Interfering with interferons : interplay between SARS-CoV-2 and interferon response

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic, which has been an ongoing global health crisis. At the beginning of the pandemic, all the efforts were directed toward understanding the pathogenesis of the virus. An early interferon (IFN) response is crucial in initiating and boosting the antiviral response. It was identified that the IFN response is dim and delayed in COVID-19 patients, accompanied by pro-inflammatory cytokine production. Circumvention and dysregulation of interferon (IFN) response were found to be characteristic of the SARS-CoV-2 infection, leading to its pathogenicity and severity in a group of COVID-19 patients. Thus, a better understanding of the pathogenic mechanisms of SARS-CoV-2 infection is crucial for a better therapeutic strategy against the disease. The thesis aimed to characterize the interplay between SARS-CoV-2 and host IFN response. In Paper I, we assessed the susceptibility and cytotoxicity of the first Swedish isolate of SARSCoV- 2 in six cell lines of human origin in comparison to other globally isolated strains. Furthermore, we determined the proteomic landscape during SARS-CoV-2 infection in the susceptible cell lines, using LC-MS/MS-based tandem mass tags (TMT) labeling quantitative proteomics technology. The studies provided an overview of the signaling pathways altered by the SARS-CoV-2, elucidating IFN-signaling pathways. In Paper II, we identified and characterized the expression of antiviral ISGs during SARSCoV- 1, MERS-CoV, and SARS-CoV-2 infection of the Huh7 cell line using TMT-labeled LCMS/ MS. Transcriptomic ISG signatures were identified for SARS-CoV-2 in a time-dependent manner. Furthermore, we identified that SARS-CoV-2 inhibited IFN-b production and showed a muted and delayed activation of ISGs in Huh7 cells. IFN treatment was found to be effective in controlling the virus prior to the establishment of the infection, and IFN treatment postinfection had no effect on the virus. We also showed increased virus production in a senescent Huh cell model. Paper III explored how the virus infection impacts the IFN signaling pathways (IFN-I/ IFNIII) and interferon-stimulated gene (ISG) expression in COVID-19 patients. Irrespective of the disease status, heterogeneity was observed in the expression of ISGs. We categorized the patients based on type-I, type-II, and antiviral-response-related ISG scores obtained from whole-blood transcriptomics data. We investigated factors like immune cell proportions, neutrophil extracellular traps (NETs), inflammatory factors, metabolic status, and autoimmunity against IFNs, to try to find any association with the ISG score status of the patients. Autoimmune antibodies against IFNs were more prominent in patients with low ISG scores. Furthermore, the expression of ISGs was associated with a perturbation in amino acid and lipid metabolism. In Paper IV, we investigated a potential innate immune evasion mechanism by SARS-CoV- 2. We studied the role of a crucial virus protease: papain-like protease (PLpro), which has a potent deubiquitinating and deISGylating activity in inhibiting type-I IFN response. Using immunoprecipitation, we have identified that SARS-CoV-2 interacts with RIG-I signalosome components TRIM25 and RIG-I. Catalytically active PLpro could deubiquitinate the constitutively active 2CARD domain, which leads to the inhibition of interferon response. The SARS-CoV-2 homologs in other coronaviruses also interacted with TRIM25 and RIG-I and inhibited IFN production. These findings show another innate immune regulatory mechanism by Ub/UbL deconjugated activity of coronavirus PLpro. In summary, the research covered in this thesis deciphers the significance of interferon response during SARS-CoV-2 infection.