Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells

  1. Megan L. Stanifer
  2. Carmon Kee
  3. Mirko Cortese
  4. Sergio Triana
  5. Markus Mukenhirn
  6. Hans-Georg Kraeusslich
  7. Theodore Alexandrov
  8. Ralf Bartenschlager
  9. Steeve Boulant

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Abstract

SARS-CoV-2 is an unprecedented worldwide health problem that requires concerted and global approaches to better understand the virus in order to develop novel therapeutic approaches to stop the COVID-19 pandemic and to better prepare against potential future emergence of novel pandemic viruses. Although SARS-CoV-2 primarily targets cells of the lung epithelium causing respiratory infection and pathologies, there is growing evidence that the intestinal epithelium is also infected. However, the importance of the enteric phase of SARS-CoV-2 for virus-induced pathologies, spreading and prognosis remains unknown. Here, using both colon-derived cell lines and primary non-transformed colon organoids, we engage in the first comprehensive analysis of SARS-CoV-2 lifecycle in human intestinal epithelial cells. Our results demonstrate that human intestinal epithelial cells fully support SARS-CoV-2 infection, replication and production of infectious de-novo virus particles. Importantly, we identified intestinal epithelial cells as the best culture model to propagate SARS-CoV-2. We found that viral infection elicited an extremely robust intrinsic immune response where, interestingly, type III interferon mediated response was significantly more efficient at controlling SARS-CoV-2 replication and spread compared to type I interferon. Taken together, our data demonstrate that human intestinal epithelial cells are a productive site of SARS-CoV-2 replication and suggest that the enteric phase of SARS-CoV-2 may participate in the pathologies observed in COVID-19 patients by contributing in increasing patient viremia and by fueling an exacerbated cytokine response.

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  1. ScreenIT

    SciScore for 10.1101/2020.04.24.059667: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: This study was carried out in accordance with the recommendations of the University Hospital Heidelberg with informed written consent from all subjects in accordance with the Declaration of Helsinki.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Antibodies and Inhibitors: Mouse monoclonal antibody against SARS-CoV NP (Sino biologicals MM05), mouse monoclonal against J2 (scions), mouse monoclonal against E-cadherin (BD Transductions #610181), and rabbit polyclonal anti-Mucin-2 (Santa Graz Biotechnology# sc-15334) were used at 1:500 for immunofluorescence.
    SARS-CoV NP
    suggested: (Sino Biological Cat# 40143-MM05, RRID:AB_2827977)
    J2
    suggested: None
    E-cadherin
    suggested: (BD Biosciences Cat# 610181, RRID:AB_397580)
    anti-Mucin-2
    suggested: (Acris Antibodies GmbH Cat# SM1709, RRID:AB_1619486)
    Secondary antibody (anti-mouse CW800) and DNA dye Draq5 (Abcam) were diluted 1/10,000 in blocking buffer and incubated for 1h at RT.
    anti-mouse CW800
    suggested: None
    Draq5
    suggested: (Biostatus Cat# DR50050, RRID:AB_2314341)
    Experimental Models: Cell Lines
    SentencesResources
    Caco-2 human colorectal adenocarcinoma (ATCC HTB-37) and Vero E6 (ATCC CRL 1586) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (GibCo) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Gibco).
    Caco-2
    suggested: None
    In-cell Western: 20,000 Vero E6 cells were seeded per well into a 96-well dish 24h prior to infection.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Statistics: Unless otherwise stated, statistical analysis was performed by a two-tailed unpaired t test using the GraphPad Prism software package.
    GraphPad Prism
    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: 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 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.

    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.

  2. Version published to 10.1101/2020.04.24.059667v1 on bioRxiv