Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.

The investigation and analysis of critical incidents and adverse events in healthcare.

OBJECTIVES: To carry out a review of published and unpublished work on the analysis on methods of accident investigation in high-risk industries, and of critical incidents in healthcare. To develop and pilot guidelines for the analysis of critical incidents in healthcare for the hospital sector, mental health and primary care. DATA SOURCES: Literature already available in the Clinical Risk Unit, University College London. Work by known experts in the field of accident investigation and analysis. Electronic databases including PsycINFO and MEDLINE. Websites for accident investigation reports. REVIEW METHODS: Twelve techniques from other high-risk industries were reviewed in detail using criteria developed for the purpose. This review provided a conceptual framework for the healthcare review and appraisal process, as well as providing a critical assessment of the industry techniques. Rigorous searching and screening identified 138 papers for formal appraisal and a further 114 were designated as providing potentially useful background information. A formal appraisal instrument was designed, piloted and modified until acceptable reliability was achieved. From the 138 papers, six techniques were identified as representing clearly definable approaches to incident investigation and analysis. All relevant papers were reviewed for each of the six techniques: Australian Incident Monitoring System, the Critical Incident Technique, Significant Event Auditing, Root Cause Analysis, Organisational Accident Causation Model and Comparison with Standards approach. RESULTS: All healthcare techniques had the potential of being applied in any specialty or discipline related to healthcare. While a few studies looked solely at death as an outcome, most used a variety of outcomes including near misses. Most techniques used interviewing and primary document review to investigate incidents. All techniques included papers that identified clinical issues and some attempt to assess underlying errors, causes and contributory factors. However the extent and sophistication of the various attempts varied widely. Only a third of papers referred to an established model of accident causation. In most studies examined there was little or no information on the training of investigators, how the data was extracted or any information on quality assurance for data collection and analysis. There was some variation in the level of expertise and training required but to undertake the investigation to an acceptable depth all required some expertise. In most papers there was little or no discussion of implementation of any changes as a result of the investigations. A quarter of publications gave some description of the implementation of changes, though few addressed evaluation of changes. CONCLUSIONS: The reviews demonstrate that, while much valuable work has been accomplished, there is considerable potential for further development of techniques, the utilisation of a wider range of techniques and a need for validation and evaluation of existing methods which would make incident investigation more versatile and use limited resources more effectively. Further exploration of techniques used in high-risk industries, with interviews and observation of actual investigations should prove valuable. Existing healthcare techniques would benefit from formal evaluation of their outcomes and effectiveness. Studies should examine depth of investigation and analysis, adequacy and feasibility of recommendations and cost effectiveness. Examining implementation of recommendations is a key issue.

An evaluation of adverse incident reporting.

To examine the reliability of adverse incident-reporting systems we carried out a retrospective review of the mother and baby case notes from a series of 250 deliveries in each of two London obstetric units. Notes were screened for the presence of adverse incidents defined by lists of incidents to be reported in accordance with unit protocols. We assessed the percentage of adverse incidents reported by staff to the maternity risk manager at each unit; the percentage of incidents detected by each risk manager, but not reported; and the percentage of incidents identified only by retrospective case note review. A total of 196 adverse incidents was identified from the 500 deliveries. Staff reported 23% of these and the risk managers identified a further 22%. The remaining 55% of incidents were identified only by retrospective case-note review and not known to the risk manager. Staff reported about half the serious incidents (48%), but comparatively few of the moderately serious (24%) or minor ones (15%). The risk managers identified an additional 16% of serious incidents that staff did not report. Drug errors were analysed separately; only two were known to the risk managers and a further 44 were found by case-note review. Incident-reporting systems may produce much potentially valuable information, but seriously underestimate the true level of reportable incidents. Where one risk manager covers an entire trust, rather than a single unit, reporting rates are likely to be very much lower than in the present study. Greater clarity is needed regarding the definition of reportable incidents (including drug errors). Staff should receive continuing education about the purposes and aims of clinical risk management and incident reporting and consideration should be given to designating specific members of staff with responsibility for reporting.

The validation of three human reliability quantification techniques--THERP, HEART and JHEDI: Part II--Results of validation exercise.

This is the second of three papers dealing with the validation of three Human Reliability Assessment (HRA) techniques. The first paper introduced the need for validation, the techniques themselves and pertinent validation issues. This second paper details the results of the validation study carried out on the Human Reliability Quantification techniques THERP, HEART and JHEDI. The validation study used 30 real Human Error Probabilities (HEPs) and 30 active Human Reliability Assessment (HRA) assessors, 10 per technique. The results were that 23 of the assessors showed a significant correlation between their estimates and the real HEPs, supporting the predictive accuracy of the techniques. Overall precision showed 72% (60-87%) of all HEPs to be within a factor of 10 of the true HEPs, with 38% of all estimates being within a factor of three of the true values. Techniques also tended to be pessimistic rather than optimistic, when they were imprecise. These results lend support to the empirical validity of these three approaches.