Structural under-reporting of informed consent, data handling and sharing, ethical approval, and application of Open Science principles as proxies for study quality conduct in COVID-19 research: a systematic scoping review.

BACKGROUND: The COVID-19 pandemic required science to provide answers rapidly to combat the outbreak. Hence, the reproducibility and quality of conducting research may have been threatened, particularly regarding privacy and data protection, in varying ways around the globe. The objective was to investigate aspects of reporting informed consent and data handling as proxies for study quality conduct. METHODS: A systematic scoping review was performed by searching PubMed and Embase. The search was performed on November 8th, 2020. Studies with hospitalised patients diagnosed with COVID-19 over 18 years old were eligible for inclusion. With a focus on informed consent, data were extracted on the study design, prestudy protocol registration, ethical approval, data anonymisation, data sharing and data transfer as proxies for study quality. For reasons of comparison, data regarding country income level, study location and journal impact factor were also collected. RESULTS: 972 studies were included. 21.3% of studies reported informed consent, 42.6% reported waivers of consent, 31.4% did not report consent information and 4.7% mentioned other types of consent. Informed consent reporting was highest in clinical trials (94.6%) and lowest in retrospective cohort studies (15.0%). The reporting of consent versus no consent did not differ significantly by journal impact factor (p=0.159). 16.8% of studies reported a prestudy protocol registration or design. Ethical approval was described in 90.9% of studies. Information on anonymisation was provided in 17.0% of studies. In 257 multicentre studies, 1.2% reported on data sharing agreements, and none reported on Findable, Accessible, Interoperable and Reusable data principles. 1.2% reported on open data. Consent was most often reported in the Middle East (42.4%) and least often in North America (4.7%). Only one report originated from a low-income country. DISCUSSION: Informed consent and aspects of data handling and sharing were under-reported in publications concerning COVID-19 and differed between countries, which strains study quality conduct when in dire need of answers.

Decoding the Fundamental Drivers of Phylodynamic Inference.

Despite its increasing role in the understanding of infectious disease transmission at the applied and theoretical levels, phylodynamics lacks a well-defined notion of ideal data and optimal sampling. We introduce a method to visualize and quantify the relative impact of pathogen genome sequence and sampling times-two fundamental sources of data for phylodynamics under birth-death-sampling models-to understand how each drives phylodynamic inference. Applying our method to simulated data and real-world SARS-CoV-2 and H1N1 Influenza data, we use this insight to elucidate fundamental trade-offs and guidelines for phylodynamic analyses to draw the most from sequence data. Phylodynamics promises to be a staple of future responses to infectious disease threats globally. Continuing research into the inherent requirements and trade-offs of phylodynamic data and inference will help ensure phylodynamic tools are wielded in ever more targeted and efficient ways.

COVID-19 Lockdown Effects on a Highly Contaminated Coastal Site: The Mar Piccolo Basin of Taranto

The COVID-19 pandemic has had a dramatic socio-economic impact on mankind;however, the COVID-19 lockdown brought a drastic reduction of anthropic impacts on the environment worldwide, including the marine–coastal system. This study is concentrated on the Mar Piccolo basin of Taranto, a complex marine ecosystem model that is important in terms of ecological, social, and economic activities. Although many numerical studies have been conducted to investigate the features of the water fluxes in the Mar Piccolo basin, this is the first study conducted in order to link meteo-oceanographic conditions, water quality, and potential reduction of anthropic inputs. In particular, we used the model results in order to study the response of the Mar Piccolo basin to a drastic reduction in the leakage of heavy metal IPAs from industrial discharges during the two months of the mandated nationwide lockdown. The results show the different behavior of the two sub-basins of Mar Piccolo, showing the different times necessary for a reduction in the concentrations of heavy metals even after a total stop in the leakage of heavy metal IPAs. The results highlight the high sensitivity of the basin to environmental problems and the different times necessary for the renewal of the water in both sub-basins. © 2023 by the authors.

