Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53 (preprint)

COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. SARS-CoV-2 infection induces TP53 stabilization on chromatin, which contributes to its host cytopathic effect. We mapped this TP53 stabilization to the SARS-CoV-2 spike and its propensity to form syncytia, a consequence of cell-cell fusion. Differences in SARS-CoV-2 spike variant-induced syncytia formation modify chromatin accessibility, cellular senescence, and inflammatory cytokine release via TP53. Our findings suggest that differences in syncytia formation alter senescence-associated inflammation, which varies among SARS-CoV-2 variants.

Apolipoprotein ε in Brain and Retinal Neurodegenerative Diseases.

Alzheimer's disease (AD) is the most common form of dementia that remains incurable and has become a major medical, social, and economic challenge worldwide. AD is characterized by pathological hallmarks of senile plaques (SP) and neurofibrillary tangles (NFTs) that damage the brain up to twenty years before a clinical diagnosis is made. Interestingly these pathological features have also been observed in retinal neurodegenerative diseases including age related macular degeneration (ARMD), glaucoma and diabetic retinopathy (DR). An association of AD with these diseases has been suggested in epidemiological studies and several common pathological events and risk factors have been identified between these diseases. The E4 allele of Apolipoprotein E (APOE) is a well-established genetic risk factor for late onset AD. The ApoE ε4 allele is also associated with retinal neurodegenerative diseases however in contrast to AD, it is considered protective in AMD, likewise ApoE E2 allele, which is a protective factor for AD, has been implicated as a risk factor for AMD and glaucoma. This review summarizes the evidence on the effects of ApoE in retinal neurodegenerative diseases and discusses the overlapping molecular pathways in AD. The involvement of ApoE in regulating amyloid beta (Aß) and tau pathology, inflammation, vascular integrity, glucose metabolism and vascular endothelial growth factor (VEGF) signaling is also discussed.

A urine-based ELISA with recombinant non-glycosylated SARS-CoV-2 spike protein for detecting anti-SARS-CoV-2 spike antibodies.

Serological assays have been widely used to detect anti-SARS-CoV-2 antibodies, which are generated from previous exposure to the virus or after vaccination. The presence of anti-SARS-CoV-2 Nucleocapsid antibodies was recently reported in patients´ urine using an in-house urine-based ELISA-platform, allowing a non-invasive way to collect clinical samples and assess immune conversion. In the current study, we evaluated and validated another in-house urine-based ELISA for the detection of anti-SARS-CoV-2 Spike antibodies. Three partial recombinant SARS-CoV-2 Spike proteins comprising the Receptor Binding Domain, expressed in eukaryotic or prokaryotic systems, were tested in an ELISA platform against a panel of over 140 urine and paired serum samples collected from 106 patients confirmed positive for SARS-CoV-2 by qRT-PCR. The key findings from our study were that anti-SARS-CoV-2 Spike antibodies could be detected in urine samples and that the prokaryotic expression of the rSARS-CoV-2 Spike protein was not a barrier to obtain relatively high serology efficiency for the urine-based assay. Thus, use of a urine-based ELISA assay with partial rSARS-CoV-2 Spike proteins, expressed in a prokaryotic system, could be considered as a convenient tool for screening for the presence of anti-SARS-CoV-2 Spike antibodies, and overcome the difficulties arising from sample collection and the need for recombinant proteins produced with eukaryotic expression systems.

Assessment of Psychosocial Risk Factors in Nurses one year after the start of the COVID-19 pandemic

Objective: To assess psychosocial risk factors in Portuguese nurses one year after the pandemic. Method(s): A questionnaire in digital format consisting of a sociodemographic and professional component and the COPSOQ II scale was applied, which assesses the psychosocial risks that influence health and well-being. The total sample is 188 nurses. Result(s): All nurses reported that the COVID-19 situation increased psychosocial risk factors at work level, with an average intensity of 8.54 (scale 0-10). In fact, 91.5% said that life will never be like it was before the pandemic. The factors that showed the greatest impact on health and well-being were cognitive demands (M=4.13) emotional (M=3.95), meaning of work (M=3.93) and high work rate (M=3 .86). In the mean values of the COPSOQ II scale, there were no significant differences regarding gender (Pillai's trace=0.206, F(35.152)=1.129, p=0.167. Age was significantly correlated with cognitive requirements factors (r=0.165;p=0.024), influence at work (r=0.248;p=0.001), social support from superiors (r=0.150;p=0.040), quality of leadership and headship (r=0.175;p=0.016), justice and respect (r=0.144;p=0.048), commitment to the workplace (r=0.202;p=0.005), job satisfaction in general (r=0.224;p=0.002) and sleep problems (r=0.168;p=0.021). Conclusion(s): One year after the start of the pandemic, nurses feel physically and emotionally exhausted due to the high work rate and not very optimistic about the improvement of the situation. The older the age, the more positive is the perception of influence at work, social support from superiors, quality of leadership and headship, justice and respect, commitment to the workplace and job satisfaction.

Characteristics of Oral Corticosteroid Users Among Persons with Asthma on GINA Step 3 Therapy and Above: A Cross-Sectional Study in Portuguese Community Pharmacies.

Purpose: Oral corticosteroids (OCS) are frequently used in asthma management but have an important risk-profile. The aim of the study is to characterize and compare the sociodemographic and clinical characteristics, treatment regimen and asthma control between OCS users and non-users among the population of asthma patients (≥18 years) at GINA step 3 and above treated with a fixed combination of an inhaled corticosteroid and a long-acting beta-agonist (ICS/LABA). Methods: Cross-sectional study in Portuguese community pharmacies. Data was collected via paper-based interview delivered at the pharmacy (sociodemographic characteristics and asthma treatment regimen, namely ICS/LABA and OCS utilization), followed by a telephonic interview collecting smoking history, comorbidities, body mass index (BMI), history of exacerbations and asthma-related healthcare resource utilization (HCRU) in the previous 12 months, as well as asthma control using the Control of Allergic Rhinitis and Asthma Test (CARAT®). Results: A total of 347 patients recruited in 98 pharmacies were included in the analysis. Of those, 328 had completed both questionnaires. A quarter of the individuals reported OCS use in the previous 12 months (OCS users), either as add-on therapy (6%) or exacerbation treatment (19%). Patients were mostly females (72%), with an average age of 59.5 years (SD=15.4). OCS users were significantly older and reported more frequently having conjunctivitis (25.9% vs 15.0%), osteoporosis (25.9% vs 13.4%), arthritis (14.6% vs 6.9%), and gastrointestinal disease (16.1% vs 8.1%). OCS users also reported greater urgent HCRU: unscheduled consultations (33.3% vs 9.3%) and emergency department (ED) visits (32.1% vs 12.1%). Both groups presented poor disease control (85.2% of OCS users vs 72.9% of non-OCS users). Conclusion: These results highlight the burden of OCS therapy to asthma patients and the need to improve asthma management, by adopting OCS sparing strategies in this subgroup of patients.

Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England (preprint)

Random genetic drift in the population-level dynamics of an infectious disease outbreak results from the randomness of inter-host transmission and the randomness of host recovery or death. The strength of genetic drift has been found to be high for SARS-CoV-2 due to superspreading, and this is expected to substantially impact the disease epidemiology and evolution. Noise that results from the measurement process, such as biases in data collection across time, geographical areas, etc., can potentially confound estimates of genetic drift as both processes contribute "noise" to the data. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude. Corrections taking into account epidemiological dynamics (susceptible-infected-recovered or susceptible-exposed-infected-recovered models) do not explain the discrepancy. Moreover, the levels of genetic drift that we observe are higher than the estimated levels of superspreading found by modeling studies that incorporate data on actual contact statistics in England. We discuss how even in the absence of superspreading, high levels of genetic drift can be generated via community structure in the host contact network. Our results suggest that further investigations of heterogeneous host contact structure may be important for understanding the high levels of genetic drift observed for SARS-CoV-2 in England.

