SARS-CoV-2 Viral Clearance and Evolution Varies by Extent of Immunodeficiency (preprint)

Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged SARS-CoV-2 infection, but the immune defects that predispose to persistent COVID- 19 remain incompletely understood. In this study, we performed detailed viro-immunologic analyses of a prospective cohort of participants with COVID-19. The median time to nasal viral RNA and culture clearance in the severe hematologic malignancy/transplant group (S-HT) were 72 and 21 days, respectively, which were significantly longer than clearance rates in the severe autoimmune/B-cell deficient (S-A), non-severe, and non-immunocompromised groups (P<0.001). Participants who were severely immunocompromised had greater SARS-CoV-2 evolution and higher risk of developing antiviral treatment resistance. Both S-HT and S-A participants had diminished SARS-CoV-2-specific humoral, while only the S-HT group had reduced T cell-mediated responses. This highlights the varied risk of persistent COVID-19 across immunosuppressive conditions and suggests that suppression of both B and T cell responses results in the highest contributing risk of persistent infection.

Clinical and Immunological Characteristics of Prolonged SARS-CoV-2 Omicron Infection in Hematologic Disease (preprint)

Prolonged viral shedding (PVS) occurs when severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is not adequately cleared and has been associated with poor outcomes. However, it remains unclear whether the immunological and clinical characteristics of Omicron PVS in hematologic disease (HD) are identical to those of earlier variants. We retrospectively analyzed 160 patients with HD with Omicron breakthrough infections. Although the hospitalization rate was high (21.3 %), deaths attributable to COVID-19 occurred in only 2.5% of the cases. PVS developed in 36.9% of the evaluable patients. Factors such as B- and CD4+ T-cell depletion, recent use of anti-CD20 antibodies and bendamustine were found to be significant predictors of PVS. Analysis of T cell phenotypes showed an increase in exhausted CD4+ T cells in PVS, but not in CD8+ cells.  Neutralizing activities against recombinant spike proteins for three Omicron subvariants were significantly reduced. Notably, despite the high frequency of PVS, many patients previously treated with anti-CD20 antibodies and bendamustine ultimately recovered. Late-onset interstitial pneumonia is a fatal complication that can occur regardless of viral clearance. Despite the use of high-dose corticosteroids and potent antivirals, the optimal treatment for PVS remains unclear and should be individualized until a more effective strategy is established.

Adherence to Sars-CoV2 vaccination in hematological patients.

Background: SARS-CoV2 vaccination efficiently prevents severe COVID-19, although hematological patients, particularly under therapy, respond less well. Besides vaccine efficacy, adherence to vaccination is essential for ensuring adequate protection of this vulnerable population. Methods: We evaluated the impact of a program aimed at maximizing patient adherence by comparing the rate of SARS-CoV2 vaccination of our hematological patients and a matched sample of the general population. Results: Vaccination rates were 88.9% among 2,156 patients, aged 65.2 ± 15.8 years (M ± SD, range 19-86 years). Rates differed considerably with age, i.e. 84.2% between 18-64 years and 92.4% above 65 years (p<0.0001), but not with sex. In the general population, rates were 76.3% overall, 73.0% between 18-64 and 86.7% above 65 years, all significantly lower than among patients, overall (Standardized Incidence ratio (SIR) 1.17; 95%CI 1.12-1.22, p<0.0001) as well as among younger (SIR 1.15; 1.07-1.24, p<0.0001) or older (SIR 1.06; 1.00-1.13, p=0.046) people. Vaccination rates increased to 92.2% overall (SIR 1.21; 1.16-1.27, p<0.0001), 88.5% in younger (SIR 1.21; 1.13-1.30, p<0.0001) and 94.8% in older (SIR 1.09; 1.03-1.12, p=0.0043) patients, after excluding those with medical contraindications, and further to 95.6% overall (SIR 1.26; 1.20-1.32, p<0.0001), 93.8% in younger (SIR 1.29; 1.20-1.38, p<0.0001) and 96.9% in older (SIR 1.11; 1.05-1.18, p=0.0004) patients, after excluding those not seen in hematology in 2021. Conclusions: Vaccination rates were significantly higher in hematological patients compared to the general population regardless of age, sex and municipality. Acceptance of Covid vaccines by hematological patients may be improved by targeted information campaigns carried out by trusted health care professionals.

