Prognostic factors for mortality, ICU, MIS-C and hospital admission due to SARS-CoV-2 in paediatric patients: A systematic review and meta-analysis (preprint)

ABSTRACT Background: There is a paucity of data on the factors associated with severe COVID-19 disease, especially in children. This systematic review and meta-analysis aim to identify the risk factors for acute adverse outcomes of COVID-19 within paediatric populations, using the recruitment setting as a proxy of initial disease severity. Methods: A systematic review and meta-analysis were performed representing published evidence from the start of the pandemic up to 14 February 2022. Our primary outcome was the identification of risk factors for adverse outcomes, stratified by recruitment setting (community, hospital). No geographical restrictions were imposed. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to evaluate the certainty in the body of evidence for each meta-analysis. In anticipation of significant clinical and methodological heterogeneity in the meta-analyses, we fitted logistic regression models with random effects. Findings: Our review identified 47 studies involving 94,210 paediatric cases of COVID-19. Infants up to 3 months were more likely to be hospitalised than older children. Gender and ethnicity were not associated with an increased likelihood of adverse outcomes among children within the community setting. Concerning comorbidities, having at least one pre-existing disease increased the odds of hospitalisation. Concerning BMI, underweight children and severely obese were noted to have an increased likelihood of hospital admission. The presence of metabolic disorders and children with underlying cardiovascular diseases, respiratory disorders, neuromuscular disorders and neurologic conditions were also more likely to be hospitalised. Concerning underlying comorbidities, paediatric hospitalised patients with congenital/genetic disease, those obese, with malignancy, cardiovascular diseases and respiratory disease were associated with higher odds of being admitted to ICU or ventilated. Interpretation: Our findings suggest that age, male, gender, and paediatric comorbidities increased the likelihood of hospital and ICU admission. Obesity, malignancy, and respiratory and cardiovascular disorders were among the most important risk factors for hospital and ICU admission among children with COVID-19. The extent to which these factors were linked to actual severity or where the application of cautious preventive care is an area in which further research is needed.

MIS-C, inherited metabolic diseases and methylmalonic acidemia: a case report and review of the literature (preprint)

Bacground Methylmalonic acidemia (MMA) secondary to mutase deficiency, mut0, is an inborn error of metabolism causing complete enzyme deficiency. Multisystem Inflammatory Syndrome in Children (MIS-C) is a hyperinflammatory syndrome characterized by fever, inflammation, multiorgan impairment that manifests 14–60 days after the SARS-CoV-2 infection in patients aged < 21 years. Case presentation We describe the clinical case of a 2-year-old child with MMA secondary to mutase deficiency, with the documented homozygous mutation c.2179 C > T of MMUT gene, associated to mut0 phenotype. One month after SARS-CoV-2 infection, he presented fever, rash, significant increase of C-reactive protein (CRP), ferritin, triglycerides, (interleukin) IL-6, PRO-BNP, compatible with the diagnosis of MIS-C. He was treated with intravenous immunoglobulins (2gr/Kg), methylprednisolone (2 mg/Kg/day), with rapid clinical improvement. Ten days later, he showed the worsening of clinical conditions, with the recurrence of fever, vasculitic rash with palmoplantar extension, further increase of ferritin (1033 ug/l), IL-6 (146 pg/ml), PRO-BNP (5117 pg/ml), triglycerides, anemia, thrombocytopenia, metabolic acidosis with hyperlactatemia (180 mg/dl), increased urinary methylmalonic acid (200 mmol/mCreat), multiorgan failure. He was treated with sodium bicarbonate, thiamine, coenzyme Q, vitamin C, methylprednisolone and anakinra (2 mg/Kg/day). Three days after the start of anakinra, he showed a significant improvement of clinical and biochemical parameters and defervescence. 20 days later, a sepsis from Staphylococcus Aureus and Candida Albicans required the interruption of anakinra, with the worsening of the clinical and haematological parameters and the exitus. Conclusions Only a few cases of patients with inherited metabolic diseases (IMD) and MIS-C are described. However, to our knowledge, this is the first case of MIS-C in MMA described. The description of these clinical cases is a precious lesson for pediatricians to manage IMD therapeutic emergencies. Anakinra must be considered as a safe treatment of choice in IMD patients with MIS-C. The use of anakinra in patients with a severe form of MMA is safe and can be employed to treat MIS-C, gaining a substantial clinical and biochemical improvement.

