PT - JOURNAL ARTICLE AU - Xufang Deng AU - Aaron Volk AU - Yafang Chen AU - Kristina R. Kesely AU - Matthew Hackbart AU - Robert C. Mettelman AU - Amornrat O’Brien AU - Andrew D. Mesecar AU - Susan C. Baker TI - Coronavirus Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages AID - 10.1101/782409 DP - 2019 Jan 01 TA - bioRxiv PG - 782409 4099 - http://biorxiv.org/content/early/2019/09/25/782409.short 4100 - http://biorxiv.org/content/early/2019/09/25/782409.full AB - Coronaviruses encode multiple interferon antagonists that modulate the host response to virus replication. Here, we evaluated pathogenesis and host transcription in response to infection with murine coronaviruses encoding independent mutations in two different viral antagonists: the deubiquitinase (DUB) within nonstructural protein 3 and the endoribonuclease (EndoU) within nonstructural protein 15. The virus with reduced ability to deubiquitinate proteins, herein termed the DUBmut virus, was engineered via X-ray structure-guided mutagenesis and activates an earlier interferon response than the wild type virus. However, the replication kinetics of DUBmut in cultured cells are similar to wild type virus and pathogenesis in mice is also similar to what was observed during infection with wild type virus. On the other hand, we previously reported that an EndoUmut virus containing an inactivated endoribonuclease activity elicited rapid and robust activation of type I interferon, which limited virus replication and pathogenesis. Here, using a transcriptomics approach, we compared the scope and kinetics of the host response to the wild type, DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response, predominantly involving type I interferons and a subset of interferon-responsive genes, within 12 hours after infection. In contrast, the wild type and DUBmut viruses stimulate upregulation of over 2,800 genes, including activation of unfolded protein response (UPR) pathways and a proinflammatory profile associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in shaping the kinetics and magnitude of the host response during virus infection and demonstrates that inactivation of a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages and the disease process.Author Summary Macrophages are an important cell type during coronavirus infections because they “notice” the infection and respond by activating type I interferons, which then act to establish antiviral defenses and limit virus replication. In turn, coronaviruses encode proteins that mitigate the cell’s ability to detect virus replication or amplify the interferon response. Here, we evaluated the host macrophage response to two independent mutant coronaviruses: one with a reduced deubiquitinating activity (DUBmut), and the other containing an inactivated endoribonuclease (EndoUmut). We observed a rapid, robust, and focused response to the EndoUmut virus, which was characterized by enhanced expression of interferon and interferon-stimulated genes. These results indicate that coronaviruses utilize EndoU activity for preventing early activation of interferon in macrophages, thereby allowing for viral replication. In contrast, DUBmut elicited a transient interferon response and ultimately activated over 2,800 genes, including many well-known players in pro-inflammatory pathways and the unfolded protein response. These DUBmut-induced pathways are associated with development and progression of significant disease, similar to what is observed during wild type virus infection. This study demonstrates the distinct consequences of mutating different viral interferon antagonists and reveals that intact coronaviral EndoU activity substantially contributes to the ability of coronaviruses to replicate in macrophages.