Circulating Ubiquitous RNA, A Highly Predictive and Prognostic Biomarker in Hospitalized Coronavirus Disease 2019 (COVID-19) Patients.

BACKGROUND: Approximately 15-30% of hospitalized coronavirus disease 2019 (COVID-19) patients develop acute respiratory distress syndrome, systemic tissue injury, and/or multi-organ failure leading to death in around 45% of cases. There is a clear need for biomarkers that quantify tissue injury, predict clinical outcomes, and guide the clinical management of hospitalized COVID-19 patients. METHODS: We herein report the quantification by droplet-based digital polymerase chain reaction (ddPCR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNAemia and the plasmatic release of a ubiquitous human intracellular marker, the ribonuclease P (RNase P) in order to evaluate tissue injury and cell lysis in the plasma of 139 COVID-19 hospitalized patients at admission. RESULTS: We confirmed that SARS-CoV-2 RNAemia was associated with clinical severity of COVID-19 patients. In addition, we showed that plasmatic RNase P RNAemia at admission was also highly correlated with disease severity (P < .001) and invasive mechanical ventilation status (P < .001) but not with pulmonary severity. Altogether, these results indicate a consequent cell lysis process in severe and critical patients but not systematically due to lung cell death. Finally, the plasmatic RNase P RNA value was also significantly associated with overall survival. CONCLUSIONS: Viral and ubiquitous blood biomarkers monitored by ddPCR could be useful for the clinical monitoring and the management of hospitalized COVID-19 patients. Moreover, these results could pave the way for new and more personalized circulating biomarkers in COVID-19, and more generally in infectious diseases, specific from each patient organ injury profile.

Highly Sensitive Quantification of Plasma Severe Acute Respiratory Syndrome Coronavirus 2 RNA Sheds Light on its Potential Clinical Value.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662 000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury, and/or multiple organ failure, suggesting a spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We intend to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAemia) in hospitalized COVID-19 patients. METHODS: Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild to moderate in 17 patients, severe in 16, and critical in 26. Plasma SARS-CoV-2 RNAemia was quantified by droplet digital Crystal Digital PCR next-generation technology (Stilla Technologies, Villejuif, France). RESULTS: Overall, SARS-CoV-2 RNAemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (P = .036). Levels of SARS-CoV-2 RNAemia were associated with severity (P = .035). Among 9 patients who experienced clinical deterioration during follow-up, 8 had positive SARS-CoV-2 RNAemia at baseline, whereas only 1 critical patient with undetectable SARS-CoV-2 RNAemia at the time of analysis died at day 27. CONCLUSION: SARS-CoV-2 RNAemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients.

HPV circulating tumoral DNA quantification by droplet-based digital PCR: A promising predictive and prognostic biomarker for HPV-associated oropharyngeal cancers.

We aimed to determine whether pretherapeutic assessment of HPV circulating tumoral DNA (HPV ctDNA) by droplet-based digital PCR (ddPCR) could constitute a predictive and prognostic biomarker for HPV-associated oropharyngeal squamous cell carcinoma (OPSCC). A mono-institutional prospective biomarker study on 66 patients with p16+/HPV16-positive oropharyngeal squamous cell carcinoma (OPSCC) was conducted in European Georges Pompidou Hospital, Paris, France. Blood samples were collected at the time of diagnosis before any treatment. Optimized digital PCR assays were used to quantify HPV16 ctDNA. Forty-seven (71%) patients showed a positive pretherapeutic HPV ctDNA at time of diagnosis. Interestingly, the quantity of HPV16 ctDNA at baseline, as assessed by ddPCR, was significantly correlated with the T/N/M status or OPSCC stages according to the 2018 new staging criteria for high-risk human papillomavirus (HR HPV) related OPSCC from American Joint Committee on Cancer (AJCC). Moreover, all recurrences and the majority (83%) of death reported events occurred in patients with positive HPV16 ctDNA at baseline. Finally, when posttreatment blood samples were available (n = 6), the kinetic of pretreatment/posttreatment HPV16 ctDNA was clearly associated with treatment success or failure. HPV ctDNA monitoring by ddPCR could constitute a useful and noninvasive dynamic biomarker to select HR HPV-related OPSCC patients eligible for potential treatment de-escalation and to monitor treatment response.

Impact of a Model Used to Simulate Chronic Socio-Environmental Stressors Encountered during Spaceflight on Murine Intestinal Microbiota.

During deep-space travels, crewmembers face various physical and psychosocial stressors that could alter gut microbiota composition. Since it is well known that intestinal dysbiosis is involved in the onset or exacerbation of several disorders, the aim of this study was to evaluate changes in intestinal microbiota in a murine model used to mimic chronic psychosocial stressors encountered during a long-term space mission. We demonstrate that 3 weeks of exposure to this model (called CUMS for Chronic Unpredictable Mild Stress) induce significant change in intracaecal ß-diversity characterized by an important increase of the Firmicutes/Bacteroidetes ratio. These alterations are associated with a decrease of Porphyromonadaceae, particularly of the genus Barnesiella, a major member of gut microbiota in mice and humans where it is described as having protective properties. These results raise the question of the impact of stress-induced decrease of beneficial taxa, support recent data deduced from in-flight experimentations and other ground-based models, and emphasize the critical need for further studies exploring the impact of spaceflight on intestinal microbiota in order to propose strategies to countermeasure spaceflight-associated dysbiosis and its consequences on health.

Evaluation of the Theoretical Teaching of Postgraduate Radiation Oncology Medical Residents in France: a Cross-Sectional Study.

This study's purpose was to have residents evaluate Radiation Oncology (RO) theoretical teaching practices in France. An anonymous electronically cross-functional survey on theoretical teaching practices in the RO residents was conducted by (i) collecting data from residents in the medical faculties in France, (ii) comparing the data across practices when possible and (iii) suggesting means of improvement. A total of 103 out of 140 RO residents responded to the survey (73.5% response rate). National, inter-university, university and internships courses do not exist in 0% (0), 16.5% (17), 53.4% (55) and 40.8% (42) of residents, respectively. Residents need additional training due to the shortage of specialised postgraduate degree training (49.5% (51)), CV enhancement to obtain a post-internship position (49.5% (51)) or as part of a career plan (47.6% (49)). The topics covered in teaching to be improved were the following: basic concept 61.2% (63), advanced concept 61.2 (63) and discussion of frequent clinical cases 50.5% (52). The topics not covered in teaching to be improved were the following: the development of career (66.0% (68)), medical English (56.3% (58)), the organisation of RO speciality (49.5% (51)) and the hospital management of RO department (38.8% (40)). This is the first national assessment of theoretical teaching of RO residents in France.

Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports.

The heterogeneity of patient phenotype data are an impediment to the research into the origins and progression of neuropsychiatric disorders. This difficulty is compounded in the case of rare disorders such as Phelan-McDermid Syndrome (PMS) by the paucity of patient clinical data. PMS is a rare syndromic genetic cause of autism and intellectual deficiency. In this paper, we describe the Phelan-McDermid Syndrome Data Network (PMS_DN), a platform that facilitates research into phenotype-genotype correlation and progression of PMS by: a) integrating knowledge of patient phenotypes extracted from Patient Reported Outcomes (PRO) data and clinical notes-two heterogeneous, underutilized sources of knowledge about patient phenotypes-with curated genetic information from the same patient cohort and b) making this integrated knowledge, along with a suite of statistical tools, available free of charge to authorized investigators on a Web portal https://pmsdn.hms.harvard.edu. PMS_DN is a Patient Centric Outcomes Research Initiative (PCORI) where patients and their families are involved in all aspects of the management of patient data in driving research into PMS. To foster collaborative research, PMS_DN also makes patient aggregates from this knowledge available to authorized investigators using distributed research networks such as the PCORnet PopMedNet. PMS_DN is hosted on a scalable cloud based environment and complies with all patient data privacy regulations. As of October 31, 2016, PMS_DN integrates high-quality knowledge extracted from the clinical notes of 112 patients and curated genetic reports of 176 patients with preprocessed PRO data from 415 patients.

