Animals can mount potent and rapid innate immune responses to invading viruses. The classic signaling pathway by which this response occurs is via type I interferons (IFNs), including IFN-beta (IFN-β) and multiple IFN-alphas (IFN-α) (1). When cells sense viral products, type I IFNs are produced, which stimulate transcription of antiviral molecules that act in autocrine and paracrine fashion. However, in the past decade, an important paradigm shift has occurred in how we consider the compartmentalization of viral responses into systemic versus mucosal responders, driven in large part by the discovery of type III IFNs, or IFN-λ.

First described in 2003 (2, 3), the IFN-λ family of cytokines includes up to four members in humans, dependent on genetic polymorphisms (4, 5), and two functional orthologs in mice (6, 7). The family, likely arising from a common ancestral fish IFN gene that gave rise to both type I and III IFN families, is conserved to chickens (8, 9). The type III IFNs are under positive selection, with long-term persistence of duplicate copies suggesting a critical biological role for type III IFNs independent from type I IFNs (9). Pattern-recognition receptors, including RIG-I and MDA5, detect viruses and induce type I and III IFNs via MAVS and IRF3/IRF7 signaling (10–12) (Figure 1). IRF1 plays a unique role in type III IFN induction, however, being specifically stimulated by peroxisome-associated MAVS in contrast to mitochondrial-associated MAVS, which better induces type I IFNs (13). Intestinal epithelial cells (IECs) produce type III IFNs with in vivo viral infection (14–16). However, leukocytes generate IFN-λ in vitro (10, 17), and intestinal eosinophils (18) and plasmacytoid dendritic cells (pDCs) (19) can produce IFN-λ in vivo, suggesting the possibility of additional cellular IFN-λ contributors.

While the antiviral programs induced by type I and type III IFNs exhibit substantial overlap (20–22) (Figure 1), a critical difference between the two is the cell types they affect secondary to receptor expression. The IFN-λ receptor consists of IFNLR1 and IL10Rβ. While the receptor for type I IFNs, IFNAR1, is expressed broadly on the majority of cell types, IFNLR1 exhibits a much more restricted pattern of expression (23). In the intestine, IFNLR1 is expressed preferentially on IECs, allowing for a compartmentalized response to viruses infecting at this mucosal surface (24, 25). While IFNLR1 expression has also been reported on NK cells, T cells, B cells, and pDCs (26–30), no role has been found for these cells in IFN-λ-mediated antiviral responses. Type I IFNs, on the other hand, are critical for preventing a virus from moving past this initial epithelial barrier into systemic tissues (24, 25, 31). The host may benefit by inducing specific and local barrier defenses at a site commonly exposed to pathogens via IFN-λ signaling, and thus avoid potentially detrimental systemic inflammatory responses by type I IFNs. Many autoimmune diseases, as well as the congenital interferonopathies, are secondary to excessive type I IFN activity (32, 33).

There is an ever-expanding set of roles being discovered for IFN-λ signaling, from control of viral infections in liver (34), lung (35), and brain (36), to regulation of non-infectious diseases like inflammatory bowel disease (37) and cancer (38). Many of these intriguing advances are addressed elsewhere in this Frontiers in Immunology topic, “Interferon-λs: New Regulators of Inflammatory Processes.” Here, however, we will focus exclusively on the regulation of enteric viruses by IFN-λ. We review the current literature about IFN-λ-mediated regulation of specific intestinal viruses, discuss interplay of IFN-λ with other cytokines and its regulation of viral–bacterial interactions, and highlight areas ripe for future research enterprises.

Enteric viruses, including rotavirus (RV), reovirus, norovirus (NoV), and others, generally infect via the fecal–oral route, though other transmission routes have been described. As such, the IECs comprising the mucosal barrier of the intestine likely represent the first eukaryotic cells with which an enteric virus interacts. Here, we describe what is known about specific enteric viruses and their relationship with both the intestinal epithelium and IFN-λ (Table 1).

Interferon-lambda-mediated antiviral immunity in the intestine against rotavirus (EDIM-RV) and MNoV does not redundantly overlap with type I IFNs, while there is redundancy between type I and III IFNs to control influenza, SARS coronavirus, and respiratory syncytial virus in the lung, and herpes simplex virus-2 in the genital tract [reviewed in Ref. (76)]. There are two potential reasons for a non-redundant role for IFN-λ in the intestine. First, the IFN-λ receptor is highly expressed in IECs but is minimally detectable in other intestinal cell types such as lamina propria cells (50). Second, expression of IFN-α receptor subunits (i.e., IFNAR1 and IFNAR2) is less abundant in IECs than in lamina propria cells (14), and surface expression of the IFN-α receptor is polarized to the apical side (41). Interestingly, in neonatal mice, IECs are sensitive to both IFN-α/β and IFN-λ, and both IFN-α/β and IFN-λ can control RV (RRV strain) infection in suckling mice (24). It has not been explored whether this IFN-α/β-sensitivity in neonatal IECs is from altered trafficking of the IFN-α receptor to the basolateral side. Further work is needed to explore the consequences of age-related IFN-α/β sensitivity in IECs and the pathogenesis of enteric virus infection (Figure 1).

