Innate Immune Response and Inflammasome Activation During SARS-CoV-2 Infection

Abstract

The novel coronavirus SARS-CoV-2, responsible for the COVID-19 outbreak, has become a pandemic threatening millions of lives worldwide. Recently, several vaccine candidates and drugs have shown promising effects in preventing or treating COVID-19, but due to the development of mutant strains through rapid viral evolution, urgent investigations are warranted in order to develop preventive measures and further improve current vaccine candidates. Positive-sense-single-stranded RNA viruses comprise many (re)emerging human pathogens that pose a public health problem. Our innate immune system and, in particular, the interferon response form an important first line of defense against these viruses. Flexibility in the genome aids the virus to develop multiple strategies to evade the innate immune response and efficiently promotes their replication and infective capacity. This review will focus on the innate immune response to SARS-CoV-2 infection and the virus' evasion of the innate immune system by escaping recognition or inhibiting the production of an antiviral state. Since interferons have been implicated in inflammatory diseases and immunopathology along with their protective role in infection, antagonizing the immune response may have an ambiguous effect on the clinical outcome of the viral disease. This pathology is characterized by intense, rapid stimulation of the innate immune response that triggers activation of the Nod-like receptor family, pyrin-domain-containing 3 (NLRP3) inflammasome pathway, and release of its products including the pro-inflammatory cytokines IL-6, IL-18, and IL-1β. This predictive view may aid in designing an immune intervention or preventive vaccine for COVID-19 in the near future.

Keywords: COVID-19; Inflammasome; Innate immune response; NLRP3; SARS-CoV2; Vaccine..

Fig. 1

Pictures depicting the structure organization and ORFs of SARS-CoV2. A Structure of SARS-CoV2: it is an enveloped virus, nonsegmented with positive‐sense single‐stranded RNA genome. Various components of the virion are shown as follows: spike protein (S), the envelope (E) protein together with the membrane (M) protein, and the nucleocapsid (N) protein bound to the RNA genome forming nucleocapsid. B Graph representing genomic organization of SARS-CoV2: genome of the virus encodes two large open reading frames (ORF1a and ORF1b) as shown in 5′ to 3′ orientation. About two-thirds (67%) of the complete virus genome consist of two ORFs: ORF1 a and b. Both these ORFs encode for 16 nonstructural proteins. The remaining ORFs occupy the remaining one-third of the genome encoding the four structural proteins (S, spike; E, envelope; M, membrane; N, nucleocapsid) and other accessory proteins of the virus.

Fig. 2

Schematic representation of elements involved in generating innate immune response against SARS-CoV-2. SARS‐CoV2 infects permissible cells via angiotensin‐converting enzyme 2 (ACE2). After entering the alveolar epithelium, the virus is recognized by important innate immune sensors including endosomal RNA sensors—Toll-like receptor 3 (TLR3), TLR7/8 and cytoplasmic retinoic acid-inducible gene I (RIG-I), and melanoma differentiation-associated protein 5 (MDA5). TLRs are known to further activate TIR-domain-containing adapter-inducing IFNβ (TRIF) and myeloid differentiation primary response gene 88 (MyD88) signaling pathways. MyD88-dependent pathway proceeds via formation of “Mydossome” with TRAF6 activating TAK1 kinase via polyubiquitination. The activated TAK1 activates IKK kinase complex by phosphorylation. The activation of IKK complex leads to the activation of induced nuclear translocation of NF-κB. The TRIF-dependent pathway, on the other hand, recruits TRAF3 and TRAF6. TRAF3 activates IKK complex by polyubiquitination which in turn activates IKKε/TBK1 by phosphorylation and causes activation and nuclear translocation of IRF3 and IRF7. In addition, virus-induced mitochondria damage activates cyclic GMP-AMP synthase (cGAS) and stimulator of interferon gene (STING) pathway to induce synthesis of antiviral IFN-α/β production via IRF3 and IRF7. Transcription factor NF-κB initiates production of pro-inflammatory cytokines (TNF-α and IL-6), and the transcription factor IRF3/7 initiates production of type I interferon (IFN-α/β). Interferons are secreted and bind to the type I interferon receptor (IFNAR) in an autocrine loop to activate JAK-STAT signal transduction pathway, where STAT1-STAT2 is phosphorylated and forms heterodimer that joins IRF9 to form ISGF-3. ISGF-3 complex then binds to ISREs on the regulatory region on target genes to induce expression of interferon-stimulated genes (ISGs). ISG genes expression establishes an antiviral state in the cells.

Fig. 3

Immune evasion strategies exploited by SARS-CoV2 during infection. After viral genome entry into the host cells during infection, viral genome ssRNA as well as dsRNA intermediate found in virus life cycle is sensed by innate immune sensors, RIG-I/MDA5 in cytoplasm or Toll-like receptors TLR3/7/8 in endosome. Response generated from these sensors initiates a downstream signaling cascade leading to IFN-β gene expression. RIG-I/MDA5-dependent signaling involves a mitochondrial adaptor MAVS, whereas TLR signals through TRIF/MyD88. Both pathways involve common TRAF adaptor to activate transcription factors. The SARS-CoV-2 encoded proteins shown in yellow box are known to intervene the host innate immune signaling at various action points as evasion mechanisms to sustain viral replication and propagation. One key strategy is to effectively suppress the activation of TNF receptor-associated factors (TRAF) 3 and 6, thereby limiting activation of the transcription factors NFκB and IRF3 and 7. This leads to severely dampened early pro-inflammatory response mediated by type I interferons (IFN) and pro-inflammatory effector cytokines IL-1, IL-6, and TNF-α. Furthermore, novel SARS-CoV-2 inhibits activation of STAT transcription factors (ISRE) in response to type I IFN receptor activation, which further limits antiviral response mechanisms. Altogether, this prohibits virus containment through activation of antiviral programs and the recruitment of immune cells.

Fig. 4

NLRP3 activation by SARS-CoV-2. Activation of the NLRP3 inflammasome requires priming signal and activation signal. During initial priming signal, activated PRRs induce IRF3/7 and NF-kB activation, triggering the transcription of NLRP3, pro caspase-1, pro-IL-1b, and pro-IL-18. Later, activation signal involves multiple DAMPs, and PAMPs induced NLRP3 inflammasome assembly and activation. DAMPs include lysosomal or endosomal injury, aberrant ionic fluxes, mitochondrial injury, and protein aggregates. With the help of ZBP1, NLRP3 is activated by sensing viral proteins and RNA and promotes inflammasome assembly. Lysosomal maturation and mitochondria damage induce the production of ROS to activate the NLRP3 inflammasome. NLRP3 recruits the adapter protein, ASC and the protease caspase-1. Association with these factors makes NLRP3 fully matured, and NLRP3 inflammasome further drives maturation of pro-IL-1β and pro-IL-18 into their respective active forms. Activation of caspase-1 involves the auto-cleavage of pro-caspase-1 and matured caspase-1 and then mediates proteolytic cleavage-based activation and secretion of pro-IL-1b and pro-IL-18 into IL-1β and IL-18 which results in pyroptosis (programmed cell death).