Application of thermography to estimate respiratory rate in the emergency room: The journal Temperature toolbox.

Among the vital signs collected during hospital triage, respiratory rate is an important parameter associated with physiological, pathophysiological, and emotional changes. In recent years, the importance of its verification in emergency centers due to the severe acute respiratory syndrome 2 (SARS2) pandemic has become very clear, although it is still one of the least evaluated and collected vital signs. In this context, infrared imaging has been shown to be a reliable estimator of respiratory rate, with the advantage of not requiring physical contact with patients. The objective of this study was to evaluate the potential of analyzing a sequence of thermal images as an estimator of respiratory rate in the clinical routine of an emergency room. We used an infrared thermal camera (T540, Flir Systems) to obtain the respiratory rate data of 136 patients, based on nostrils' temperature fluctuation, during the peak of the COVID-19 pandemic in Brazil and compared it with the chest incursion count method, commonly employed in the emergency screening procedures. We found a good agreement between both methods, with Bland-Altman limits of agreement ranging from -4 to 4 min-1, no proportional bias (R2 = 0.021, p = 0.095), and a strong correlation between them (r = 0.95, p < 0.001). Our results suggest that infrared thermography has potential to be a good estimator of respiratory rate in the routine of an emergency room.

Detecting anti-SARS-CoV-2 antibodies in urine samples: A noninvasive and sensitive way to assay COVID-19 immune conversion.

Serum-based ELISA (enzyme-linked immunosorbent assay) has been widely used to detect anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. However, to date, no study has investigated patient urine as a biological sample to detect SARS-CoV-2 virus-specific antibodies. An in-house urine-based ELISA was developed using recombinant SARS-CoV-2 nucleocapsid protein. The presence of SARS-CoV-2 antibodies in urine was established, with 94% sensitivity and 100% specificity for the detection of anti-SARS-CoV-2 antibodies with the urine-based ELISA and 88% sensitivity and 100% specificity with a paired serum-based ELISA. The urine-based ELISA that detects anti-SARS-CoV-2 antibodies is a noninvasive method with potential application as a facile COVID-19 immunodiagnostic platform, which can be used to report the extent of exposure at the population level and/or to assess the risk of infection at the individual level.

Nitazoxanide in Patients Hospitalized With COVID-19 Pneumonia: A Multicentre, Randomized, Double-Blind, Placebo-Controlled Trial.

Background: Nitazoxanide exerts antiviral activity in vitro and in vivo and anti-inflammatory effects, but its impact on patients hospitalized with COVID-19 pneumonia is uncertain. Methods: A multicentre, randomized, double-blind, placebo-controlled trial was conducted in 19 hospitals in Brazil. Hospitalized adult patients requiring supplemental oxygen, with COVID-19 symptoms and a chest computed tomography scan suggestive of viral pneumonia or positive RT-PCR test for COVID-19 were enrolled. Patients were randomized 1:1 to receive nitazoxanide (500 mg) or placebo, 3 times daily, for 5 days, and were followed for 14 days. The primary outcome was intensive care unit admission due to the need for invasive mechanical ventilation. Secondary outcomes included clinical improvement, hospital discharge, oxygen requirements, death, and adverse events within 14 days. Results: Of the 498 patients, 405 (202 in the nitazoxanide group and 203 in the placebo group) were included in the analyses. Admission to the intensive care unit did not differ between the groups (hazard ratio [95% confidence interval], 0.68 [0.38-1.20], p = 0.179); death rates also did not differ. Nitazoxanide improved the clinical outcome (2.75 [2.21-3.43], p < 0.0001), time to hospital discharge (1.37 [1.11-1.71], p = 0.005), and reduced oxygen requirements (0.77 [0.64-0.94], p = 0.011). C-reactive protein, D-dimer, and ferritin levels were lower in the nitazoxanide group than the placebo group on day 7. No serious adverse events were observed. Conclusions: Nitazoxanide, compared with placebo, did not prevent admission to the intensive care unit for patients hospitalized with COVID-19 pneumonia. Clinical Trial Registration: Brazilian Registry of Clinical Trials (REBEC) RBR88bs9x; ClinicalTrials.gov, NCT04561219.