Initial Experience of Long-Term Prophylaxis with Lanadelumab for Hereditary Angioedema in China: a Clinical Observation of Four patients. (preprint)

Background Hereditary angioedema (HAE) is a rare genetic disorder caused by a deficiency or dysfunction of C1 esterase inhibitor (C1-INH), which leads to recurrent episodes of bradykininmediated edema. Lanadelumab is a plasma kallikrein inhibitor that is the only first line therapy for long term prophylaxis (LTP) of HAE attacks in China since 2021.Objectives To observe the clincial efficacy and safety of lanadelumab in Chinese patients with HAE in a small population of four patients.Method Four HAE patients from three academic centers in China was included. Demographic characteristics, clinical manifestions and life quality of HAE patients were recorded before and after LTP treatment of lanadelumab .The primary outcome is the attack frequence of symptoms, and disease-related work loss days. The secondary outcome is the improved life quality of patients. Health-related quality of life was assessed using the Dermatology Life Quality Index (DLQI) and the Angioedema Quality of Life Questionnaire (AE-QoL).Results Lanadelumab led to the reductions of 98.04% and 100% in attack rate and treated attack rate respectively. Three patients of four (75%) reported complete remission from attacks after starting the administration of lanadelumab. Two patients had significant improvements on AE-QoL and DLQI (both scores reduction rate were 100%) in early period of treatment (4 weeks and 2 weeks, respectively) and all the patients had significant improvement on missed work days/year (reduction rate was 100%). The efficacy of lanadelumab was stable during vaccination and infection with COVID-19. No treatment-related serious/severe treatment emergent adverse events (TEAEs) occured during the treatment of lanadelumab.Conclusions Our study first demonstrated the clinical efficacy of lanadelumab with highly safety in Chinese HAE patients. A reasonable dosage plan can ensure the stability of therapeutic effects of lanadelumab. Moreover, lanadelumab also play a protective role to prevent attack in the case of COVID-19 infection.

Caveolin-1 mediates neuroinflammation and cognitive impairment in SARS-CoV-2 infection (preprint)

Leukocyte infiltration of the CNS can contribute to neuroinflammation and cognitive impairment. Brain endothelial cells regulate adhesion, activation, and diapedesis of T cells across the blood-brain barrier (BBB) in inflammatory diseases. The integral membrane protein Caveolin-1 (Cav-1) critically regulates BBB permeability, but its influence on T cell CNS infiltration in respiratory viral infections is unknown. In this study, we sought to determine the role of Cav-1 at the BBB in neuroinflammation in a COVID-19 mouse model. We used mice genetically deficient in Cav-1 to test the role of this protein in T cell infiltration and cognitive impairment. We found that SARS-CoV-2 infection upregulated brain endothelial Cav-1. Moreover, SARS-CoV-2 infection increased brain endothelial cell vascular cell adhesion molecule-1 (VCAM-1) and CD3+ T cell infiltration of the hippocampus, a region important for short term learning and memory. Concordantly, we observed learning and memory deficits. Importantly, genetic deficiency in Cav-1 attenuated brain endothelial VCAM-1 expression and T cell infiltration in the hippocampus of mice with SARS-CoV-2 infection. Moreover, Cav-1 KO mice were protected from the learning and memory deficits caused by SARS-CoV-2 infection. These results indicate the importance of BBB permeability in COVID-19 neuroinflammation and suggest potential therapeutic value of targeting Cav-1 to improve disease outcomes.

Symptoms of SARS-CoV-2 infection and vaccine status of sixty-seven adult patients affected by inherited metabolic diseases: a phone survey. (preprint)

Background: The Covid pandemic seems to have had several detrimental effects on managing patients affected by inherited metabolic diseases (IMD), although published data about the impact of COVID-19 on patients suffering from IMD are very scarce. The scope of our work was to evaluate adherence to the vaccination plan, the side effects experienced by our adult IMD patients, and the symptoms of the SARS-CoV-2 infection. Results: sixty-seven patients agreed to respond to a phone interview. The mean age was 36.5 (±11,6 SD). Regarding the vaccination campaign, fifty-five patients (82%) joined it, of whom ten have received two doses and the remaining forty-five, three. Forty-two patients (76%) reported adverse events following vaccination, the most frequent being local reaction, fever, and asthenia, which lasted an average of two days and resolved without sequelae. Regarding SARS-CoV-2 infection, twenty-seven out of sixty-seven patients (40%) have tested positive for the virus; seven of them were not vaccinated at the time of infection; on the other hand, twenty had already had at least two doses. Regarding the prevalence of long-Covid, as many as 12 patients (44%) reported symptoms that persisted after the nasopharyngeal swab tested negative and lasted an average of 81 (±74 SD) days. There were no statistically significant differences in BMI of patients who contracted the infection and patients who did not (25.15 vs 25.20, p=.861), between those who had adverse reactions to the vaccine and those who did not (24.40 vs 25.75, p=.223), between those who had long Covid and those who did not (25.9 vs 27.7, p=.183). No relation was observed between metabolic inherited disease, SARS-CoV-2 infection symptoms and adverse vaccine reactions. Conclusions: The data indicate that IMD patients adhered to the vaccination plan comparably to the general Italian population. Adverse events to the vaccine were negligible. SARS-CoV-2 infection, which occurred in most cases after receiving at least two doses of the vaccine, did not cause serious symptoms and never required hospitalisation. A non-negligible share of patients suffered from long Covid symptoms.