Comparison and Propensity Score of Seroconversion After Two Doses Of SARS-CoV-2 Vaccine in IBD Patients And Liver Transplant Recipients

Background: Suboptimal anti-Sars-Cov2 vaccine response has been demonstrated during immunosuppressive treatments. Liver Transplant Recipients (LTRs) and Inflammatory Bowel Disease (IBD) patients are different setting of populations who are both undergoing immunosuppressive treatments. In this work, we pooled and compared, retrospectively, these two populations to evaluate anti-SARS-CoV2 seroconversion after the second dose of vaccination. Different comorbidities and therapies outcomes have been explored as well. Method(s): The antibody titres standardized of the two cohorts have been analysed. Matched patients of both populations for comorbidities and therapies with application of propensity score have been investigated. Result(s): 240 LTRs and 424 IBD patients were analysed. Most have received an mRNA based vaccine (BNT162b2 or mRNA-1273: 99.1%). The seroconversion rate of 84% for LTRs and 93% for IBD patients was recorded. To multivariate analysis, hypertension (OR 2.8618, 95% CI 1.0012 to 8.1802), the mycophenolate administration (OR 2.9733, 95% CI 1.1820 to 7.4794) and the steroid use (OR 5.4531, 95% CI 1.0706 to 27.7761) were significantly associated with reduced seroconversion in LTRs cohort;meanwhile, the older age (OR 1.0369, 95% CI 1.0076 to 1.0670) and the thiopurine consumption (OR 2.9484, 95% CI 1.0089 to 8.6166) with that in IBD population. After Propensity Score Matching application, the seroconversion rates, not statistically different, of 86% for LTRs and 92% for IBD patients were found. Hypertension (OR 2.73, 95%CI 1.1258 to 6.6138), diabetes (OR 3.16, 95% CI 1.1888 to 8.4217), age > 65y (OR 2.93, 95% CI 1.1712 to 7.3153) and the female sex (OR 2.54, 95% CI 1.0963 to 5.9104) were correlated with reduced seroconversion in both populations. Conclusion(s): After Propensity Score Matching, the seroconversion rates of IBD and LTR patients were not statistically different. Hypertension, diabetes and age > 65y revealed a significant influence on seroconversion and the female showed a reduced seroconversion in comparison to male.

SARS-CoV-2 RNA Detected in Vitreous Samples Obtained at Autopsy.

Purpose: This work aims to examine the vitreous of autopsy patients with COVID-19 for the presence of SARS-CoV-2 RNA. Methods: Four deceased patients with COVID-19 had an autopsy at Massachusetts General Hospital. Two control specimens were obtained from patients undergoing retinal detachment repair with negative preoperative polymerase chain reaction (PCR) testing for SARS-CoV-2 RNA. Vitreous specimens were obtained from autopsy patients with COVID-19 after povidone was placed on the ocular surface to decrease the risk of contamination of the vitreous specimen. SARS-CoV-2 RNA for gene N (nucleocapsid) was tested using reverse transcription-PCR. Results: SARS-CoV-2 RNA was detected in the vitreous of 2 of 4 autopsy patients who died from complications of COVID-19. Conclusions: SARS-CoV-2 RNA can penetrate into the vitreous of systemically infected patients, which might present risks to operating room personnel during ophthalmic surgical procedures.

Adipocytokine plasma concentrations reflect influence of inflammation but not body mass index (BMI) on clinical outcomes of COVID-19 patients: A prospective observational study from the Netherlands.

Obesity is recognized as a risk factor for adverse outcome in COVID-19, but the molecular mechanisms underlying this relationship remain unknown. Adipose tissue functions as an endocrine organ by secreting multiple pro-inflammatory and anti-inflammatory factors, known as adipocytokines, which could be involved in COVID-19 severity. We explored the role of adipocytokines in COVID-19 and its association with BMI, clinical outcome, and inflammation. This is an observational study in 195 hospitalized COVID-19 patients. Serial plasma concentrations of the adipocytokines leptin, adiponectin, resistin, and various inflammatory cytokines were assessed. Adipocytokines were compared between patients with normal weight (BMI: 18.5-24.9 kg/m2 ), overweight (BMI: 25.0-29.9 kg/m2 ), and obesity (BMI ≥ 30 kg/m2 ), between patients admitted to the ICU and to non-ICU clinical wards, and between survivors and non-survivors. Patients with overweight and obesity displayed higher leptin concentrations and lower adiponectin concentrations throughout hospital admission (p < .001), whereas resistin concentrations were not different from patients with normal weight (p = .12). Resistin concentrations correlated with inflammatory markers and were persistently higher in ICU patients and non-survivors compared to non-ICU patients and survivors, respectively (both p < .001), whereas no such relationships were found for the other adipocytokines. In conclusion, leptin and adiponectin are associated with BMI, but not with clinical outcomes and inflammation in COVID-19 patients. In contrast, resistin is not associated with BMI, but high concentrations are associated with worse clinical outcomes and more pronounced inflammation. Therefore, it is unlikely that BMI-related adipocytokines or differences in the inflammatory response underlie obesity as a risk factor for severe COVID-19.

