Innate immune recognition and evasion by viruses

Viral infections represent a major share of the world-wide infectious disease burden. Cell-autonomous recognition of viral pathogens, and both local and systemic antiviral cytokine responses, are critically required for limiting infection. Zika virus (ZIKV) and Varicella-Zoster virus (VZV), two viruses with significant associated morbidity, are poorly characterised regarding their interaction with the innate immune system. More specifically, cell-autonomous mechanisms that govern recognition of these viruses are virtually undescribed. In addition, strategies employed by these viruses to evade recognition and clearance by the host require investigation.
ZIKV is a Flavivirus and represents a major public health concern in the Americas. It causes Zika fever in adults and can be detrimental to foetal development if acquired during pregnancy. ZIKV is closely related to other important human pathogens such as Dengue virus (DENV). Flaviviruses are positive-sense ssRNA viruses that are commonly transmitted to humans by mosquitoes or ticks. VZV is an alpha-herpesvirus that causes chickenpox upon primary infection. The virus establishes latency and causes shingles upon reactivation. Herpesviruses are dsDNA viruses that all establish latency in the human host. ZIKV and VZV differ vastly in their virion architecture, life cycle, and associated morbidities, and are both insufficiently characterised. In this study, I elucidated the molecular requirements for cells to mount antiviral type I interferon (IFN) responses to both ZIKV and VZV. I further identified a novel antagonist of cell-autonomous recognition encoded by VZV.
Infection with ZIKV induced potent type I IFN responses in A549 cells. Transcriptional induction of the IFNb response to RNA from ZIKV-infected cells was fully dependent on recognition of immunostimulatory RNA by the RNA sensors RIG-I and MDA5 and their common adaptor protein MAVS. ZIKV genomic RNA bound to RIG-I protein in a cell-free system, indicating that viral RNA can be directly recognised by cellular sensors.
Using monocytic THP1 cells as a model system I identified the cGAS/STING DNA-sensing pathway to be critically required for type I IFN induction in response to VZV infection. Using knockout cell lines, I showed that cGAS, STING, TBK1, and IRF3 were all required for induction of the IFN transcript. Furthermore, I did not observe phosphorylation of STAT1 and STAT2 and secretion of IP-10 upon VZV infection in cells knocked-out for these factors. Given the importance of the cGAS/STING pathway for VZV recognition, I hypothesised that VZV encodes an antagonist of this pathway. I screened all unique VZV open reading frames (ORFs) and identified the tegument protein ORF9 as a novel antagonist of cGAS. Ectopically expressed ORF9 bound to endogenous cGAS and blocked the type I IFN response to transfected DNA. Confocal microscopy revealed co-localisation of ORF9 and cGAS. I further showed that this interaction occurred in VZV infected cells. ORF9 and cGAS protein also interacted directly in a cell-free system. Additional mechanistic data suggested that ORF9 blocked the production of cGAMP by cGAS.
Taken together, this work contributes to the ongoing molecular characterisation of both ZIKV and VZV. I highlighted the importance of RNA sensors for recognition of viral RNA in the context of ZIKV infection. I further demonstrated the importance of the cGAS/STING DNA sensing pathway for VZV recognition and identified a previously uncharacterised immune antagonist that directly blocks DNA sensing via cGAS.

Advisor: Rehwinkel, J