SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Biodegradation of spent pulping liquor lignins under mesophilic and thermophilic anaerobic conditions

We conducted a laboratory scale feasibility study on the anaerobic treatment of spent pulping liquor effluent in upflow anaerobic sludge bed reactors. Tests showed that, in spite of high levels of sodiuk and lignin in the liquor, up to 80% of CODs can be successfully removed at a specific removal rate of 0.22 g and 0.57 g COD g\u207b\ub9 VSS d\u207b\ub9 for mesophilic and thermophilic conditions, respectively. Throughout the experiment, lignin accumulation occurred in the mesophilic, but not in the thermophilic reactor. Lignin measurements confirmed that up to 59% of lignin was degraded under thermophilic conditions. Higher activity of thermophilic biomass coupled with higher solubility, and therefore bioavailability of lignin under thermophilic conditions, contributed to the observed lignin removal.NRC publication: Ye

Medical Management of Duodenum Inversum Presenting With Partial Proximal Intestinal Obstruction in a Pediatric Patient

Duodenum inversum is a rare congenital anomaly of unknown etiology whereby the duodenum travels superiorly to the level of the duodenal bulb and then posteriorly prior to crossing the midline above the pancreas. We describe the first pediatric case of duodenum inversum presenting as partial proximal intestinal obstruction that was medically managed without surgical intervention

Medical Management of Duodenum Inversum Presenting With Partial Proximal Intestinal Obstruction in a Pediatric Patient

Duodenum inversum is a rare congenital anomaly of unknown etiology whereby the duodenum travels superiorly to the level of the duodenal bulb and then posteriorly prior to crossing the midline above the pancreas. We describe the first pediatric case of duodenum inversum presenting as partial proximal intestinal obstruction that was medically managed without surgical intervention

Families as Partners in Hospital Error and Adverse Event Surveillance

ImportanceMedical errors and adverse events (AEs) are common among hospitalized children. While clinician reports are the foundation of operational hospital safety surveillance and a key component of multifaceted research surveillance, patient and family reports are not routinely gathered. We hypothesized that a novel family-reporting mechanism would improve incident detection.ObjectiveTo compare error and AE rates (1) gathered systematically with vs without family reporting, (2) reported by families vs clinicians, and (3) reported by families vs hospital incident reports.Design, setting, and participantsWe conducted a prospective cohort study including the parents/caregivers of 989 hospitalized patients 17 years and younger (total 3902 patient-days) and their clinicians from December 2014 to July 2015 in 4 US pediatric centers. Clinician abstractors identified potential errors and AEs by reviewing medical records, hospital incident reports, and clinician reports as well as weekly and discharge Family Safety Interviews (FSIs). Two physicians reviewed and independently categorized all incidents, rating severity and preventability (agreement, 68%-90%; κ, 0.50-0.68). Discordant categorizations were reconciled. Rates were generated using Poisson regression estimated via generalized estimating equations to account for repeated measures on the same patient.Main outcomes and measuresError and AE rates.ResultsOverall, 746 parents/caregivers consented for the study. Of these, 717 completed FSIs. Their median (interquartile range) age was 32.5 (26-40) years; 380 (53.0%) were nonwhite, 566 (78.9%) were female, 603 (84.1%) were English speaking, and 380 (53.0%) had attended college. Of 717 parents/caregivers completing FSIs, 185 (25.8%) reported a total of 255 incidents, which were classified as 132 safety concerns (51.8%), 102 nonsafety-related quality concerns (40.0%), and 21 other concerns (8.2%). These included 22 preventable AEs (8.6%), 17 nonharmful medical errors (6.7%), and 11 nonpreventable AEs (4.3%) on the study unit. In total, 179 errors and 113 AEs were identified from all sources. Family reports included 8 otherwise unidentified AEs, including 7 preventable AEs. Error rates with family reporting (45.9 per 1000 patient-days) were 1.2-fold (95% CI, 1.1-1.2) higher than rates without family reporting (39.7 per 1000 patient-days). Adverse event rates with family reporting (28.7 per 1000 patient-days) were 1.1-fold (95% CI, 1.0-1.2; P = .006) higher than rates without (26.1 per 1000 patient-days). Families and clinicians reported similar rates of errors (10.0 vs 12.8 per 1000 patient-days; relative rate, 0.8; 95% CI, .5-1.2) and AEs (8.5 vs 6.2 per 1000 patient-days; relative rate, 1.4; 95% CI, 0.8-2.2). Family-reported error rates were 5.0-fold (95% CI, 1.9-13.0) higher and AE rates 2.9-fold (95% CI, 1.2-6.7) higher than hospital incident report rates.Conclusions and relevanceFamilies provide unique information about hospital safety and should be included in hospital safety surveillance in order to facilitate better design and assessment of interventions to improve safety

