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

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Cardiac society of Australia and New Zealand position statement executive summary: Coronary artery calcium scoring

Introduction: This article summarises the Cardiac Society of Australia and New Zealand position statement on coronary artery calcium (CAC) scoring. CAC scoring is a non-invasive method for quantifying coronary artery calcification using computed tomography. It is a marker of atherosclerotic plaque burden and the strongest independent predictor of future myocardial infarction and mortality. CAC scoring provides incremental risk information beyond traditional risk calculators such as the Framingham Risk Score. Its use for risk stratification is confined to primary prevention of cardiovascular events, and can be considered as individualised coronary risk scoring for intermediate risk patients, allowing reclassification to low or high risk based on the score. Medical practitioners should carefully counsel patients before CAC testing, which should only be undertaken if an alteration in therapy, including embarking on pharmacotherapy, is being considered based on the test result. Main recommendations: • CAC scoring should primarily be performed on individuals without coronary disease aged 45e75 years (absolute 5-year cardiovascular risk of 10e15%) who are asymptomatic. • CAC scoring is also reasonable in lower risk groups (absolute 5-year cardiovascular risk, 400, or a CAC score of 100e399 and above the 75th percentile for age and sex. • It is reasonable to treat patients with CAC scores > 100 with aspirin and a statin. • It is reasonable not to treat asymptomatic patients with a CAC score of zero. Changes in management as result of this statement: • Cardiovascular risk is reclassified according to CAC score. • High risk patients are treated with a high efficacy statin and aspirin. • Very low risk patients (ie, CAC score of zero) do not benefit from treatment

Aortic annulus dimension assessment by computed tomography for transcatheter aortic valve implantation: differences between systole and diastole

Accurate assessment of aortic annular dimensions is essential for successful transcatheter aortic valve implantation (TAVI). Annular dimensions are conventionally measured in mid-systole by multidetector computed tomography (MDCT), echocardiography and angiography. Significant differences in systolic and diastolic aortic annular dimensions have been demonstrated in cohorts without aortic stenosis (AS), but it is unknown whether similar dynamic variation in annular dimensions exists in patients with severe calcific AS in whom aortic compliance is likely to be substantially reduced. We investigated the variation in aortic annular dimensions between systole and diastole in patients with severe calcific AS. Patients with severe calcific AS referred for TAVI were evaluated by 128-slice MDCT. Aortic annular diameter was measured during diastole and systole in the modified coronal, modified sagittal, and basal ring planes (maximal, minimal and mean diameters). Differences between systole and diastole were analysed by paired t test. Fifty-nine patients were included in the analysis. Three of the five aortic dimensions measured increased significantly during systole. The largest change was a 0.75 mm (3.4%) mean increase in the minimal diameter of the basal ring during systole (p = 0.004). This corresponds closely to the modified sagittal view, which also increased by mean 0.42 mm (1.9%) during systole (p = 0.008). There was no significant change in the maximal diameter of the basal ring or the modified coronal view during systole (p > 0.05). There is a small magnitude but statistically significant difference in aortic annulus dimensions of patients with severe AS referred for TAVI when measured in diastole and systole. This small difference is unlikely to alter clinical decisions regarding prosthesis size or suitability for TAVI.Angela G. Bertaso, Dennis T. L. Wong, Gary Y. H. Liew, Michael S. Cunnington, James D. Richardson, Viji S. Thomson, Brett Lorraine, George Kourlis, Diana Leech, Matthew I. Worthley, Stephen G. Worthle

In vivo non-invasive serial monitoring of FDG-PET progression and regression in a rabbit model of atherosclerosis

We investigated the ability of fluorodeoxyglucose positron emission tomography (FDG PET) imaging to serially monitor macrophage content in a rabbit model of atherosclerosis. Atherosclerosis was induced in rabbits (n = 8) by a combination of atherogenic diet and balloon denudation of the aorta. At the end of nine months, the rabbits were randomized to a further six months of the same atherogenic diet (progression group) or normal diet (regression group). In vivo uptake of FDG by the thoracic aorta was measured using aortic uptake-to-blood radioactivity ratios at the start and end of the randomized period. A significant increase in FDG uptake of the progression group after continued cholesterol feeding (aortic uptake-to-blood radioactivity: 0.57 ± 0.02 to 0.68 ± 0.02, P = 0.001), and a corresponding fall in FDG uptake of the regression group after returning to a normal chow diet (aortic uptake-to-blood radioactivity ratios: 0.67 ± 0.02 to 0.53 ± 0.02, P < 0.0001). FDG PET can quantify in vivo macrophage content and serially monitor changes in FDG activity in this rabbit model.Stephen G. Worthley, Zhuang Y. Zhang, Josef Machac, Gérard Helft, Cheuk Tang, Gary Y. H. Liew, Azfar G. Zaman, Matthew I. Worthley, Zahi A. Fayad, Monte S. Buchsbaum, Valentin Fuster and Juan J. Badimo