Another cytokine important for mucosal immunity, IL-22, has a synergistic relationship with IFN-λ. Similar to IFNLR1, the IL-22 receptor subunit, IL22Rα, associates with IL10Rβ and is expressed preferentially by IECs (77). During RV infection, IL-22 acts coordinately with IFN-λ to control virus replication and prevent tissue damage in mice (16). This antiviral activity of IL-22 is Ifnlr1 and Stat1 dependent but not Stat3 dependent. IL-22 also restricts porcine enteric coronavirus infection in the intestine, for which antiviral activity is largely Stat3 dependent (78). Since IL-22 also induces IFN-λ expression in the intestine, a Stat3-independent/IFN-λ-dependent role for IL-22 in control of porcine enteric coronavirus cannot be ruled out (78).

Finally, lactoferrin, a member of the transferrin family and a component of milk, potentiates IFN-λ production in a human IEC line (79), and in vitro lactoferrin has antiviral activity against RV (80) and MNoV (81). Thus, it would be interesting to study whether milk-derived components exhibit cross talk with IFN-λ-mediated immunity for enteric viral infections in neonatal hosts.

A final critical factor for discussion of enteric viral infections and IFN-λ is the role of the commensal bacterial microbiome. For these viruses, infection occurs amidst the complex milieu of the oral and intestinal microbiome, which plays important roles in regulation of viral infectivity. Poliovirus, reovirus, and murine mammary tumor virus depend upon the presence of commensal bacteria for infection (82, 83), with direct viral binding to bacterial products like lipopolysacchide implicated as the mechanism of facilitation (84, 85). Depletion of the commensal microbiota also impairs RV infection and results in enhancement of both mucosal and systemic antibody responses against the virus (86). Human NoV binds directly to bacterial products that mimic the histo-blood group antigens (HBGAs) known to be attachment factors for NoV (87–89), and indeed culture of human NoV in B cells depends on the presence of these HBGA-expressing bacteria (57, 90). Hence, there is a common theme for enteric viruses in interacting with and depending on intestinal bacteria for infectivity, though the specific mechanisms may be virus dependent (91, 92).

The link between viral dependence on the microbiome and sensitivity to IFN-λ comes from work done with MNoV. Depletion of the commensal microbiota in wild-type mice prevents persistent intestinal MNoV infection (93), similar to what has been observed with other enteric viruses. Interestingly, in mice lacking Ifnlr1, Stat1, or Irf3, all important molecules for IFN-λ induction or signaling, MNoV establishes infection even in the absence of commensal microbes, implicating IFN-λ in regulation of these transkingdom viral–bacterial interactions (93) (Figure 1). Other enteric viruses share both a dependence on the microbiome and a sensitivity to IFN-λ; whether interplay between the microbiome and IFN-λ signaling also regulates other intestinal viruses such as RV and reovirus remains to be seen.

While the past decade yielded many exciting insights into regulation of enteric viruses by IFN-λ, many important questions remain. Type I and III IFNs share significant overlap in induction and signaling pathways, though there are distinctions in promoter sequences, upstream regulatory elements, and kinetics of downstream gene stimulation [reviewed in Ref. (76)]. However, most previous studies were performed in vitro outside of the complex environment of the gut. How is IFN-λ production regulated in the intestine, and by what pathways is it induced in vivo by viral infection? Are specific ISGs induced by IFN-λ necessary for antiviral activity against enteric infections? Conversely, viruses rapidly evolve mechanisms to evade the host immune system. Are there viral factors that specifically target IFN-λ induction or signaling pathways for evasion or suppression?

In addition to important mechanistic questions for enteric viruses already known to be IFN-λ regulated, there are a number of intestinal viruses for which sensitivity to IFN-λ has not yet been explored. Astroviruses, parvoviruses, enteroviruses, and adenoviruses are among the enteric viruses for which data on IFN-λ-sensitivity in both cell culture and animal models is currently lacking. Finally, of great interest is the in vivo effect of IFN-λ regulation on enteric viruses in humans. Single-nucleotide polymorphisms (SNPs) in human IFN-λ genes are associated with differential responses to hepatitis B and C, human cytomegalovirus, herpes simplex virus 1, and influenza virus vaccination [reviewed in Ref. (76, 94)]. Enteric infections cause a spectrum of disease in different individuals, including variable severity and duration of infection, which may correlate with host genetic variation. Do these same SNPs correlate with differential responses to enteric viruses or to vaccination? IFN-λ is clearly an important innate immune regulator for many gut viruses, and defining the breadth of its effects and the mechanisms underlying its enteric activity represent exciting areas for future research endeavors.

All authors contributed equally to this work. SL and MB conceptualized, wrote, and edited the manuscript.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer, YT, and handling editor declared their shared affiliation, and the handling editor states that the process nevertheless met the standards of a fair and objective review.