Distinct and overlapping immunological responses to SARS-CoV-2 and Mycobacterium tuberculosis identified by single-cell RNA-seq of co-infected whole blood (preprint)

Introduction: COVID-19 and tuberculosis (TB) exhibit similar symptomatic presentation and clinical parameters. Common underlying immunological mechanisms also highlight potential routes of immunopathogenic interaction between these diseases during co-infection. To explore immunological similarities, differences and interactions, single-cell RNA-seq (scRNA-seq) was performed on whole blood infected with Mycobacterium tuberculosis (Mtb), SARS-CoV-2, or both pathogens. Methods: Whole blood from four healthy adults, were subjected to ex vivo infection with Mtb and/or SARS-CoV-2 ancestral strain, or were maintained in an uninfected state, for 24 or 96 hours. At each timepoint, for each condition, the four biological replicates were captured, fixed and cryopreserved to be processed for scRNA-seq as a single batch. Following quality control filtering, genotype-based demultiplexing was performed to obtain data from each biological replicate for pseudobulk differential expression analysis. Results: Thirteen distinct clusters of cells were identified based on marker gene expression. Profound differences in the proportions of monocytes, T cells and neutrophils were observed between infection conditions and timepoints. The greatest divergence between pathogen responses occurred within myeloid cells at early timepoints of infection. Co-infection had the greatest synergistic effect 24 hours post-infection with 238 immunological pathways uniquely enriched, including IFN-{gamma} and TNF production, whilst by 96 hours post-infection there was a large overlap of 182 shared pathways between Mtb, SARS-CoV-2 and co-infection. SARS-CoV-2-only infection resulted in widespread cell death by 96 hours post-infection, while Mtb-only and co-infected samples remained enriched for monocyte, T cell and NK cell signatures, sharing negative regulation of extrinsic apoptotic signalling. Distinct from Mtb, SARS-Co-V-2 had unique regulating of {beta} T cell activation and differentiation at both time points. Conclusion: These data provide a high-resolution characterisation of distinct and overlapping immunological responses generated by SARS-CoV-2 and Mtb when a single infection or co-infection occurs. This sheds light on the potential effects of novel or existing host-directed therapies that target these pathways, which is particularly crucial for settings where dual presentation is common.

Viral infection of hematopoietic stem cells (preprint)

Hematopoietic stem cells (HSCs) are critical for maintaining healthy blood and immune cell populations. They’re also valuable resources and targets for medical treatments, such as HSC transplantation and gene therapy. However, these blood cell precursors are susceptible to viral infection, which can cause blood disorders and limit the efficacy of HSC-based therapies. In fact, viral infection is a leading cause of complications and death among HSC transplant recipients. For example, latent cytomegalovirus can become reactivated after transplantation leading to immunosuppression, pneumonia, encephalitis, and graft failure. HSC transplantation also reduces the numbers of T cells that are specifically cytotoxic toward the mononucleosis- inducing Epstein–Barr virus. Furthermore, recipients of HSC transplants are more susceptible to infection by SARS-CoV-2, the cause of the COVID-19 pandemic. SARS-CoV-2, in turn, can induce numerous blood abnormalities, such as thrombocytopenia, lymphocytopenia, anemia, hypercoagulability, and systemic thrombosis in part because HSCs express SARS-CoV-2 receptors. More research is needed to determine the best ways to prevent viral infection of these essential cells in both endogenous and transplantation contexts, in order to reduce serious blood disorders and related mortality in the clinic.

Hyperviscosity syndromes; hemorheology for physicians and the use of microfluidic devices.

PURPOSE OF REVIEW: Hyperviscosity syndromes can lead to significant morbidity and mortality. Existing methods to measure microcirculatory rheology are not readily available and limited in relevance and accuracy at this level. In this review, we review selected hyperviscosity syndromes and the advancement of their knowledge using microfluidic platforms. RECENT FINDINGS: Viscosity changes drastically at the microvascular level as the physical properties of the cells themselves become the major determinants of resistance to blood flow. Current, outdated viscosity measurements only quantify whole blood or serum. Changes in blood composition, cell number, or the physical properties themselves lead to increased blood viscosity. Given the significant morbidity and mortality from hyperviscosity syndromes, new biophysical tools are needed and being developed to study microvascular biophysical and hemodynamic conditions at this microvascular level to help predict those at risk and guide therapeutic treatment. SUMMARY: The use of 'lab-on-a-chip' technology continues to rise to relevance with point of care, personalized testing and medicine as customizable microfluidic platforms enable independent control of many in vivo factors and are a powerful tool to study microcirculatory hemorheology.

Immunogenicity profile after COVID-19 vaccination in patients with onco-hematological diseases.

OBJECTIVE: To evaluate the influence of onco-hematological pathologies on seroconversion to COVID-19 vaccines, in addition to the effects of chemotherapy treatment on this response. METHODS: The present study evaluated the immunogenic response of 76 patients with onco-hematological diseases to multiple vaccine platforms compared to 25 control individuals. RESULTS: Our results showed positive response rates of 74.02% in patients with onco-hematological diseases and 100% in controls. When analyzed according to etiological group, patients with lymphoproliferative disorders achieved a positive vaccine response rate of 58.7%, whereas those with myeloproliferative diseases achieved a 100% response rate. We also observed that patients previously exposed to COVID-19 presented a 75% increase in their antibody values after vaccination, and these values were 37% higher than those of patients who did not have such exposure. We found that patients who underwent B-lymphocyte-depleting therapy in the last 2 years before vaccination had a worse response rate of 18.75%. CONCLUSION: Despite the immunosuppression of patients with onco-hematological diseases, caused by the biology of their diseases and treatment, benefit and safety in vaccinating these patients are observed, in view of the important recall immune response and incidence of adverse effects similar to those of the healthy population.

Outcome of COVID-19 in allogeneic stem cell transplant recipients: Results from the EPICOVIDEHA registry.

Background: The outcome of COVID-19 in allogeneic hematopoietic stem cell transplantation (HSCT) recipients is almost uniformely considered poor. The aim of present study was to retrospectively analyse the outcome and risk factors for mortality in a large series of patients who developed COVID-19 infection after an allogeneic HSCT. Methods: This multicenter retrospective study promoted by the European Hematology Association - Infections in Hematology Study Working Group, included 326 adult HSCT patients who had COVID-19 between January 2020 and March 2022. Results: The median time from HSCT to the diagnosis of COVID-19 was 268 days (IQR 86-713; range 0-185 days). COVID-19 severity was mild in 21% of the patients, severe in 39% and critical in 16% of the patients. In multivariable analysis factors associated with a higher risk of mortality were, age above 50 years, presence of 3 or more comorbidities, active hematologic disease at time of COVID-19 infection, development of COVID-19 within 12 months of HSCT, and severe/critical infections. Overall mortality rate was 21% (n=68): COVID-19 was the main or secondary cause of death in 16% of the patients (n=53). Conclusions: Mortality in HSCT recipients who develop COVID-19 is high and largely dependent on age, comorbidities, active hematologic disease, timing from transplant and severity of the infection.

Outcome of early treatment of SARS-CoV-2 infection in patients with haematological disorders.

Outcome of early treatment of COVID-19 with antivirals or anti-spike monoclonal antibodies (MABs) in patients with haematological malignancies (HM) is unknown. A retrospective study of HM patients treated for mild/moderate COVID-19 between March 2021 and July 2022 was performed. The main composite end-point was treatment failure (severe COVID-19 or COVID-19-related death). We included 328 consecutive patients who received MABs (n = 120, 37%; sotrovimab, n = 73) or antivirals (n = 208, 63%; nirmatrelvir/ritonavir, n = 116) over a median of two days after symptoms started; 111 (33.8%) had non-Hodgkin lymphoma (NHL); 89 (27%) were transplant/CAR-T (chimaeric antigen receptor T-cell therapy) recipients. Most infections (n = 309, 94%) occurred during the Omicron period. Failure developed in 31 patients (9.5%). Its independent predictors were older age, fewer vaccine doses, and treatment with MABs. Rate of failure was lower in the Omicron versus the pre-Omicron period (7.8% versus 36.8%, p < 0.001). During the Omicron period, predictors of failure were age, fewer vaccine doses and diagnosis of acute myeloid leukaemia/myelodysplastic syndrome (AML/MDS). Independent predictors of longer viral shedding were age, comorbidities, hospital admission at diagnosis, NHL/CLL, treatment with MABs. COVID-19-associated mortality was 3.4% (n = 11). The mortality in those who developed severe COVID-19 after early treatment was 26% in the Omicron period. Patients with HM had a significant risk of failure of early treatment, even during the Omicron period, with high mortality rate.