Estimating Remaining Lifespan from the Face (preprint)

The face is a rich source of information that can be utilized to infer a person's biological age, sex, phenotype, genetic defects, and health status. All of these factors are relevant for predicting an individual's remaining lifespan. In this study, we collected a dataset of over 24,000 images (from Wikidata/Wikipedia) of individuals who died of natural causes, along with the number of years between when the image was taken and when the person passed away. We made this dataset publicly available. We fine-tuned multiple Convolutional Neural Network (CNN) models on this data, at best achieving a mean absolute error of 8.3 years in the validation data using VGGFace. However, the model's performance diminishes when the person was younger at the time of the image. To demonstrate the potential applications of our remaining lifespan model, we present examples of using it to estimate the average loss of life (in years) due to the COVID-19 pandemic and to predict the increase in life expectancy that might result from a health intervention such as weight loss. Additionally, we discuss the ethical considerations associated with such models.

The Eating Disorders Genetics Initiative (EDGI) United Kingdom (preprint)

Objective The Eating Disorders Genetics Initiative United Kingdom (EDGI UK), part of the National Institute for Health and Care Research (NIHR) Mental Health BioResource, aims to deepen our understanding of the environmental and genetic aetiology of eating disorders. EDGI UK launched in February 2020 and is partnered with the UK eating disorders charity, Beat. There are multiple EDGI branches worldwide. Method EDGI UK recruits via media and clinical services. Anyone living in England, at least 16 years old, with a lifetime probable or clinical eating disorder is eligible to sign up online: edgiuk.org . Participants complete online questionnaires, donate a saliva sample for genetic analysis, and consent to medical record linkage and recontact for future studies. Results As of September 2022, EDGI UK has recruited 8,397 survey participants: 98% female, 93% white, 97.7% cisgender, 67% heterosexual, and 52% have a university degree. Half (51.7%) of participants have returned their saliva kit. The most common diagnoses are anorexia nervosa (42.7%), atypical anorexia nervosa (31.4%), bulimia nervosa (33.2%), binge-eating disorder (14.6%), and purging disorder (33.5%). Conclusion EDGI UK is the largest UK eating disorders study but needs to increase its diversity, and efforts are underway to do so. It also offers a unique opportunity to accelerate eating disorder research, and collaboration between researchers and participants with lived experience, with unparalleled sample size.

Improving the preclinical and clinical success rates of LMW drugs depends on radical revisions to the status quo scientific foundations of medicinal chemistry: a case study on COVID Mpro inhibition (preprint)

The poor preclinical and clinical success rates of low molecular weight compounds is partially attributable to the inherent trial-and-error nature of pharmaceutical research, which is limited largely to retrospective data-driven, rather than prospective prediction-driven workflows stemming from: 1) inadequate scientific understanding of structure-activity, structure-property, and structure-free energy relationships; 2) disconnects between empirical models derived from in vitro equilibrium data (e.g., Hill and Michaelis-Menten models) vis-a-vis the native non-equilibrium cellular setting (where the pertinent metrics consist of rates, rather than equilibrium state distributions); and 3) inadequate understanding of the non-linear dynamic (NLD) basis of cellular function and disease. We argue that the limit of understanding of cellular function/dysfunction and pharmacology based on empirical principles (observation/inference) has been reached, and that further progress depends on understanding these phenomena at the first principles theoretical level. Toward that end, we are developing and applying a theory on the mechanisms by which: 1) cellular functions are conveyed by dynamic multi-molecular/-ionic (multi-flux) systems operating in the NLD regime; 2) cellular dysfunction results from molecular dysfunction; 3) molecular structure and function are powered by covalent/non-covalent forms of free energy; and 4) cellular dysfunction is corrected pharmacologically. Our theory represents a radical departure from the status quo empirical science and reduction to practice thereof, replacing: 1) the interatomic contact model of structure-free energy and structure-property relationships with a solvation free energy model; 2) equilibrium drug-target occupancy models with dynamic models accounting for time-dependent drug and target/off-target binding site buildup and decay; and 3) linear models of molecular structure-function and multi-molecular/-ionic systems conveying cellular function and dysfunction with NLD models that more realistically capture the emergent behaviors of such systems. Here, we apply our theory to COVID Mpro inhibition and overview its implications for a holistic, in vivo relevant approach to drug design.

Innate Immunity in Cardiovascular Diseases – Identification of Novel Molecular Players and Targets (preprint)

During the past few years unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking ad-vantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss emerging clinical relevance of advanced diagnostics for cardiovascular diseases - includ-ing those associated with COVID-19 - with a focus on the role of inflammation in cardiomyopa-thies and arrhythmias. Second, we consider newly identified immunological interactions at or-gan and systems level which affect cardiovascular pathogenesis. Thus, studies into immune in-fluences arising from the intestinal system are moving towards therapeutic exploitation. Fur-ther, powerful new research tools have enabled novel insight into brain – immune system inter-actions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress - acting through defined brain regions - upon viral and cardiovas-cular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Post-COVID Syndrome: A Common Neuroimmune Ground? (preprint)

A Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic disease of unknown aetiology under growing interest now in view of the increasingly recognized post-COVID syndrome as a new entity with similar clinical presentation. We performed the first cross-sectional study of ME/CFS in community population in Russia and then described and compared some clinical and pathophysiological characteristics of ME/CFS and post-COVID syndrome as neuroimmune disorders. Of the cohort of 76 individuals who suggested themselves suffering from ME/CFS 56 subsequently were confirmed as having CFS/ME according to ≥1 of the 4 most commonly used case definition. Of the cohort of 14 individuals with post-COVID-19 syndrome 14 met diagnostic criteria for ME/CFS. The prevalence of clinically expressed and subclinical anxiety and depression in ME / CFS and post-COVID ME/CFS did not differ significantly from that in healthy individuals. Severity of anxiety / depressive symptoms did not correlate with the severity of fatigue neigther in ME / CFS nor in post-COVID ME/CFS, but the positive correlation was found between the severity of fatigue and 20 other symptoms of ME / CFS related to the domains of “post-exertional exhaustion”, “immune dysfunction”, “sleep disturbances”, "dysfunction of the autonomic nervous system", "neurological sensory / motor disorders" and "pain syndromes". Immunological abnormalities were identified in 12/12 patients with ME / CFS according to the results of laboratory testing. The prevalence of postural orthostatic tachycardia assessed by the active standing test was 37.5% in ME / CFS and 75.0% in post-COVID ME/CFS (the latter was higher than in healthy controls, p = 0.02) There was a more pronounced increase in heart rate starting from the 6th minute of the test in post-COVID ME/CFS compared with the control group. Assessment of the functional characteristics of microcirculation by laser doppler flowmetry revealed obvious and very similar changes in ME/CFS and post-COVID ME/CFS compared to the healthy controls. The identified pattern corresponded to the hyperemic form of microcirculation disorders, usually observed in acute inflammatory processes or in deficiency of systemic vasoconstriction influences.

Accelerated ensemble generation for cyclic peptides using a Reservoir-REMD implementation in GROMACS (preprint)

Cyclic peptides naturally occur as antibiotics, fungicides, and immunosuppressants, and have been adapted for use as potential therapeutics. Scaffolded cyclic peptide antigens have many protein characteristics such as reduced toxicity, increased stability over linear peptides, and conformational selectivity, but with fewer amino acids than whole proteins. The profile of shapes presented by a cyclic peptide modulates its therapeutic efficacy, and is represented by the ensemble of its sampled conformations. Although some algorithms excel in creating a diverse ensemble of cyclic peptide conformations, they seldom address the entropic contribution of flexible conformations, and they often have significant practical difficulty producing an ensemble with converged and reliable thermodynamic properties. In this study, an accelerated molecular dynamics (MD) method, reservoir replica exchange MD (R-REMD or Res-REMD), was implemented in GROMACS-4.6.7, and benchmarked on three small cyclic peptide model systems: a cyclized segment of A β (cyclo-(CGHHQKLVG)), a cyclized furin cleavage site of SARS-CoV-2 spike (cyclo-(CGPRRARSG)), and oxytocin (disulfide bonded CY-IQNCPLG). Additionally, we also benchmarked Res-REMD on Alanine dipeptide and Trpzip2 to demonstrate its validity and efficiency over REMD. Compared to REMD, Res-REMD significantly accelerated the ensemble generation of cyclo-(CGHHQKLVG), but not cyclo-(CGPRRARSG) or oxytocin. This difference is due to the longer auto-correlation time of torsional angles in cyclo-(CGHHQKLVG) v s. the latter two cyclic peptide systems; The randomly seeded reservoir in Res-REMD thus accelerates sampling and convergence. The auto-correlation time of the torsional angles can thus be used to determine whether Res-REMD is preferable to REMD for cyclic peptides. We provide a github page with modified GROMACS source code for running Res-REMD at https://github.com/PlotkinLab/Reservoir-REMD .

