Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication

  1. Elizabeth R. Vanderwall
  2. Kaitlyn A. Barrow
  3. Lucille M. Rich
  4. David F. Read
  5. Cole Trapnell
  6. Oghenemega Okoloko
  7. Steven F. Ziegler
  8. Teal S. Hallstrand
  9. Maria P. White
  10. Jason S. Debley

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Common alphacoronaviruses and human rhinoviruses (HRV) induce type I and III interferon (IFN) responses important to limiting viral replication in the airway epithelium. In contrast, highly pathogenic betacoronaviruses including SARS-CoV-2 may evade or antagonize RNA-induced IFN I/III responses. In airway epithelial cells (AECs) from children and older adults we compared IFN I/III responses to SARS-CoV-2 and HRV-16, and assessed whether pre-infection with HRV-16, or pretreatment with recombinant IFN-β or IFN-λ, modified SARS-CoV-2 replication. Bronchial AECs from children (ages 6–18 years) and older adults (ages 60–75 years) were differentiated ex vivo to generate organotypic cultures. In a biosafety level 3 (BSL-3) facility, cultures were infected with SARS-CoV-2 or HRV-16, and RNA and protein was harvested from cell lysates 96 h. following infection and supernatant was collected 48 and 96 h. following infection. In additional experiments cultures were pre-infected with HRV-16, or pre-treated with recombinant IFN-β1 or IFN-λ2 before SARS-CoV-2 infection. In a subset of experiments a range of infectious concentrations of HRV-16, SARS-CoV-2 WA-01, SARS-CoV-2 Delta variant, and SARS-CoV-2 Omicron variant were studied. Despite significant between-donor heterogeneity SARS-CoV-2 replicated 100 times more efficiently than HRV-16. IFNB1, INFL2, and CXCL10 gene expression and protein production following HRV-16 infection was significantly greater than following SARS-CoV-2. IFN gene expression and protein production were inversely correlated with SARS-CoV-2 replication. Treatment of cultures with recombinant IFNβ1 or IFNλ2, or pre-infection of cultures with HRV-16, markedly reduced SARS-CoV-2 replication. In addition to marked between-donor heterogeneity in IFN responses and viral replication, SARS-CoV-2 (WA-01, Delta, and Omicron variants) elicits a less robust IFN response in primary AEC cultures than does rhinovirus, and heterologous rhinovirus infection, or treatment with recombinant IFN-β1 or IFN-λ2, reduces SARS-CoV-2 replication, although to a lesser degree for the Delta and Omicron variants.

Article activity feed

  1. Version published to 10.1038/s41598-022-10763-2
  2. ScreenIT

    SciScore for 10.1101/2021.11.20.469409: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: AECs from children were obtained under study #12490 approved by the Seattle Children’s Hospital Institutional Review Board.
    Consent: Parents of subjects provided written consent and children over 7 years of age provided assent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Primary bronchial AECs from adults were purchased from Lonza® or obtained from a tracheal segment lung transplant donor lung tissue.
    Lonza®
    suggested: (Lonza, RRID:SCR_000377)
    Data was analyzed using Prism® 9.0 software (GraphPad Software Inc.
    Prism®
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:
    However, there are several limitations of our primary airway epithelial model system. First, our ex vivo system lacks interaction with immune cells and the complex immune responses that occur in vivo in the context of COVID-19, and therefore we cannot assess how heterogeneity in interferon responses to SARS-CoV-2 at the level of the airway epithelium relate to systemic immune responses or clinical outcomes in vivo. Second, in this study we did not investigate potential genetic or epigenetic factors that may explain the between subject heterogeneity in interferon responses and viral replication that we observed. Finally, given the limitations posed by the complex logistics of completing these experiments in a biosafety level 3 (BSL-3) facility, together with limitations in available material from organotypic cultures from a sizeable number of human donors, we were constrained in the number of feasible sample harvesting timepoints which prevented us from conducting a high resolution assessment of the time kinetics of viral infection and interferon responses in the present study; however, our choice to harvest supernatant 48 hours following SARS-CoV-2 infection and RNA 96 hours following infection was informed by both our prior work with RSV(29) and preliminary experiments with SARS-CoV-2 (data not shown) where we observed that in organotypic primary ALI cultures type I and III interferon responses peak between 24-48 hours while expression of downstream ISGs peak between 72-96 h...

    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: 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.

    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.

  3. Version published to 10.1101/2021.11.20.469409v1 on bioRxiv