Exploratory analysis of interleukin-38 in hospitalized COVID-19 patients.

INTRODUCTION: A major contributor to coronavirus disease 2019 (COVID-19) progression and severity is a dysregulated innate and adaptive immune response. Interleukin-38 (IL-38) is an IL-1 family member with broad anti-inflammatory properties, but thus far little is known about its role in viral infections. Recent studies have shown inconsistent results, as one study finding an increase in circulating IL-38 in COVID-19 patients in comparison to healthy controls, whereas two other studies report no differences in IL-38 concentrations. METHODS: Here, we present an exploratory, retrospective cohort study of circulating IL-38 concentrations in hospitalized COVID-19 patients admitted to two Dutch hospitals (discovery n = 148 and validation n = 184) and age- and sex-matched healthy subjects. Plasma IL-38 concentrations were measured by enzyme-linked immunosorbent assay, disease-related proteins by proximity extension assay, and clinical data were retrieved from hospital records. RESULTS: IL-38 concentrations were stable during hospitalization and similar to those of healthy control subjects. IL-38 was not associated with rates of intensive care unit admission or mortality. Only in men in the discovery cohort, IL-38 concentrations were positively correlated with hospitalization duration. A positive correlation between IL-38 and the inflammatory biomarker d-dimer was observed in men of the validation cohort. In women of the validation cohort, IL-38 concentrations correlated negatively with thrombocyte numbers. Furthermore, plasma IL-38 concentrations in the validation cohort correlated positively with TNF, TNFRSF9, IL-10Ra, neurotrophil 3, polymeric immunoglobulin receptor, CHL1, CD244, superoxide dismutase 2, and fatty acid binding protein 2, and negatively with SERPINA12 and cartilage oligomeric matrix protein. CONCLUSIONS: These data indicate that IL-38 is not associated with disease outcomes in hospitalized COVID-19 patients. However, moderate correlations between IL-38 concentrations and biomarkers of disease were identified in one of two cohorts. While we demonstrate that IL-38 concentrations are not indicative of COVID-19 severity, its anti-inflammatory effects may reduce COVID-19 severity and should be experimentally investigated.

Plasma with high titers of anti-SARS-Cov2 antibodies improves outcome of COVID-19 in patients with hematological malignancy and cancer in a randomized controlled trial

Background. Patients with hematological malignancy or other cancers as well as immunosuppression bear a high risk for severe COVID-19. Monoclonal antibodies (mAb) are efficient at early stages of the disease but may lose potency with new variants. Trials on plasma from convalescent donors in unselected patients have not shown clinical benefit. No randomized trials focussing on patients with underlying disease have been published. Methods. We conducted an open-label, multicenter, randomized controlled trial to evaluate efficacy of plasma (CVP - convalescent or after vaccination) in patients with COVID-19 at high risk for adverse outcome in Germany. We assessed the effect of high-titer CVP (2 units from different donors, 238-337 ml each, on subsequent days). Patients with hematological or other malignancy (group 1), immunosuppression (group 2), age >50 and <=75 years and lymphopenia and/or high D-dimers (group 3) or age >75 years (group 4) who were hospitalized with confirmed SARS-CoV-2 infection and with an oxygen saturation <=94% were included. Primary outcome measure was time to clinical improvement on a seven-point ordinal scale, secondary outcome was mortality (Janssen et al. Trials 2020 Oct 6;21(1):828). Results. Overall, 133 patients were randomized, 68 received CVP with an additional 10 patients as a crossover on day 10. Median age (range) was 68 years (39-95) in the CVP group and 70 (38-90) in controls. For the entire cohort, no significant difference was seen in time to improvement (median days: CVP 12.5 vs. control 18;HR 1.24 (95% confidence interval (CI) 0.83-1.85), p=0.29). Subgroup analysis (group 1+2) revealed shortened time to improvement (median days CVP 13 vs. control 32;HR 2.03 (95%CI 1.17-3.6), p=0.01) and mortality was reduced (mortality CVP n=6 (18%) vs. control n=10 (29%). No significant differences in time to improvement were observed in group 3 or 4 (HR 0.72 (95%CI 0.41-1.28), p=0.26). No relevant adverse events were observed. Conclusion. CVP improves time to clinical improvement and mortality for COVID-19 patients with underlying hematological disease/cancer or other reasons of impaired immune response. Even with new variants, high-titer CVP may offer a widely available and inexpensive therapy option in high-risk groups. Funding. BMBF FKZ 01KI20152;EudraCT 2020-001632-10.