Families as Partners in Hospital Error and Adverse Event Surveillance

ImportanceMedical errors and adverse events (AEs) are common among hospitalized children. While clinician reports are the foundation of operational hospital safety surveillance and a key component of multifaceted research surveillance, patient and family reports are not routinely gathered. We hypothesized that a novel family-reporting mechanism would improve incident detection.ObjectiveTo compare error and AE rates (1) gathered systematically with vs without family reporting, (2) reported by families vs clinicians, and (3) reported by families vs hospital incident reports.Design, setting, and participantsWe conducted a prospective cohort study including the parents/caregivers of 989 hospitalized patients 17 years and younger (total 3902 patient-days) and their clinicians from December 2014 to July 2015 in 4 US pediatric centers. Clinician abstractors identified potential errors and AEs by reviewing medical records, hospital incident reports, and clinician reports as well as weekly and discharge Family Safety Interviews (FSIs). Two physicians reviewed and independently categorized all incidents, rating severity and preventability (agreement, 68%-90%; κ, 0.50-0.68). Discordant categorizations were reconciled. Rates were generated using Poisson regression estimated via generalized estimating equations to account for repeated measures on the same patient.Main outcomes and measuresError and AE rates.ResultsOverall, 746 parents/caregivers consented for the study. Of these, 717 completed FSIs. Their median (interquartile range) age was 32.5 (26-40) years; 380 (53.0%) were nonwhite, 566 (78.9%) were female, 603 (84.1%) were English speaking, and 380 (53.0%) had attended college. Of 717 parents/caregivers completing FSIs, 185 (25.8%) reported a total of 255 incidents, which were classified as 132 safety concerns (51.8%), 102 nonsafety-related quality concerns (40.0%), and 21 other concerns (8.2%). These included 22 preventable AEs (8.6%), 17 nonharmful medical errors (6.7%), and 11 nonpreventable AEs (4.3%) on the study unit. In total, 179 errors and 113 AEs were identified from all sources. Family reports included 8 otherwise unidentified AEs, including 7 preventable AEs. Error rates with family reporting (45.9 per 1000 patient-days) were 1.2-fold (95% CI, 1.1-1.2) higher than rates without family reporting (39.7 per 1000 patient-days). Adverse event rates with family reporting (28.7 per 1000 patient-days) were 1.1-fold (95% CI, 1.0-1.2; P = .006) higher than rates without (26.1 per 1000 patient-days). Families and clinicians reported similar rates of errors (10.0 vs 12.8 per 1000 patient-days; relative rate, 0.8; 95% CI, .5-1.2) and AEs (8.5 vs 6.2 per 1000 patient-days; relative rate, 1.4; 95% CI, 0.8-2.2). Family-reported error rates were 5.0-fold (95% CI, 1.9-13.0) higher and AE rates 2.9-fold (95% CI, 1.2-6.7) higher than hospital incident report rates.Conclusions and relevanceFamilies provide unique information about hospital safety and should be included in hospital safety surveillance in order to facilitate better design and assessment of interventions to improve safety

Whole-genome sequencing reveals host factors underlying critical COVID-19

Altres ajuts: Department of Health and Social Care (DHSC); Illumina; LifeArc; Medical Research Council (MRC); UKRI; Sepsis Research (the Fiona Elizabeth Agnew Trust); the Intensive Care Society, Wellcome Trust Senior Research Fellowship (223164/Z/21/Z); BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070, BBS/E/D/30002275); UKRI grants (MC_PC_20004, MC_PC_19025, MC_PC_1905, MRNO2995X/1); UK Research and Innovation (MC_PC_20029); the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z); the Edinburgh Clinical Academic Track (ECAT) programme; the National Institute for Health Research, the Wellcome Trust; the MRC; Cancer Research UK; the DHSC; NHS England; the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health (CTSA award number UL1TR001878); the Perelman School of Medicine at the University of Pennsylvania; National Institute on Aging (NIA U01AG009740); the National Institute on Aging (RC2 AG036495, RC4 AG039029); the Common Fund of the Office of the Director of the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA; NIMH; NINDS.Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care or hospitalization after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease