Effector memory T cell subset CD45RA-CCR7-CD27-CD28- EM3 increases in direct proportion to the disease severity of COVID-19

COVID-19, which emerged in December 2019 and continues to wreak havoc, has led to the death of many people around the world. In this study, we aimed to uncover the variables underlying the exacerbation of the disease by considering the changes in T cell subsets in adults and juveniles with different disease severity of COVID-19. Peripheral blood samples of 193 patients (128 adults and 65 juveniles) diagnosed with COVID-19 were evaluated in a flow cytometer, and a broad T cell profile was revealed by examining T cell subsets in terms of exhaustion and senescence. We found remarkable differences in the effector memory (EM;CD45RA-CCR7-) cell subsets of severe pneumonia cases. The frequencies of EM2 CD4+ T, EM3 CD4+ T, EM3 CD8+ T, EM2 DN T and EM3 DN T cells were found to increase in severe pneumonia cases. Consistently, these cells were found in juveniles and uncomplicated adults in similar or lower proportions to healthy controls. The findings of our study provide a view of the T cell profile that may underlie differences in the course of COVID-19 cases in juveniles and adults and may provide new insights into the development of effective treatment strategies.

Effector memory T cell subset CD45RA−CCR7−CD27−CD28− EM3 increases in direct proportion to the disease severity of COVID-19

COVID-19, which emerged in December 2019 and continues to wreak havoc, has led to the death of many people around the world. In this study, we aimed to uncover the variables underlying the exacerbation of the disease by considering the changes in T cell subsets in adults and juveniles with different disease severity of COVID-19. Peripheral blood samples of 193 patients (128 adults and 65 juveniles) diagnosed with COVID-19 were evaluated in a flow cytometer, and a broad T cell profile was revealed by examining T cell subsets in terms of exhaustion and senescence. We found remarkable differences in the effector memory (EM;CD45RA−CCR7−) cell subsets of severe pneumonia cases. The frequencies of EM2 CD4+ T, EM3 CD4+ T, EM3 CD8+ T, EM2 DN T and EM3 DN T cells were found to increase in severe pneumonia cases. Consistently, these cells were found in juveniles and uncomplicated adults in similar or lower proportions to healthy controls. The findings of our study provide a view of the T cell profile that may underlie differences in the course of COVID-19 cases in juveniles and adults and may provide new insights into the development of effective treatment strategies. © 2022 The Scandinavian Foundation for Immunology.

Treatment With Monoclonal Antibodies Is Safe and Effective for Kidney Transplant Recipients With COVID-19

Background: Monoclonal antibodies have been the mainstay of treatment of COVID-19 in patients at high-risk of mortality from COVID-19. We aimed to study our experience with monoclonal antibodies (mAb) in kidney transplant recipients with COVID-19 at our center. Method(s): We reviewed 93 of our kidney transplant recipients who were infected with COVID-19 and received mAb treatment. The mAb infusion received was the one active against the variant that was circulating during that period (39 received either bamlanivimab or casirivimab/imdevimab, 41 received sotrovimab and 13 received bebtelovimab). All patients were on standard immunosuppression with tacrolimus and prednisone, and 88% were on mycophenolate prior to COVID-19 diagnosis, which was subsequently reduced or held for at least 2 weeks. Result(s): Of the 93 patients, median age was 54 (IQR 44-64), 44% were male, 42% were Hispanic, 36% were African American. 76% have received deceased donor kidney transplant, 94% had history of hypertension, 47% diabetes mellitus, 18% coronary artery disease. All the patients had mild symptoms without initial hypoxia requiring supplemental O2 and only 5 patients (5.4%) were admitted to the hospital. While 33 patients (35%) were unvaccinated at the time of COVID-19 diagnosis, 60 patients (65%) have received at least 2 doses of COVID vaccination at time of diagnosis and of those 27 patients (29%) have received a third dose. There was only one death (1%) in a patient that was re-hospitalized with severe COVID-19. There was no allograft loss. The rate of re-infection after mAb treatment was 6.5%. There was no serious adverse event related to the mAb infusion. Conclusion(s): Our experience suggests that monoclonal antibodies are a safe therapeutic to reduce the need for COVID-19 related hospitalization in this high-risk kidney transplant population, while one third of those were unvaccinated at the time of COVID-19 diagnosis.

