Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

There are no SARS-CoV-2 protein terms in the subcorpus


SARS-CoV-2 Proteins
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    Development and validation of a predictive model for critical illness MESHD in adult patients requiring hospitalization for COVID-19 MESHD

    Authors: Neha Paranjape; Lauren Staples; Christina Stradwick; Herman Ray; Ian Saldanha

    doi:10.1101/2021.01.22.21250289 Date: 2021-01-22 Source: medRxiv

    Background: Identifying factors that can predict severe disease in patients needing hospitalization for COVID-19 MESHD is crucial for early recognition of patients at greatest risk. Objective: (1) Identify factors predicting intensive care unit (ICU) transfer and (2) develop a simple calculator for clinicians managing patients hospitalized with COVID-19 MESHD. Methods: A total of 2,685 patients with laboratory-confirmed COVID-19 MESHD admitted to a large metropolitan health system in Georgia, USA between March and July 2020 were included in the study. Seventy-five percent of patients were included in the training dataset (admitted March 1 HGNC to July 10). Through multivariable logistic regression, we developed a prediction model (probability score) for ICU transfer. Then, we validated the model by estimating its performance accuracy (area under the curve [AUC]) using data from the remaining 25% of patients (admitted July 11 to July 31). Results: We included 2,014 and 671 patients in the training and validation datasets, respectively. Diabetes mellitus MESHD, coronary artery disease MESHD, chronic kidney disease MESHD, serum C-reactive protein HGNC, and serum lactate dehydrogenase were identified as significant risk factors for ICU transfer, and a prediction model was developed. The AUC was 0.752 for the training dataset and 0.769 for the validation dataset. We developed a free, web-based calculator to facilitate use of the prediction model (https://icu covid19 COVID19 MESHD/). Conclusion: Our validated, simple, and accessible prediction model and web-based calculator for ICU transfer may be useful in assisting healthcare providers in identifying hospitalized patients with COVID-19 MESHD, who are at high risk for clinical deterioration. Triage of such patients for early aggressive treatment can impact clinical outcomes for this potentially deadly disease.

    Low-density lipoprotein cholesterol levels are associated with poor clinical outcomes in COVID-19 MESHD

    Authors: Alvaro Aparisi; Carolina Iglesias-Echeverria; Cristina Ybarra-Falcon; Ivan Cusacovich; Aitor Uribarri; Mario Garcia-Gomez; Raquel Ladron; Raul Fuertes; Jordi Candela; Williams Hinojosa; Carlos Duenas; Roberto Gonzalez; Leonor Nogales-Martin; Dolores Calvo; Manuel Carrasco-Moraleja; J. Alberto San Roman; Ignacio J Amat-Santos; David Andaluz Ojeda

    doi:10.1101/2020.10.06.20207092 Date: 2020-10-08 Source: medRxiv

    Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the sole causative agent of coronavirus infectious disease MESHD-19 ( COVID-19 MESHD). Methods: We performed a retrospective single-center study of consecutively admitted patients between March 1 HGNCst and May 15th, 2020, with a definitive diagnosis of SARS-CoV-2 infection MESHD. The primary endpoint was to evaluate the association of lipid markers with 30-days all-cause mortality in COVID-19 MESHD. Results: A total of 654 patients were enrolled, with an estimated 30-day mortality of 22.8% (149 patients). Non-survivors had lower total cholesterol (TC) and low-density lipoprotein cholesterol ( LDL-c HGNC) levels during the entire course of the disease with complete resolution among survivors. Both showed a significant inverse correlation with inflammatory markers and a positive correlation with lymphocyte count. In a multivariate analysis, LDL-c HGNC < 69 mg/dl (hazard ratio [HR] 1.94; 95% confidence interval [CI] 1.14-3.31), C-reactive protein HGNC > 88 mg/dl (HR 2.44; 95% CI, 1.41-4.23) and lymphopenia MESHD < 1000 cells/ml (HR 2.68; 95% CI, 1.91-3.78) at admission were independently associated with 30-day mortality. This association was maintained 7 days after admission. Conclusion: Hypolipidemia in SARS-CoV-2 infection MESHD SARS-CoV-2 infection MESHD may be secondary to an immune-inflammatory response, with complete recovery in survivors. Low LDL-c HGNC serum levels are independently associated with higher 30-day mortality in COVID-19 MESHD patients.

