Betacoronaviruses: activation and antagonism of host innate immune responses

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Human betacoronaviruses induce a wide spectrum of respiratory disease. MERS-CoV (MERS) and SARS-CoV- 2 (SARS-2), cause severe lethal pneumonia, while SARS-2 can also cause mild to asymptomatic disease in some individuals. In contrast, infections with the “common” respiratory human beta-CoV OC43 are largely limited to the upper respiratory tract. With only a few drugs that show promise against human CoVs, it remains imperative to develop therapeutics for current and future emergent human CoVs. For this, we need to identify and understand the host-virus interactions common to all or different among these viruses. A major focus of our lab has been on the double-stranded (ds)RNA induced host responses to beta-CoVs: interferon production and signaling; oligoadenylate synthetase-ribonuclease L and protein kinase R (PKR), that are both antiviral and pro- inflammatory. We have shown that the conserved CoV replicase encoded nsp15 endoribonuclease (Endo)U reduces dsRNA accumulation and activation of all three pathways while subgenera specific accessory proteins add to the antagonism. Merbeco (MERS-CoV) and embeco (OC43) viruses shut down these pathways effectively; in contrast, the sarbecovirus, SARS-2, replicates in respiratory derived cells despite activation of all three. Preliminary data suggest that downstream effects of RNase L on inflammation and cell death may be more impactful during SARS-2 infection than the modest antiviral effects. PKR and PKR-like ER kinase (PERK), both kinases of the integrated stress response, when activated, phosphorylate protein synthesis initiation factor eIF2a, leading to protein synthesis attenuation, providing an important control point in infection. Activation of PERK also initiates a pathways of the unfolded protein response (UPR) to ER stress, which produces antiviral effects and inflammation. We found that MERS and OC43 infection suppress phosphorylation of eIF2a by preventing PKR activation and through a PERK pathway feedback loop, dephosphorylating eIF2a. In contrast SARS-2 promotes p-eIF2a through both PKR and PERK, but maintains viral protein synthesis. This may occur in part via the CoV replicase nsp1 protein, which promotes selective attenuation of host, but not viral, protein synthesis. Our overall hypothesis is that betacoronaviruses of each subgenus have evolved unique ways to interact with host responses to optimize replication and spread and that these differences influence pathogenic outcomes. We propose to determine: the role of the conserved CoV EndoU and subgenera specific accessory proteins in antagonizing host innate response pathways; the impact of OAS-RNase L activation on viral replication, inflammation and cell death; and the effects of host PKR/PERK and viral nsp1 on control of protein synthesis and virus replication. Our overall goal is to understand the similarities and differences in host interactions among beta-CoVs of three subgenera. Our findings may identify novel therapeutic interventions targeting host or viral proteins and indicate whether they may work as pan-CoV therapies or be unique to each beta-CoV subgenus, and thus help prepare for future CoV outbreaks.