IFN-I and IL-22 mediate protective effects of intestinal viral infection


Products derived from bacterial members of the gut microbiota evoke immune signalling pathways of the host that promote immunity and barrier function in the intestine. How immune reactions to enteric viruses support intestinal homeostasis is unknown. We recently demonstrated that infection by murine norovirus (MNV) reverses intestinal abnormalities following depletion of bacteria, indicating that an intestinal animal virus can provide cues to the host that are typically attributed to the microbiota. Here, we elucidate mechanisms by which MNV evokes protective responses from the host. We identify an important role for the viral protein NS1/2 in establishing local replication and a type I interferon (IFN-I) response in the colon. We further show that IFN-I acts on intestinal epithelial cells to increase the proportion of CCR2-dependent macrophages and interleukin (IL)-22-producing innate lymphoid cells, which in turn promote pSTAT3 signalling in intestinal epithelial cells and protection from intestinal injury. In addition, we demonstrate that MNV provides a striking IL-22-dependent protection against early-life lethal infection by Citrobacter rodentium. These findings demonstrate novel ways in which a viral member of the microbiota fortifies the intestinal barrier during chemical injury and infectious challenges.

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Fig. 1: Sequence variation in NS1/2 contributes to protection from intestinal injury.
Fig. 2: NS1/2 sequence variation contributes to intestinal persistence, IFN-I signalling and epithelial cell proliferation following intestinal injury.
Fig. 3: Protection of ABX-treated mice from intestinal injury is dependent on IL-22.
Fig. 4: Protection from intestinal injury and IL-22 expression is associated with CCR2-dependent cells.
Fig. 5: IFN-I signalling in IEC is required for protection from intestinal injury.
Fig. 6: IECs react to IFN-I stimulation and promote an IL-22 response.
Fig. 7: MNV protects young mice from enteric bacterial infection.

Data availability

The data that support the findings of this study are available from the corresponding author on request. FASTQ files corresponding to the RNA–seq and 16S rRNA sequencing have been deposited in a public database (RNA–seq accession no. GSE129384 and 16S accession no. PRJNA532632).


  1. 1.

    Cadwell, K. The virome in host health and disease. Immunity 42, 805–813 (2015).

    CAS  Article  Google Scholar 

  2. 2.

    Neil, J. A. & Cadwell, K. The intestinal virome and immunity. J. Immunol. 201, 1615–1624 (2018).

    CAS  Article  Google Scholar 

  3. 3.

    Cadwell, K. et al. Virus-plus-susceptibility gene interaction determines Crohn’s disease gene Atg16L1 phenotypes in intestine. Cell 141, 1135–1145 (2010).

    CAS  Article  Google Scholar 

  4. 4.

    Basic, M. et al. Norovirus triggered microbiota-driven mucosal inflammation in interleukin 10-deficient mice. Inflamm. Bowel Dis. 20, 431–443 (2014).

    Article  Google Scholar 

  5. 5.

    Seamons, A. et al. Obstructive lymphangitis precedes colitis in murine norovirus-infected Stat1-deficient mice. Am. J. Pathol. 188, 1536–1554 (2018).

    Article  Google Scholar 

  6. 6.

    Cadwell, K. et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456, 259–263 (2008).

    CAS  Article  Google Scholar 

  7. 7.

    Matsuzawa-Ishimoto, Y. et al. Autophagy protein ATG16L1 prevents necroptosis in the intestinal epithelium. J. Exp. Med. 214, 3687–3705 (2017).

    CAS  Article  Google Scholar 

  8. 8.

    Kernbauer, E., Ding, Y. & Cadwell, K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 516, 94–98 (2014).

    CAS  Article  Google Scholar 

  9. 9.

    Abt, M. C. et al. TLR-7 activation enhances IL-22-mediated colonization resistance against vancomycin-resistant enterococcus. Sci. Transl. Med. 8, 327ra325 (2016).

    Article  Google Scholar 

  10. 10.

    Thepaut, M. et al. Protective role of murine norovirus against Pseudomonas aeruginosa acute pneumonia. Vet. Res. 46, 91 (2015).

    Article  Google Scholar 

  11. 11.

    Yang, J. Y. et al. Enteric viruses ameliorate gut inflammation via toll-like receptor 3 and toll-like receptor 7-mediated interferon-β production. Immunity 44, 889–900 (2016).

    CAS  Article  Google Scholar 

  12. 12.

    Vijay-Kumar, M. et al. Activation of toll-like receptor 3 protects against DSS-induced acute colitis. Inflamm. Bowel Dis. 13, 856–864 (2007).

    Article  Google Scholar 

  13. 13.

    Bailey, D., Thackray, L. B. & Goodfellow, I. G. A single amino acid substitution in the murine norovirus capsid protein is sufficient for attenuation in vivo. J. Virol. 82, 7725–7728 (2008).

    CAS  Article  Google Scholar 

  14. 14.

    Strong, D. W., Thackray, L. B., Smith, T. J. & Virgin, H. W. Protruding domain of capsid protein is necessary and sufficient to determine murine norovirus replication and pathogenesis in vivo. J. Virol. 86, 2950–2958 (2012).