Rapid reversible osmoregulation of cytoplasmic biomolecular condensates of human interferon-α-induced antiviral MxA GTPase (preprint)

Cellular and tissue-level edema is a common feature of acute viral infections such as covid-19, and of many hyponatremic hypoosmolar disorders. However, there is little understanding of the effects of cellular edema on antiviral effector mechanisms. We previously discovered that cytoplasmic human MxA, a major antiviral effector of Type I and III interferons against several RNA- and DNA-containing viruses, existed in the cytoplasm in phase-separated membraneless biomolecular condensates of varying sizes and shapes. In this study we investigated how hypoosmolar conditions, mimicking cellular edema, might affect the structure and antiviral function of MxA condensates. Cytoplasmic condensates of both IFN-α-induced endogenous MxA and of exogenously expressed GFP-MxA in human A549 lung and Huh7 hepatoma cells rapidly disassembled within 1-2 min when cells were exposed to hypotonic buffer (~ 40-50 mOsm), and rapidly reassembled into new structures within 1-2 min of shifting of cells to isotonic culture medium (~ 330 mOsm). MxA condensates in cells continuously exposed to culture medium of moderate hypotonicity (in the range one-fourth, one-third or one-half isotonicity; range 90-175 mOsm) first rapidly disassembled within 1-3 min, and then, in most cells, spontaneously reassembled 7-15 min later into new structures. Condensate reassembly, whether induced by isotonic medium or occurring spontaneously under continued moderate hypotonicity, was preceded by crowding of the cytosolic space by large vacuole-like dilations (VLDs) derived from internalized plasma membrane. Remarkably, the antiviral activity of GFP-MxA against vesicular stomatitis virus survived hypoosmolar disassembly. Overall, the data highlight the exquisite sensitivity of MxA condensates to rapid reversible osmoregulation.

Genome-wide determinants of mortality and clinical progression in Parkinson’s disease (preprint)

ABSTRACT Background There are 90 genetic risk variants for Parkinson’s disease (PD) but currently only five nominated loci for PD progression. The biology of PD progression is likely to be of central importance in defining mechanisms that can be used to develop new treatments. Methods We studied 6,766 PD patients, over 15,340 visits with a mean follow-up of between 4.2 and 15.7 years and carried out a genome wide survival study for time to motor progression, defined by reaching Hoehn and Yahr stage 3 or greater, cognitive impairment as defined by serial cognitive examination, and death (mortality). Findings There was a robust effect of the APOE ε4 allele on mortality and cognitive impairment in PD. We identified three novel loci for mortality and motor progression, and nominated genes based on physical proximity or expression quantitative trait loci data. One locus within the TBXAS1 gene encoding thromboxane A synthase 1 was associated with mortality in PD (HR = 2.04 [95% CI 1.63 to 2.56], p-value = 7.71 x 10 -10 ). Another locus near the SYT10 gene encoding synaptotagmin 10 was associated with mortality just above genome-wide significance (HR=1.36 [95% CI 1.21 to 1.51], p-value=5.31×10 -8 ). A genomic variant associated with the expression of ADORA2A , encoding the A2A adenosine receptor, was associated with motor progression (HR=4.83 [95% CI 2.89 to 8.08], p-value=1.94×10 -9 ). Only the non-Gaucher disease causing GBA PD risk variant E326K, of the known PD risk variants, was associated with progression in PD. Interpretation We report three novel loci associated with PD progression or mortality. Further work is needed to understand the links between these genomic variants and the underlying disease biology. However, thromboxane synthesis, vesicular peptidergic neurotransmitter release and the A2A adenosine receptor may represent new candidates for disease modification in PD. RESEARCH IN CONTEXT Evidence before this study We searched PubMed for articles on Parkinson’s disease (PD) with no language restrictions from database inception up to February 9, 2022. We used the search terms “Parkinson disease AND genetics” and “disease progression OR survival OR mortality OR prognosis OR longitudinal studies”. We also conducted this search with the addition of “genome-wide association study” (GWAS) to focus on these genome-wide analyses. There are now three published large-scale GWASs investigating PD progression, and many candidate variant studies. However, no genome-wide studies have reported on survival/mortality in PD. Added value of this study To our knowledge, this is the first GWAS of survival in PD. Our study highlights new loci influencing survival in PD, including TBXAS1 and SYT10 . We also conducted GWASs of progression to other clinical milestones, Hoehn and Yahr stage 3 or greater, and cognitive impairment. We show that APOE influences both mortality and cognitive progression in PD, and report an additional locus influencing expression of ADORA2A which affects the rate of motor progression. Implications of all the available evidence With the exception of APOE , we report new loci which have not been previously associated with PD progression or for mortality and ageing in the general population. These loci could be investigated in functional studies as potential drug targets to stop or slow progression of PD. In addition, new genetic loci can help to improve our understanding of the biology of PD progression and prediction of progression. Further replication of these loci is also needed in independent, longitudinal PD cohorts.

