Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics

The interaction between the SARS-CoV-2 virus Spike protein receptor binding domain (RBD) and the ACE2 cell surface protein is required for viral infection of cells. Mutations in the RBD are present in SARS-CoV-2 variants of concern that have emerged independently worldwide. For example, the B.1.1.7 lineage has a mutation (N501Y) in its Spike RBD that enhances binding to ACE2. There are also ACE2 alleles in humans with mutations in the RBD binding site. Here we perform a detailed affinity and kinetics analysis of the effect of five common RBD mutations (K417N, K417T, N501Y, E484K, and S477N) and two common ACE2 mutations (S19P and K26R) on the RBD/ACE2 interaction. We analysed the effects of individual RBD mutations and combinations found in new SARS-CoV-2 Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P1) variants. Most of these mutations increased the affinity of the RBD/ACE2 interaction. The exceptions were mutations K417N/T, which decreased the affinity. Taken together with other studies, our results suggest that the N501Y and S477N mutations enhance transmission primarily by enhancing binding, the K417N/T mutations facilitate immune escape, and the E484K mutation enhances binding and immune escape

Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19:A case study in affinity predictions of interface variants

SARS-CoV-2 Spike (Spike) binds to human angiotensin-converting enzyme 2 (ACE2) and the strength of this interaction could influence parameters relating to virulence. To explore whether population variants in ACE2 influence Spike binding and hence infection, we selected 10 ACE2 variants based on affinity predictions and prevalence in gnomAD and measured their affinities and kinetics for Spike receptor binding domain through surface plasmon resonance (SPR) at 37°C. We discovered variants that reduce and enhance binding, including three ACE2 variants that strongly inhibited (p.Glu37Lys, ΔΔG = –1.33 ± 0.15 kcal mol(-1) and p.Gly352Val, predicted ΔΔG = –1.17 kcal mol(-1)) or abolished (p.Asp355Asn) binding. We also identified two variants with distinct population distributions that enhanced affinity for Spike. ACE2 p.Ser19Pro (ΔΔG = 0.59 ± 0.08 kcal mol(-1)) is predominant in the gnomAD African cohort (AF = 0.003) whilst p.Lys26Arg (ΔΔG = 0.26 ± 0.09 kcal mol(-1)) is predominant in the Ashkenazi Jewish (AF = 0.01) and European non-Finnish (AF = 0.006) cohorts. We compared ACE2 variant affinities to published SARS-CoV-2 pseudotype infectivity data and confirmed that ACE2 variants with reduced affinity for Spike can protect cells from infection. The effect of variants with enhanced Spike affinity remains unclear, but we propose a mechanism whereby these alleles could cause greater viral spreading across tissues and cell types, as is consistent with emerging understanding regarding the interplay between receptor affinity and cell-surface abundance. Finally, we compared mCSM-PPI2 ΔΔG predictions against our SPR data to assess the utility of predictions in this system. We found that predictions of decreased binding were well-correlated with experiment and could be improved by calibration, but disappointingly, predictions of highly enhanced binding were unreliable. Recalibrated predictions for all possible ACE2 missense variants at the Spike interface were calculated and used to estimate the overall burden of ACE2 variants on Covid-19

Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand the human ACE2 receptor on binding affinity and kinetics

The interaction between the SARS-CoV-2 virus Spike protein receptor binding domain (RBD) and the ACE2 cell surface protein is required for viral infection of cells. Mutations in the RBD are present in SARS-CoV-2 variants of concern that have emerged independently worldwide. For example, the B.1.1.7 lineage has a mutation (N501Y) in its Spike RBD that enhances binding to ACE2. There are also ACE2 alleles in humans with mutations in the RBD binding site. Here we perform a detailed affinity and kinetics analysis of the effect of five common RBD mutations (K417N, K417T, N501Y, E484K, and S477N) and two common ACE2 mutations (S19P and K26R) on the RBD/ACE2 interaction. We analysed the effects of individual RBD mutations and combinations found in new SARS-CoV-2 Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P1) variants. Most of these mutations increased the affinity of the RBD/ACE2 interaction. The exceptions were mutations K417N/T, which decreased the affinity. Taken together with other studies, our results suggest that the N501Y and S477N mutations enhance transmission primarily by enhancing binding, the K417N/T mutations facilitate immune escape, and the E484K mutation enhances binding and immune escape

Retrospective observational study to assess the clinical management and outcomes of hospitalised patients with complicated urinary tract infection in countries with high prevalence of multidrug resistant Gram-negative bacteria (RESCUING)

