Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity

Abstract

The innate immune response to viruses is initiated when specialized cellular sensors recognize viral danger signals. Here we show that truncated forms of viral genomes that accumulate in infected cells potently trigger the sustained activation of the transcription factors IRF3 and NF-κB and the production type I IFNs through a mechanism independent of IFN signaling. We demonstrate that these defective viral genomes (DVGs) are generated naturally during respiratory infections in vivo even in mice lacking the type I IFN receptor, and their appearance coincides with the production of cytokines during infections with Sendai virus (SeV) or influenza virus. Remarkably, the hallmark antiviral cytokine IFNβ is only expressed in lung epithelial cells containing DVGs, while cells within the lung that contain standard viral genomes alone do not express this cytokine. Together, our data indicate that DVGs generated during viral replication are a primary source of danger signals for the initiation of the host immune response to infection.

Defective Viral Genomes: Critical Danger Signals of Viral Infections

“…In support of this idea, MAVS deficiency abrogates the generation of the antiviral response to DVGs (12). In addition, RIG-I binds DVGs preferentially over standard virus genomes in cells infected with SeV or influenza virus (18) and RIG-I overexpression enhances the response to SeV DVGs (14).…”

“…Although both deletion and copy-back DVGs preserve the RIG-I stimulatory uncapped 5=ppp motif, copy-back DVGs have significantly more potent immunostimulatory activity than that of other forms of the genome (8,14). While the potent activity of DVGs may be partially explained by a faster accumulation in infected cells (12) due to their strong flanking antigenomic promoters, infection with large amounts of standard virus lacking DVGs does not compensate for their poor immunostimulatory activity (12,14), suggesting that the relative level of PAMPs does not fully account for the more potent recognition of DVGs. Interestingly, treatment of SeV DVGs with phosphatase to eliminate the 5=ppp motif significantly diminishes but does not eliminate their immunostimulatory ability (11,12), suggesting that other RNA motifs play a role in DVG recognition.…”

“…DI particles rendered these cells fully capable of stimulating T cells, thereby promoting the transition from the innate to the adaptive immune response (11)(12)(13)(14). Stocks of SeV lacking DI particles failed to induce a potent response even at a high multiplicity of infection, but potent activation of dendritic cells was restored following supplementation with purified DI particles.…”

“…While the potent activity of DVGs may be partially explained by a faster accumulation in infected cells (12) due to their strong flanking antigenomic promoters, infection with large amounts of standard virus lacking DVGs does not compensate for their poor immunostimulatory activity (12,14), suggesting that the relative level of PAMPs does not fully account for the more potent recognition of DVGs. Interestingly, treatment of SeV DVGs with phosphatase to eliminate the 5=ppp motif significantly diminishes but does not eliminate their immunostimulatory ability (11,12), suggesting that other RNA motifs play a role in DVG recognition. Using in vitro-transcribed RNA from a highly immunostimulatory SeV DVG, a critical role for secondary structures in the immunostimulatory activity of DVG RNA is beginning to emerge (11,20).…”

Plasmacytoid Dendritic Cells Require Direct Infection To Sustain the Pulmonary Influenza A Virus-Specific CD8 T Cell Response

“…Defective interfering genomes have been demonstrated to be produced following IAV infection and can stimulate innate immune responses and enhance DC maturation, which could modulate induction of antiviral CD8 T cell responses (16,18,19). Therefore, differences in the amounts of defective genomes produced in the lungs of DC donors infected with ctrl-or 142t-IAV could potentially lead to alterations in antigen presentation capabilities of DC subsets.…”