    Universal health care access for all residents reduce mortality in COVID-19 MESHD patients in Abu Dhabi, UAE: A retrospective multicenter cohort study

    Authors: Nawal Al kaabi; Asma Al Nuaimi; Mariam Al Harbi; Jehad Abdalla; Tehmina Khan; Huda Gasmelseed; Asad Khan; Osama Hamdoun; Stefan Weber

    doi:10.21203/ Date: 2020-10-04 Source: ResearchSquare

    Background: SARS‐CoV‐2 was first reported in December 2019. The severity of COVID-19 MESHD infection ranges from being asymptomatic to severe infection leading to death. The aim of the study is to describe the clinical characteristics and outcomes of hospitalized COVID-19 MESHD patients within the largest government healthcare facilities in the Emirate of Abu Dhabi, the capital of UAE. Methods:  This paper is a retrospective cross-sectional study of all patients admitted to Abu Dhabi Healthcare services facilities (SEHA) between the period of March 1 HGNCst until May 31st with a laboratory-confirmed test of SARS-CoV2, known as Coronavirus disease MESHD ( COVID19 MESHD). Variation in characteristics, comorbidities, laboratory values, length of hospital stay, treatment received and outcomes were examined. Data was collected from electronic health records available at SEHA health information system.Results: There were 9390 patients included; patients were divided into severe and non-severe groups. 721 (7.68%) patients required intensive care while the remaining majority (92.32 %) were mild-moderate cases. The mean age (41.8 years) is less than the mean age reported globally. Our population had a male predominance and variable representation of different nationalities. Three major comorbidities were noted, hypertension MESHD, diabetes mellitus MESHD and chronic kidney disease MESHD. The laboratory tests that were significantly different between the severe and the non-severe groups were LDH, Ferritin, CRP HGNC, neutrophil count, IL6 HGNC and creatinine level. The major antiviral therapies the patients have received were a combination of hydroxychloroquine and favipiravir. The overall in hospital mortality was 1.63% while severe group mortality rate was 19.56 %. The Death rate in the adults younger than 30 years was noted to be higher compared to elderly patients above 60 years, 2.3% and 0.9 % respectively. Conclusion: our analysis suggests that Abu Dhabi had a relatively low morbidity and mortality rate and a high recovery rate compared to published rates in China, Italy and The United States. The demographic of the population is younger and has an international representation. The country had the highest testing rate in relation to the population volume. We believe the early identification and younger demographic had affected the favorable comparative outcome in general with early identification of cases leading to a lower mortality rate. 

    Arterial Carboxyhemoglobin Levels In Covid-19 MESHD Critically Ill Patients

    Authors: Paul Paccaud; Diego Castanares-Zapatero; Ludovic Gerard; Virginie Montiel; Xavier Wittebole; Christine Collienne; Pierre-François Laterre; Philippe Hantson

    doi:10.21203/ Date: 2020-08-29 Source: ResearchSquare

    Background : Oxidative stress conditions may be responsible for an up-regulation of the expression of heme oxygenase, the enzyme synthesizing carbon monoxide (CO) in cells. Elevated levels of arterial carboxyhemoglogin (CO-Hb) have been found in critically ill patients, including those suffering from acute lung injury MESHD. We aimed to investigate the changes of arterial CO-Hb levels in COVID-19 MESHD critically ill MESHD patients.Methods : A retrospective cohort study was conducted on the medical charts of 63 patients admitted in the ICU for severe COVID-19 MESHD infection over the period March 1 HGNC – May 31, 2020.Results : The overall ICU mortality rate was 39%. Non-survivors had a significantly higher profile of arterial CO-Hb levels than survivors (p<0.001), but arterial CO-Hb increased significantly from admission to day 30 in both groups (p<0.001). Mortality could not be predicted by the changes in arterial CO-Hb, but there was a correlation between the maximal arterial CO-Hb value and SOFA score on admission. No correlation could be demonstrated between arterial CO-Hb and serum C-reactive protein HGNC ( CRP HGNC) as a marker of the inflammatory response.Conclusions : A greater increase of arterial CO-Hb levels over time may represent another marker of severity of COVID-19 MESHD infection in ICU patients. 

    Trends in Covid-19 MESHD risk-adjusted mortality rates in a single health system

    Authors: Leora Horwitz; Simon A. Jones; Robert J. Cerfolio; Fritz Francois; Joseph Greco; Bret Rudy; Christopher M Petrilli

    doi:10.1101/2020.08.11.20172775 Date: 2020-08-14 Source: medRxiv

    Early reports showed high mortality from Covid-19 MESHD; by contrast, the current outbreaks in the southern and western United States are associated with fewer deaths, raising hope that treatments have improved. However, in Texas for instance, 63% of diagnosed cases are currently under 50, compared to only 52% nationally in March-April. Current demographics in Arizona and Florida are similar. Therefore, whether decreasing Covid-19 MESHD mortality rates are a reflection of changing demographics or represent improvements in clinical care is unknown. We assessed outcomes over time in a single health system, accounting for changes in demographics and clinical factors. Methods We analyzed biweekly mortality rates for admissions between March 1 HGNC and June 20, 2020 in a single health system in New York City. Outcomes were obtained as of July 14, 2020. We included all hospitalizations with laboratory-confirmed Covid-19 MESHD disease. Patients with multiple hospitalizations (N=157, 3.3%) were included repeatedly if they continued to have laboratory-confirmed disease. Mortality was defined as in-hospital death MESHD or discharge to hospice care. Based on prior literature, we constructed a multivariable logistic regression model to generate expected risk of death MESHD, adjusting for age; sex; self-reported race and ethnicity; body mass index; smoking history; presence of hypertension MESHD, heart failure MESHD, hyperlipidemia MESHD, coronary artery disease MESHD, diabetes MESHD, cancer MESHD, chronic kidney disease MESHD, or pulmonary disease MESHD individually as dummy variables; and admission oxygen saturation, D-dimer, C reactive protein HGNC, ferritin, and cycle threshold for RNA detection. All data were obtained from the electronic health record. We then calculated the sum of observed and expected deaths in each two-week period and multiplied each period's observed/expected (O/E) risk by the overall average crude mortality to generate biweekly adjusted rates. We calculated Poisson control limits and indicated points outside the control limits as significantly different, following statistical process control standards. The NYU institutional review board approved the study and granted a waiver of consent. Results We included 4,689 hospitalizations, of which 4,661 (99.4%) had died or been discharged. The median age, and the proportion male or with any comorbidity decreased over time; median real-time PCR cycle threshold increased (indicating relatively less concentration of virus) (Table). For instance, median age decreased from 67 years in the first two weeks to 49 in the last two. Peak hospitalizations were during the fifth and sixth study weeks, which accounted for 40% of the hospitalizations. Median length of stay for patients who died or were discharged to hospice was 8 days (interquartile range, 4-16). Unadjusted mortality dropped each period, from 30.2% in the first two weeks to 3% in the last two weeks, with the last eight weeks being lower than the 95% control limits. Risk adjustment partially attenuated the mortality decline, but adjusted mortality rates in the second-to-last two weeks remained outside the control limits (Figure, Table). The O/E risk of mortality decreased from 1.07 (0.64-1.67) in the first two weeks to 0.39 (0.08-1.12) in the last two weeks. Discussion In this 16-week study of Covid-19 MESHD mortality at a single health system, we found that changes in demographics and severity of illness at presentation account for some, but not all, of the decrease in unadjusted mortality. Even after risk adjustment for a variety of clinical and demographic factors, mortality was significantly lower towards the end of the study period. Incremental improvements in outcomes are likely a combination of increasing clinical experience, decreasing hospital volume, growing use of new pharmacologic treatments (such as corticosteroids, remdesivir and anti-cytokine treatments), non-pharmacologic treatments (such as proning), earlier intervention, community awareness, and lower viral load exposure from increasing mask wearing and social distancing. It is also possible that earlier periods had a more virulent circulating strain. In summary, data from one health system suggest that Covid-19 MESHD remains a serious disease for high risk patients, but that outcomes may be improving.

    Neutrophil-to-Lymphocyte Ratio on Admission Predicts In-hospital Mortality in Patients with COVID-19 MESHD

    Authors: Jin Hu; Jun Zhou; Fang Dong; Jie Tan; Shuntao Wang; Zhi Li; Ximeng Zhang; Huiqiong Zhang; Jie Ming; Tao Huang

    doi:10.21203/ Date: 2020-07-26 Source: ResearchSquare

    Background: A novel coronavirus caused an outbreak of acute infectious pneumonia MESHD are spreading over the globe. However, studies predicting prognosis are limited. We predicted outcomes of patients with coronavirus disease 2019 MESHD ( COVID-19 MESHD) using the neutrophil-to-lymphocyte ratio (NLR) on admission.Methods: We retrospectively analyzed the characteristics of COVID-19 MESHD patients diagnosed from February 6 to March 1 HGNC. The outcomes, including the occurrence of in-hospital mortality, acute kidney injury MESHD ( AKI MESHD), and endotracheal intubation (ETI), were recorded. The relationships of neutrophils, lymphocytes, C-reactive protein HGNC, lactate dehydrogenase, and NLR with outcomes were assessed using multivariate regression model. P-values for trends across quartiles of NLR was examined.Results: A total of 182 patients were included. 37 (20.3%) patients died during the hospitalization, 41 (22.5%) developed AKI MESHD, and 36 (19.8%) received ETI. The NLR had a superior predictive performance than others. Using an NLR cutoff of 11.4, the area under the curves (AUC) were 0.766 for in-hospital mortality, 0.755 for AKI MESHD, and 0.733 for ETI. In multivariate analysis, NLR >11.4 was further identified as an independent prognostic factor. Following stratification with quartiles of NLR, a positive trend between the increasing quartiles of NLR and the three outcomes were observed (p-values for trends across quartiles were 0.043, <0.001, and 0.041, respectively). The multivariate adjusted odds ratio (OR) in the highest quartile vs. the lowest quartile were 5.738 for mortality, 25.307 for AKI MESHD, and 5.136 for ETI.Conclusions: Increasing NLR obtained on admission is a powerful predictor for inpatient mortality, AKI MESHD, and ETI in COVID-19 MESHD patients.