The 2000HIV study: Design, multi-omics methods and participant characteristics.

Background: Even during long-term combination antiretroviral therapy (cART), people living with HIV (PLHIV) have a dysregulated immune system, characterized by persistent immune activation, accelerated immune ageing and increased risk of non-AIDS comorbidities. A multi-omics approach is applied to a large cohort of PLHIV to understand pathways underlying these dysregulations in order to identify new biomarkers and novel genetically validated therapeutic drugs targets. Methods: The 2000HIV study is a prospective longitudinal cohort study of PLHIV on cART. In addition, untreated HIV spontaneous controllers were recruited. In-depth multi-omics characterization will be performed, including genomics, epigenomics, transcriptomics, proteomics, metabolomics and metagenomics, functional immunological assays and extensive immunophenotyping. Furthermore, the latent viral reservoir will be assessed through cell associated HIV-1 RNA and DNA, and full-length individual proviral sequencing on a subset. Clinical measurements include an ECG, carotid intima-media thickness and plaque measurement, hepatic steatosis and fibrosis measurement as well as psychological symptoms and recreational drug questionnaires. Additionally, considering the developing pandemic, COVID-19 history and vaccination was recorded. Participants return for a two-year follow-up visit. The 2000HIV study consists of a discovery and validation cohort collected at separate sites to immediately validate any finding in an independent cohort. Results: Overall, 1895 PLHIV from four sites were included for analysis, 1559 in the discovery and 336 in the validation cohort. The study population was representative of a Western European HIV population, including 288 (15.2%) cis-women, 463 (24.4%) non-whites, and 1360 (71.8%) MSM (Men who have Sex with Men). Extreme phenotypes included 114 spontaneous controllers, 81 rapid progressors and 162 immunological non-responders. According to the Framingham score 321 (16.9%) had a cardiovascular risk of >20% in the next 10 years. COVID-19 infection was documented in 234 (12.3%) participants and 474 (25.0%) individuals had received a COVID-19 vaccine. Conclusion: The 2000HIV study established a cohort of 1895 PLHIV that employs multi-omics to discover new biological pathways and biomarkers to unravel non-AIDS comorbidities, extreme phenotypes and the latent viral reservoir that impact the health of PLHIV. The ultimate goal is to contribute to a more personalized approach to the best standard of care and a potential cure for PLHIV.

Targeted proteomics identifies circulating biomarkers associated with active COVID-19 and post-COVID-19.

The ongoing Coronavirus Disease 2019 (COVID-19) pandemic is caused by the highly infectious Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). There is an urgent need for biomarkers that will help in better stratification of patients and contribute to personalized treatments. We performed targeted proteomics using the Olink platform and systematically investigated protein concentrations in 350 hospitalized COVID-19 patients, 186 post-COVID-19 individuals, and 61 healthy individuals from 3 independent cohorts. Results revealed a signature of acute SARS-CoV-2 infection, which is represented by inflammatory biomarkers, chemokines and complement-related factors. Furthermore, the circulating proteome is still significantly affected in post-COVID-19 samples several weeks after infection. Post-COVID-19 individuals are characterized by upregulation of mediators of the tumor necrosis (TNF)-α signaling pathways and proteins related to transforming growth factor (TGF)-ß. In addition, the circulating proteome is able to differentiate between patients with different COVID-19 disease severities, and is associated with the time after infection. These results provide important insights into changes induced by SARS-CoV-2 infection at the proteomic level by integrating several cohorts to obtain a large disease spectrum, including variation in disease severity and time after infection. These findings could guide the development of host-directed therapy in COVID-19.

