COVID-19: The Emerging Immunopathological Determinants for Recovery or Death

Abstract

Hyperactivation of the host immune system during infection by SARS-CoV-2 is the leading cause of death in COVID-19 patients. It is also evident that patients who develop mild/moderate symptoms and successfully recover display functional and well-regulated immune response. Whereas a delayed initial interferon response is associated with severe disease outcome and can be the tipping point towards immunopathological deterioration, often preceding death in COVID-19 patients. Further, adaptive immune response during COVID-19 is heterogeneous and poorly understood. At the same time, some studies suggest activated T and B cell response in severe and critically ill patients and the presence of SARS-CoV2-specific antibodies. Thus, understanding this problem and the underlying molecular pathways implicated in host immune function/dysfunction is imperative to devise effective therapeutic interventions. In this comprehensive review, we discuss the emerging immunopathological determinants and the mechanism of virus evasion by the host cell immune system. Using the knowledge gained from previous respiratory viruses and the emerging clinical and molecular findings on SARS-CoV-2, we have tried to provide a holistic understanding of the host innate and adaptive immune response that may determine disease outcome. Considering the critical role of the adaptive immune system during the viral clearance, we have presented the molecular insights of the plausible mechanisms involved in impaired T cell function/dysfunction during various stages of COVID-19.

Keywords: COVID-19; SARS-CoV-2; T cell response; interferon response; lymphocytopaenia; viral evasion.

FIGURE 1

Proposed model of SARS-CoV-2 entry into the host cells. Based on available literature on SARS-CoV and recent findings on SARS-CoV-2, we suggest two different mechanisms that can be employed by SARS-CoV-2 to enter into the ACE2 expressing cells. (1) Initially the virus may use the cell membrane mode of entry. The first step is the binding of the spike protein of the virus with ACE2 receptors expressed on the plasma membrane of host cells. (2) The attachment with ACE2 is followed by the cleavage of S protein by membrane bound proteases like TMPRSS2. TMPRSS2 cleaves the membrane bound virus at both S1/S2 boundary as well as at S2’ site. (3) This activates the fusion machinery, and subsequently, the viral membrane fuses with the host cell plasma membrane. (4) This leads to release of the viral nucleocapsid into the cytoplasm. (5) The replication, assembly, and maturation of virus takes places in the cytoplasm. (6) Before dissemination, SARS-CoV-2 may also undergo pre-activation in the golgi apparatus by furin proteases. (7) The fully mature and pre-activated SARS-CoV-2 eventually disseminates from host cells by exocytosis. During subsequent infection cycles, the virus may utilize either cell membrane or (8–11) the more probable endocytic entry route. In the endocytic mode of entry, (8) after attachment with ACE2, (9) the virus gets endocytosed and (10) then processed at the S2’ region by endosomal proteases like cathepsins, to activate membrane fusion. (11) Finally, the viral components are released into the cytoplasm by fusion of the viral membranes with endosomal membrane, leading to repeat of the cycle.

FIGURE 2

Molecular and signaling pathway implicated in host cell antiviral response. (A) After the viral contents are released into the cytoplasm, the viral RNA is recognized by host cell NASs like RIG-I and MDA5. Counter-defense may be provided by the viral proteins, NSP14 and NSP16 to shield the viral RNA from sensing by the NASs. However, if successfully recognized, RIG-I and MDA5 get activated and subsequently activate the centrally placed MAVS located on mitochondria. MAVS acts as a molecular adaptor that further recruits TRAF2/3/5/6. Association of the type of TRAF with MAVS is suggested to determine the type of downstream signaling, i.e., IRF3/7 and/or NF-κB. At the MAVS junction, the association of TRAF5/6 with TRADD, FADD, and RIPK1 activates NF-κB. Whereas, binding of MAVS with STING activates TBK1 and IKKε by interacting with TRAF2/3, which eventually results in the activation of IRF3 and IRF7 (Chen et al., 2014). Activated IRF3, IRF7, and NF-κB translocate to the nucleus and induce the expression of IFN genes. (B) The transcribed IFNs act on the respective IFN receptors (IFNRs) present on the host cells as well as on other innate immune cells, thus signaling in a both autocrine and paracrine manner. Signaling via IFNRs activates the JAK/STAT signaling pathway and subsequently induces the expression of ISGs. These molecular events were recently reviewed (Rehwinkel and Gack, 2020). ISGs transcribed will eventually inhibit viral propagation. However, SARS-CoV and likely SARS-CoV-2 have developed counter-defense mechanisms to interfere at various steps in the NAS signaling pathway. NSP4a inhibits TRIM25, which is required for RIG-I activation. N protein inhibits MDA5, NSP14 inhibits MAVS, ORF9b inhibits RIG-I/MDA5 activation complex, M protein interferes with TANK, IKKε, and TBK1 signaling, and PLpro inhibits various RIG-I, MDA5, and MAVs downstream signaling steps. SARS-CoV-2 proteins acting at various steps in blocking NAS and IFN signaling are shown in the red box. NAS, Nucleic acid sensors; RIG-I, Retinoic acid-inducible gene I; MDA5, melanoma differentiation-associated protein 5; TRAF, TNF receptor-associated factor; STING, ER-associated stimulator of interferon genes; FADD, FAS-associated death domain protein; IRF, Interferon regulatory factor (IRF3/7); TRADD, TNFR1-associated death domain protein; IKKε, IκB kinase-ε; RIPK1, Receptor-interacting protein 1; TANK, TRAF family member-associated NF-kappa-B activator; TBK1, TANK-binding kinase 1; ISG, Interferon stimulatory gene; TRIM25, Tripartite motif-containing protein 25.