Personality, dopamine, and Parkinson's disease: Insights from subthalamic stimulation.

BACKGROUND: Subthalamic stimulation improves the motor and neuropsychiatric symptoms of Parkinson's disease. However, the impact of this treatment on impulse control and personality is the subject of heavy debate. The objective of this study was to investigate personality changes after subthalamic stimulation. METHODS: Using Cloninger's biosocial model, we assessed personality in 73 Parkinson's disease patients before and 12 months after subthalamic stimulation accompanied by a drastic reduction in dopaminergic medication. Changes in psychobehavioral symptoms were measured using a battery of validated clinical scales (apathy, depression, anxiety, hyperemotionality, mania, psychosis, punding, and impulse control behaviors). RESULTS: One year after surgery, the harm avoidance personality domain total score increased compared with the baseline (+2.8; 34 patients; P < 0.001), as did 3 of its 4 subdomains: anticipatory worry (+0.7; 10 patients; P = 0.005), shyness (+0.6; 7 patients; P = 0.03), and fatigability (+1.1; 10 patients; P = 0.0014). Evolution of the shyness personality trait correlated with the decrease in dopaminergic medication. Total scores in the other personality domains remained unchanged, except for extravagance, a subdomain of novelty seeking, and persistence, a subdomain of reward dependence, which both decreased following surgery (-0.3; 7 patients; and -0.6; 9 patients; P = 0.03 and P = 0.0019, respectively). Although apathy increased, other psychobehavioral symptoms, including impulse control behaviors and neuropsychiatric nonmotor fluctuations, improved. Depression and anhedonia remained stable. Scores in hypodopaminergia and neuropsychiatric nonmotor OFF correlated with harm avoidance. Scores in hyperdopaminergia and neuropsychiatric nonmotor ON correlated with novelty seeking. CONCLUSIONS: When subthalamic stimulation is applied in Parkinson's disease, significant changes in personality traits are observed, which may be related to postoperative tapering of dopaminergic treatment. © 2017 International Parkinson and Movement Disorder Society.

Posterior Radioscaphoid Angle as a Predictor of Wrist Degenerative Joint Disease in Patients With Scapholunate Ligament Tears.

OBJECTIVE: The purpose of this study is to determine whether the posterior radioscaphoid angle, a marker of posterior displacement of the scaphoid, is associated with degenerative joint disease in patients with scapholunate ligament tears. MATERIALS AND METHODS: Images from 150 patients with wrist pain who underwent CT arthrography and radiography were retrospectively evaluated. Patients with and without scapholunate ligament ruptures were divided into two groups according to CT arthrography findings. The presence of degenerative changes (scapholunate advanced collapse [SLAC] wrist) was evaluated and graded on conventional radiographs. Images were evaluated by two readers independently, and an adjudicator analyzed the discordant cases. Posterior radioscaphoid angle values were correlated with CT arthrography and radiographic findings. The association between posterior radioscaphoid angle and degenerative joint disease was evaluated. Scapholunate and radiolunate angles were considered in the analysis. RESULTS: The posterior radioscaphoid angle was measurable in all patients, with substantial interobserver agreement (intraclass correlation coefficient, 0.75). The posterior radioscaphoid angle performed better than did the scapholunate and radiolunate angles in the differentiation of patients with and without SLAC wrist (p < 0.02). Posterior radioscaphoid angles greater than 114° presented an 80.0% sensitivity and 89.7% specificity for the detection of SLAC wrist. CONCLUSION: Posterior radioscaphoid angles were strongly associated with degenerative wrist disease, with potential prognostic implications in patients with wrist trauma and scapholunate ligament ruptures.

