Broader Epstein-Barr virus-specific T-cell receptor repertoire in patients with multiple sclerosis

Introduction: Epstein-Barr virus (EBV) infection precedes signs of multiple sclerosis (MS) pathology and cross-reactive antibodies might link EBV infection mechanistically to CNS autoimmunity. Objective(s): As an altered immune reaction against EBV antigens in T cells of MS patients has been suggested, we queried deep, peripheral blood T-cell receptor beta chain (TCRbeta) repertoires of 1395 MS patients, 887 controls, and 35 monozygotic, MS-discordant twin pairs for multimerconfirmed, viral antigen-specific TCRbeta sequences. Aim(s): Quantification of HLA-matched EBV-specific, CMV-specific, Influenza A virus-specific, and SARS-CoV-2-specific TCRbeta sequences in MS patients, controls, and COVID-19 patients. Result(s): We detected higher numbers of MHC-I restricted EBVspecific TCRbeta sequences in MS patients, and validated this with independent cohorts and sequencing methods. Genetic as well as early environmental factors could be excluded by validation in diseased siblings of monozygotic twin pairs discordant for MS. Therapeutic blockade of VLA-4-mediated T-cell extravasation amplified this observation, while interferon beta treatment and B-cell depletion did not modulate occurrence of EBV-specific T cells. EBV-specific CD8+ T cells were characterized as effectormemory cells in peripheral blood and cerebrospinal fluid of healthy controls. In MS patients, the cerebrospinal fluid also contained EBV-specific central-memory CD8+ T cells, suggesting recent priming. Conclusion(s): MS is not only preceded by EBV infection, but also associated with a broader EBV-specific TCR repertoire, which would be consistent with an ongoing anti-EBV immune reaction in MS patients.

A CASE OF MICROSCOPIC POLYANGIITIS (MPA) FOLLOWING SARS-COV-2 INFECTION

SESSION TITLE: Unique Inflammatory and Autoimmune Complications of COVID-19 Infections SESSION TYPE: Rapid Fire Case Reports PRESENTED ON: 10/19/2022 12:45 pm - 1:45 pm INTRODUCTION: ANCA-associated vasculitis (AAV) is a systemic disease that causes inflammation of small vessels in various organs, such as the lungs, kidneys, and nervous system. We report a case of AAV following SARS-CoV-2 infection. CASE PRESENTATION: A 64-year-old female from Albania with no known medical history, presented with intermittent low-grade hemoptysis and fever for 1 week prior to admission. She had chills, myalgias, fatigue, and poor appetite 6 weeks prior. On arrival, she was febrile (101F), and hypoxic (Spo2 92% on 3L O2). Labs were significant for anemia [Hb 6.8 g/dl], acute kidney injury (AKI) [Cr 2.5 mg/dl]. She was found to be Positive for Sars-CoV-2 by PCR. Chest X-Ray showed patchy bilateral airspace opacities with peripheral and lower lobe predominance, concerning for atypical pneumonia (Fig 1). Urinalysis was significant for proteinuria (2+) and hematuria (2+). CT (Computed Tomography) thorax showed extensive bilateral airspace disease (dense consolidations and ground-glass opacities) favoring multifocal infection and mediastinal lymphadenopathy(Fig 2). Due to the chronicity of her symptoms and atypical imaging for viral pneumonia, other diagnoses were explored including bacterial superinfection, Tuberculosis, and autoimmune disease. Sputum studies were negative for infections including Acid Fast Bacilli. Workup revealed elevated Antimyeloperoxidase antibodies (MPO) and positive COVID-19 Ig G. She was started on methylprednisolone 1g for AAV. Renal biopsy revealed pauci-immune glomerulonephritis with features of cellular crescent consistent with microscopic polyangiitis (Fig 3). Follow-up CT chest showed improved airspace abnormalities and mediastinal lymphadenopathy. After induction therapy with Rituximab was initiated, she continued to recover and was discharged home. DISCUSSION: The pathogenesis of AAV is believed to be an aberrant pathogenic autoimmune response that follows an initial insult which can include infections. SARS-CoV-2 has been associated with the emergence of autoimmune diseases in susceptible patients(1). The proposed mechanism is linked to elevated levels of circulating neutrophil extracellular traps (NETs) observed in covid infection. These NETS are covered with proteins including neutrophilic enzymes which can activate complement pathways causing tissue destruction and vasculitis. The diagnosis of new-onset AAV can be challenging in COVID-19 patients as symptoms and clinical manifestations of both diseases can overlap. AAV should be considered strongly in patients who are currently infected or have been infected with SARS-CoV-2 and present with atypical or non-resolving pneumonia and other organ involvement such as AKI to avoid permanent organ damage. CONCLUSIONS: The presence of non-resolving or atypical pneumonia and AKI in a patient with SARS-CoV-2 should prompt evaluation of immunological markers to assess or rule out AAV for early diagnosis and treatment. Reference #1: Caso F, Costa L, Ruscitti P, Navarini L, Del Puente A, Giacomelli R, Scarpa R. Could Sars-coronavirus-2 trigger autoimmune and/or autoinflammatory mechanisms in genetically predisposed subjects? Autoimmun Rev. 2020;19(5):102524. doi: 10.1016/j.autrev.2020.102524 DISCLOSURES: No relevant relationships by Tarik Al-Bermani No relevant relationships by Anant Jain No relevant relationships by Ian Kaplan No relevant relationships by Alina Kifayat No relevant relationships by Lisa Paul