    CAS  Article  Google Scholar 

  15. 15.

    Zhu, S. et al. Regulation of norovirus virulence by the VP1 protruding domain correlates with B cell infection efficiency. J. Virol. 90, 2858–2867 (2015).

    Article  Google Scholar 

  16. 16.

    Tomov, V. T. et al. Persistent enteric murine norovirus infection is associated with functionally suboptimal virus-specific CD8 T cell responses. J. Virol. 87, 7015–7031 (2013).

    CAS  Article  Google Scholar 

  17. 17.

    Nice, T. J., Strong, D. W., McCune, B. T., Pohl, C. S. & Virgin, H. W. A single-amino-acid change in murine norovirus NS1/2 is sufficient for colonic tropism and persistence. J. Virol. 87, 327–334 (2013).

    CAS  Article  Google Scholar 

  18. 18.

    Jones, M. K. et al. Enteric bacteria promote human and mouse norovirus infection of B cells. Science 346, 755–759 (2014).

    CAS  Article  Google Scholar 

  19. 19.

    Baldridge, M. T. et al. Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection. Science 347, 266–269 (2015).

    CAS  Article  Google Scholar 

  20. 20.

    Lee, S. et al. Norovirus cell tropism is determined by combinatorial action of a viral non-structural protein and host cytokine. Cell Host Microbe 22, 449–459 (2017).

    CAS  Article  Google Scholar 

  21. 21.

    Wilen, C. B. et al. Tropism for tuft cells determines immune promotion of norovirus pathogenesis. Science 360, 204–208 (2018).

    CAS  Article  Google Scholar 

  22. 22.

    Sun, L. et al. Type I interferons link viral infection to enhanced epithelial turnover and repair. Cell Host Microbe 17, 85–97 (2015).

    CAS  Article  Google Scholar 

  23. 23.

    McCartney, S. A. et al. MDA-5 recognition of a murine norovirus. PLoS Pathog. 4, e1000108 (2008).

    Article  Google Scholar 

  24. 24.

    Wang, P. et al. Nlrp6 regulates intestinal antiviral innate immunity. Science 350, 826–830 (2015).

    CAS  Article  Google Scholar 

  25. 25.

    MacDuff, D. A. et al. HOIL1 is essential for the induction of type I and III interferons by MDA5 and regulates persistent murine norovirus infection. J. Virol. 92, e01368-18 (2018).

    Article  Google Scholar 

  26. 26.

    Pickert, G. et al. STAT3 links IL-22 signaling in intestinal epithelial cells to mucosal wound healing. J. Exp. Med. 206, 1465–1472 (2009).

    CAS  Article  Google Scholar 

  27. 27.

    Seo, S. U. et al. Intestinal macrophages arising from CCR2+ monocytes control pathogen infection by activating innate lymphoid cells. Nat. Commun. 6, 8010 (2015).

    CAS  Article  Google Scholar 

  28. 28.

    Tschurtschenthaler, M. et al. Type I interferon signalling in the intestinal epithelium affects Paneth cells, microbial ecology and epithelial regeneration. Gut 63, 1921–1931 (2014).

    CAS  Article  Google Scholar 

  29. 29.

    Pott, J. et al. IFN-λ determines the intestinal epithelial antiviral host defense. Proc. Natl Acad. Sci. USA 108, 7944–7949 (2011).

    CAS  Article  Google Scholar 

  30. 30.

    Baldridge, M. T. et al. Expression of Ifnlr1 on intestinal epithelial cells is critical to the antiviral effects of interferon lambda against norovirus and reovirus. J. Virol. 91, e02079-02016 (2017).

    Article  Google Scholar 

  31. 31.

    Nice, T. J. et al. Interferon-λ cures persistent murine norovirus infection in the absence of adaptive immunity. Science 347, 269–273 (2015).

    CAS  Article  Google Scholar 

  32. 32.

    Gronke, K. et al. Interleukin-22 protects intestinal stem cells against genotoxic stress. Nature 566, 249–253 (2019).

    CAS  Article  Google Scholar 

  33. 33.

    Lim, E. S. et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat. Med. 21, 1228–1234 (2015).

    CAS  Article  Google Scholar 

  34. 34.

    Mao, K. et al. Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism. Nature 554, 255–259 (2018).

    CAS  Article  Google Scholar 

  35. 35.

    Zheng, Y. et al. Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens. Nat. Med. 14, 282–289 (2008).

    CAS  Article  Google Scholar 

  36. 36.

    Kim, Y. G. et al. Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens. Science 356, 315–319 (2017).

    CAS  Article  Google Scholar 

  37. 37.

    Ettayebi, K. & Hardy, M. E. Norwalk virus nonstructural protein p48 forms a complex with the SNARE regulator VAP-A and prevents cell surface expression of vesicular stomatitis virus G protein. J. Virol. 77, 11790–11797 (2003).

    CAS  Article  Google Scholar 

  38. 38.

    Fernandez-Vega, V. et al. Norwalk virus N-terminal nonstructural protein is associated with disassembly of the Golgi complex in transfected cells. J. Virol. 78, 4827–4837 (2004).