Safe urodynamic practices in times of COVID-19: What can be accomplished and what can be added?

AIM: To present feedback, after applying national and international urodynamic study (UDS) recommendations for safe practice during the COVID-19 pandemic. METHODS: We created a checklist to assess the feasibility of performing UDS recommendations for safe practice during the COVID-19 pandemic from the first week of May 2021 to the last week of July 2021. RESULTS: One hundred patients were analyzed during the study period. We observed that all preventive recommendations for the steps that precede UDS could be followed in full. However, some guidelines for performing the exam were not feasible in all patients. We have successfully adopted other safety measures for all patients. CONCLUSIONS: The COVID-19 pandemic will likely persist for several more years. We believe that continuous improvement, revision, and updating of existing protocols and guidelines for the safe practice of UDS in times of COVID-19, as we propose in this study, should be encouraged.

Available and affordable complementary treatments for COVID-19: From hypothesis to pilot studies and the need for implementation.

Vaccination is a highly effective preventive measure against COVID-19. However, complementary treatments are needed to better control the disease. Fermented vegetables and spices, agonists of the antioxidant transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) and TRPA1/V1 channels (Transient Receptor Potential Ankyrin 1 and Vanillin 1), may help in the control of COVID-19. Some preliminary clinical trials suggest that curcumin (spice) can prevent some of the COVID-19 symptoms. Before any conclusion can be drawn and these treatments recommended for COVID-19, the data warrant confirmation. In particular, the benefits of the foods need to be assessed in more patients, through research studies and large trials employing a double-blind, placebo-controlled design.

Associations between resources and practices of ILD centers and outcomes in patients with idiopathic pulmonary fibrosis: data from the IPF-PRO Registry.

BACKGROUND: Performance benchmarks for the management of idiopathic pulmonary fibrosis (IPF) have not been established. We used data from the IPF-PRO Registry, an observational registry of patients with IPF managed at sites across the US, to examine associations between the characteristics of the enrolling sites and patient outcomes. METHODS: An online survey was used to collect information on the resources, operations, and self-assessment practices of IPF-PRO Registry sites that enrolled ≥ 10 patients. Site variability in 1-year event rates of clinically relevant outcomes, including death, death or lung transplant, and hospitalization, was assessed. Models were adjusted for differences in patient case mix by adjusting for known predictors of each outcome. We assessed whether site-level heterogeneity existed for each patient-level outcome, and if so, we investigated potential drivers of the heterogeneity. RESULTS: All 27 sites that enrolled ≥ 10 patients returned the questionnaire. Most sites were actively following > 100 patients with IPF (70.4%), had a lung transplant program (66.7%), and had a dedicated ILD nurse leader (77.8%). Substantial heterogeneity was observed in the event rates of clinically relevant outcomes across the sites. After controlling for patient case mix, there were no outcomes for which the site variance component was significantly different from 0, but the p-value for hospitalization was 0.052. Starting/completing an ILD-related quality improvement project in the previous 2 years was associated with a lower risk of hospitalization (HR 0.60 [95% CI 0.44, 0.82]; p = 0.001). CONCLUSIONS: Analyses of data from patients with IPF managed at sites across the US found no site-specific characteristics or practices that were significantly associated with clinically relevant outcomes after adjusting for patient case mix. Trial registration ClinicalTrials.gov, NCT01915511. Registered 5 August 2013, https://clinicaltrials.gov/ct2/show/NCT01915511.

COVID-19 surveillance data quality issues: a national consecutive case series.

