Corpus overview


MeSH Disease

Human Phenotype


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    Early prognostication of COVID-19 to guide hospitalisation versus outpatient monitoring using a point-of-test risk prediction score

    Authors: Felix Chua; Rama Vancheeswaran; Adrian Draper; Tejal Vaghela; Matthew Knight; Rahul Moghal; Jaswinder Singh; Lisa G Spencer; Erica Thwaite; Harry Mitchell; Sam Calmonson; Noor Mahdi; Shershah Assadullah; Matthew Leung; Aisling O'Neill; Chhaya Popat; Radhika Kumar; Thomas J Humphries; Rebecca Talbutt; Sarika Raghunath; Philip L Molyneaux; Miriam Schechter; Jeremy Lowe; Andrew Barlow

    doi:10.1101/2020.10.19.20215426 Date: 2020-10-21 Source: medRxiv

    Introduction Risk factors of adverse outcomes in COVID-19 are defined but stratification of mortality using non-laboratory measured scores, particularly at the time of pre-hospital SARS-CoV-2 testing, is lacking. Methods Multivariate regression with bootstrapping was used to identify independent mortality predictors in a derivation cohort of COVID-19 patients. Predictions were externally validated in a large random sample of the ISARIC cohort (N=14,231) and a smaller cohort from Aintree (N=290). Results 983 patients (median age TRANS 70, IQR 53-83; in-hospital mortality 29.9%) were recruited over an 11-week study period. Through sequential modelling, a 5-predictor score termed SOARS (SpO2, Obesity HP, Age TRANS, Respiratory rate, Stroke HP Stroke MESHD history) was developed to correlate COVID-19 severity across low, moderate and high strata of mortality risk. The score discriminated well for in-hospital death, with area under the receiver operating characteristic values of 0.82, 0.80 and 0.74 in the derivation, Aintree and ISARIC validation cohorts respectively. Its predictive accuracy (calibration) in both external cohorts was consistently higher in patients with milder disease (SOARS 0-1), the same individuals who could be identified for safe outpatient monitoring. Prediction of a non-fatal outcome in this group was accompanied by high score sensitivity SERO (99.2%) and negative predictive value SERO (95.9%). Conclusion The SOARS score uses constitutive and readily assessed individual characteristics to predict the risk of COVID-19 death MESHD. Deployment of the score could potentially inform clinical triage in pre-admission settings where expedient and reliable decision-making is key. The resurgence of SARS-CoV-2 transmission TRANS provides an opportunity to further validate and update its performance SERO.

    Basrah experience among 6404 patients with COVID-19

    Authors: Saad S. Hamadi Al-Taher; Abbas K AlKanan; Mohammad N. Fares; Nihad Q. Mohammed; Ali Raheem Al-Jabery; Awatif A. Habeeb; Abbas Ali Mansour; Kerstin Klaser; Michela Antonelli; Liane S Canas; Erika Molteni; Marc Modat; M. Jorge Cardoso; Anna May; Sajaysurya Ganesh; Richard Davies; Long H Nguyen; David Alden Drew; Christina M Astley; Amit D. Joshi; Jordi Merino; Neli Tsereteli; Tove Fall; Maria F Gomez; Emma Duncan; Christina Menni; Frances MK Williams; Paul W Franks; Andrew T Chan; Jonathan Wolf; Sebastien Ourselin; Timothy Spector; Claire J Steves

    doi:10.1101/2020.10.19.20215384 Date: 2020-10-21 Source: medRxiv

    Background: The first case of COVID-19 report in Basrah was in early March 2020. This study aimed to assess some of the characteristics of patients with COVID-19 in Basrah for the period from March ,4th to September ,8th 2020. Methods: Retrospective database analysis of the University of Basrah database. All RT-PCR positive patients during the study period were enrolled. Results: Of 6404 patients included , male TRANS constituted 54.8%. Healthcare workers constituted 11.4% of the infected people. Of health care workers 16.1% were physicians . The mean age TRANS for the whole cohort was 39{+/-}16.7 years; adolescents and children TRANS younger than 20 years constituted 12.4%. The peak age TRANS was 31-40 years, those aged TRANS 61 years or more constituted 9.8% only. The case fatality rate was 3% ( males TRANS 55.2% and females TRANS 44.8%) . No death MESHD was reported in adolescents or children TRANS. The highest death rate was among those age TRANS 61 years or more. Conclusion: The situation of COVID-19 infection MESHD in Basrah is evolving like other countries. Furthers studies are needed to assess associated comorbidities, treatment lines, outcomes and variables associated with mortality.

