Lecture 8 PDF: Innate and Adaptive Immunity to Viruses

Innate immunity The adaptive immune is the initial response is responsible response for protection against During 1st few infection and the days since onset eradication of of infection. established infection. Innate and Adaptiv...

Innate immunity The adaptive immune is the initial response is responsible response for protection against During 1st few infection and the days since onset eradication of of infection. established infection. Innate and Adaptive Immunity to Viruses Characteristics of the Adaptive Immune System: T cells Different subpopulations of T cells lead to the recognition of the pathogens as well as the destruction or elimination of these foreign invaders from the body, including: Production of cytokines that activate or inhibit other cells of the immune system. Cytokines are small, soluble molecules that are secreted by most cells of the immune system including T cells. T cells may also eliminate pathogens by direct cytotoxic (i.e., killing) function against virally infected cells and cancer cells B cells produce antibodies that bind to antigens expressed by the pathogens that enter the body leading to the destruction or elimination of pathogen. Targeted portions of the pathogen are usually referred to as antigens or antigenic determinants.  Phases of the Adaptive Immune Response A. Recognition phase: early phase where pathogen is recognized by T cells and B cells. T and B cells that recognized the pathogen will multiply. B. Activation phase: once the pathogen is recognized the immune response is activated. C. Effector phase: once there are enough effector B and T cells, the effector phase begins. Both cell mediated immunity(which is mediated by T cells) and humoral immunity (mediated by antibodies) will work to eliminate the pathogen. D. Decline (homeostasis): Effector B and T cells will die by apoptosis because essential cells may be destroyed by them. E. Memory: Memory B and T cells will be generated to facilitate immune response in the case of reinfection. The body will recognize the pathogenic antigen and respond with the appropriate antibodies gained from previous infection. T Cells in Viral Infection CD4+ T (also called helper T cell) cells provide help to B cells for virus-specific antibody production. CD4+ T cells produce cytokines that augment CD8+ cytotoxic T cells and recruitment of macrophages CD8+ cytotoxic T cells (CTLs) capable of secreting an array of molecules such as perforin, granzymes, and gamma interferon to eradicate viruses from the host CD4+ and CD8+ T cells work with other cells to first resolve acute viral infections and to provide protection against reinfection. Delineation of the frequency, specificity, functionality and durability of T cells during COVID- 19 is vital to understanding how to use them as biomarkers and targets for immunotherapies and vaccines CD4+ T helper cells may differentiate into 4 different types of T helper cells depending on the environment: 1. T- helper cell 1 (Th1): cellular immunity, inflammation clearance of intracellular pathogens. In the presence of IL-12, T helper will differentiate into Th1. 2. T helper cell 2 (Th2): humoral immunity, allergic responses. IL-4 will trigger differentiation to Th2. 3. T helper cell 17 (Th17): tissue inflammation, autoimmunity, clearance of extracellular pathogens. IL-6 and IL-23 will trigger differentiation to Th17 and t-reg. 4. T-reg: tolerance, immune suppression. Antibody Molecule Variable region (antigen-binding site;Fab region) Binds antigen “antigen” = target molecule Upon binding, antibodies can neutralize or block antigen activities (e.g. toxins, viral entry receptors). Does not allow pathogenic antigen to bind anywhere else. Constant region (effector function; Fc region) Triggers immune response Engages Fc receptors on immune cells Complement binding to antibody-antigen complex results in lysis elimination of pathogen. Antibodies IgM IgM is the first antibody produced in a primary immune response. 10% of the total antibody pool, mostly in the circulation IgG Major human serum immunoglobulin (60-70% of total circulating antibodies are IgG) Key player in secondary immune response  IgG, IgM and IgA antibodies can bind and Antibodies neutralize extracellular virus. Before virus infects a cell. involvement in Only IgG antibodies may bind to infected cells Viral Infection and cause Antibody dependent cell cytotoxicity (ADCC). By ADCC, an antibody may kill antibody infected cells via complement lysis. IgG, IgM and IgA antibodies block virus/cell interactions. IgM antibodies may agglutinate (ability to be able to clump viral particles) virus particles. IgM and IgG may opsonize virus particles for clearance Opsonize refers to coating of viral particles. Induction of T cell Responses to Respiratory Virus Infection Immune response begins with direct infection of airway epithelium. Lung- resident respiratory dendritic cells (rDCs) acquire the virus or antigens from infected epithelial cells, become activated, process antigen and migrate to the draining lymph nodes (DLN). In the DLNs, rDCs present the processed antigen in the form of MHC/peptide complex to naıve circulating T cells. Engagement of the T cell receptor (TCR) with peptide–MHC complex and additional co-stimulatory signals, results in T cell activation proliferation and migration to the site of infection (the lung) to perform their effector function.  