OBJECTIVES: High-quality data are crucial for guiding decision-making and practising evidence-based healthcare, especially if previous knowledge is lacking. Nevertheless, data quality frailties have been exposed worldwide during the current COVID-19 pandemic. Focusing on a major Portuguese epidemiological surveillance dataset, our study aims to assess COVID-19 data quality issues and suggest possible solutions. SETTINGS: On 27 April 2020, the Portuguese Directorate-General of Health (DGS) made available a dataset (DGSApril) for researchers, upon request. On 4 August, an updated dataset (DGSAugust) was also obtained. PARTICIPANTS: All COVID-19-confirmed cases notified through the medical component of National System for Epidemiological Surveillance until end of June. PRIMARY AND SECONDARY OUTCOME MEASURES: Data completeness and consistency. RESULTS: DGSAugust has not followed the data format and variables as DGSApril and a significant number of missing data and inconsistencies were found (eg, 4075 cases from the DGSApril were apparently not included in DGSAugust). Several variables also showed a low degree of completeness and/or changed their values from one dataset to another (eg, the variable 'underlying conditions' had more than half of cases showing different information between datasets). There were also significant inconsistencies between the number of cases and deaths due to COVID-19 shown in DGSAugust and by the DGS reports publicly provided daily. CONCLUSIONS: Important quality issues of the Portuguese COVID-19 surveillance datasets were described. These issues can limit surveillance data usability to inform good decisions and perform useful research. Major improvements in surveillance datasets are therefore urgently needed-for example, simplification of data entry processes, constant monitoring of data, and increased training and awareness of healthcare providers-as low data quality may lead to a deficient pandemic control.

Role of Imaging in Diagnosis and Management of COVID-19: A Multiorgan Multimodality Imaging Review.

In this pandemic of Coronavirus disease 2019 (COVID-19), a vast proportion of healthcare resources, including imaging tools, have been dedicated to the management of affected patients; yet, the frequent reports of unknown presentations and complications of disease over time have been changing the usual standard of care and resource allocation in health centers. As of now, we have witnessed multisystemic symptoms requiring the collaboration of different clinical teams in COVID-19 patients' care. Compared to previous viral pandemics, imaging modalities are now playing an essential role in the diagnosis and management of patients. This widespread utility of imaging modalities calls for a deeper understanding of potential radiologic findings in this disease and identifying the most compatible imaging protocol with safety precautions. Although initially used for respiratory tract evaluation, imaging modalities have also been used for cardiovascular, neurologic, and gastrointestinal evaluation of patients with COVID-19. In this narrative review article, we provide multimodality and multisystemic review of imaging techniques and features that can aid in the diagnosis and management of COVID-19 patients.

Prognostic value of pre-hospitalization stress perfusion cardiovascular magnetic resonance to predict death in patients hospitalized for COVID-19.

BACKGROUND: Inducible ischaemia is a strong marker of vascular vulnerability. Knowing the important role of the vascular tropism of COVID-19 to explain its severity, the presence of a prior inducible ischaemia may be a key pathogenetic determinant of COVID-19 severity. AIMS: To investigate the prognostic value of prior inducible ischaemia on stress cardiovascular magnetic resonance (CMR) to predict death in patients hospitalized for COVID-19. METHODS: We retrospectively analysed consecutive patients referred for stress perfusion CMR during 1/1/18-1/1/20 who were later hospitalized for COVID-19. The primary outcome was all-cause death, including in-hospital and post-hospitalization deaths, based on the electronic national death registry. RESULTS: Among the patients referred for stress CMR, 481 were hospitalized for COVID-19 (mean age 68.4±9.6years, 61.3% male) and completed the follow-up (median [interquartile range] 73 [36-101] days). There were 93 (19.3%) all-cause deaths, of which 13.7% occurred in hospital and 5.6% were post-hospitalization deaths. Age, male sex, hypertension, diabetes, known coronary artery disease (CAD), the presence of prior inducible ischaemia, the number of ischaemic segments, the presence of late gadolinium enhancement and left ventricular ejection fraction were significantly associated with all-cause death. In multivariable stepwise Cox regression analysis, age (hazard ratio [HR]: 1.04, 95% confidence interval [CI]: 1.01-1.07; P=0.023), hypertension (HR: 2.77; 95% CI: 1.71-4.51; P<0.001), diabetes (HR: 1.72; 95% CI: 1.08-2.74; P=0.022), known CAD (HR: 1.78; 95% CI: 1.07-2.94; P=0.025) and prior inducible ischaemia (HR 2.05; 95% CI: 1.27-3.33; P=0.004) were independent predictors of all-cause death. CONCLUSIONS: In COVID-19 patients, prior inducible ischaemia by stress CMR during the 2years preceding the COVID-19 pandemic was independently associated with all-cause death.