[Analysis of anti-SARS-CoV-2 IgG antibody titers after mRNA booster vaccination in patients with nonmalignant hematological disorders].

In our facility, anti-SARS-CoV-2 mRNA vaccines were given to 21 patients, including 8 with aplastic anemia (AA), 3 with pure red cell aplasia (PRCA), and 10 with immune thrombocytopenic purpura (ITP), and IgG antibody titers were assessed one month after vaccinations. After receiving both a second vaccine and a booster shot, all patients with AA/PRCA treated with cyclosporine A aside from one, had IgG titers that were lower than the median levels of healthy controls. Even if prednisolone (PSL) doses did not go over 10 mg/day, ITP patients receiving PSL therapy were unable to achieve adequate levels of IgG after booster immunizations.

[Outcomes of COVID-19 due to omicron variant infection complicated with hematological disorders].

When the omicron variant became the most dominant severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) variant causing coronavirus disease 2019 (COVID-19) in Japan, 11 patients with hematological diseases infected with this new variant were treated at our institution. Among them, four of the five patients who had been treated with chemotherapy progressed to moderate-II COVID-19, and two of them died. In contrast, five of the six patients who did not receive the treatment remained at mild to moderate-I stage of COVID-19, except for a single case progressing to moderate-II COVID-19. While all four patients infused with anti-coronavirus monoclonal antibodies within 8 days after the onset survived, the other two patients, being withheld from treatment or treated later, died. In these two cases, anti-SARS-Cov-2 immunoglobulin G antibodies remained at low titers. Although the omicron variant is considered a less harmful SARS-Cov-2 variant, patients with hematological disorders, particularly those who are immunosuppressed caused by chemotherapy, should be continuously cared for as they remain at a higher risk of severe COVID-19 due to insufficient or delayed anti-viral humoral immunity development. Thus, the rapid introduction of antiviral monoclonal antibodies together with anti-viral reagents may rescue these patients.

Use of convalescent plasma in COVID-19: is clinical severity more important than the intervention? (preprint)

Background COVID-19 convalescent plasma (CCP) was used in the early period of the pandemic, but the effectivity of this treatment showed different results, especially because of the possible ineffectiveness of passive antibodies, when an inflammatory response is already established. Objectives: The aim of this study is to compare the outcomes of two different cohorts of COVID-19 patients that received CCP transfusion in the years 2020 and 2021. Design and setting: This is a retrospective study from a tertiary hospital in São Paulo, Brazil. Methods: We included a retrospective cohort of patients that received convalescent compassionate plasma and another group with patients from a previous clinical study. We collected clinical and laboratory data on the day of transfusion and five days later. Patients with hematological or immunological conditions were excluded. A p-value < 0·05 was considered significant.Results CCP did not show to interfere in the outcomes of severe COVID-19 patients, when comparing two different cohorts transfused with different volumes and titles of neutralizing antibodies. Despite the improvement in some laboratory parameters, there was not impact on clinical outcomes. Dialysis had a negative impact on the ICU stay, days of hospitalization and days of mechanical ventilation. Each higher point on the day 0 WHO scale reduced the probability of hospital and ICU discharge, and the risk of mechanical ventilation discontinuation. Conclusions: In conclusion, the use of dialysis and the assessed clinical severity represented by WHO scale on day 0 had influence on the outcomes, but not the CCP transfusion.