Ivory: Learning Network Adaptive Streaming Codes

With the growing interest in web services during the current COVID-19 outbreak, the demand for high-quality low-latency interactive applications has never been more apparent. Yet, packet losses are inevitable over the Internet, since it is based on UDP. In this paper, we propose Ivory, a new real-world system framework designed to support network adaptive error control in real-time communications, such as VoIP, using a recently proposed low-latency streaming code. We design and implement our prototype over UDP that can correct or retransmit lost packets conditional on network conditions and application requirements.To maintain the highest quality, Ivory attempts to correct as many lost packets as possible on-the-fly, yet incurring the smallest footprint in terms of coding overhead over the network. To achieve such an objective, Ivory uses a deep reinforcement learning agent to estimate the best coding parameters in real-time based on observed network states and experience learned. It learns offline the best coding parameters to use based on previously observed loss patterns and takes into account the round-trip time observed to decide on the optimum decoding delay for a low-latency application. Our extensive array of experiments shows that Ivory achieves a better trade-off between recovering packets and using lower redundancy than the state-of-the-art network adaptive streaming codes algorithms. © 2022 IEEE.

THE T-CELL RESPONSE TO SARS-COV-2 VACCINATION IN PATIENTS WITH INFLAMMATORY BOWEL DISEASE IS OFTEN DEFICIENT IN ANTIBODY-RESPONDERS, AND AUGMENTED BY ANTI-TNF THERAPY

Background: Vaccination against SARS-CoV-2 is a highly effective strategy to protect against infection, which is predominantly mediated by vaccine-induced antibodies. Postvaccination antibodies are robustly produced by those with inflammatory bowel disease (IBD) even on immune-modifying therapies but are blunted by anti-TNF therapy. In contrast, T-cell response which primarily determines long-term efficacy against disease progression, , is less well understood. We aimed to assess the post-vaccination T-cell response and its relationship to antibody responses in patients with inflammatory bowel disease (IBD) on immunemodifying therapies. Methods: We evaluated IBD patients who completed SARS-CoV-2 vaccination using samples collected at four time points (dose 1, dose 2, 2 weeks after dose 2, 8 weeks after dose 2). T-cell clonal analysis was performed by T-cell Receptor (TCR) immunosequencing. The breadth (number of unique sequences to a given protein) and depth (relative abundance of all the unique sequences to a given protein) of the T-cell clonal response were quantified using reference datasets and were compared to antibody responses. Results: Overall, 303 subjects were included (55% female;5% with prior COVID) (Table). 53% received BNT262b (Pfizer), 42% mRNA-1273 (Moderna) and 5% Ad26CoV2 (J&J). The Spike-specific clonal response peaked 2 weeks after completion of the vaccine regimen (3- and 5-fold for breadth and depth, respectively);no changes were seen for non-Spike clones, suggesting vaccine specificity. Reduced T-cell clonal depth was associated with chronologic age, male sex, and immunomodulator treatment, and was preserved by nonanti- TNF biologic therapies;augmented clonal depth was associated with anti-TNF treatment (Figure). TCR depth and breadth were associated with vaccine type;after adjusting for age and gender, Ad26CoV2 (J&J) exhibited weaker metrics than mRNA-1273 (Moderna) (p= 0.01 for each) or BNT262b (Pfizer) (p=0.056 for depth). Antibody and T-cell responses were only modestly correlated;while those with robust humoral responses also had robust TCR clonal expansion, a substantial fraction of patients with high antibody levels had only a minimal T-cell clonal response (Figure). Conclusion: Age, sex and select immunotherapies are associated with the T-cell clonal response to SARS-CoV-2 vaccines, and T-cell responses are low in many patients despite high antibody levels. These factors, as well as differences seen by vaccine type may help guide reimmunization vaccine strategy in immune-impaired populations. Further study of the effects of anti-TNF therapy on vaccine responses are warranted. (Table Presented)