    Characteristics and outcomes of clinically diagnosed RT-PCR swab negative COVID-19: a retrospective cohort study

    Authors: Paul Middleton; Pablo N Perez-Guzman; Alexandra Cheng; Naveenta Kumar; Mara Kont; Anna Daunt; Sujit Mukherjee; Graham Cooke; Timothy B Hallett; Katharina D Hauck; Peter J White; Mark R Thursz; Shevanthi Nayagam; Brendan Flannery; Ricardo Gilead Baibich; Iris Bigler; Matan Malul; Rotem Rishti; Asher Brenner; Yair E. Lewis; Eran Friedler; Yael Gilboa; Sara Sabach; Yuval Alfiya; Uta Cheruti; Nadav Davidovitch; Natalya Bilenko; Jacob Moran-Gilad; Yakir Berchenko; Itay Bar-Or; Ariel Kushmaro; Timothy Spector; Claire J Steves

    doi:10.1101/2020.10.20.20204651 Date: 2020-10-21 Source: medRxiv

    Patients with strong clinical features of COVID-19 with negative real time polymerase chain reaction (RT-PCR) SARS-CoV-2 testing are not currently included in official statistics. The scale, characteristics and clinical relevance of this group are thus unknown. We performed a retrospective cohort study in two large London hospitals to characterize the demographic, clinical, and hospitalization outcome characteristics of swab-negative clinical COVID-19 patients. We found 1 in 5 patients with a negative swab and clinical suspicion of COVID-19 received a clinical diagnosis of COVID-19 within clinical documentation, discharge summary or death MESHD certificate. We compared this group to a similar swab positive cohort and found similar demographic composition, symptomology and laboratory findings. Swab-negative clinical COVID-19 patients had better outcomes, with shorter length of hospital stay, reduced need for >60% supplementary oxygen and reduced mortality. Patients with strong clinical features of COVID-19 that are swab-negative are a common clinical challenge. Health systems must recognize and plan for the management of swab-negative patients in their COVID-19 clinical management, infection control policies and epidemiological assessments.

    A placebo-controlled double blind trial of hydroxychloroquine in mild-to-moderate COVID-19

    Authors: Vincent Dubee; Pierre-Marie Roy; Bruno Vielle; Elsa Parot-Schinkel; Odile Blanchet; Astrid Darsonval; Caroline Lefeuvre; Chadi Abbara; Sophie Boucher; Edouard Devaud; Olivier Robineau; Patrick Rispal; Thomas Guimard; Emma D'Anglejan; Sylvain Diamantis; Marc-Antoine Custaud; Isabelle Pellier; Alain Mercat

    doi:10.1101/2020.10.19.20214940 Date: 2020-10-21 Source: medRxiv

    Background The efficacy of hydroxychloroquine in coronavirus disease MESHD 2019 (COVID-19) remains controversial. Methods We conducted a multicentre randomized double-blind placebo-controlled trial evaluating hydroxychloroquine in COVID-19 patients with at least one of the following risk factors for worsening: age TRANS 75 years or more, age TRANS between 60 and 74 years, and presence of at least one comorbidity, or need for supplemental oxygen (3 L/min or more). Eligible patients were randomized in a 1:1 ratio to receive either 800 mg hydroxychloroquine on Day 0 followed by 400 mg per day for 8 days or a placebo. The primary endpoint was a composite of death MESHD or tracheal intubation within 14 days following randomization. Secondary endpoints included mortality and clinical evolution at Day 14 and 28, viral shedding at Day 5 and 10. Results The trial was stopped after 250 patients were included due to a slowdown of the pandemic in France. The intention-to-treat population comprised 123 and 124 patients in the placebo and hydroxychloroquine groups, respectively. The median age TRANS was 77 years and 151 patients required oxygen therapy. The primary endpoint occurred in nine patients in the hydroxychloroquine group and eight patients in the placebo group (relative risk 1.12; 95% confidence interval 0.45-2.80; P=0.82). No difference was observed between the two groups in any of the secondary endpoints. Conclusion In this trial involving mainly older patients with mild-to-moderate COVID-19, patients treated with hydroxychloroquine did not experience better clinical or virological outcomes than those receiving the placebo.

