11. Sandra Murphy
  12. Jonathan Scott
  13. James P. Garnett
  14. Sean Carrie
  15. Jason Powell
  16. C. M. Anjam Khan
  17. Lei Huang
  18. Rafiqul Hussain
  19. Jonathan Coxhead
  20. Tracey Davey
  21. A. John Simpson
  22. Muzlifah Haniffa
  23. Sophie Hambleton
  24. Malcolm Brodlie
  25. Chris Ward
  26. Matthias Trost
  27. Gary Reynolds
  28. Christopher J. A. Duncan

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon (IFN) responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we apply single-cell RNA sequencing and proteomics to a primary cell model of human nasal epithelium differentiated at air-liquid interface. SARS-CoV-2 demonstrates widespread tropism for nasal epithelial cell types. The host response is dominated by type I and III IFNs and interferon-stimulated gene products. This response is notably delayed in onset relative to viral gene expression and compared to other respiratory viruses. Nevertheless, once established, the paracrine IFN response begins to impact on SARS-CoV-2 replication. When provided prior to infection, recombinant IFNβ or IFNλ1 induces an efficient antiviral state that potently restricts SARS-CoV-2 viral replication, preserving epithelial barrier integrity. These data imply that the IFN-I/III response to SARS-CoV-2 initiates in the nasal airway and suggest nasal delivery of recombinant IFNs to be a potential chemoprophylactic strategy.

Article activity feed

  1. Version published to 10.1038/s41467-021-27318-0
  2. Version published to 10.1101/2021.02.17.431591v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.02.17.431591: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical approval for sample collection was provided (Research Ethics Committee Reference 17/NE/0361).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    The initial stock was propagated once in Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    All spectra were analysed using MaxQuant 1.6.10.43 and searched against SwissProt Homo sapiens and Trembl SARS-CoV-2 FASTA files.
    MaxQuant
    suggested: (MaxQuant, RRID:SCR_014485)
    Moderated t-tests, with patient accounted for in the linear model, was performed using Limma, where proteins with an adjusted P < 0.05 were considered as statistically significant.
    Limma
    suggested: (LIMMA, RRID:SCR_010943)
    Images were captured using a Nikon A1 confocal microscope (Nikon, Japan) and analysed via Fiji (Version 2.0) using the Cell Counter plugin.
    Fiji
    suggested: (Fiji, RRID:SCR_002285)
    Statistical analysis: Statistical analysis was performed and figures assembled using GraphPad Prism V8 (GraphPad Software, USA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The main limitation of our data in this nasal epithelial culture system is that it did not account for professional immune cells present in the nasal mucosa, for example plasmacytoid dendritic cells36, which are capable of more rapidly mounting an IFN-I/III response to SARS-CoV-237, potentially tipping the scales in favour of the host. We studied cells derived from adult donors, however it is possible that nasal cells from paediatric donors may behave differently in terms of their permissiveness to SARS-CoV-2 and/or the efficiency of their innate immune response. Furthermore, SARS-CoV-2 variants with mutations in the spike gene have emerged worldwide whilst we were undertaking the experiments described here; these variants may impact viral replication and/or host immunity, and should be included in future studies. Nevertheless, our data, employing a variety of complementary methods, indicate that SARS-CoV-2 has a relatively broad tropism for nasal epithelial cells, confirming suggestions from prior scRNA-seq studies7,9 and other in vitro studies of primary nasal13 and tracheobronchial cells22. These findings contrast with the results of Hou and colleagues, who reported exclusive tropism of SARS-CoV-2 for ciliated cells in the airway12. It is not immediately clear how to reconcile these findings, given that secretory cells express relevant entry receptors12. Hou and colleagues used a fluorescent reporter virus, the tropism of which might have been slightly narrower than clinic...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 8. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2021.02.17.431591v1 on bioRxiv