Rethinking the landscape of host defences against emerging viruses

All recent viral pandemics originated following human adaptation of zoonotic viruses. Our front-line antiviral defences are a major barrier to these viruses. Specifically, our cells encode antiviral proteins -that can be species-specific-, and directly inhibit viral entry, replication, and spread, thus influencing the outcome of infection. Current dogma states that antiviral proteins induced by interferon signalling, named interferon stimulated genes (ISGs), are the most significant front-line of defence. However, as ISGs are induced upon recognition of an already replicating virus, I hypothesize that an array of proteins that are constitutively expressed act to contain the initial wave of viral infection before the more specific and potent ISGs are expressed, thus providing a critical first-line of defence that influences pathogenesis and interspecies transmission. Supporting this hypothesis, my recent genome-wide multi-OMICs investigation of dengue (DENV) and influenza virus (IAV) restriction revealed that 75% of the proteins that inhibited viral infection are non-ISGs. Integrative analysis of these proteins revealed enrichment in general cellular pathways, -many not previously linked to viral restriction-, with significant enrichment in homeostasis maintenance. Moreover, depletion of one single of these proteins resulted in 100% mortality in infected mice, confirming their role in pathogenesis. Using DENV as a model of emergent WHO-priority virus, I will now characterize how these proteins inhibit DENV and other related (west Nile and zika) and unrelated viruses (IAV) (Objective 1). I will investigate their impact on DENV pathogenesis using attenuated and virulent clinical isolates (Objective 2) and as barriers of interspecies transmission using ex vivo models (Objective 3). Overall, this work will shift our understanding of antiviral defences, opening a new area of research that offers signatures of pathogenesis, surveillance, and broad-acting antiviral targets.