From Molecular Dynamics to Supramolecular Organization: The Role of PIM Lipids in the Originality of the Mycobacterial Plasma Membrane (preprint)

Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis, a disease that claims ~1.5 million lives annually. The current treatment regime is long and expensive, and missed doses contribute to drug resistance. There is much to be understood about the Mtb cell envelope, a complicated barrier that antibiotics need to negotiate to enter the cell. Within this envelope, the plasma membrane is the ultimate obstacle and is proposed to be comprised of over 50% mannosylated phosphatidylinositol lipids (phosphatidyl- myo inositol mannosides, PIMs), whose role in the membrane structure remains elusive. Here we used multiscale molecular dynamics (MD) simulations to understand the structure-function relationship of the PIM lipid family and decipher how they self-organize to drive biophysical properties of the Mycobacterial plasma membrane. To validate the model, we tested known anti-tubercular drugs and replicated previous experimental results. Our results shed new light into the organization of the Mycobacterial plasma membrane and provides a working model of this complex membrane to use for in silico studies. This opens the door for new methods to probe potential antibiotic targets and further understand membrane protein function. Abstract Figure

Immunogenicity of the mRNA-1273 COVID-19 vaccine in adult patients with inborn errors of immunity.

BACKGROUND: Patients with inborn errors of immunity (IEI) are at increased risk of severe coronavirus disease-2019 (COVID-19). Effective vaccination against COVID-19 is therefore of great importance in this group, but little is known about the immunogenicity of COVID-19 vaccines in these patients. OBJECTIVES: We sought to study humoral and cellular immune responses after mRNA-1273 COVID-19 vaccination in adult patients with IEI. METHODS: In a prospective, controlled, multicenter study, 505 patients with IEI (common variable immunodeficiency [CVID], isolated or undefined antibody deficiencies, X-linked agammaglobulinemia, combined B- and T-cell immunodeficiency, phagocyte defects) and 192 controls were included. All participants received 2 doses of the mRNA-1273 COVID-19 vaccine. Levels of severe acute respiratory syndrome coronavirus-2-specific binding antibodies, neutralizing antibodies, and T-cell responses were assessed at baseline, 28 days after first vaccination, and 28 days after second vaccination. RESULTS: Seroconversion rates in patients with clinically mild antibody deficiencies and phagocyte defects were similar to those in healthy controls, but seroconversion rates in patients with more severe IEI, such as CVID and combined B- and T-cell immunodeficiency, were lower. Binding antibody titers correlated well to the presence of neutralizing antibodies. T-cell responses were comparable to those in controls in all IEI cohorts, with the exception of patients with CVID. The presence of noninfectious complications and the use of immunosuppressive drugs in patients with CVID were negatively correlated with the antibody response. CONCLUSIONS: COVID-19 vaccination with mRNA-1273 was immunogenic in mild antibody deficiencies and phagocyte defects and in most patients with combined B- and T-cell immunodeficiency and CVID. Lowest response was detected in patients with X-linked agammaglobulinemia and in patients with CVID with noninfectious complications. The assessment of longevity of immune responses in these vulnerable patient groups will guide decision making for additional vaccinations.

Discovery of multitargeting inhibitors for the treatment of COVID-19: An in- silico studies (preprint)

Coronavirus disease-2019 (COVID-19), a global pandemic has currently infected more than 247 million people around the world. Nowadays, several receptors of COVID-19 have been reported, and few of them are explored for drug discovery. New mutant strains of COVID-19 are emerging since the first outbreak of disease and causing significant morbidity and mortality across the world. Although, few of drugs were approved for an emergency uses, however, promising drug with well proven clinical efficacy is yet to be discovered. Hence, researchers are continuously attempting for search of potential drug candidates targeting the well-established enzymatic targets of the virus. The present study is aiming to discover the antiviral compounds as potential inhibitors against the five targets in various stages of the SARS-CoV-2 life cycle, i.e., virus attachments (ACE2 and TMPRSS2), viral replication and transcription (M pro , PL pro and RdRp), using the most reliable molecular docking and molecular dynamics method. The ADMET study was then carried out to determine the pharmacokinetics and toxicity of several compounds with the best docking results. To provide a more effective mechanism for demonstrating protein-ligand interactions, molecular docking data were subjected to a molecular dynamic (MD) simulation at 300K for 100 ns. In terms of structural stability, structure compactness, solvent accessible surface area, residue flexibility, and hydrogen bond interactions, the dynamic features of complexes have been compared.