INTRODUCTION: The emergence of multidrug resistant (MDR) Gram-negative bacteria (GNB), including carbapenemase-producing strains, has become a major therapeutic challenge. These MDR isolates are often involved in complicated urinary tract infection (cUTI), and are associated with poor clinical outcomes. The study has been designed to gain insight into the epidemiology, clinical management, outcome and healthcare cost of patients with cUTI, especially in countries with high prevalence of MDR GNB. METHODS AND ANALYSIS: This multinational and multicentre observational, retrospective study will identify cases from 1 January 2013 to 31 December 2014 in order to collect data on patients with cUTI as a cause of hospital admission, and patients who develop cUTI during their hospital stay. The primary end point will be treatment failure defined as the presence of any of the following criteria: (1) signs or symptoms of cUTI present at diagnosis that have not improved by days 5–7 with appropriate antibiotic therapy, (2) new cUTI-related symptoms that have developed within 30 days of diagnosis, (3) urine culture taken within 30 days of diagnosis, either during or after completion of therapy, that grows ≥104 colony-forming unit/mL of the original pathogen and (4) death irrespective of cause within 30 days of the cUTI diagnosis. SAMPLE SIZE: 1000 patients afford a power of 0.83 (α=0.05) to detect an absolute difference of 10% in the treatment failure rate between MDR bacteria and other pathogens. This should allow for the introduction of about 20 independent risk factors (or their interaction) in a logistic regression model looking at risk factors for failure. ETHICS AND DISSEMINATION: Approval will be sought from all relevant Research Ethics Committees. Publication of this study will be considered as a joint publication by the participating investigator leads, and will follow the recommendations of the International Committee of Medical Journal Editors (ICMJE)

Impact of age and sex on heart rate variability and cardiometabolic function in healthy adults

Heart rate variability (HRV) is a non-invasive measure of cardiac autonomic function. A clearer understanding as to whether resting autonomic function represented by HRV could be associated with changes in peak exercise cardiac function remains unanswered. This study evaluated the effect of age and sex on HRV, cardiometabolic function, and determined the correlation between HRV and cardiac function in healthy individuals. Sixty-eight participants (age range: 19–78 years old, females, n = 28) were recruited. Participants were stratified according to age (younger (&lt;40 years old, n = 43, females, n = 17) and older age groups (&gt;55 years old, n = 25, females, n = 11). Firstly, HRV was measured using non-invasive impedance cardiography method (TaskForce, CNSystems, Graz, Austria) and recorded at rest (supine position) for 30 min. HRV measures included: low frequency (LF) power, high frequency (HF) power (both normalised (nu) and absolute units (ms2)) and LF/HF ratio. Participants then completed a progressive cardiorespiratory exercise test using a semi-recumbent cycle ergometer (Corival, Lode, Groningen, Netherlands) with simultaneous gas exchange measurements (Metalyzer 3B, Cortex, Leipzig, Germany). Cardiac function was represented by peak exercise cardiac power output index (CPO). After controlling for body mass index and physical activity, males had significantly higher mean vales of RR interval than females (males = 1043 ± 165; females = 952 ± 128 ms, p = 0.02). There was no significant main effect of age, sex or their interaction on any of the other HRV measures. In younger and older females, resting RR interval had a significant relationship with peak exercise CPO (young females: r = 0.54, p &lt; 0.05; old females: r = 0.81, p &lt; 0.01). There was also a significant relationship between resting HF power and peak exercise CPO in younger females (r = 0.70, p &lt; 0.01). HRV was not influenced by age but RR interval was associated with peak exercise CPO in females regardless of age, whilst HF power was significantly associated with CPO in younger females only.</p

Adsorption of para-Hydrogen on Krypton pre-plated graphite

Adsorption of para-Hydrogen on the surface of graphite pre-plated with a single layer of atomic krypton is studied thoretically by means of Path Integral Ground State Monte Carlo simulations. We compute energetics and density profiles of para-hydrogen, and determine the structure of the adsorbed film for various coverages. Results show that there are two thermodynamically stable monolayer phases of para-hydrogen, both solid. One is commensurate with the krypton layer, the other is incommensurate. No evidence is seen of a thermodynamically stable liquid phase, at zero temperature. These results are qualitatively similar to what is seen for for para-hydrogen on bare graphite. Quantum exchanges of hydrogen molecules are suppressed in this system.Comment: 12 pages, 6 figures, to appear in the proceedings of "Advances in Computational Many-Body Physics", Banff, Alberta (Canada), January 13-16 200