Virus-infected cells trigger a robust innate immune response and facilitate virus replication. Here, we review the role of autophagy in virus infection, focusing on both pro-viral and anti-viral host responses using a select group of viruses. Autophagy is a cellular degradation pathway operated at the basal level to maintain homeostasis and is induced by external stimuli for specific functions. The degradative function of autophagy is considered a cellular anti-viral immune response. However, autophagy is a double-edged sword in viral infection; viruses often benefit from it, and the infected cells can also use it to inhibit viral replication. In addition to viral regulation, autophagy pathway proteins also function in autophagy-independent manners to regulate immune responses. Since viruses have co-evolved with hosts, they have developed ways to evade the anti-viral autophagic responses of the cells. Some of these mechanisms are also covered in our review. Lastly, we conclude with the thought that autophagy can be targeted for therapeutic interventions against viral diseases.

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The transcription factor interferon (IFN) regulatory factor 3 (IRF3) provides cellular antiviral response by expressing IFN and antiviral genes. In addition to the transcriptional activation, IRF3 triggers a direct pro-apoptotic pathway, RIPA, in virus-infected cells. The pathway of IRF3 activation in RIPA is independent of and distinct from the transcriptional activation of IRF3 (Chattopadhyay et al. Immunity, 2016, J Virol, 2013, 2011, EMBO J, 2010). Using knock-in mice expressing transcriptionally-inactive, but RIPA-competent, IRF3 mutant, we demonstrated that RIPA contributes to the antiviral response of the host. Because RIPA is a cellular antiviral pathway, we hypothesized that RIPA-promoting small molecules would act as antiviral agents. To test this, we conducted a high throughput screen of a library of 1,200 FDA-approved compounds to identify RIPA activators. Our screen isolated twenty-four primary candidates with diverse therapeutic activities, e.g. anti-cancer, anti-inflammatory, anti-bacterial, etc. We screened these primary candidates for their antiviral activities against RNA (vesicular stomatitis virus) and DNA (herpes simplex virus-1) viruses. The antiviral screen revealed a small subset of antiviral compounds, which specifically promote RIPA but not the transcriptional pathway of IRF3. We further validated their antiviral activities against additional viruses, e.g. respiratory syncytial virus and vector-borne flaviviruses. Therefore, we report a high throughput screen, which identified novel antiviral compounds that are specific activators of RIPA branch of IRF3. Currently, we are investigating the mechanisms of these RIPA-promoting antiviral compounds.