Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; p = 0.40). There was no significant effect of DMF on any secondary outcome

Characterisation of the (Y1–xLax)2Ti2O7 system by powder diffraction and nuclear magnetic resonance methods

Structural characteristics of the (Y1–xLax)2Ti2O7 system have been determined using time-of-flight (TOF) neutron and constant wavelength powder X-ray diffraction (XRD), scanning electron microscopy (SEM), electron probe micro-analysis (EPMA) and 89Y (I = ½) magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR). Lattice parameters obtained from neutron data suggest that a pyrochlore (Fdm, Z = 8) solid solution exists from x = 0 to x = 0.134, whereupon a monoclinic La2Ti2O7-type phase (P21, Z = 4) exsolves. Both phases coexist for 0.134 x 0.807 and a single-phase solid solution with the monoclinic structure is stable for x > 0.807. Unit cell volumes from X-ray diffraction of samples synthesised within the pyrochlore regime show excellent agreement with the expected linear increase in unit cell volume across a solid solution, increasing from 1028.46 Å3 for Y2Ti2O7 to 1037.49 Å3 for (Y0.90825La0.09175)2Ti2O7. The limit of the monoclinic solid solution as observed by XRD is higher than that found from neutron diffraction (0.88 compared to 0.807), but this difference is attributed to variation in the sintering temperatures employed. Spectral analysis of NMR spectra for Y-rich compositions suggests that increasing proportions of La are incorporated onto the pyrochlore A-site randomly, up to the limit of solid solution. The NMR spectra of the monoclinic phase show four resonances – two broad and two sharp. These have been attributed to the four crystallographically distinct A-type sites within the structure. At lower Y concentrations, the sites corresponding to the broad NMR resonances are preferentially occupied. We have tentatively assigned these broad resonances to the slab-edge sites in the monoclinic perovskite structure, based on their relatively small size and lower average coordination numbers compared to the perovskite-like sites within the centre of the slabs

Composition driven structural phase transitions in the (Y1-xLax)2Ti2O7 system

The structural characteristics of samples in the (Y1-xLax)2Ti2O system have been studied as a function of bulk composition using time-of-flight (TOF) powder neutron diffraction, powder X-ray diffraction (XRD), Electron Microscopy and 89Y (I = ½) Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR). Analysis of the neutron diffraction data suggests the following: For compositions where 0 ≤ x ≤ 0.132, a single cubic phase is present (Fd3,¯ m, Z = 8). Between 0.832 ≤ x ≤ 1, a solid solution with the La2Ti2O7 structure (P21, Z = 4) forms. The two phases coexist between x values of 0.132 and 0.832. XRD suggests that the limits of the two regions of solid solution fall within the ranges of x = 0.1-0.125 and x = 0.875-0.9. The variation in the limits found by the two diffraction methods may be due to stoichiometric errors in the samples. Line-shape analysis of NMR spectra for Y rich compositions suggests that increasing proportions of La are incorporated onto the pyrochlore A site in a statistically random manner, up to the limit of solid solution. The NMR spectra of the monoclinic phase suggest that occupation of the four crystallographically distinct ‘A’ type sites within the structure is not random. At low Y concentrations, two of these sites are preferentially occupied by Y. These sites are suggested to be those found at the edge of the perovskite slabs, which exhibit smaller coordination numbers (based on the number of oxygens within bonding distance of the ‘A’ type cation) than the true perovskite A sites found at the slab centres

Composition driven structural phase transitions in the (Y1-xLax)2Ti2O7 system

The structural characteristics of samples in the (Y1-xLax)2Ti2O system have been studied as a function of bulk composition using time-of-flight (TOF) powder neutron diffraction, powder X-ray diffraction (XRD), Electron Microscopy and 89Y (I = ½) Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR). Analysis of the neutron diffraction data suggests the following: For compositions where 0 ≤ x ≤ 0.132, a single cubic phase is present (Fd3,¯ m, Z = 8). Between 0.832 ≤ x ≤ 1, a solid solution with the La2Ti2O7 structure (P21, Z = 4) forms. The two phases coexist between x values of 0.132 and 0.832. XRD suggests that the limits of the two regions of solid solution fall within the ranges of x = 0.1-0.125 and x = 0.875-0.9. The variation in the limits found by the two diffraction methods may be due to stoichiometric errors in the samples. Line-shape analysis of NMR spectra for Y rich compositions suggests that increasing proportions of La are incorporated onto the pyrochlore A site in a statistically random manner, up to the limit of solid solution. The NMR spectra of the monoclinic phase suggest that occupation of the four crystallographically distinct ‘A’ type sites within the structure is not random. At low Y concentrations, two of these sites are preferentially occupied by Y. These sites are suggested to be those found at the edge of the perovskite slabs, which exhibit smaller coordination numbers (based on the number of oxygens within bonding distance of the ‘A’ type cation) than the true perovskite A sites found at the slab centres

Characterisation of the (Y1–xLax)2Ti2O7 system by powder diffraction and nuclear magnetic resonance methods

Structural characteristics of the (Y1–xLax)2Ti2O7 system have been determined using time-of-flight (TOF) neutron and constant wavelength powder X-ray diffraction (XRD), scanning electron microscopy (SEM), electron probe micro-analysis (EPMA) and 89Y (I = ½) magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR). Lattice parameters obtained from neutron data suggest that a pyrochlore (Fdm, Z = 8) solid solution exists from x = 0 to x = 0.134, whereupon a monoclinic La2Ti2O7-type phase (P21, Z = 4) exsolves. Both phases coexist for 0.134 x 0.807 and a single-phase solid solution with the monoclinic structure is stable for x > 0.807. Unit cell volumes from X-ray diffraction of samples synthesised within the pyrochlore regime show excellent agreement with the expected linear increase in unit cell volume across a solid solution, increasing from 1028.46 Å3 for Y2Ti2O7 to 1037.49 Å3 for (Y0.90825La0.09175)2Ti2O7. The limit of the monoclinic solid solution as observed by XRD is higher than that found from neutron diffraction (0.88 compared to 0.807), but this difference is attributed to variation in the sintering temperatures employed. Spectral analysis of NMR spectra for Y-rich compositions suggests that increasing proportions of La are incorporated onto the pyrochlore A-site randomly, up to the limit of solid solution. The NMR spectra of the monoclinic phase show four resonances – two broad and two sharp. These have been attributed to the four crystallographically distinct A-type sites within the structure. At lower Y concentrations, the sites corresponding to the broad NMR resonances are preferentially occupied. We have tentatively assigned these broad resonances to the slab-edge sites in the monoclinic perovskite structure, based on their relatively small size and lower average coordination numbers compared to the perovskite-like sites within the centre of the slabs

Thigh-length compression stockings and DVT after stroke

Controversy exists as to whether neoadjuvant chemotherapy improves survival in patients with invasive bladder cancer, despite randomised controlled trials of more than 3000 patients. We undertook a systematic review and meta-analysis to assess the effect of such treatment on survival in patients with this disease