Biochemical, Biophysical, and Immunological Characterization of Respiratory Secretions in Severe SARS-CoV-2 (COVID-19) Infections (preprint)

Thick, viscous respiratory secretions are a major pathogenic feature of COVID19 disease, but the composition and physical properties of these secretions are poorly understood. We characterized the composition and rheological properties (i.e. resistance to flow) of respiratory secretions collected from intubated COVID19 patients. We find the percent solids and protein content are greatly elevated in COVID19 compared to heathy control samples and closely resemble levels seen in cystic fibrosis, a genetic disease known for thick, tenacious respiratory secretions. DNA and hyaluronan (HA) are major components of respiratory secretions in COVID19 and are likewise abundant in cadaveric lung tissues from these patients. COVID19 secretions exhibit heterogeneous rheological behaviors with thicker samples showing increased sensitivity to DNase and hyaluronidase treatment. In histologic sections from these same patients, we observe increased accumulation of HA and the hyaladherin versican but reduced tumor necrosis factor stimulated gene 6 (TSG6) staining, consistent with the inflammatory nature of these secretions. Finally, we observed diminished type I interferon and enhanced inflammatory cytokines in these secretions. Overall, our studies indicate that increases in HA and DNA in COVID19 respiratory secretion samples correlate with enhanced inflammatory burden and suggest that DNA and HA may be viable therapeutic targets in COVID19 infection.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes (preprint)

The gut microbiome has been identified as a key to immune and metabolic health, especially in industrialized populations 1 . Non-industrialized individuals harbor more diverse microbiomes and distinct bacterial lineages 2 , but systemic under-sampling has hindered insight into the extent and functional consequences of these differences 3 . Here, we performed ultra-deep metagenomic sequencing and laboratory strain isolation on fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophage, and eukaryotes, and find that 43% are novel upon aggregating with existing unified datasets 4,5 . Analysis of in situ growth rates, genetic pN/pS signatures, and high-resolution strain tracking reveal dynamics in the hunter-gatherer gut microbiome that are distinct from industrialized populations. Industrialized versus Hadza gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. We use phylogenomics to reveal that global spread of the spirochaete Treponema succinifaciens parallels historic human migration prior to its extinction in industrialized populations. When combined with a detailed definition of gut-resident strains that are vanishing in industrialized populations, our data demonstrate extensive perturbation in many facets of the gut microbiome brought on by the industrialized lifestyle. Recognition of work with indigenous communities Research involving indigenous communities is needed for a variety of reasons including to ensure that scientific discoveries and understanding appropriately represent all populations and do not only benefit those living in industrialized nations 3,6 . Special considerations must be made to ensure that this research is conducted ethically and in a non-exploitative manner. In this study we performed deep metagenomic sequencing on fecal samples that were collected from Hadza hunter-gatherers in 2013/2014 and were analyzed in previous publications using different methods 2,7 . A material transfer agreement with the National Institute for Medical Research in Tanzania specifies that stool samples collected are used solely for academic purposes, permission for the study was obtained from the National Institute of Medical Research (MR/53i 100/83, NIMR/HQ/R.8a/Vol.IX/1542) and the Tanzania Commission for Science and Technology, and verbal consent was obtained from the Hadza after the study’s intent and scope was described with the help of a translator. The publications that first described these samples included several scientists and Tanzanian and Nepali field-guides as co-authors for the critical roles they played in sample collection, but as no new samples were collected in this study, only scientists who contributed to the analyses described here were included as co-authors in this publication. It is currently not possible for us to travel to Tanzania and present our results to the Hadza people, however we intend to do so once the conditions of the COVID-19 pandemic allow it.

The relationship between BMI and COVID-19: exploring misclassification and selection bias in a two-sample Mendelian randomisation study (preprint)