    Suicide Deaths during the Stay-at-Home Advisory in Massachusetts.

    Authors: Jeremy Faust; Sejal B Shah; Chengan Du; Shu-Xia Li; Zhenqiu Lin; Harlan M Krumholz; Qin Zhou; Chenyu Sun; Manuel M Vicente; Angela Fernandes; Ana M Dias; Ivan-Christian Kurolt; Alemka Markotic; Dragan Primorac; Adriana Soares; Luis Malheiro; Irena Trbojevic-Akmacic; Miguel Abreu; Rui Sarmento e Castro; Silvia Bettinelli; Annapaola Callegaro; Marco Arosio; Lorena Sangiorgio; Luca Lorini; Xavier Castells; Juan P Horcajada; Salome Pinho; Massimo Allegri; Clara Barrios; Gordan Lauc

    doi:10.1101/2020.10.20.20215343 Date: 2020-10-20 Source: medRxiv

    Many believe that shelter-in-place or stay-at-home policies might cause an increase in so-called deaths of despair. While increases in psychiatric MESHD stressors during the COVID-19 pandemic are anticipated, whether suicide rates changed during stay-at-home periods has not been described. This was an observational cohort study that assembled suicide death data for persons aged TRANS 10 years or older from the Massachusetts Department of Health Registry of Vital Records and Statistics from January 2015 through May 2020. Using autoregressive integrated moving average (ARIMA) and seasonal ARIMA to analyze suicide deaths in Massachusetts, we compared the observed number of suicide deaths MESHD in Massachusetts during the stay-at-home period (March through May, 2020) in Massachusetts to the projected number of expected deaths. To be conservative, we also accounted for the deaths still pending final cause determination The incident rate for suicide deaths MESHD in Massachusetts was 0.67 per 100,000 person-month (95% CI 0.56-0.79) versus 0.81 per 100,000 person-month (95% CI 0.69-0.94) during the 2019 corresponding period (incident rate ratio of 0.83; 95% CI 0.66-1.03). The addition of the 57 deaths pending cause determination occurring from March through May 2020 and the 33 cases still pending determination from the 2019 corresponding period did not change these findings. The observed number of suicide deaths during the stay-at-home period did not deviate from ARIMA projected expectations using either preliminary data or an alternate scenario in which deaths pending investigation (exceeding the average remaining number of deaths still pending investigation which occurred during the corresponding 2015-2019 period) were ascribed to suicide. Decedent age TRANS and sex demographics were unchanged during the pandemic period compared to 2015-2019. The stable rates of suicide deaths during the stay-at-home advisory in Massachusetts parallel findings following ecological disasters. As the pandemic persists, uncertainty about its scope and economic impact may increase. However, our data are reassuring that an increase in suicide deaths MESHD in Massachusetts during the stay-at-home advisory period did not occur.

    Excess deaths MESHD, baselines, Z-scores, P-scores and peaks

    Authors: Laurie Davies

    id:2010.10320v1 Date: 2020-10-20 Source: arXiv

    The recent Covid-19 epidemic has lead to comparisons of the countries suffering from it. These are based on the number of excess deaths attributed either directly or indirectly to the epidemic. Unfortunately the data on which such comparisons rely are often incomplete and unreliable. This article discusses problems of interpretation of data even when the data is largely accurate and delayed by at most two to three weeks. This applies to the Office of National Statistics in the UK, the Statistisches Bundesamt in Germany and the Belgian statistical office Statbel. The data in the article is taken from these three sources. The number of excess deaths MESHD is defined as the number of deaths minus the baseline, the definition of which varies from country to country. In the UK it is the average number of deaths over the last five years, in Germany it is over the last four years and in Belgium over the last 11 years. This means that in all cases the individual baselines depend strongly on the timing and intensity of adverse factors such as past influenza epidemics and heat waves. This makes cross-country comparisons difficult. A baseline defined as the number the number of deaths in the absence of adverse factors can be operationalized by taking say the 10\% quantile of the number of deaths. This varies little over time and European countries within given age groups TRANS. It therefore enables more robust and accurate comparisons of different countries. The article criticizes the use of Z-scores which distort the comparison between countries. Finally the problem of describing past epidemics by their timing, that is start and finish and time of the maximum, and by their effect, the height of the maximum and the total number of deaths MESHD, is considered.