Safety of Covid-19 Vaccine in Patients with Inflammatory Bowel Disease: Data of a National Study (Escape-Ibd)

Introduction: Vaccination is the most effective method to prevent and control the SARS-CoV-2 infection. Recommendations consider patients with inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC), a high-priority population to COVID-19 vaccine administration. There were a lot of concerns about vaccination safety in the setting of biological and immunomodulatory drugs. The purpose of this study was to present data on safety about anti-SARSCoV- 2 vaccination in a cohort of IBD patients. These are data of an ongoing multicenter study assessing effectiveness and safety of COVID-19 vaccines in patients with IBD treated with immunomodulatory or biological drugs (ESCAPE-IBD) sponsored by the Italian Group for the study of Inflammatory Bowel Disease (IG-IBD - ClinicalTrials.gov Identifier: NCT04769258). Aims & Methods: Anti-SARS-CoV-2 vaccination was administrated to 809 IBD patients. Afterwards completed vaccination, telephone or in-person interviews were conducted from February to July 2021 by gastroenterologists from referral center to report local and/or systemic adverse events (AEs) related to vaccination. Data on medical history and treatment was collected from electronic health records. Of these 809, 346 patients were surveyed on the pandemic burden and the main reason for hesitancy in Covid-19 vaccination. Chi-square test was used to compare categorical variables. Logistic regression was used to assess the relationship between disease-related characteristics and the onset of AEs. Result(s): 809 patients, 456 CD and 353 UC, regularly followed in IBD unit, were enrolled. All patients received a complete SARS-CoV-2 vaccination cycle. Most of them (68%) were in biological or immunomodulatory therapy. About 45% of patients had at least one side effect, following the first dose (10%), the second (15%) or both doses (20%). Local pain at site of injection (24%), fatigue (33%) and fever (30%) were the three most common AEs. Flares of the underlying IBD were not reported. The vast majority of AE were mild and lasted only a few days. No serious AEs were reported and no patient was hospitalized. Logistic regression analysis revealed that female gender (p<0.001), younger age (p=0.001), seroconversion (p=0.002) and comorbidity (p<0.001) were significantly associated with the occurrence of AEs. Futhermore the survey showed that the pandemic did not affect IBD at all in 37.5%, and a lot in 9.2% of participants. The majority (95%) of patients welcomed the possibility of getting vaccinated;only 7% feared the vaccine's influence on the course of the IBD. The main concerns were the possibility of adverse effects (33%) and the failure to achieve immunity (17%), few for the type of vaccine (3%) and for the need to a further booster (6%). Almost all patients (99%) felt safer to have vaccinated at their IBD reference center. Conclusion(s): The short-term vaccine reactions experienced in this cohort of IBD patients were mostly self-limiting, including local pain at the injection site, fatigue and fever. We found a high acceptance rate and a good safety profile of SARS-CoV-2 vaccination in our cohort.

A RANDOMIZED CONTROLLED CLINICAL TRIAL DEMONSTRATES THAT PLASMA FROM CONVALESCENT AND VACCINATED DONORS IMPROVES OUTCOME OF COVID-19 IN PATIENTS WITH HEMATOLOGICAL DISEASE, CANCER OR IMMUNOSUPPRESSION