Decreased Mortality From SARS-CoV-2 in Kidney Transplant Recipients Over the Course of the Pandemic

Background: We aimed to investigate the variation in mortality from SARS-CoV-2 infection in kidney transplant recipients Methods: Between March 16, 2020 and May 4, 2022, 537 patients were diagnosed with SARS-CoV-2 infection by RT-PCR. Result(s): 59% were male, median age 58 (IQR: 45-67), predominantly Hispanic (51.2%) and African American (29%). 75.4% received a deceased-donor renal transplant, 55% received anti-thymocyte induction. Most patients were on triple immunosuppression (96% on calcineurin inhibitors, 87% on anti-metabolite, and 99% on prednisone). While the mortality rate was 37 % (47/128) during first peak between March 16 and April 30, 2020, it has significantly decreased to 11% (7/61) from May 1, 2020 to end of December 2020 with social distancing and use of facemask. Between January 1, 2021 and November 5, 2021 with use of vaccination and monoclonal antibodies, the mortality rate further decreased to 7.7% (10/129). Between November 6, 2021 till May 4, 2022 which corresponds to the period when the Omicron variant and subvariants are prevalent, the mortality rate was 5.5% (12/219). Among those diagnosed during the period when Omicron was prevalent, 188/219 (85.8%) have received 2 doses of COVID vaccine and 82/219 (37.4%) have received a third dose. Since the beginning of use of monoclonal antibodies, 93 patients received a combination of casirivimab/imdevimab when initial SARS-CoV-2 variants were dominant and sotrovimab then bebtelovimab during the period of Omicron and its subvariants. Only one death occurred in patients who received monoclonal antibody treatment and that patient was hospitalized for severe COVID-19. We identified 23 re-infections. Most of re-infected patients have already received at least 2 doses of COVID vaccine but only 5 received a third dose. None of the re-infected patients was hospitalized and none of them died. Conclusion(s): In summary, mortality from SARS-CoV-2 infection in kidney transplant recipients has significantly decreased over time. This could be explained by initial exposure to higher viral load due to lack of personal protection and social distancing. However, since the judicious use of monoclonal antibodies and vaccination, in addition to social distancing protocols and use of facemask, the mortality in kidney transplant recipients has decreased over time.

Blood Transcriptomes of Kidney Recipients with Covid-19 Demonstrate Deficient Adaptive Immune Activation

Purpose: Kidney transplant recipients (KTRs) have poor outcomes compared to non-KTRs with acute COVID-19. To provide insight into management of immunosuppression (IS) during COVID-19, we studied immune signatures from the peripheral blood during and after COVID-19 infection from a multicenter KTR cohort. Method(s): Clinical data were collected by chart review. Paxgene blood RNA was polyA-selected and sequenced at enrollment Results: A total of 64 KTRs affected with COVID-19 were enrolled (31 Early cases (<4weeks from a positive SARS-CoV-2 PCR test) and 33 late cases). Out of the 64 patients, eight died and three encountered graft losses during follow-up. Among 31 early cases, we detected differentially expressed genes (nominal p-value < 0.01) in the blood transcriptome that were positively or negatively associated with the COVID-19 severity score (scale of 1 to 7 with increasing severity;Fig 1A). Enrichment analyses showed upregulation of neutrophil and innate immune pathways and downregulation of adaptive immune activation pathways with increasing severity score (Fig 1B). This observation was independent of lymphocyte count, despite reduction in immunosuppression (IS) in 75% of KTRs. Interestingly, compared with early cases, the blood transcriptome in late cases showed "normalization" of these enriched pathways after 4 weeks, suggesting return of adaptive immune system activation despite re-initiation of immunosuppression (Fig 1C). The latter analyses were adjusted for the severity score. Interestingly, similar pathway enrichment with worsening severity of COVID-19 was identifiable from a public dataset of non-KTRs (GSE152418), showing overlapped signatures for acute COVID-19 between KTRs and non-KTRs (overlap P<0.05) (Fig 1D). Conclusion(s): Blood transcriptome of COVID-KTRs shows marked decrease in adaptive immune system activation during acute COVID-19, even during IS reduction, which show recovery after acute illness. (Figure Presented).