Differentiation of COVID-19 signs and symptoms from allergic rhinitis and common cold: An ARIA-EAACI-GA2 LEN consensus.

BACKGROUND: Although there are many asymptomatic patients, one of the problems of COVID-19 is early recognition of the disease. COVID-19 symptoms are polymorphic and may include upper respiratory symptoms. However, COVID-19 symptoms may be mistaken with the common cold or allergic rhinitis. An ARIA-EAACI study group attempted to differentiate upper respiratory symptoms between the three diseases. METHODS: A modified Delphi process was used. The ARIA members who were seeing COVID-19 patients were asked to fill in a questionnaire on the upper airway symptoms of COVID-19, common cold and allergic rhinitis. RESULTS: Among the 192 ARIA members who were invited to respond to the questionnaire, 89 responded and 87 questionnaires were analysed. The consensus was then reported. A two-way ANOVA revealed significant differences in the symptom intensity between the three diseases (p < .001). CONCLUSIONS: This modified Delphi approach enabled the differentiation of upper respiratory symptoms between COVID-19, the common cold and allergic rhinitis. An electronic algorithm will be devised using the questionnaire.

Impact of non-pharmacological initiatives for COVID-19 on hospital admissions due to pediatric acute respiratory illnesses.

INTRODUCTION: Interventions to deal with the COVID-19 pandemic may impact the burden of other respiratory diseases. The aim of this study is to analyze the impact of non-pharmacological initiatives (NPI) against COVID-19 on the number of hospitalizations due to pediatric acute respiratory illnesses (ARIs). MATERIAL AND METHODS: This is a retrospective analysis of pediatric hospitalizations in Porto Alegre, Brazil. We analyzed the monthly incidence of hospital admissions from 2018 to 2020 due to ARIs included in the study. The time series was divided into the period before introducing NPI (2018 and 2019), and the period when NPI were running (2020). We compared means between the years with Student's t-test. The Dickey-Fuller test was used for secular trend analysis. For seasonality, Fischer's G test was performed. Dynamic linear univariate and multivariate models were used to estimate the association between the predictors (the introduction of NPI, secular trend, and seasonality) and outcome (the incidence of ARI admissions). For the statistical analysis, the cut-off probability for rejecting the null hypothesis was defined as <5%. RESULTS: From 2018 to 2020, 10,109 hospital admissions were due to the respiratory causes included in this study. There was a significant decrease in 2020 in the mean incidence of the ARIs studied compared with 2018 and 2019. The number of hospitalizations due to respiratory diseases in children decreased by 64% for asthma and 93% for bronchiolitis. A secular trend of monthly admissions rates due to ARIs was only observed in the laryngotracheitis data (p = 0.485), but seasonality was detected in all analyses. According to the univariate and multivariate analysis, the introduction of NPI was associated with a decrease in the incidence of ARI admissions. CONCLUSION: There was a significant reduction in hospital admissions due to ARIs in children. Our data suggest a significant impact of NPI on reducing the spread of viruses associated with ARIs in children. These results support respiratory illness prevention strategies.