Systematic Brain Natriuretic Peptide Measurement for Cardiac Screening in Patients with Severe Obesity: The OLECOEUR Study.

INTRODUCTION: Heart failure (HF) is difficult to diagnose in obese patients because of cardiovascular and pulmonary comorbidities associated with physical deconditioning, all of which lead to dyspnea. METHODS: The OLECOEUR study is a prospective screening for HF using systematic brain natriuretic peptide (BNP) measurement in ambulatory patients with obesity from a department of Nutrition (Paris, France). Clinical, biological, and echocardiographic data were extracted from electronic medical records. RESULTS: We included 1,506 patients middle-aged (mean age: 47.2 ± 14.6 years old) with severe obesity (mean body mass index: 40.4 ± 6.6 kg/m2). Patients with BNP ≥35 pg/mL had left heart remodeling including thicker interventricular septum (10.4 ± 2.0 vs. 9.6 ± 1.8 mm; p = 0.0008), higher left ventricular mass (89.9 ± 24.3 vs. 77.2 ± 20.0 g/m2; p = 0.0009), and significant changes in both left and right atria consistent with a higher proportion of prior atrial fibrillation. Markers of right heart remodeling on echocardiography were also significantly higher (pulmonary artery systolic pressure: 33.3 ± 17.3 vs. 24.5 ± 6.3 mm Hg; p = 0.0002). CONCLUSION: The OLECOEUR study shows left and right subclinical cardiac remodeling in obese patients screened for HF with systematic dosing of BNP with usual cut-off of 35 pg/mL.

Phenome-wide profiling identifies genotype-phenotype associations in Phelan-McDermid syndrome using family-sourced data from an international registry.

BACKGROUND: Phelan-McDermid syndrome (PMS) is a rare neurodevelopmental disorder caused by 22q13 deletions that include the SHANK3 gene or pathogenic sequence variants in SHANK3. It is characterized by global developmental delay, intellectual disability, speech impairment, autism spectrum disorder, and hypotonia; other variable features include epilepsy, brain and renal malformations, and mild dysmorphic features. Here, we conducted genotype-phenotype correlation analyses using the PMS International Registry, a family-driven registry that compiles clinical data in the form of family-reported outcomes and family-sourced genetic test results. METHODS: Data from the registry were harmonized and integrated into the i2b2/tranSMART clinical and genomics data warehouse. We gathered information from 401 individuals with 22q13 deletions including SHANK3 (n = 350, ranging in size from 10 kb to 9.1 Mb) or pathogenic or likely pathogenic SHANK3 sequence variants (n = 51), and used regression models with deletion size as a potential predictor of clinical outcomes for 328 phenotypes. RESULTS: Our results showed that increased deletion size was significantly associated with delay in gross and fine motor acquisitions, a spectrum of conditions related to poor muscle tone, renal malformations, mild dysmorphic features (e.g., large fleshy hands, sacral dimple, dysplastic toenails, supernumerary teeth), lymphedema, congenital heart defects, and more frequent neuroimaging abnormalities and infections. These findings indicate that genes upstream of SHANK3 also contribute to some of the manifestations of PMS in individuals with larger deletions. We also showed that self-help skills, verbal ability and a range of psychiatric diagnoses (e.g., autism, ADHD, anxiety disorder) were more common among individuals with smaller deletions and SHANK3 variants. LIMITATIONS: Some participants were tested with targeted 22q microarrays rather than genome-wide arrays, and karyotypes were unavailable in many cases, thus precluding the analysis of the effect of other copy number variants or chromosomal rearrangements on the phenotype. CONCLUSIONS: This is the largest reported case series of individuals with PMS. Overall, we demonstrate the feasibility of using data from a family-sourced registry to conduct genotype-phenotype analyses in rare genetic disorders. We replicate and strengthen previous findings, and reveal novel associations between larger 22q13 deletions and congenital heart defects, neuroimaging abnormalities and recurrent infections.

viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome.