SARS-COV-2 VACCINATION INDUCES A PREDOMINENTLY CLASS II (CYTOKINE EFFECTOR) T CELL RESPONSE, BUT THE CLASS I RESPONSE IS AUGMENTED BY ANTI-TNF THERAPY AND VACCINE TYPE

BACKGROUND: In response to COVID-19 vaccination, cytotoxic and cytokine effector T cell immune responses are elicited in the T-cell compartment, based on recognition of epitopes presented by Class I or Class II MHC molecules, respectively. The levels of these distinct T-cell responses may have significant implications for immunization strategies and risk assessment. Knowledge of these two responses after vaccination is still largely unknown, especially in the context of immunomodulatory treatment regimens. METHODS: We performed T-cell receptor (TCR) immunosequencing (Adaptive Biotechnologies, Seattle WA) of IBD patients (N=303) and health care worker controls (HCW, N=224) at up to four time points (prior to dose 1, prior to dose 2, 2 weeks after dose 2, 8 weeks after dose 2). Two metrics of TCR response, breadth (# of unique antigen-specific sequences) and depth (expansion of antigen-specific sequences), were calculated for all sequences and Class I- and Class II-specific sequences, and compared to demographics, IBD treatment, and vaccine type. Subjects with exceptional Class I or Class II responses were calculated as significant residuals relative to the Class I vs. Class II regression line. Similar associations were observed for both breadth and depth: breadth is presented here for brevity. RESULTS: Both Class I- and Class II-specific T-cell responses peaked 2 weeks after dose 2, and significantly correlated with lower age, female gender, and mRNA vaccine type (mRNA-1273/Moderna and BNT262b/Pfizer, versus vector vaccine AD26CoV2/J&J) (FIGURE). Class II responses comprised ~85% of detected TCR response in both IBD and HCW subjects. Among IBD patients, there was a significant elevation of the class I response with anti-TNF treatment (p=0.04). This effect was most pronounced at later timepoints, suggesting that anti-TNF permitted a more persistent Class I-specific response. Among patients with exceptionally high or low Class I TCR response, there were significant differences in TCR metrics across vaccine types (p=0.0035). 21% of AD26CoV2 patients were highly Class I-biased (Zscore>1, 9.4% and 7.3% for BNT162 and mRNA-1273, respectively), and this was correlated with lower anti-spike serology 2 and 8 weeks after vaccination (p<1E-10). Conversely, mRNA- 1273 patients were Class I-deficient, representing 25.3% of patients but 44.1% of highly Class I-deficient patients (Zscore<1, 0% for AD26CoV2). CONCLUSION: The T-cell clonal response to SARS-CoV-2 vaccine is Class II-predominant, but the Class I-response is augmented by anti-TNF therapy and vector vaccine type. These factors may help guide reimmunization vaccine strategy in immune-impaired populations, and warrant further study of the effects of anti-TNF therapies on vaccine efficacy.(Figure Presented)Figure: TCR response time course (left);effect of anti-TNF (middle);effect of vaccine type (right). Breadth was predominantly Class II for most patients, with maximum response at 2 weeks after full vaccination (left). The balance of Class I vs. Class II response was significantly biased towards Class I at 8 weeks after full vaccination for patients receiving anti-TNF treatment for IBD (asterisk, p=0.036). Patients receiving AD26CoV2 vaccines were significantly increased in Class I responses, while patients receiving mRNA-1273 vaccines were significantly reduced for Class I responses (t-tests: p=0.0036 at 8 weeks [asterisk], p=0.051 at 2 weeks).

