PRESERVED SARS-COV-2 VACCINE CELL-MEDIATED IMMUNOGENICITY IN INFLAMMATORY BOWEL DISEASE PATIENTS ON IMMUNEMODULATING THERAPIES

BACKGROUND: Immune-modulating medications for inflammatory bowel diseases (IBD) have been associated with suboptimal vaccine responses. There is conflicting data with SARS-CoV-2 vaccination. METHODS: We measured SARS-CoV-2 vaccine immunogenicity at 2 weeks post 2nd mRNA vaccine in IBD patients as compared to normal healthy donors (NHD). We measured humoral immune responses to SARS-CoV-2: anti-spike Immunoglobulin G (IgG) and anti-receptor binding domain (RBD) IgG were measured by ELISA, and neutralizing antibody titers were measured using recombinant, reporter SARS-CoV-2. Antigen specific memory B cells were measured using recombinant SARS-CoV-2 proteins. Activation induced marker T cell (AIM) assays were performed using SARS-CoV-2 spike megapools. Immunophenotyping was performed by flow cytometry. RESULTS: We enrolled 29 patients with IBD (19 with Crohn's disease, 10 with ulcerative colitis) on infliximab (IFX) monotherapy (N=9), IFX combination therapy with a thiopurine (N=9), vedolizumab monotherapy (N= 11) as compared to matched NHD (N=12). At 2 weeks post vaccination, all subjects made detectable anti-spike IgG and anti-RBD IgG. There were no differences in anti-spike IgG titers among the different groups. IBD patients on IFX monotherapy, but not IBD patients on IFX combination therapy or vedolizumab monotherapy, had lower anti-RBD and neutralization titers as compared to NHD (p-value: 0.041 and 0.023, respectively) (Fig. 1). There were no significant differences in the percentage of spike-specific or RBD-specific memory B cells in IBD patients as compared to NHD (Fig. 1). There were no differences in the percentage of spike-specific CD4+ or CD8+ T cells in all IBD patients as compared to NHDs (Fig. 2). CONCLUSIONS: We demonstrate overall comparable and perserved cell-mediated immunity to SARS-CoV-2 vaccination in a small cohort of IBD patients treated with a range of different immune-modulating medications as compared to healthy controls. Larger numbers of patients are needed to validate these findings.

T-CELL RESPONSE QUALITY to ACUTE SARS-CoV-2 INFECTION, IMMUNE MEMORY, and HCoV

Background: SARS-CoV-2 specific T-cell response has been associated with disease severity, immune memory and heterologous response to endemic coronaviruses (HCoV). However, an integrative approach combining a comprehensive analysis of the quality of SARS-CoV-2 specific T-cell response and antibody levels is needed. Methods: We assayed SARS-CoV-2 specific T-cell response in 103 participants. Thirty-seven (18 mild and 19 severe) were hospitalized during acute COVID-19 and 33 were recruited seven months after SARS-CoV-2 infection (19 previously hospitalized (H) and 14 non-hospitalized (NH) during acute infection). Pre-COVID-19 healthy donors (HD, n=33) were included. PBMCs were stimulated with Spike (S) and Nucleocapside (N) SARS-CoV-2 peptide pools. Likewise, an optimized peptide pool of HCoV S protein was used in HD. T-cell polyfunctionality by intracellular cytokine staining (IFN-γ, IL-2, TNF-α, CD107a and perforin (PRF)) was assayed by multiparametric flow cytometry together with measurements of T cell subsets, activation, exhaustion and senescence. Anti-S SARS-CoV-2 and HCoV IgG titers and pro-inflammatory markers were measured in plasma. Non-parametric statistic was used for the analysis. Results: Mild disease was associated with high T-cell polyfunctionality biased to IL-2 production and inversely correlated with anti-S IgG levels (eg, N-specific EM CD4+ IL-2+ T-cell, r=-0.594, p=0.004). However, only IFN-γ combinations without PRF production was mostly observed for severe disease (eg, S-specific TEMRA CD4+ CD107a-IFN-γ+IL-2-PRF-TNF-α-T-cells, p=0.008). Moreover, this response was long-lasting seven months after SARS-CoV-2 infection. Both NH and H individuals presented robust anti-S IgG levels and SARS-CoV-2 specific T-cell response. In addition, only H individuals showed a T-cell exhaustion profile (eg, TEMRA CD4+ TIGIT+ T cells, p=0.0004). Combinations including IL-2, but not IFN-γ, in response to HCoV S protein, were associated with SARS-CoV-2 S-specific T-cell response in HD (eg, S-specific CM CD8+ CD107a-IFN-γ-IL-2+PRF-TNF-α-T-cells, r=5414, p=0.001). Conclusion: T-cell polyfunctionality features were associated with disease severity. Moreover, T-cell response was robust seven months after infection, although previously hospitalized patients showed signs of exhaustion. SARS-CoV-2 and HCoV immune cross-reactivity have implications for protective immunity against SARS-CoV-2 to design new prototypes of vaccines in order to achieve of broader long-lasting protection against COVID-19.