INTRODUCTION: The implication of viruses in human cancers, as well as the emergence of next generation sequencing has permitted to investigate further their role and pathophysiology in the development of this disease. One such mechanism is the integration of portions of viral genomes in the human genome, as well as the specific action of viral oncogenes.inding integration sites and preserved oncogenes is still relying on heavy manual intervention. METHODS: We developed an analysis and interpretation pipeline to determine viral insertions. Using data from directed viral capture, the pipeline conducts a crude genotyping phase to select reference viral genomes, identifies chimeric reads, extracts the putative human sequences to locate in the human reference genome, scores and ranks candidate junctions, and exports tabular and visual results. RESULTS: We leverage common bioinformatics tools (bowtie2, samtools, blat), and a dedicated filtering and ranking algorithm, implemented in R, to infer candidate junctions and insertions. Static results (tables, figures) are produced, as well as an interactive interpretation tool developed as a shiny web app. DISCUSSION: We validated this pipeline against published results of HPV, HBV, and AAV2 insertions and show good information retrieval.

Determining the Set of Items to Include in Breast Operative Reports, Using Clustering Algorithms on Retrospective Data Extracted from Clinical DataWarehouse.

Medical reports are key elements to guarantee the quality, and continuity of care but their quality remains an issue. Standardization and structuration of reports can increase their quality, but are usually based on expert opinions. Here, we hypothesize that a structured model of medical reports could be learnt using machine learning on retrospective medical reports extracted from clinical data warehouses (CDW). To investigate our hypothesis, we extracted breast cancer operative reports from our CDW. Each document was preprocessed and split into sentences. Clustering was performed using TFIDF, Paraphrase or Universal Sentence Encoder along with K-Means, DBSCAN, or Hierarchical clustering. The best couple was TFIDF/K-Means, providing a sentence coverage of 89 % on our dataset; and allowing to identify 7 main categories of items to include in breast cancer operative reports. These results are encouraging for a document preset creation task and should then be validated and implemented in real life.

Aetiological classification and prognosis in patients with heart failure with preserved ejection fraction.

AIMS: Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome with various causes that may influence prognosis. METHODS AND RESULTS: We extracted the electronic medical records for 2180 consecutive patients hospitalized between 2016 and 2019 for decompensated heart failure. Using a text mining algorithm looking for a left ventricular ejection fraction ≥50% and plasma brain natriuretic peptide level >100 pg/mL, we identified 928 HFpEF patients. We screened for a prevailing cause of HFpEF according to European guidelines and found that 418 (45.0%) patients had secondary HFpEF due to either myocardial (n = 125, 13.5%) or loading condition abnormalities (n = 293, 31.5%), while the remaining 510 (55.0%) patients had idiopathic HFpEF. We assessed the association between the causes of HFpEF and survival collected up to 31 December 2020 using Cox proportional hazards analysis. Even though patients with idiopathic HFpEF were older, frequently female, and had frequent co-morbidities and a higher crude mortality rate compared with secondary HFpEF patients, their prognosis was similar after adjustment for age and sex. Unsupervised clustering analysis revealed three main phenogroups with different distribution of idiopathic vs. secondary HFpEF. The phenogroup with the highest proportion of idiopathic HFpEF (69%) had (i) an excess rate of non-cardiac co-morbidities including chronic obstructive pulmonary disease (31%) or obesity (41%) and (ii) a better prognosis compared with the two other phenogroups enriched with secondary HFpEF. CONCLUSIONS: Aetiological classification provides clinical and prognostic information and may be useful to better decipher the clinical heterogeneity of HFpEF.

Assessing rare diseases prevalence using literature quantification.