ObjectiveTo use the example of the effect of body mass index (BMI) on COVID-19 susceptibility and severity to illustrate methods to explore potential selection and misclassification bias in Mendelian randomisation (MR) of COVID-19 determinants. DesignTwo-sample MR analysis. SettingSummary statistics from the Genetic Investigation of ANthropometric Traits (GIANT) and COVID-19 Host Genetics Initiative (HGI) consortia. Participants681,275 participants in GIANT and more than 2.5 million people from the COVID-19 HGI consortia. ExposureGenetically instrumented BMI. Main outcome measuresSeven case/control definitions for SARS-CoV-2 infection and COVID-19 severity: very severe respiratory confirmed COVID-19 vs not hospitalised COVID-19 (A1) and vs population (those who were never tested, tested negative or had unknown testing status (A2)); hospitalised COVID-19 vs not hospitalised COVID-19 (B1) and vs population (B2); COVID-19 vs lab/self-reported negative (C1) and vs population (C2); and predicted COVID-19 from self-reported symptoms vs predicted or self-reported non-COVID-19 (D1). ResultsWith the exception of A1 comparison, genetically higher BMI was associated with higher odds of COVID-19 in all comparison groups, with odds ratios (OR) ranging from 1.11 (95%CI: 0.94, 1.32) for D1 to 1.57 (95%CI: 1.57 (1.39, 1.78) for A2. As a method to assess selection bias, we found no strong evidence of an effect of COVID-19 on BMI in a no-relevance analysis, in which COVID-19 was considered the exposure, although measured after BMI. We found evidence of genetic correlation between COVID-19 outcomes and potential predictors of selection determined a priori (smoking, education, and income), which could either indicate selection bias or a causal pathway to infection. Results from multivariable MR adjusting for these predictors of selection yielded similar results to the main analysis, suggesting the latter. ConclusionsWe have proposed a set of analyses for exploring potential selection and misclassification bias in MR studies of risk factors for SARS-CoV-2 infection and COVID-19 and demonstrated this with an illustrative example. Although selection by socioeconomic position and arelated traits is present, MR results are not substantially affected by selection/misclassification bias in our example. We recommend the methods we demonstrate, and provide detailed analytic code for their use, are used in MR studies assessing risk factors for COVID-19, and other MR studies where such biases are likely in the available data. SummaryO_ST_ABSWhat is already known on this topicC_ST_ABS- Mendelian randomisation (MR) studies have been conducted to investigate the potential causal relationship between body mass index (BMI) and COVID-19 susceptibility and severity. - There are several sources of selection (e.g. when only subgroups with specific characteristics are tested or respond to study questionnaires) and misclassification (e.g. those not tested are assumed not to have COVID-19) that could bias MR studies of risk factors for COVID-19. - Previous MR studies have not explored how selection and misclassification bias in the underlying genome-wide association studies could bias MR results. What this study adds- Using the most recent release of the COVID-19 Host Genetics Initiative data (with data up to June 2021), we demonstrate a potential causal effect of BMI on susceptibility to detected SARS-CoV-2 infection and on severe COVID-19 disease, and that these results are unlikely to be substantially biased due to selection and misclassification. - This conclusion is based on no evidence of an effect of COVID-19 on BMI (a no-relevance control study, as BMI was measured before the COVID-19 pandemic) and finding genetic correlation between predictors of selection (e.g. socioeconomic position) and COVID-19 for which multivariable MR supported a role in causing susceptibility to infection. - We recommend studies use the set of analyses demonstrated here in future MR studies of COVID-19 risk factors, or other examples where selection bias is likely.

Inflammation in the COVID-19 airway is due to inhibition of CFTR signaling by the SARS-CoV-2 Spike protein (preprint)

Background: SARS-CoV-2-contributes to sickness and death in COVID-19 patients partly by inducing a hyper-proinflammatory immune response in the host airway. This hyper- proinflammatory state involves activation of signaling by NF{kappa}B and ENaC, and expression of high levels of cytokines and chemokines. Post-infection inflammation may contribute to "Long COVID", and there are also other long term consequences of acute severe COVID-19, which double or triple the chances of dying from any cause within a year. Enhanced signaling by NF{kappa}B and ENaC also marks the airway of patients suffering from cystic fibrosis, a lethal proinflammatory genetic disease due to inactivating mutations in the CFTR gene. We therefore hypothesized that inflammation in the COVID-19 airway might similarly be due to inhibition of CFTR signaling by SARS-CoV-2 Spike protein. Methods: This hypothesis was tested using the hTERT-transformed BCi-NS1.1 basal stem cell, previously derived from small airway epithelia, which were differentiated into a model of small airway epithelia on an air-liquid-interface (ALI). Cyclic AMP-activated CFTR chloride channel activity was measured using an Ussing Chamber. Cell surface-CFTR was labeled with the impermeant biotin method. Results: Exposure of differentiated airway epithelia to SARS-CoV-2 Spike protein resulted in loss of CFTR protein expression. As hypothesized, TNF/NF{kappa}B signaling was activated, based on increased protein expression of TRADD, the first intracellular adaptor for the TNF/TNFR1 complex, TNFR1, the TNF receptor, phosphorylated I{kappa}B, and the chemokine IL8. ENaC activity was also activated, based on specific changes in molecular weights for and{gamma}ENaC. Exposure of the epithelia to viral Spike protein suppressed cAMP-activated CFTR chloride channel activity. However, addition of 30 nM concentrations of cardiac glycoside drugs ouabain, digitoxin and digoxin, prevented loss of channel activity. ACE2 and CFTR were found to co-immunoprecipitate (co-IP) in both basal cells and epithelia, suggesting that the mechanism for Spike-dependent CFTR loss might involve ACE2 as a bridge between Spike and CFTR. In addition, Spike exposure to the epithelia resulted in failure of endosomal recycling to return CFTR to the plasma membrane, suggesting that failure of CFTR recovery from endosomal recycling might be a mechanism for Spike-dependent loss of CFTR. Conclusion: Based on experiments with this model of small airway epithelia, we predict that inflammation in the COVID-19 airway may be mediated by inhibition of CFTR signaling by SARS-CoV-2 Spike protein, thus inducing a CFTR-null, cystic fibrosis-like clinical phenotype. Descriptions of COVID-19 in CF carriers with only one copy of wildtype CFTR suggest that this model-based conclusion might be consistent with patient-based experience.