Immunologic Monitoring of a Breakthrough Infection in a Heart and Kidney Transplant Recipient

Introduction Solid organ transplant recipients (SOTR) have lower SARS-CoV-2 spike seroconversion than healthy subjects (HS) following vaccination. A breakthrough (BT) infection is defined as the detection of SARS-CoV-2 in a respiratory specimen after a person is ≥14 days after completing the recommended doses for a vaccine. We report a case of SARS-CoV-2 BT infection in a SOTR who was immunologically followed longitudinally following vaccination. Case Report A 44-year-old man with a history of non-ischemic cardiomyopathy (NICM) and end stage renal disease had undergone heart and kidney transplantation in December 2017 with thymoglobulin induction. His NICM was secondary to radiation for non-Hodgkin's lymphoma treated with autologous bone marrow transplant in 2001. Maintenance immunosuppression consisted of sirolimus 2mg daily, tacrolimus 2mg twice daily (BID), and prednisone 5mg daily at his 1st Moderna vaccine in April 2021. In anticipation of surgery, sirolimus was stopped and mycophenolate mofetil (MMF) 500mg BID was started. He was on this regimen at the time of his 2nd Moderna vaccine. Sirolimus was restarted in July and increased to 1mg daily while continuing MMF 500mg BID, tacrolimus, and prednisone. At the end of July, the patient was exposed to several family members with COVID-19. He tested positive 89 days after his 2nd Moderna vaccine (cycle threshold of 33.5). He was asymptomatic at the time, but later developed fever, myalgias, headache, and loss of taste and smell and was treated with casirivimab and imdevimab monoclonal antibody (mAb) infusion. We assessed the patient's immunologic response 14 days post 2nd Moderna vaccination and at BT infection prior to mAb infusion and compared this to HS. The patient developed SARS-CoV-2 spike-specific CD4+ T cells at 14 days post 2nd mRNA vaccine at a frequency below the average frequency for HS. At BT infection, the patient did not have SARS-CoV-2 spike-specific CD4+ T cells, partly due to virus induced lymphopenia. The patient did not develop spike-specific CD8+ T cells, spike IgG or neutralizing antibodies at 14 days post 2nd Moderna vaccination or at BT infection. Summary The patient developed SARS-CoV-2-specific CD4+ T cells following vaccination. His uneventful recovery may be secondary to these SARS-CoV-2 specific CD4+ T cells post vaccination as well as receiving mAb therapy 8 days post infection.

Adoptive Immune Responses to Sars-Cov2 Vaccination in CART19 Treated Patients

Background: The two FDA approved mRNA-based SARS-CoV2 vaccines have shown >90% efficacy at preventing COVID and eliciting protective immunity in nearly all healthy individuals. However, the extent of vaccine induced antibody and T cell immunity in immunocompromised patients is not well known. Our study objective is to determine if patients with hematologic malignancies treated with B-cell targeting chimeric antigen receptor (CAR) T cell therapies can mount antibody and T cell immune responses to SARS-CoV2 vaccines. A prospective single-center study to evaluate the SARS-CoV2 immune responses in immunocompromised individuals (COVAX Study) was initiated at University of Pennsylvania following the IRB guidelines. The study enrolled 8 healthy adults,12 patients are in remission after treatment (average of 40.6 months) with CART cells targeting either CD19 or CD19+CD22 and received both doses of SARS-CoV2 vaccine. Methods and Results: Serology to SARS-CoV2 spike-receptor binding domain (RBD) IgG, RBD-IgA, RBD-IgM and spike-specific T cell responses were measured prior to vaccination and serially up to 28 days after booster vaccination. RBD-IgG and RBD-IgA were detected in 8/8 and 7/8 healthy subjects compared to 5/12 and 2/12 CART patients, respectively (Figure A). In the CART cohort, several patients who demonstrated an induction of RBD-IgG (57.2/uL +/- 20.2) compared to those who were RBD-IgG-negative (9/uL +/- 10.1, ANOVA with multiple comparisons test p=0.017) have higher level of circulating B cells. No association was found with time since CART infusion, age, disease type, or vaccine manufacturer. All 8 healthy subjects demonstrated induction of SARS-Cov2 spike-specific CD4 + T cell immunity compared to 7 out of 11 CART patients (Figure B). RBD-IgG responses were not correlated with CD4 + T cell activation (Pearson correlation, R=0.21, p=0.53). Indeed, 3 CART patients demonstrated robust CD4 + T cell activation despite absence of antibody induction. Overall, 8/12 CART patients demonstrated induction of either or both humoral and T cell immune responses. Conclusions: We show that immune responses to SARS-CoV2 mRNA vaccines are induced in majority of patients who have been treated with CART therapies targeting B-cell lineage antigens. Induction of vaccine-specific antibody was strongly associated with the level of circulating B cells. However, in CART cohort patients despite severe humoral immune deficiency, strong CD4 + T cell responses were observed suggestive of a sufficient protective immunity. [Formula presented] Disclosures: Frey: Novartis: Research Funding;Sana Biotechnology: Consultancy;Kite Pharma: Consultancy;Syndax Pharmaceuticals: Consultancy. Garfall: Amgen: Honoraria;CRISPR Therapeutics: Research Funding;GlaxoSmithKline: Honoraria;Janssen: Honoraria, Research Funding;Novartis: Research Funding;Tmunity: Research Funding. Porter: American Society for Transplantation and Cellular Therapy: Honoraria;Genentech: Current equity holder in publicly-traded company, Ended employment in the past 24 months;ASH: Membership on an entity's Board of Directors or advisory committees;DeCart: Membership on an entity's Board of Directors or advisory committees;Incyte: Membership on an entity's Board of Directors or advisory committees;Janssen: Membership on an entity's Board of Directors or advisory committees;Kite/Gilead: Membership on an entity's Board of Directors or advisory committees;National Marrow Donor Program: Membership on an entity's Board of Directors or advisory committees;Novartis: Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding;Tmunity: Patents & Royalties;Wiley and Sons Publishing: Honoraria. June: AC Immune, DeCART, BluesphereBio, Carisma, Cellares, Celldex, Cabaletta, Poseida, Verismo, Ziopharm: Consultancy;Tmunity, DeCART, BluesphereBio, Carisma, Cellares, Celldex, Cabaletta, Poseida, Verismo, Ziopharm: Current equity holder in publicly-traded company;Novartis: Patents & Royalties.