Immune Dysregulation During Chronic Viral Infection T cell–mediated adaptive immune response is essential for clearing and maintaining long- term suppression of viral infections. Effective viral clearance, which occurs within a week of initial infection, requires both CD8+ effector T cell–mediated killing of virally infected cells as well as CD4+ T cell–dependent enhancement of CD8+ and B cell responses. Following viral clearance, the majority of virus- specific T cells undergo apoptosis; however, retention of a virus-specific memory T cell population is required for long-term antiviral immunity Chronic viral infections must either evade or suppress adaptive immunity. Infections are characterized by persistent antigenic activation of T cells - driving a nonresponsive cell state or T cell “exhaustion”.  T cell immune responses to SARS-CoV Marked leukopenia - dramatic loss of CD4 T cells and CD8 T cells Severe infection - delayed development of the adaptive immune response and prolonged virus clearance T cell epitopes found in the S, N and M viral proteins – most CD4 T cells specific for S protein Th1 response - key for successful control of SARS-CoV Magnitude and frequency of CD8 memory T cells exceeded that of CD4 memory T cells Virus-specific memory CD4 and CD8 T cells - found in individuals who recovered from the infection at least 10 years after acute infection  T cell immune response to MERS High frequencies of MERS-CoV-reactive CD8+ T cells - observed in patients with severe/moderate illness, before detection of Abs and CD4+ T cell responses. Strong specific T-cell response against the MERS-CoV S protein on day 24 after disease onset All deceased patients displayed rapid drops in their lymphocyte counts IL-12 and interferon gamma levels - lower in a fatal case than in a patient who survived the infection Early rise of CD8+ T cells - correlates with disease severity and at the convalescent phase, dominant Th1 type helper T cells are observed Plasma cytokine levels in patients with COVID-19: The Cytokine Storm Levels of interleukin 2R (IL-2R), IL-6, IL- 10, and tumor necrosis factor α (TNF-α) were markedly higher in severe cases than in moderate cases.  Lymphopenia Marked lymphopenia (drop in lymphocytes) observed in T cells in patients with acute phase of infection Changes in the phenotype of T cells in the peripheral blood Reduced CD4+ and CD8+ T cells in moderate and severe COVID-19 in acute phase Decreases in CD8+ T cells in patients admitted to ICU – correlates with COVID- associated disease severity and mortality Increases in activated CD4 and CD8 T cells which display an exhausted phenotype – upregulated expression of inhibitory markers such as PD-1 and Tim-3 in persistent COVID Production of inflammatory cytokines such as GM-CSF by CD4 T cells in critically ill patients Reduced frequencies of T regulatory cells in severe COVID-19.  Mechanisms contributing to reduced T cells in the blood Cause of peripheral T cell loss in moderate to severe COVID-19 remains elusive Similar phenomenon is observed in other viral infections Cytokines such as IFN-α,IL-6 and TNF-α may inhibit T cell circulation in blood by promoting retention in the lymphoid organs and attachment to endothelium T cell recruitment to sites of infection may reduce their presence in the peripheral blood - increase in CD8 T cell infiltrate in bronchoalveolar lavage fluid Direct viral infection has not been reported  CD4 and CD8 T Cell Responses T cell responses specific for Spike, Matrix and Nucleocapsid proteins found in convalescent (recovering patients) COVID patients. T cell reactivity to SARS-CoV-2 is detected in non-exposed individuals  Anti-viral T cell responses SARS-CoV2 specific T cells are observed in most individuals CD4 and CD8 T cell responses directed against different antigens but mostly against the spike and nucleocapsid proteins Majority of SARS-CoV2 CD4+ T cells exhibit a CCR7+CD45- phenotype (central memory 50-60%) and some exhibit a CCR7-CD45- phenotype (effector memory 25-40%) SARS-CoV2 CD8+ T cells are predominately express the effector memory phenotype SARS-CoV2 specific CD4 and CD8 T cells display a Th1 profile with increased cytotoxic activity and elevated expression of immune activation markers  Pro-inflammatory cytokine secretion profile Activated CD4+ T cells produce high amounts of cytokines whether they are activated to the spike or non-spike protein.  SARS-CoV2- specific T cells and associations with disease severity Detection of early SARS-Cov2 CD4+ T cell response associated with less severe disease more so than antibody response or CD8+ T cell response Early induction of CD4+ T cells secreting interferon gamma are found much earlier in patients with mild disease and correlates with viral clearance Preliminary evidence shows that very rapid induction of CD8+ T cells could be cause of asymptomatic disease Severe COVID 19 is associated with poor polyfunctionality and proliferative capacity and enhanced immune activation Cytokine profile of CD4 and CD8-specific T cells to SARS-CoV2 proteins SARS-CoV-2 reactive CD4+ T cells have been detected in unexposed individuals.  A range of pre-existing memory CD4+ T cells that are cross-reactive with SARS-CoV-2 and the common cold coronaviruses - HCoV-OC43, HCoV-229E, HCoV-NL63, HCoV-HKU1 Healthy individuals were previously exposed to common cold coronaviruses and responded better to SARS-CoV-2 infection.  