Background: Therapy options are limited for COVID-19 patients with hematological disease, cancer, immunosuppression or adanced age. Een though no benefit was obsered for conalescent plasma in unselected patients with COVID-19, retrospectie data suggest that it could be effectie in patients unable to mount a sufficient immune response upon SARS-CoV-2 infection. Plasma from accinated donors has not been systematically assessed for COVID-19 treatment. Aims: We conducted a randomized clinical trial to address plasma efficacy in patients at high risk for an aderse outcome. Methods: COVID-19 patients with confirmed SARS-CoV-2 infections and oxygen saturation <=94% were randomized (NCT05200754). Patients receied conalescent or accinated SARS-CoV-2 plasma in two bags (238 - 337 ml plasma each) from different donors on day 1 and 2 (PLASMA) or standard of care (CONTROL). Randomization was stratified according to four clinical patient groups, hematological/solid cancer (group-1), treatment or disease associated immunosuppression (group 2), high risk disease by standard parameters (group-3) or age >=75 years (group-4). Mechanically entilated patients were not eligible. Plasma was obtained from donors with high leel neutralizing actiity (titer >=1:80) either after SARS-CoV-2 infection (conalescent) or after accination with at least two doses of mRNA accines (accinated). Crossoer for the control group was allowed at day 10. The primary endpoint was time to improement as two points on a seen-point ordinal scale or lie discharge from the Hospital (IMPROVEMENT) with prespecified analyses of subgroups (Janssen M, et al. Trials 2020 Oct 6;21(1):828). Results: A total of 133 patients were randomized with 68 receiing PLASMA with a median age of 68 years (range 36-95) or CONTROL (n=65, of which n=10 (15.4%) crossed oer at day 10) with a median age of 70 years (range 38-90). The distribution of the four predefined groups was group-1, n=53;group-2, n=18;group-3, n=35;and group-4, n=27. The intention to treat analysis reealed a non-significant shorter time to IMPROVEMENT for patients in PLASMA (median 12.5 days, 95%-CI [10;16]) compared to patients in CONTROL (median 18 days, 95%-CI [11;28] ), hazard ratio 1.24, 95% confidence interal [0.83;1.85], p=0.29). Oerall, 27 patients died (PLASMA, n=12;CONTROL, n=15;p=0.80). Predefined subgroup analysis reealed a clinically significant benefit in patients with hematological malignancies, other cancers or immunosuppression (group-1, group-2, n=71). With a median time to improement of 13 days (95%-CI [9;19]) for PLASMA and 32 days (95%-CI [17;57]) for CONTROL(HR 2.03, 95%-CI [1.17;3.6], p=0.01). A sensitiity analysis reealed that IMPROVEMENT appeared to be seen een earlier with accinated (median 10 days, 95%-CI [8;14]) compared to conalescent SARS-CoV-2 plasma (median 13 days, 95%-CI [6;38]) and CONTROL. Within group-1 and group-2, six patients in PLASMA (18.2%) and 10 in CONTROL (28.6%) died. No significant differences in improement were obsered in group-3 and group-4 with a HR of 0.72 (95%-CI [0.41;1.28], p=0.26). Within group-3 and group-4, six patients in PLASMA (18.8%) and fie in CONTROL (16.7%) died. No preiously unknown side effects of plasma therapy emerged within the trial. Summary/Conclusion: Plasma from conalescent and particularly accinated donors improed outcome of COVID-19 patients with an underlying hematological disease /cancer or other reasons of impaired immune response. Plasma did not improe outcome in immune-competent patients with other risk factors and/or older age. (Figure Presented).

The Genetic Risk for COVID-19 Severity Is Associated With Defective Immune Responses.

Recent genome-wide association studies (GWASs) of COVID-19 patients of European ancestry have identified genetic loci significantly associated with disease severity. Here, we employed the detailed clinical, immunological and multi-omics dataset of the Human Functional Genomics Project (HFGP) to explore the physiological significance of the host genetic variants that influence susceptibility to severe COVID-19. A genomics investigation intersected with functional characterization of individuals with high genetic risk for severe COVID-19 susceptibility identified several major patterns: i. a large impact of genetically determined innate immune responses in COVID-19, with ii. increased susceptibility for severe disease in individuals with defective cytokine production; iii. genetic susceptibility related to ABO blood groups is probably mediated through the von Willebrand factor (VWF) and endothelial dysfunction. We further validated these identified associations at transcript and protein levels by using independent disease cohorts. These insights allow a physiological understanding of genetic susceptibility to severe COVID-19, and indicate pathways that could be targeted for prevention and therapy.

Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.

Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology, and statistical inference. It has also experienced more intense application than ever before amid the SARS-CoV-2 pandemic. In light of this, we present a review of phylodynamic models beginning with foundational models and assumptions. Our target audience is public health researchers, epidemiologists, and biologists seeking a working knowledge of the links between epidemiology, evolutionary models, and resulting epidemiological inference. We discuss the assumptions linking evolutionary models of pathogen population size to epidemiological models of the infected population size. We then describe statistical inference for phylodynamic models and list how output parameters can be rearranged for epidemiological interpretation. We go on to cover more sophisticated models and finish by highlighting future directions.

The impact of pre-existing thyroid diseases on susceptibility to respiratory infections or self-reported sickness during the SARS-CoV-2 pandemic.