    Indirect effects of the COVID-19 pandemic on paediatric health-care use and severe disease: a retrospective national cohort study

    Authors: Thomas C Williams; Clare MacRae; Olivia Swann; Haris Haseeb; Steve Cunningham; Philip Davies; Neil Gibson; Christopher Lamb; Richard Levin; Catherine McDougall; Jillian McFadzean; Ian Piper; Alastair Turner; Steve Turner; Margrethe Van Dijke; Don Urquhart; Bruce Guthrie; Ross Langley; Progyaparamita Saha; Yvenie Desire; Russell Saltzman; Kim G Hankey; Sixto A Arias; Folusakin Ayoade; Jairo A. Tovar; Rejane Lamazares; Hayley B Gershengorn; Fontaine J Magali; Matthias Loebe; Kristin Mullins; Muthukumar Gunasekaran; Vela Karakeshishyan; Dushyantha T Jayaweera; Anthony Atala; Ali Ghodsizad; Joshua M Hare

    doi:10.1101/2020.10.15.20212308 Date: 2020-10-20 Source: medRxiv

    Background: Severe disease directly associated with SARS-CoV-2 infection MESHD in children TRANS is rare. However, the indirect consequences of the COVID-19 pandemic on paediatric health have not been fully quantified. We examined paediatric health-care utilisation, incidence of severe disease, and mortality during the lockdown period in Scotland. Methods: This national retrospective cohort study examined national data for emergency childhood primary and secondary care utilisation following national lockdown on March 23, 2020. To determine whether social distancing measures and caregiver behavioural changes were associated with delayed care-seeking and increased disease severity on presentation, unplanned, emergency admissions requiring invasive mechanical ventilation for the two national Paediatric Intensive Care Units (PICUs) were analysed. PICU admissions were grouped by diagnostic category, and disease severity on presentation calculated. National statutory death MESHD records were consulted to establish childhood mortality rates and causes of death MESHD. For all observations, the lockdown period was compared to equivalent dates in 2016-2019. Findings: We identified 273,455 unscheduled primary care attendances; 462,437 emergency department attendances; 54,076 emergency hospital admissions; 413 PICU emergency admissions; and 415 deaths during the lockdown study period and equivalent dates in previous years. The rates of emergency presentations to primary and secondary care fell HP during lockdown in comparison to previous years. Emergency PICU admissions for children TRANS requiring invasive mechanical ventilation also fell HP, with an odds ratio of 0.52 for chance of admission during lockdown (95% CI 0.37-0.73, p < 0.001). Clinical severity scores did not suggest children TRANS were presenting with more advanced disease. The greatest reduction in PICU admissions was for diseases of the respiratory system; those for injury, poisoning MESHD or other external causes were equivalent to previous years. Mortality during lockdown did not change significantly compared to 2016-2019. Interpretation: National lockdown led a reduction in paediatric emergency care utilisation, without associated evidence of severe harm. Funding: None.

    Age TRANS-Stratified SARS-CoV-2 Infection MESHD Fatality Rates in New York City estimated from serological data

    Authors: Chloe G Rickards; A. Marm Kilpatrick; Deborah A. Lawlor; Fady I. Sharara; Scott M. Nelson; Maryam Poursadeghfard; Isabelle Delpierre; Sophie Henrard; Niloufar Sadeghi; Jean-Christophe Goffard; Serge Goldman; Xavier De Tiège; Javier Colomina; David Navarro

    doi:10.1101/2020.10.16.20214023 Date: 2020-10-20 Source: medRxiv

    Importance: COVID-19 has killed hundreds of thousands of people in the US and >1 million globally. Estimating the age TRANS-specific infection fatality rate (IFR) of SARS-CoV-2 for different populations is crucial for assessing the fatality of COVID-19 and for appropriately allocating limited vaccine supplies to minimize mortality. Objective: To estimate IFRs for COVID-19 in New York City and compare them to IFRs from other countries. Design, Setting, Participants: We used data from a published serosurvey of 5946 individuals 18 years or older conducted April 19-28, 2020 with time series of COVID-19 confirmed cases TRANS and deaths MESHD for five age TRANS-classes from the New York City Department of Health and Mental Hygiene MESHD. We inferred age TRANS-specific IFRs using a Bayesian framework that accounted for the distribution of delay between infection MESHD and seroconversion and infection MESHD and death MESHD. Main Outcome and Measure: Infection fatality rate. Results: We found that IFRs increased approximately 77-fold with age TRANS, with a nearly linear increase on a log scale, from 0.07% (0.055%-0.086%) in 18-44 year olds to 5.4% (4.3%-6.3%) in individuals 75 and older. New York City IFRs were higher for 18-44 year olds and 45-64 year olds (0.58%; 0.45%-0.75%) than Spanish, English, and Swiss populations, but IFRs for 75+ year olds were lower than for English populations and similar to Spanish and Swiss populations. Conclusions and Relevance: These results suggest that the age TRANS-specific fatality of COVID-19 differs among developed countries and raises questions about factors underlying these differences.