Anti-HLA Antibodies Do Not Increase in Kidney Transplant Recipients During COVID-19 Infection

Purpose: To determine if HLA allo-antibody levels are affected by COVID-19 in renal transplanted patients and to compare the immunoglobulin class and subclass profiles as well as the epitope binding patterns of anti-HLA and anti-SARS-CoV-2 antibodies. Method(s): A cross-sectional study of 46 kidney transplant recipients diagnosed with PCR+ SARS-CoV-2 infection was conducted. Serum samples were collected at the time of infection. For 21 patients, we obtained historical anti-HLA antibody information before COVID-19. Using a single-antigen bead Luminex assay, we determined IgG, IgG1/2/3/4, IgM, and IgA antibodies against Class I and Class II HLA, as well as against five SARS-CoV-2 (Wuhan strain) protein fragments: nucleocapsid, whole spike (S), spike S1, spike S2 and spike receptor binding domain (RBD). Result(s): 26/46 subjects had anti-HLA antibodies of which fourteen had donorspecific anti-HLA antibodies (DSA) compared with 45/46 had anti-SARS-CoV2 antibodies. The majority of DSA were specific to HLA-DQ (10/14), with a dominant IgG/IgG1/IgG3 subclass prevalence. Anti-SARS-CoV-2 antibodies exhibited stronger reactivity towards S and RBD and had increased IgM (38/43, 79%) and IgA (41/42, 85%) prevalence when compared to DSAs (5/14, 35% and 2/14, 14%, p<0.001).Out of 21 patients with pre-COVID-19 data available, calculated panel antibody reactivity (cPRA) levels did not change after COVID-19 in 14 cases (67%);cPRA increased in two cases (10%), both of them with allograft nephrectomy and immunosuppression discontinuation, and decreased in five patients (20%) (from 65.4+/-12.6% before COVID-19, to 29.4+/-33.6% after COVID-19) (Figure 1). Patients with DSA exhibited significantly lower anti-S IgG (9453+/-9945 vs 17975+/-12792;P=0.001), anti-RBD IgM (4464+/-3693 vs 8751+/-6468;P=0.03) and anti-nucleoprotein IgA (998+/-835 vs 5476+/-6895;P=0.001) anti-SARS-CoV2 antibody MFI values than patients without DSA. Conclusion(s): cPRA values did not increase following PCR confirmed COVID-19 diagnosis in renal transplant recipients and those subjects with pre-existing DSA had lower antibody strength directed at SARS-CoV-2 antigens. The lack of increase in alloantibody response is quite remarkable, since over 80% of the patients underwent either significant reduction or withdrawal of mycophenolate mofetil after COVID-19 diagnosis. (Figure Presented).

Decreased Mortality from Sars-CoV-2 Infection in Kidney Transplant Recipients Over the Course of the Pandemic

Purpose: We aimed to investigate the mortality from SARS-CoV-2 in kidney transplant recipients in the Bronx, New York since the beginning of the pandemic Methods: Between March 16, 2020 and November 5, 2021, 453 patients were diagnosed with SARS-CoV-2 infection. 316 were diagnosed by RT-PCR while the remaining 137 tested positive for anti-SARS-CoV-2 nucleocapsid IgG and did not have significant symptoms and had not been previously tested by RT-PCR Results: Of the 316 patients diagnosed by RT-PCR, 214 patients were hospitalized while 102 patients were managed at home as outpatient. 194 (61.3%) were male, median age 61 years old (IQR: 48-69), predominantly Hispanic (56.2%) and African American (29.5%). 75% received a deceased-donor renal transplant, 58% received anti-thymocyte induction. Most patients were on triple immunosuppression (95% on calcineurin inhibitors, 87% on anti-metabolite, and 97% on prednisone). Hypertension was the most common comorbidity followed by diabetes mellitus, heart disease and lung disease. A total of 65 patients (20.5%) died. The mortality rate was 37 % (47/128) in patients diagnosed between March 16 and April 30, 2020. From May 1, 2020 to end of December 2020 mortality rate has significantly decreased to 11% (7/61). Since the beginning of 2021 till November 5, 2021 the mortality rate is 7.7% (10/129). Twenty-seven patients were diagnosed with COVID-19 despite being partially of fully vaccinated (25 fully vaccinated, 2 after one dose of vaccine). 13/27 (48%) were managed at home while 14/27 (52%) were hospitalized and 2 (7%) of them died. Twenty-eight patients received treatment with casirivimab and imdevimab post diagnosis of SARS-CoV-2 starting 2021 and none of those patients have died. Conclusion(s): In summary, mortality from SARS-CoV-2 infection in kidney transplant recipients was higher earlier at the pandemic and has significantly decreased over time. This could be explained by initial exposure of the patients with higher viral load due to lack of personal protection and social distancing. However, since the judicious use of monoclonal antibodies and vaccination, in addition to social distancing protocols and use of facemask, the mortality in kidney transplant recipients has decreased over time.