Introduction: This study aimed to evaluate the incidence, severity and presence of symptoms of respiratory tract infections and COVID-19, in patients with pre-existing thyroid dysfunction compared to individuals without thyroid diseases, during the peak month of the COVID-19 pandemic in the Netherlands. Subjects and methods: In this retrospective observational cohort study, all patients currently under follow-up at the Radboud UMC for thyroid dysfunction received a digital questionnaire. Primary outcomes were incidence of self-reported sickness and cases diagnosed with COVID-19. We compared these primary outcomes between these patients and individuals without thyroid diseases that received the same questionnaire, recruited from the Human Functional Genomics Cohort at the Radboud UMC. Results: In total, 238 patients with pre-existing thyroid dysfunction and 161 controls were included. Patients did not report more sickness (30.7% vs. 29.2%; p = 0.752) or microbiologically confirmed SARS-CoV-2 infections (1.7% vs. 0.6%; p = 0.351). COVID-19 clinical diagnosis was more frequently made in patients with thyroid diseases (4.2% vs. 0.6%; p = 0.032), despite overall lower incidence of self-reported respiratory related symptoms (52.8% vs. 63.8%; p = 0.028), compared to controls. Sub-group analysis between patients with autoimmune and not-autoimmune thyroid dysfunction did not reveal significant associations with respect to any of the outcome measures. Conclusion: This retrospective survey of a cohort of patients with from a tertiary academic hospital suggests that pre-existing thyroid dysfunction, independent from the aetiology, does not lead to an apparent risk to develop respiratory tract infections and COVID-19 related symptoms.

Multi-Omics Integration Reveals Only Minor Long-Term Molecular and Functional Sequelae in Immune Cells of Individuals Recovered From COVID-19.

The majority of COVID-19 patients experience mild to moderate disease course and recover within a few weeks. An increasing number of studies characterized the long-term changes in the specific anti-SARS-CoV-2 immune responses, but how COVID-19 shapes the innate and heterologous adaptive immune system after recovery is less well known. To comprehensively investigate the post-SARS-CoV-2 infection sequelae on the immune system, we performed a multi-omics study by integrating single-cell RNA-sequencing, single-cell ATAC-sequencing, genome-wide DNA methylation profiling, and functional validation experiments in 14 convalescent COVID-19 and 15 healthy individuals. We showed that immune responses generally recover without major sequelae after COVID-19. However, subtle differences persist at the transcriptomic level in monocytes, with downregulation of the interferon pathway, while DNA methylation also displays minor changes in convalescent COVID-19 individuals. However, these differences did not affect the cytokine production capacity of PBMCs upon different bacterial, viral, and fungal stimuli, although baseline release of IL-1Ra and IFN-γ was higher in convalescent individuals. In conclusion, we propose that despite minor differences in epigenetic and transcriptional programs, the immune system of convalescent COVID-19 patients largely recovers to the homeostatic level of healthy individuals.

SARS-CoV-2 infection in liver transplantation is associated with favorable outcomes: an Italian transplant registry study

Background and aims: Solid organ transplant recipients (SOTRs) have been considered as an extremely vulnerable population in respect to SARS-CoV-2 infection. We aimed to assess the incidence and lethality rate of SARS-CoV-2 infection in different organ transplant settings using the liver as a comparator. Methods: In this nationwide population-based study we compared the crude incidence and lethality rates of SARS-CoV-2 infection [95% Bonferroni adjusted CI (Ba-CI)] among Italian LTRs as compared to non-liver SOTRs and to general population. The following independent groups had been compared: Italian general population, all SOTRs, liver transplant recipients (LTRs) and non-Liver SOTRs in area with different incidence of infection. Incidence rate ratio (IRR) and lethality rate ratio (LRR) was assessed. Community risk exposures in transplant settings were assessed. Results: From February 21 to June 22, 2020, there were 450 cases of SARS-CoV-2 infections over 14168 LTRs (n=89) and 29815 non-liver SOTRs (n= 361). A significantly lower risk of infection [IRR 0.56 (Ba-CI 0.34-0.92), 0.45 (Ba-CI 0.26-0.79), 0.52 (Ba-CI 0.36-0.75)] and a lower lethality rate ratio [(LRR 0.61 (Ba-CI 0.23-1.57), 0.37 (0.08-1.76), 0.52 (0.23-1.18] was found among LTRs as compared to non-liver SOTRs in the three areas. Excluding Lombardy, the risk of infection and lethality in LTRs was lower compared to general population. Non-Liver SOTRs showed an increased risk of infection and lethality at all geographic levels compared to general population. No significant difference in the adherence to mitigation policies was found. Conclusions: Liver transplantation was associated with a significantly lower risk of SARS-CoV-2 infection and lethality in respect to non-liver solid organ transplants. A separate evaluation of organ-specific risk stratification analysis and vaccination responses in transplant population is needed.