    Evaluating the use of the reproduction number TRANS as an epidemiological tool, using spatio-temporal trends of the Covid-19 outbreak in England

    Authors: Katharine Sherratt; Sam Abbott; Sophie Meakin; Joel Hellewell; James D Munday; Nikos Bosse; - CMMID Covid-19 working group; Mark Jit; Sebastian Funk; Angela Fernandes; Ana M Dias; Ivan-Christian Kurolt; Alemka Markotic; Dragan Primorac; Adriana Soares; Luis Malheiro; Irena Trbojevic-Akmacic; Miguel Abreu; Rui Sarmento e Castro; Silvia Bettinelli; Annapaola Callegaro; Marco Arosio; Lorena Sangiorgio; Luca Lorini; Xavier Castells; Juan P Horcajada; Salome Pinho; Massimo Allegri; Clara Barrios; Gordan Lauc

    doi:10.1101/2020.10.18.20214585 Date: 2020-10-20 Source: medRxiv

    The time-varying reproduction number TRANS (Rt: the average number secondary infections TRANS infections MESHD caused by each infected person) may be used to assess changes in transmission TRANS potential during an epidemic. Since new infections usually are not observed directly, it can only be estimated from delayed and potentially biased data. We estimated Rt using a model that mapped unobserved infections to observed test-positive cases, hospital admissions, and deaths MESHD with confirmed Covid-19, in seven regions of England over March through August 2020. We explored the sensitivity SERO of Rt estimates of Covid-19 in England to different data sources, and investigated the potential of using differences in the estimates to track epidemic dynamics in population sub-groups. Our estimates of transmission TRANS potential varied for each data source. The divergence between estimates from each source was not consistent within or across regions over time, although estimates based on hospital admissions and deaths MESHD were more spatio-temporally synchronous than compared to estimates from all test-positives. We compared differences in Rt with the demographic and social context of transmission TRANS, and found the differences between Rt may be linked to biased representations of sub-populations in each data source: from uneven testing rates, or increasing severity of disease with age TRANS, seen via outbreaks in care home populations and changing age TRANS distributions of cases. We highlight that policy makers should consider the source populations of Rt estimates. Further work should clarify the best way to combine and interpret Rt estimates from different data sources based on the desired use.

    2.5 Million Person-Years of Life Have Been Lost Due to COVID-19 in the United States


    doi:10.1101/2020.10.18.20214783 Date: 2020-10-20 Source: medRxiv

    The COVID-19 pandemic, caused by tens of millions of SARS-CoV-2 infections MESHD world-wide, has resulted in considerable levels of mortality and morbidity. The United States has been hit particularly hard having 20 percent of the world's infections MESHD but only 4 percent of the world population. Unfortunately, significant levels of misunderstanding exist about the severity of the disease and its lethality. As COVID-19 disproportionally impacts elderly TRANS populations, the false impression that the impact on society of these deaths is minimal may be conveyed by some because elderly TRANS individuals are closer to a natural death MESHD. To assess the impact of COVID-19 in the US, I have performed calculations of person-years of life lost as a result of 194,000 premature deaths due to SARS-CoV-2 infection MESHD as of early October, 2020. By combining actuarial data on life expectancy and the distribution of COVID-19 associated deaths we estimate that over 2,500,000 person-years of life have been lost so far in the pandemic in the US alone, averaging over 13.25 years per person with differences noted between males TRANS and females TRANS. Importantly, nearly half of the potential years of life lost occur in non- elderly TRANS populations. Issues impacting refinement of these models and the additional morbidity caused by COVID-19 beyond lethality are discussed.

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MeSH Disease
Human Phenotype

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