Blood Transcriptomes of Covid-19 Infected Kidney Recipients Demonstrate Frequent and Persistent SARS-CoV-2 Virome Gene Expression

Purpose: Kidney transplant recipients (KTRs) have poor outcomes vs non-KTRs with acute COVID-19. To provide insight into management of immunosuppression during acute COVID-19, we studied peripheral blood transcriptomes during and after COVID-19 from a multicenter KTR cohort. Method(s): Clinical data were collected by chart review. Paxgene blood RNA was polyA-selected and sequenced at enrollment. Result(s): A total of 64 KTRs with COVID-19 were enrolled (31 Early cases (<4weeks from a positive SARS-CoV-2 PCR test) and 33 late cases). Out of the 64 patients, eight died and three encountered graft losses during follow-up. Due to presence of mRNA reads in the blood transcriptome unmapped to the human genome, we aligned the mRNA short reads to the SARS-CoV-2 genome. Surprisingly, our strategy detected the SARS-Cov2 mRNA, especially Spike mRNA in 27 (87%) early cases, and 18 (54%) of late cases (Fig 1A and B). We then analyzed the raw reads from a public dataset of non-KTRs with Paxgene RNA (GSE172114). The SARS-CoV-2 Spike mRNA was detected in 2/47 (4.2%) critically ill COVID-19 cases and 0/25 noncritically ill cases in this non-KTR dataset (compared to KTRs, Chi-square P<0.001;Fig 1B). Among our KTRs, the amount of Spike mRNA was associated positively with the COVID-19 severity score (scale of 1 to 7 of increasing severity;Fig 1C) and inversely with time from initial positive PCR (Fig 1D). More interestingly, 7/64 patients had detectable Spike RNA-emia beyond 60 days after COVID-19 diagnosis. Of the 3 graft losses in our cohort, 2 occurred among these 7 patients. Conclusion(s): Blood transcriptome of KTRs with COVID-19 demonstrated a risk for persistent viremia with implications for pathogenesis of COVID-19 disease. This finding also supports using passive immune strategies in COVID-KTRs. (Figure Presented).

Effector memory T cell subset CD45RA‐CCR7‐CD27‐CD28‐EM3 increases in direct proportion to the disease severity of COVID‐19

COVID‐19, which emerged in December 2019 and continues to wreak havoc, has led to the death of many people around the world. In this study, we aimed to uncover the variables underlying the exacerbation of the disease by considering the changes in T cell subsets in adults and juveniles with different disease severity of COVID‐19. Peripheral blood samples of 193 patients (128 adults and 65 juveniles) diagnosed with COVID‐19 were evaluated in a flow cytometer, and a broad T cell profile was revealed by examining T cell subsets in terms of exhaustion and senescence. We found remarkable differences in the effector memory (EM;CD45RA‐CCR7‐) cell subsets of severe pneumonia cases. The frequencies of EM2 CD4+ T, EM3 CD4+ T, EM3 CD8+ T, EM2 DN T and EM3 DN T cells were found to increase in severe pneumonia cases. Consistently, these cells were found in juveniles and uncomplicated adults in similar or lower proportions to healthy controls. The findings of our study provide a view of the T cell profile that may underlie differences in the course of COVID‐19 cases in juveniles and adults, and may provide new insights into the development of effective treatment strategies.