FIGURE 3

Clearance of virus infected cells by engaging adaptive immune cells. Virus infected ATII cells activate the neighboring lung resident AMs by minimizing the CD200-200L interaction. Additional requisite activation signals are provided by DAMPs, viral derived PAMPs, and cytokines like IFN-γ. Activated AMs along with infected ATII derived molecules activate and recruit other innate immune cells, like circulating monocytes, dendritic cells, NK cells, and neutrophils which act in a coordinated manner to eventually recruit the adaptive effector immune cells like CTLs and CD4⁺T cells. These adaptive immune cells then specifically eliminate virus infected cells while minimizing the damage to the nearby uninfected cells. Thus, a well-coordinated and regulated adaptive immune response with help from innate immune cells is critical for initial antiviral response to limit the further spread of the virus. Green arrows indicate the cytokines released by the respective activated immune cells which activate other immune cells as well as mount an antiviral response by acting on lung epithelial cells.

FIGURE 4

T and B cell immune response during SARS-CoV-2 infection. (A) The activation status of CD4⁺ and CD8⁺ T in the circulation is indicated by CD38⁺ HLA-DR⁺. These activated T cells are further recruited at the sites of infection (initially lungs) in the presence of their respective chemokines. The activated CD4⁺ T cells are marked by the presence of cytokines like IFN-γ, IL-2, IL-12, IL-6, and GM-CSF, whereas activated CD8⁺T (cytotoxic T cells) are marked by the secretion of granzymes, perforins, and IFN-γ. During SARS-CoV-2 infection, activated CD8⁺T cells exhibiting increased expression of granzyme A, B, and K (GZM-B, GZM-A, and GZM-K) were found in the lungs (Liao et al., 2020; Song et al., 2020; Zheng M. et al., 2020). (B) T cells were also found to exhibit exhausted state as marked by the expression of PD-1, Tim3, and NKG2A. However, most studies showing exhausted T cells were confined to the peripheral blood, while lungs were mostly shown to have activated T cells but with concomitant expression of some exhaustive markers, suggesting that the activation state is followed by exhaustion. The exhaustive T cells are marked by the reduced expression of respective chemokines and cytolytic granules. (C) Similarly, antibody-producing B cells (plasmablasts; PB) were shown to exhibit activation status as reflected by the expression of IL4R, TNFSF13B, and XBP1, while at the same time, the exhausted status of these cells was also reported in the peripheral blood. Exhaustive state of B cells is reflected by a decrease in antibody production.

FIGURE 5

Immunopathological changes during different stages of COVID-19. (A) Immunological response in mild/moderate COVID-19 patients are overtly conferred by the adaptive immune cells with assistance from the innate immune system. Infected ATII cells and activated AMs produce a repertoire of cytokines and chemokines to recruit innate and adaptive immune cells and limit the viral propagation. The functional immune system thus acts in a well-coordinated manner to eliminate the virus specific ATII cells. Due to the relatively stem cell-like property of ATII cells, the eliminated cells are subsequently regenerated, thus ensuring recovery of the damaged lung tissue. (B) However, in severe/critically ill patients, an exaggerated inflammatory response is mounted by hyperactivated innate immune cells, and to a lower degree by adaptive immune cells. A hyperinflammatory state is created in the lungs which is characterized by the robust accumulation of inflammatory cells like monocytes/macrophages, dendritic cells, and neutrophils. This leads to the excessive release of cytokines and chemokines by these cells, thus inducing a vicious hyperinflammatory cycle. Damage to the lung parenchyma is inflicted by this hyperinflammatory state, along with other cytotoxic molecules like MMPs, NETs, ROS and NO. The latter two combine to form more cytotoxic peroxynitrite ions. The combined action of these events results in epithelial denudation, vascular leak, platelet and RBC infiltration, vascular edema, and hyaline membrane formation, resulting in ARDS.