Assessment of the influence of non-ionizing radiation to the morbidity of MRI and ultrasound diagnostics specialists in Kazakhstan (preprint)

The state of health of healthcare practitioners with occupational exposure to a complex of hazards may differ from the state of health of general population and justify the need to develop a number of preventive measures for healthcare practitioners. The purpose of the study was assessment of the prevalence of morbidity among medical specialists (MRI and ultrasound diagnostics). Design: retrospective (2018-2021), nonrandomized. Participants: MRI and ultrasound diagnostics specialists, ophthalmologists (as control). An analysis of data on healthcare practitioners seeking for medical care was done (diagnosis by ICD-10). Morbidity was also compared with general population of the RK. Higher morbidity of healthcare practitioners of the listed above specialties with genitourinary and musculoskeletal systems diseases, eye diseases and oncopathology was revealed. Comparing with ophthalmologists, ultrasound diagnostic specialists had higher morbidity with malignant and benign neoplasms (RR 2.74 and RR 9.58, respectively), MRI specialists had higher morbidity with malignant neoplasms and blood diseases (RR 4.73 and RR 1.89, respectively). The incidence rates of SARS-COV-2 in MRI and ultrasound diagnostic specialists and ophthalmologists exceeded those in the general population of the RK. Identified features of the morbidity of healthcare practitioners should be taken into account in labor ergonomics and organization of preventive and screening measures for diagnosing diseases.

Coronavirus pathogenesis in mice explains the SARS-CoV-2 multi-organ spread by red blood cell hitch-hiking (preprint)

SARS-CoV-2 infection causes a multisystemic disease that affects numerous organs beyond the respiratory system. Thus, it is well known that COVID-19 is associated with a wide range of hematological disorders; however, it remains unclear how the SARS-CoV-2 virus is able to navigate from tissue to tissue. In this work, we performed a comprehensive analysis of the pleiotropic effects of a prototypical coronavirus in its natural host, the validated preclinical model of murine hepatitis virus (MHV). Throughout this study we compared our results with the real-world data from COVID-19 patients (including autopsies). Thus, the presence of viral RNA was only detected in less than 25% of the human serum samples, whereas all had multiple positive nasal swabs for SARS-CoV-2. Notably, we found viral RNA not only in lungs, but also in heart and kidney of deceased COVID-19 patients. Subsequently, we investigated the association between viral organotropism and clinical manifestations employing the MHV murine model. Results from RT-qPCR and viral infectivity showcased the presence of viral RNA and infectious particles in multiple organs including liver, lung, brain, heart, kidney, spleen and pancreas, and even the blood of infected mice. Surprisingly, when comparing plasma and red blood cells (RBCs)-enriched fraction, higher viral load levels were detected in RBCs, with decreased RBC count, and hematocrit and hemoglobin levels in infected mice. Next, we treated infected mice with hemin triggering more aggressive symptoms. Strikingly, when combining hemin treatment with chloroquine (a compound that known to interact with the heme group and induces a conformational change in its structure) the infection and its clinical manifestations were distinctly attenuated. Computational docking suggested that heme is able to bind to MHV Spike protein in a similar way to the one, experimentally observed for SARS-CoV-2. Overall, our results lead to a global perspective of COVID-19 beyond the canonical focus on the respiratory system, and strongly support the multi-organ extent of coronavirus infection through specific interactions with RBC hemoproteins.

The Epidemiological Pattern of Seasonal Influenza in Four Sentinel Sites in Iraq (preprint)

ABSTRACT Introduction: Influenza is an acute viral infection with significant morbidity and mortality. Its occur annually each winter is called seasonal influenza and is preventable through safe vaccine. Aim: To know the epidemiological pattern of patients with seasonal influenza in Iraqi sentinel sites. Methods: A cross- sectional study carried out on records of patients who attended four sentinel sites and registered to have influenza-like illness (ILI) or severe acute respiratory infection (SARI), and laboratory investigated. Results: The total number of cases was 1124, 36.2% of them aged 19-39 years; 53.9% were female; 74.9% lived in urban areas; 64.3% diagnosed as ILI and 35.7% as SARI. 15.9% had diabetes, 12.7% had heart disease, 4.8% had asthma, 3% had a chronic lung disease, and 2% had hematological disease. 94.6% did not get influenza vaccine. About COVID-19 vaccine, 69.4% did not vaccinated, 3.5% get only 1 dose, and 27.1% completed 2 doses. Only the SARI cases needed admission, among them 95.7% were cured. 6.5% were diagnosed as influenza- A virus, 26.1% had COVID-19, and 67.5% were negative. Among those with influenza, 97.3% had H3N2 subtype, and 2.7% had H1N1 pdm09. Conclusions: The percentage of influenza virus in Iraq is relatively small. The age, classification of case (ILI or SARI), having diabetes, heart disease, or immunological disease, and taking COVID-19 vaccine have a significant association with influenza. Recommendations: It’s needed for similar sentinel sites in other health directorates and for rising health education about seasonal influenza and its vaccine.