PATIENTS WITH INFLAMMATORY BOWEL DISEASE HAVE IMPAIRED HUMORAL BUT PRESERVED CELLULAR RESPONSES TO SARS-COV-2 MRNA VACCINATION

Background: Vaccine-induced protection against SARS-CoV-2 infection is predominantly mediated by humoral immunity;protection against disease progression is primarily determined by cellular immunity. Patients with inflammatory bowel disease (IBD) have high rates of post-vaccination anti-Spike IgG [IgG(S)] seroconversion, but postvaccination immune responses relative to non-IBD controls have not been well described. We aimed to assess post-vaccination humoral (antibody) and cellular (T-cell) responses in IBD relative to healthcare worker (HCW) controls. Methods: We evaluated IBD patients enrolled in a US registry referred from 26 centers at 2, 8, and 16 weeks after completing 2 doses of SARSCoV- 2 mRNA vaccination and compared results to non-IBD non-immunosuppressed HCW participating in a parallel study. We analyzed plasma antibodies to the receptor binding domain of the viral spike protein using the SARS-CoV-2 IgG-II assay (Abbott Labs, Abbott Park, IL);IgG(S) > 50 AU/mL was defined as positive. Those with prior COVID were excluded. We also performed T-cell clonal analysis by T-cell receptor (TCR) immunosequencing at 8 weeks (Adaptive Biotechnologies, Seattle, WA). The breadth (number of unique sequences to a given protein) and depth (relative abundance of all the unique sequences to a given protein) of the T-cell clonal response were quantified using reference datasets. Analyses were adjusted for age, sex and vaccine type. Results: Overall, 1805 subjects were included (IBD n=1074 (65% Crohn's disease, 35% ulcerative colitis);HCW n=731). Age and sex were similar between both cohorts;Hispanic ethnicity and Asian race were less common among IBD than HCW (Table). Vaccine type included BNT162b2 (Pfizer) (75% of IBD, 98% of HCW) and the remainder mRNA-1274 (Moderna). IBD treatments included anti- TNF (46%), other biologics (33%), other immune suppressing therapy (9%), and no immune suppression (12%). Postvaccination antibody levels were lower among IBD than HCW both before and after adjusting for vaccine type (p<0.0001 each timepoint;Figure). After further restricting the IBD cohort to those on no immune-suppressive therapies, antibodies remained lower in IBD vs HCW at 2w (p=0.008) and 8w (p<0.0001), but not 16w (p=0.07). Among 321 subjects with available whole cell samples at 8 weeks (IBD n=163, HCW =158), Spikespecific TCR responses were similar between IBD and HCW for both clonal breadth and depth in both unadjusted and adjusted analyses;sub-analyses of those on biologics yielded similar results. Conclusion: Patients with IBD have dampened humoral responses, but similar cellular responses, after SARS-CoV-2 mRNA vaccination relative to HCW. These findings suggest a potentially greater risk of infection, but not of disease progression, among those with IBD, and should be considered to help guide booster dosing strategies for the IBD population. (Figure Presented) (Figure Presented) Figure: Post-vaccination immune responses: (A) Antibody responses are lower in IBD relative to non-IBD healthcare workers at 2, 8, and 16 weeks (p<0.0001 at each timepoint). In contrast, post-vaccination Spike-specific T-cell receptor clonal breadth (B1) and clonal depth (B2) at 8 weeks are similar in IBD compared to healthcare workers.

Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection and Vaccination

Background. T cells are central to the early identification and clearance of viral infections and support antibody generation by B cells, making them desirable for assessing the immune response to SARS-CoV-2 infection and vaccines. We combined 2 high-throughput immune profiling methods to create a quantitative picture of the SARS-CoV-2 T-cell response that is highly sensitive, durable, diagnostic, and discriminatory between natural infection and vaccination. Methods. We deeply characterized 116 convalescent COVID-19 subjects by experimentally mapping CD8 and CD4 T-cell responses via antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I and 284 class II viral peptides. We also performed T-cell receptor (TCR) repertoire sequencing on 1815 samples from 1521 PCR-confirmed SARS-CoV-2 cases and 3500 controls to identify shared public TCRs from SARS-CoV-2-associated CD8 and CD4 T cells. Combining these approaches with additional samples from vaccinated individuals, we characterized the response to natural infection as well as vaccination by separating responses to spike protein from other viral targets. Results. We find that T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the SARS-CoV-2 T-cell response peaks about 1-2 weeks after infection and is detectable at least several months after recovery. Applying these data, we trained a classifier to diagnose past SARS-CoV-2 infection based solely on TCR sequencing from blood samples and observed, at 99.8% specificity, high sensitivity soon after diagnosis (Day 3-7 = 85.1%;Day 8-14 = 94.8%) that persists after recovery (Day 29+/convalescent = 95.4%). Finally, by evaluating TCRs binding epitopes targeting all non-spike SARS-CoV-2 proteins, we were able to separate natural infection from vaccination with > 99% specificity. Conclusion. TCR repertoire sequencing from whole blood reliably measures the adaptive immune response to SARS-CoV-2 soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points, and distinguishes post-infection vs. vaccine immune responses with high specificity. This approach to characterizing the cellular immune response has applications in clinical diagnostics as well as vaccine development and monitoring.

Clinical Validation and Performance of a T-cell Immunosequencing Assay to Identify Past SARS-CoV-2 Infection

Background. Our understanding of the SARS-CoV-2 immune response has critical gaps that are inadequately addressed with available tools. We report the clinical performance of T-Detect COVID, the first T-cell assay to identify prior SARS-CoV-2 infection using T-cell receptor (TCR) sequencing and repertoire profiling from whole blood samples. Methods. The T-Detect COVID assay combines high-throughput immunosequencing of the TCRß gene from blood samples with a statistical classifier demonstrating 99.8% specificity for identifying prior SARS-CoV-2 infection. The assay was employed in several retrospective and prospective cohorts to assess primary and secondary Positive Percent Agreement (PPA) with SARS-CoV-2 RT-PCR (N=205;N=77);primary and secondary Negative Percent Agreement (NPA;N=87;N=79);PPA compared to SARS-CoV-2 serology (N=55);and pathogen cross-reactivity (N=38). The real-world performance of the test was also evaluated in a retrospective review of test ordering (N=69) at a single primary care clinic in Park City, Utah. Results. In validation studies, T-Detect COVID demonstrated high PPA (97.1% ≥15 days from diagnosis) in subjects with prior PCR-confirmed SARSCoV-2 infection;high NPA (~100%) in SARS-CoV-2 negative cases;equivalent or higher PPA with RT-PCR compared to two commercial EUA antibody tests;and no evidence of pathogen cross-reactivity. Review of assay use in a single clinic showed 100% PPA with RT-PCR in individuals with past confirmed SARS-CoV-2 vs. 85.7% for antibody testing, 100% agreement with positive antibody results, and positive results in 2/4 convalescent subjects with seroreversion to a negative antibody. In addition, 12/69 (17.3%) individuals with absent or negative RT-PCR tested positive by T-Detect COVID, nearly all of whom had compatible symptoms and/or exposure. TCR positivity was observed up to 12+ months (median 118 days) from the date of positive RT-PCR. Conclusion. A T-cell immunosequencing assay shows high clinical performance for identifying past SARS-CoV-2 infection from whole blood samples. This assay can provide additional insights on the SARS-CoV-2 immune response, with practical implications for clinical management, risk stratification, surveillance, assessing vaccine immunity, and understanding long-term sequelae.