Phenotype and function of T cell subsets Increase in activated T cells characterized by expression of HLA-DR, CD38, CD69, CD25, CD44 and Ki-67 CD8 T cells seem to be more activated than CD4 T cells Higher expression of various co-stimulatory and inhibitory molecules such as OX-40, CD137, CTLA-4, NKG2a and TIGIT Levels of most markers tended to increase in severe versus non-severe cases Impaired functionality in CD4 and CD8 T cells in critically ill patients T cells in severe COVID-19 seem to be more activated and exhausted based on the continuous expression of inhibitory markers such as PD-1 and Tim-3 Increase in follicular helper T cells (Tfh) and effector molecules such as Gzm A, Gzm B and perforin but a decrease in levels of inhibitory molecules in recovering patients  B cell immunity to SARS-CoV IgG antibodies appear early on between day 4-45 after onset of symptoms. IgG antibody and neutralizing antibodies (Nab) titers were highly correlated, peaking at month 4 after the onset of disease. Marked decease in antibodies at two years post infection. Nabs to Spike protein peak at 20–30 days after infection and are sustained for over 150 days. NAb titers decreased markedly after month 16. IgG level of mild patients was significantly higher than that of severe patients. SARS-CoV-infected patients with fatal outcomes display deficient antibody production against the S protein compared to non-severe patients.  Antibody responses to SARS-CoV One year after infection, Spike-specific IgG and neutralizing antibodies are detected in the individuals who recovered compared to at high-risk healthy controls. Healthy individuals did not have any spike-specific antibodies. Specific SpecificMemory Memory TT and and B B cell cell Responses to Responses to SARS-CoV Memory T cell responses were detected in 60% of SARS Tpatients Memory cell six yearswere responses afterdetected in infection. 60% of SARS patients six years after T cell response much stronger than B cell or infection. antibody. No SARS-specific No SARS-specific memory memory B cell B cell responses responses werewere detected. detected. Specific SARS-CoV Specific IgG were responses responses were notin not detected detected >90% in of >90% of patients. patients.  IgM and IgG to SARS-CoV-2 proteins IgM and IgG antibodies to different areas of SARS-CoV-2 proteins (spike, nucleocapsid, other receptor binding domains) were seen in patients with COVID- 19. IgM always generated in response to acute infection, then turned into IgG antibodies. IgG and IgM levels in acute and convalescent phases There is not a signficant difference between IgM in symptomatic vs non- symptomatic individuals. There is a difference in amount of IgG between symptomatic and non- symptomatic individuals. During the convalescent phase: response in symptomatic antibodies was noticeably greater than the asymptomatic individuals. Antibody-mediated immunity in SARS-COV-2 Virus-specific IgM and IgG are detected in serum between 7-14 days after onset of symptoms Antibodies binding to the receptor binding domain of S protein are neutralizing and block virus interactions with host entry receptor ACE2 Viral RNA is inversely correlated with neutralizing antibody titers SARS-CoV2 humoral response is short-lived and memory B cells may disappear  SARS-CoV-2-specific humoral immunity COVID-19 patients - IgM and IgG responses to SARS-CoV-2 proteins, especially Nucleocapsid Protein and Spike-Receptor Binding Domain Infected patients could maintain their IgG levels, at least for two weeks after discharge. Sera from several patients could inhibit SARS-CoV-2 entry in target cells. COVID-19 patients had neutralizing anti-Spike-Receptor Binding Domain IgG post discharge. Correlation between the neutralizing antibody titers and the numbers of Nucleocapsid Protein-specific T cells, indicating that the development of neutralizing antibodies may be correlated with the activation of anti-viral T cells.  Serological signatures track with SARS-CoV-2 survival Limited early differences were seen in titers and neutralization Shift in the balance of spike to nucleocapsid antibodies in convalescent versus deceased group Spike-specific phagocytic and complement fixing activity was increased in convalescent individuals Individuals that passed away from SARS- CoV-2 had increased Nucleocapsid protein specific antibodies.  2003 CoV pandemic SARS-CoV viral particles markedly activated TLR-mediated innate immune Immunological responses Lymphopenia occurred in the majority of patients and was associated with similarities severe disease. SARS also significantly affected children, in whom lymphopenia was also a common feature between COVID- Development of virus-specific memory T cells was associated with resolution 19 and recent of disease and protection from subsequent infection 2009 H1N1 influenza A pandemic pandemics? Lymphopenia occurred in the majority of patients. Occurred frequently and caused lymphopenia and significant morbidity in children Marked elevation of systemic innate inflammatory factors including MCP-1 and IL-6, and elevated IL-6 correlated with disease severity. 2013 MERS-CoV pandemic Lymphopenia occurred less frequently was associated with disease severity, and recovery was associated with improved outcomes Neutralizing antibodies to MERS and MERS-CoV–specific CD4+ T cells correlated with disease severity. Elevations in serum IL-6 levels were also observed in patients whose clinical course worsened  Long CoVID 10% of individuals report persistent symptoms after CoVID whether it was asymptomatic, mild, or severe problem Disease burden varies from mild symptoms to profound disability – major health challenge Increases in activated B cells Presence of exhausted T cells – PD1+TIM3+ Decreased levels of dendritic cells Decreased levels of central memory T cells Higher levels of IgG specific for SARS-CoV2-spike protein Higher levels of IgG specific for EBV and VZV Persistent viral antigens, latent herpes virus reactivation and chronic inflammation – may contribute to long CoVID