INTRODUCTION: Estimating the prevalence of diseases is crucial for the organization of healthcare. The amount of literature on a rare pathology could help differentiate between rare and very rare diseases. The objective of this work was to evaluate to what extent the number of publications can be used to predict the prevalence of a given pathology. METHODS: We queried Orphanet for the global prevalence class for all conditions for which it was available. For these pathologies, we cross-referenced the Orphanet, MeSH, and OMIM vocabularies to assess the number of publication available on Pubmed using three different query strategies (one proposed in the literature, and two built specifically for this study). We first studied the association of the number of publications obtained by each of these query strategies with the prevalence class, then their predictive ability. RESULTS: Class prevalence was available for 3128 conditions, 2970 had a prevalence class < 1/1,000,000, 41 of 1-9/1,000,000, 84 of 1-9/100,000, and 33 of 1-9/10,000. We show a significant association and excellent predictive performance of the number of publication, with an AUC over 94% for the best query strategy. CONCLUSION: Our study highlights the link and the excellent predictive performance of the number of publications on the prevalence of rare diseases provided by Orphanet.

Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites.

BACKGROUND: The increasing complexity of data streams and computational processes in modern clinical health information systems makes reproducibility challenging. Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. Workflow management systems (WMS) have been widely used in bioinformatics to handle the reproducibility bottleneck. OBJECTIVE: To evaluate if WMS and other bioinformatics practices could impact the reproducibility of clinical NLP frameworks. MATERIALS AND METHODS: Based on the literature across multiple researcho fields (NLP, bioinformatics and clinical informatics) we selected articles which (1) review reproducibility practices and (2) highlight a set of rules or guidelines to ensure tool or pipeline reproducibility. We aggregate insight from the literature to define reproducibility recommendations. Finally, we assess the compliance of 7 NLP frameworks to the recommendations. RESULTS: We identified 40 reproducibility features from 8 selected articles. Frameworks based on WMS match more than 50% of features (26 features for LAPPS Grid, 22 features for OpenMinted) compared to 18 features for current clinical NLP framework (cTakes, CLAMP) and 17 features for GATE, ScispaCy, and Textflows. DISCUSSION: 34 recommendations are endorsed by at least 2 articles from our selection. Overall, 15 features were adopted by every NLP Framework. Nevertheless, frameworks based on WMS had a better compliance with the features. CONCLUSION: NLP frameworks could benefit from lessons learned from the bioinformatics field (eg, public repositories of curated tools and workflows or use of containers for shareability) to enhance the reproducibility in a clinical setting.

No SARS-CoV-2 reinfection among staff health-care workers: Prospective hospital-wide screening during the first and second waves in Paris.

OBJECTIVES: Risk of reinfection with SARS-CoV-2 among health-care workers (HCWs) is unknown. We assessed the incidence rate of SARS-CoV-2 reinfection in the real-life setting of a longitudinal observational cohort of HCWs from the Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, France, during the first and second waves of COVID-19 epidemic. METHODS: From March to December 2020, HCWs were subjected to molecular and serology testing of SARS-CoV-2. Reinfection was defined as a positive test result during the first wave, either by serology or PCR, followed by a positive PCR during the second wave. Evolution of COVID-19 status of HWCs was assessed by a Sankey diagram. RESULTS: A total of 7765 tests (4579 PCR and 3186 serology) were carried out and 4168 HCWs had at least one test result during the follow-up period with a positivity rate of 15.9%. No case of reinfection during the second wave could be observed among 102 positive HCWs of the first wave, nor among 175 HCWs found positive by PCR during the second wave who were negative during the first wave. CONCLUSIONS: SARS-CoV-2 reinfection was not observed among HCWs, suggesting a protective immunity against reinfection that lasts at least 8 months post infection.

Episomal HPV16 responsible for aggressive and deadly metastatic anal squamous cell carcinoma evidenced in peripheral blood.

