Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines

Abstract

The innate immune system acts as the first line of defense against pathogens, including coronaviruses (CoVs). Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV are epidemic zoonotic CoVs that emerged at the beginning of the 21st century. The recently emerged virus SARS-CoV-2 is a novel strain of CoV that has caused the coronavirus 2019 (COVID-19) pandemic. Scientific advancements made by studying the SARS-CoV and MERS-CoV outbreaks have provided a foundation for understanding pathogenesis and innate immunity against SARS-CoV-2. In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. We also discuss how the pathogenesis of these viruses influences these biological processes.

Keywords: COVID-19; MERS-CoV; MHV; PANoptosis; PANoptosome; RNA virus; SARS-CoV; SARS-CoV-2; cell death; coronavirus; cytokines; inflammasome; inflammation; innate immunity.

Figure 1

Coronavirus (CoV) RNA Genome and Replication. (A) Schematic diagram of representative positive-sense RNA genomes of severe acute respiratory syndrome (SARS)-CoV (29.7 kB), Middle East respiratory syndrome (MERS)-CoV (30.1 kB), SARS-CoV-2 (29.9 kB), and murine hepatitis virus (MHV) (31.3 kB). The 5′-end encodes a polyprotein (ORF1a/b), and the 3′-end encodes four structural proteins [spike (S), membrane (M), envelope (E), nucleocapsid (N)], hemagglutinin-esterase (HE), internal (I) protein, and accessory proteins (ORF2a, 3, 3a, 3b, 4, 4a, 4b, 5a, 5, 6, 7a, 7b, 8a, 8b, 9a, 9b, and/or 10). The S, M, E, and N proteins are unique to each virus. (B) Representative diagram of CoV replication. After host receptor interaction with S viral protein [angiotensin-converting enzyme 2 (ACE2) for SARS-CoV, SARS-CoV-2, and HCoV-NL63; dipeptidyl peptidase 4 (DPP4) for MERS-CoV; murine carcinoembryonic antigen-related adhesion molecule 1 (mCEACAM1) for MHV; aminopeptidase N (APN) for HCoV-229E; 9-O-acetylated sialic acid for HCoV-OC43 and HCoV-HKU1], viral RNA and proteins are released to the cytoplasm, and open reading frame (ORF)-1a and ORF1ab are translated to produce pp1a and pp1ab. Next, pp1a and pp1ab form the replicase–transcriptase complex through cotranslational proteolytic processing. The complex produces an antisense negative-strand template, and the subgenomic mRNAs are synthesized. Subsequent translation of subgenomic mRNAs generates structural viral proteins, including the N, E, M, and S proteins, which are assembled at the endoplasmic reticulum (ER)–Golgi intermediate compartment (ERGIC). Newly synthesized virion-containing vesicles fuse with the plasma membrane to release the virus [15., 16., 17., 18.]. ACE2, angiotensin-converting enzyme 2; APN, aminopeptidase N; CoV, coronavirus; DPP4, dipeptidyl peptidase 4; mCEACAM1, murine carcinoembryonic antigen-related adhesion molecule 1; ORF, open reading frame.

Figure 2

Innate Immune-Sensing Pathways in Coronavirus (CoV) Infection and Immune Evasion. Upon CoV infection, incoming double-stranded RNA (dsRNA) and genomic single-stranded RNA (ssRNA) are recognized by Toll-like receptor 3 (TLR3) and TLR7, respectively. Signaling downstream of these TLRs induces activation of nuclear factor-κB (NF-κB) to produce proinflammatory cytokines and phosphorylation of interferon regulatory factor 3 (IRF3) and IRF7 to drive type I interferon (IFN) production. Viral RNA in the cytosol is recognized by retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5). The helicases of RIG-I and MDA5 associate with mitochondrial antiviral signaling protein (MAVS), leading to the activation of NF-κB and phosphorylation of IRF3. Severe acute respiratory syndrome (SARS)-CoV open reading frame (ORF)-3a, ORF8b, and envelope (E) protein stimulate the inflammasome, which results in caspase-1 activation and release of the cytokines interleukin-1β (IL-1β) and IL-18. Many CoV viral proteins [red: SARS-CoV, blue: Middle East respiratory syndrome (MERS)-CoV, green: murine hepatitis virus (MHV)] antagonize type I IFN signaling [85., 86., 87., 88., 89., 90., 91.]. Abbreviations: ASC, apoptosis-associated speck-like protein containing a caspase activation domain; M, membrane protein; N, nucleocapsid protein; NLRP3, nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3; nsp, nonstructural protein; PLP, papain-like protease.

Figure 3

Key Figure. Programmed Cell Death Pathways during Coronavirus (CoV) Infection. Upon severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, SARS-CoV-2, and murine hepatitis virus (MHV) infection, CoV viral proteins can function as cytosolic pathogen-associated molecular patterns (PAMPs) and stimulate inflammasome assembly, resulting in activation of caspase-1. Active caspase-1 then cleaves pro-interleukin (IL)-1β, pro-IL-18, and gasdermin D (GSDMD). The N-terminal fragment of GSDMD may then oligomerize within membranes to form membrane pores and execute pyroptosis [26., 27., 28., 29.,42,51,52]. SARS-CoV, MERS-CoV, SARS-CoV-2, and MHV infections also initiate a signaling cascade mediated by caspase-8 activation. Caspase-8 activates caspase-3 to drive apoptosis [52,60., 61., 62., 63., 64., 65., 66.]. Human (H)CoV-OC43 and MHV infection initiate necroptosis, a receptor-interacting serine/threonine-protein kinase 1 (RIPK1) and RIPK3 complex-dependent form of inflammatory cell death that depends on activation of the protein mixed lineage kinase domain-like pseudokinase (MLKL) to form channels in the membrane. PANoptosis, the coordinated regulation of pyroptosis, apoptosis, and necroptosis, is induced by MHV infection, and IL-1β, IL-18, and alarmins are released through GSDMD and MLKL membrane pores [52,57]. Broken lines represent connections that are known to exist in the context of inflammatory signaling but have not been shown for CoVs specifically. Abbreviations: DAMPs, danger-associated molecular patterns; GSDME, gasdermin E.