    CAS  Article  Google Scholar 

  39. 39.

    McCune, B. T. et al. Noroviruses co-opt the function of host proteins VAPA and VAPB for replication via a phenylalanine-phenylalanine-acidic-tract-motif mimic in nonstructural viral protein NS1/2. mBio 8, e00668-17 (2017).

    Article  Google Scholar 

  40. 40.

    Baker, E. S. et al. Inherent structural disorder and dimerisation of murine norovirus NS1-2 protein. PLoS ONE 7, e30534 (2012).

    CAS  Article  Google Scholar 

  41. 41.

    Broggi, A., Tan, Y., Granucci, F. & Zanoni, I. IFN-λ suppresses intestinal inflammation by non-translational regulation of neutrophil function. Nat. Immunol. 18, 1084–1093 (2017).

    CAS  Article  Google Scholar 

  42. 42.

    Martin, P. K. et al. Autophagy proteins suppress protective type I interferon signalling in response to the murine gut microbiota. Nat. Microbiol. 3, 1131–1141 (2018).

    CAS  Article  Google Scholar 

  43. 43.

    Van Winkle, J. A. et al. Persistence of systemic murine norovirus is maintained by inflammatory recruitment of susceptible myeloid cells. Cell Host Microbe 24, 665–676 (2018).

    Article  Google Scholar 

  44. 44.

    Phillips, G., Tam, C. C., Rodrigues, L. C. & Lopman, B. Prevalence and characteristics of asymptomatic norovirus infection in the community in England. Epidemiol. Infect. 138, 1454–1458 (2010).

    CAS  Article  Google Scholar 

  45. 45.

    Bouziat, R. et al. Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Science 356, 44–50 (2017).

    CAS  Article  Google Scholar 

  46. 46.

    Bouziat, R. et al. Murine norovirus infection induces TH1 inflammatory responses to dietary antigens. Cell Host Microbe 24, 677–688 (2018).

    CAS  Article  Google Scholar 

  47. 47.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).

    CAS  Article  Google Scholar 

  48. 48.

    Chen, J. et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28, 2106–2113 (2012).

    CAS  Article  Google Scholar 

  49. 49.

    Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169–172 (2011).

    Article  Google Scholar 

  50. 50.

    Vazquez-Baeza, Y., Pirrung, M., Gonzalez, A. & Knight, R. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2, 16 (2013).

    Article  Google Scholar 

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We wish to thank the following NYU facilities for the use of their instruments and technical assistance: Microcopy Core (grant no. RR023704), Histopathology and Immunohistochemistry Core (grant nos P30CA016087, NIH S10 OD010584-01A1 and S10 OD018338-01), the Cytometry and Cell Sorting Laboratory (grant no. P30CA016087), the Genome Technology Center (grant no. P30CA016087) and the Gnotobitoic Facility (Colton Center for Autoimmunity). We also wish to thank S. Fujii (Washington University School of Medicine in St. Louis) for his technical support in human organoid culture. This research was supported by US National Institute of Health (NIH) grant nos R01 HL123340 (K.C.), R01 DK093668 (K.C.), R01 DK103788 (K.C. and P.L.), R01 AI121244 (K.C.) and R01 AI130945 (P.L.). This work was also supported by a Vilcek Fellowship (J.A.N.), Sir Keith Murdoch Fellowship (J.A.N.), Crohn’s & Colitis Foundation Research Fellowship Award (Y.M.-I.), Faculty Scholar grant from the Howard Hughes Medical Institute (K.C.), Advanced Research Grant from the Merieux Institute (K.C.), Rainin Foundation Innovator Award (K.C.), Stony Wold-Herbert Fund (K.C.), PureTech Health (K.C.), Pfizer (K.C. and P.L.), NYU CTSI (grant no. NIH/NCATS 1UL TR001445; K.C. and P.L.) and philanthropy from Bernard Levine (K.C. and P.L.). K.C. is a Burroughs Wellcome Fund Investigator in the Pathogenesis of Infectious Diseases.

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J.A.N. and K.C. formulated the original hypothesis and designed the study. J.A.N. performed the experiments and analyses, and received assistance from E.K.-H. (DSS experiments), S.S. (in vitro MNV responses) and Y.M.-I. (organoids). S.L.S. and M.V. processed and analysed the samples for 16S rRNA sequencing. A.G.N. performed the histopathology analysis. P.L., D.H. and A.H. provided the human colon biopsies. S.D. performed the sorting of IECs. T.L.N. provided the cDNA clones of MNV and advice. J.A.N. and K.C. wrote the manuscript. All authors commented on the manuscript, data and conclusions.

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Correspondence to Ken Cadwell.

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K.C. has consulted for PureTech Health and AbbVie Inc. and is an inventor on US patent application 62/608,404.

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Neil, J.A., Matsuzawa-Ishimoto, Y., Kernbauer-Hölzl, E. et al. IFN-I and IL-22 mediate protective effects of intestinal viral infection. Nat Microbiol 4, 1737–1749 (2019). https://doi.org/10.1038/s41564-019-0470-1

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