Aspergillus Infections in Intensive Care Units: Before and after the COVID-19 Pandemic

Introduction: Aspergillus species have begun to cause invasive pulmonary aspergillosis (IPA) with increasing frequency in patients with known risk factors in intensive care units (ICU). An international multicenter cohort study (AspICU) established criteria for diagnosis of invasive pulmonary aspergillosis (IPA) in intensive care units. In our study, patients with Aspergillus spp. growth in deep tracheal aspirate (DTA) samples in ICU were evaluated according to AspICU criteria. Materials and Methods: This study is a retrospective study. DTA samples were collected from the Pandemic and Reanimation ICU and performed in the Medical Microbiology Laboratory by separated two periods;pre-pandemic (1 March 2019-31 December 2019) and post-pandemic (1 March 2020-31 December 2020). Cases with Aspergillus spp. growth in the DTA samples in the Pandemic ICU were evaluated as COVID 19 associated pulmonary aspergillosis (CAPA) according to AspICU criteria. Results: While Aspergillus spp. was grown in the DTA of three patients in 2019 and five patients in 2020 in the Reanimation ICU, and 11 patients in the Pandemic ICU. Growths belonging to one patient from both Reanimation (2019) and Pandemic ICUs were considered as colonization. Other growths were interpreted as IPA according to AspICU criteria. When the incidence rates according to 10000 patient days were compared, the incidence rate increased significantly in 2020 (19.1) (p< 0.001) compared to 2019 (3.4);In 2020, it was determined that it increased significantly in the Pandemic ICU (40.4) (p< 0.001) compared to Reanimation ICU (9.2). Conclusion: It should not be forgotten that intensive care patients are also at risk for IPA, especially after viral infections (such as COVID-19, Influenza). Although the incidence of IPA was not very high, it was observed that it tended to increase according to our study. The diagnosis of IPA is problematic, therefore it is necessary to increase awareness and sample diversity and to use biomarkers more widely other than hematology patients.

The Age-Dependent Role of Th22, Tc22, and Tc17 Cells in the Severity of Pneumonia in COVID-19 Immunopathogenesis.

Coronavirus disease 2019 (COVID-19) has clinical manifestations ranging from mild symptoms to respiratory failure, septic shock, and multi-organ failure. Lymphocytes are divided into different subtypes based on their cytokine production pattern. In this study, we investigated the role of cytokine expressions of CD4+ T (T helper [Th]1, Th2, Th17, Th22) and CD8+ T cell subtypes (T cytotoxic [Tc]1, Tc2, Tc17, Tc22) in the pathogenesis of COVID-19. Peripheral blood mononuclear cells (PBMCs) were extracted with Ficoll by density gradient centrifugation from blood samples of 180 COVID-19 patients (children and adults) and 30 healthy controls. PBMCs were stimulated with PMA and Ionomycin and treated with Brefeldin A in the fourth hour, and a 10-colored monoclonal antibody panel was evaluated at the end of the sixth hour using flow cytometry. According to our findings, the numbers of Th22 (CD3+, CD4+, and interleukin [IL]-22+) and Tc22 (CD3+, CD8+, IL-22+) cells increased in adult patients regardless of the level of pneumonia (mild, severe, or symptom-free) as compared with healthy controls (p < 0.05). In addition, the number of Tc17 (CD3+, CD8+, and IL-17A+) cells increased in low pneumonia and severe pneumonia groups compared with the healthy controls (p < 0.05). Both IL-22 and IL-17A production decreased during a follow-up within 6 weeks of discharge. Our findings suggest that the increase in only IL-22 expressed Tc22 cells in the 0-12 age group with a general symptom-free course and higher levels of Th22 and Tc22 in uncomplicated adult cases may indicate the protective effect of IL-22. On the contrary, the association between the severity of pneumonia and the elevation of Tc17 cells in adults may reveal the damaging effect of IL-22 when it is co-expressed with IL-17.

Assessment of CD39 expression in regulatory T-cell subsets by disease severity in adult and juvenile COVID-19 cases.

COVID-19 is a disease characterized by acute respiratory failure and is a major health problem worldwide. Here, we aimed to investigate the role of CD39 expression in Treg cell subsets in COVID-19 immunopathogenesis and its relationship to disease severity. One hundred and ninety COVID-19 patients (juveniles, adults) and 43 volunteers as healthy controls were enrolled in our study. Flow cytometric analysis was performed using a 10-color monoclonal antibody panel from peripheral blood samples. In adult patients, CD39+ Tregs increased with disease severity. In contrast, CD39+ Tregs were decreased in juvenile patients in an age-dependent manner. Overall, our study reveals an interesting profile of CD39-expressing Tregs in adult and juvenile cases of COVID-19. Our results provide a better understanding of the possible role of Tregs in the mechanism of immune response in COVID-19 cases.