Association between SARS-CoV-2 Infection and Select Symptoms and Conditions 31 to 150 Days After Testing among Children and Adults (preprint)

Background An increasing number of studies have described new and persistent symptoms and conditions as potential post-acute sequelae of SARS-CoV-2 infection (PASC). However, it remains unclear whether certain symptoms or conditions occur more frequently among persons with SARS-CoV-2 infection compared with those never infected with SARS-CoV-2. We compared the occurrence of specific COVID-associated symptoms and conditions as potential PASC 31 to 150 days following a SARS-CoV-2 test among adults ([≥]20 years) and children (<20 years) with positive and negative test results documented in the electronic health records (EHRs) of institutions participating in PCORnet, the National Patient-Centered Clinical Research Network. Methods and Findings This study included 3,091,580 adults (316,249 SARS-CoV-2 positive; 2,775,331 negative) and 675,643 children (62,131 positive; 613,512 negative) who had a SARS-CoV-2 laboratory test (nucleic acid amplification or rapid antigen) during March 1, 2020-May 31, 2021 documented in their EHR. We identified hospitalization status in the day prior through the 16 days following the SARS-CoV-2 test as a proxy for the severity of COVID-19. We used logistic regression to calculate the odds of receiving a diagnostic code for each symptom outcome and Cox proportional hazard models to calculate the risk of being newly diagnosed with each condition outcome, comparing those with a SARS-CoV-2 positive test to those with a negative test. After adjustment for baseline covariates, hospitalized adults and children with a positive test had increased odds of being diagnosed with [≥]1 symptom (adults: adjusted odds ratio[aOR], 1.17[95% CI, 1.11-1.23]; children: aOR, 1.18[95% CI, 1.08-1.28]) and shortness of breath (adults: aOR, 1.50[95% CI, 1.38-1.63]; children: aOR, 1.40[95% CI, 1.15-1.70]) 31-150 days following a SARS-CoV-2 test compared with hospitalized individuals with a negative test. Hospitalized adults with a positive test also had increased odds of being diagnosed with [≥]3 symptoms (aOR, 1.16[95% CI, 1.08 - 1.26]) and fatigue (aOR, 1.12[95% CI, 1.05 - 1.18]) compared with those testing negative. The risks of being newly diagnosed with type 1 or type 2 diabetes (aHR, 1.25[95% CI, 1.17-1.33]), hematologic disorders (aHR, 1.19[95% CI, 1.11-1.28]), and respiratory disease (aHR, 1.44[95% CI, 1.30-1.60]) were higher among hospitalized adults with a positive test compared with those with a negative test. Non-hospitalized adults with a positive SARS-CoV-2 test had higher odds of being diagnosed with fatigue (aOR, 1.11[95% CI, 1.05-1.16]) and shortness of breath (aOR, 1.22[95% CI, 1.15-1.29]), and had an increased risk (aHR, 1.12[95% CI, 1.02-1.23]) of being newly diagnosed with hematologic disorders (i.e., venous thromboembolism and pulmonary embolism) 31-150 days following SARS-CoV-2 test compared with those testing negative. The risk of being newly diagnosed with certain conditions, such as mental health conditions and neurological disorders, was lower among patients with a positive viral test relative to those with a negative viral test. Conclusions Patients with SARS-CoV-2 infection were at higher risk of being diagnosed with certain symptoms and conditions, particularly fatigue, respiratory symptoms, and hematological abnormalities, after acute infection. The risk was highest among adults hospitalized after SARS-CoV-2 infection.