Immune signatures underlying post-acute COVID-19 lung sequelae.

Severe coronavirus disease 2019 (COVID-19) pneumonia survivors often exhibit long-term pulmonary sequelae, but the underlying mechanisms or associated local and systemic immune correlates are not known. Here, we have performed high-dimensional characterization of the pathophysiological and immune traits of aged COVID-19 convalescents, and correlated the local and systemic immune profiles with pulmonary function and lung imaging. We found that chronic lung impairment was accompanied by persistent respiratory immune alterations. We showed that functional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)­specific memory T and B cells were enriched at the site of infection compared with those of blood. Detailed evaluation of the lung immune compartment revealed that dysregulated respiratory CD8+ T cell responses were associated with the impaired lung function after acute COVID-19. Single-cell transcriptomic analysis identified the potential pathogenic subsets of respiratory CD8+ T cells contributing to persistent tissue conditions after COVID-19. Our results have revealed pathophysiological and immune traits that may support the development of lung sequelae after SARS-CoV-2 pneumonia in older individuals, with implications for the treatment of chronic COVID-19 symptoms.

SARS-CoV-2 specific and cross-reactive t cell responses

Understanding adaptive immune responses to SARS-CoV-2 is important for vaccine development efforts, interpreting disease pathogenesis, and calibration of future pandemic control measures. We have developed HLA class I and class II predicted peptides, collected into “Megapools” (MP), to identify SARSCoV- 2-specific CD4+ and CD8+ T cells in coronavirus disease 2019 (COVID-19) convalescent patients. Importantly, we detected SARS-CoV-2 reactive CD4+ T cells in 40-60% unexposed individuals sampled before 2019, implicating pre-existing cross-reactive T-cell memory. Using human blood samples derived pre-2019, we demonstrated a range of preexisting memory CD4+ T cells that are cross-reactive with comparable affinity to SARS-CoV-2 and HCoV-OC43, HCoV- 229E, HCoV-NL63, or HCoV-HKU1. Thus, variegated T-cell memory to common cold coronaviruses may underlie at least some of the extensive heterogeneity observed in COVID-19 clinical and subclinical disease.

Pipelines Bent, Pipelines Broken: Interdisciplinary Self-Reflection on the Impact of COVID-19 on Current and Future Research (Position Paper)

Among the many changes brought about by the COVID-19 pandemic, one of the most pressing for scientific research concerns user testing. For the researchers who conduct studies with human participants, the requirements for social distancing have created a need for reflecting on methodologies that previously seemed relatively straightforward. It has become clear from the emerging literature on the topic and from first-hand experiences of researchers that the restrictions due to the pandemic affect every aspect of the research pipeline. The current paper offers an initial reflection on user-based research, drawing on the authors' own experiences and on the results of a survey that was conducted among researchers in different disciplines, primarily psychology, human-computer interaction (HCI), and visualization communities. While this sampling of researchers is by no means comprehensive, the multi-disciplinary approach and the consideration of different aspects of the research pipeline allow us to examine current and future challenges for user-based research. Through an exploration of these issues, this paper also invites others in the VIS - as well as in the wider - research community, to reflect on and discuss the ways in which the current crisis might also present new and previously unexplored opportunities. © 2020 IEEE.