Archival tissue samples collected longitudinally from a patient who died from HPV16-induced high-grade anal intraepithelial squamous cell carcinoma with vertebral HPV16-positive metastasis were retrospectively analyzed by the Capture-HPV method (Capt-HPV) followed by Next-Generation Sequencing (NGS). Full length nucleotide sequences of the same HPV16 were identified from the initial and second anal biopsy samples, from plasma sample and from vertebral metastasis biopsy. Remarkably, HPV was episomal in each sample. The HPV genome sequence was closest to the HPV16 Qv18158E variant subtype (A1 lineage) exhibiting base substitutions and deletions in 7 and 2 HPV loci, respectively. In conclusion, the powerful Capt-HPV followed by NGS allows evidencing the detailed cartography of tumoral and circulating HPV DNA, giving rise to a unique and unexpected episomal virus molecular status in a context of aggressive carcinoma, underlying the importance of HPV status and its association with clinical features for further prospective studies.

Release of infectious virus and cytokines in nasopharyngeal swabs from individuals infected with non-alpha or alpha SARS-CoV-2 variants: an observational retrospective study.

BACKGROUND: The dynamics of SARS-CoV-2 alpha variant shedding and immune responses at the nasal mucosa remain poorly characterised. METHODS: We measured infectious viral release, antibodies and cytokines in 426 PCR+ nasopharyngeal swabs from individuals harboring non-alpha or alpha variants. FINDINGS: With both lineages, viral titers were variable, ranging from 0 to >106 infectious units. Rapid antigenic diagnostic tests were positive in 94% of samples with infectious virus. 68 % of individuals carried infectious virus within two days after onset of symptoms. This proportion decreased overtime. Viable virus was detected up to 14 days. Samples containing anti-spike IgG or IgA did not generally harbor infectious virus. Ct values were slightly but not significantly lower with alpha. This variant was characterized by a fast decrease of infectivity overtime and a marked release of 13 cytokines (including IFN-b, IP-10 and IL-10). INTERPRETATION: The alpha variant displays modified viral decay and cytokine profiles at the nasopharyngeal mucosae during symptomatic infection. FUNDING: This retrospective study has been funded by Institut Pasteur, ANRS, Vaccine Research Institute, Labex IBEID, ANR/FRM and IDISCOVR, Fondation pour la Recherche Médicale.

Genetic, Cellular, and Molecular Heterogeneity in Adrenals With Aldosterone-Producing Adenoma.

Aldosterone-producing adenoma (APA) cause primary aldosteronism-the most frequent form of secondary hypertension. Somatic mutations in genes coding for ion channels and ATPases are found in APA and in aldosterone-producing cell clusters. We investigated the genetic, cellular, and molecular heterogeneity of different aldosterone-producing structures in adrenals with APA, to get insight into the mechanisms driving their development and to investigate their clinical and biochemical correlates. Genetic analysis of APA, aldosterone-producing cell clusters, and secondary nodules was performed in adrenal tissues from 49 patients by next-generation sequencing following CYP11B2 immunohistochemistry. Results were correlated with clinical and biochemical characteristics of patients, steroid profiles, and histological features of the tumor and adjacent adrenal cortex. Somatic mutations were identified in 93.75% of APAs. Adenoma carrying KCNJ5 mutations had more clear cells and cells expressing CYP11B1, and fewer cells expressing CYP11B2 or activated ß-catenin, compared with other mutational groups. 18-hydroxycortisol and 18-oxocortisol were higher in patients carrying KCNJ5 mutations and correlated with histological features of adenoma; however, mutational status could not be predicted using steroid profiling. Heterogeneous CYP11B2 expression in KCNJ5-mutated adenoma was not associated with genetic heterogeneity. Different mutations were identified in secondary nodules expressing aldosterone synthase and in independent aldosterone-producing cell clusters from adrenals with adenoma; known KCNJ5 mutations were identified in 5 aldosterone-producing cell clusters. Genetic heterogeneity in different aldosterone-producing structures in the same adrenal suggests complex mechanisms underlying APA development.