    A tertiary center experience of multiple myeloma patients with COVID-19 MESHD: lessons learned and the path forward

    Authors: Bo Wang; Oliver Van Oekelen; Tarek Mouhieddine; Diane Marie Del Valle; Joshua Richter; Hearn Jay Cho; Shambavi Richard; Ajai Chari; Sacha Gnjatic; Miriam Merad; Sundar Jagannath; Samir Parekh; Deepu Madduri

    doi:10.1101/2020.06.04.20122846 Date: 2020-06-05 Source: medRxiv

    Background: The COVID-19 pandemic MESHD COVID-19 pandemic MESHD, caused by SARS-CoV-2 virus, has resulted in over 100,000 deaths in the United States. Our institution has treated over 2,000 COVID-19 MESHD patients during the pandemic in New York City. The pandemic directly impacted cancer MESHD patients and the organization of cancer MESHD care. Mount Sinai Hospital has a large and diverse multiple myeloma MESHD ( MM MESHD) population. Herein, we report the characteristics of COVID-19 MESHD infection and serological response in MM MESHD patients in a large tertiary care institution in New York. Methods: We performed a retrospective study on a cohort of 58 patients with a plasma-cell disorder (54 MM MESHD, 4 smoldering MM MESHD) who developed COVID-19 MESHD between March 1 HGNC, 2020 and April 30, 2020. We report epidemiological, clinical and laboratory characteristics including persistence of viral detection by polymerase chain reaction (PCR) and anti-SARS-CoV-2 antibody testing, treatments initiated, and outcomes. Results: Of the 58 patients diagnosed with COVID-19 MESHD, 36 were hospitalized and 22 were managed at home. The median age was 67 years; 52% of patients were male and 63% were non-white. Hypertension MESHD (64%), hyperlipidemia MESHD (62%), obesity MESHD (37%), diabetes mellitus MESHD (28%), chronic kidney disease MESHD (24%) and lung disease MESHD (21%) were the most common comorbidities. In the total cohort, 14 patients (24%) died. Older age (>70 years), male sex, cardiovascular risk, and patients not in complete remission (CR) or stringent CR were significantly (p<0.05) associated with hospitalization. Among hospitalized patients, laboratory findings demonstrated elevation of traditional inflammatory markers ( CRP HGNC, ferritin, D-dimer) and a significant (p<0.05) association between elevated inflammatory markers, severe hypogammaglobulinemia MESHD, non-white race, and mortality. Ninety-six percent (22/23) of patients developed antibodies to SARS-CoV-2 at a median of 32 days after initial diagnosis. Median time to PCR negativity was 43 (range 19-68) days from initial positive PCR. Conclusions: Drug exposure and MM MESHD disease status at the time of contracting COVID-19 MESHD had no bearing on mortality. Mounting a severe inflammatory response to SARS-CoV-2 and severe hypogammaglobulinemia MESHD were associated with higher mortality. The majority of patients mounted an antibody response to SARS-CoV-2. These findings pave a path to identification of vulnerable MM MESHD patients who need early intervention to improve outcome in future outbreaks of COVID-19 MESHD.

    Factors associated with hospitalization and critical illness among 4,103 patients with COVID-19 MESHD disease in New York City

    Authors: Christopher M. Petrilli; Simon A. Jones; Jie Yang; Harish Rajagopalan; Yelena Chernyak; Katie Tobin; Robert J. Cerfolio; Fritz Francois; Leora I. Horwitz

    doi:10.1101/2020.04.08.20057794 Date: 2020-04-11 Source: medRxiv

    Background: Little is known about factors associated with hospitalization and critical illness in Covid-19 MESHD positive patients. Methods: We conducted a cross-sectional analysis of all patients with laboratory-confirmed Covid-19 MESHD treated at a single academic health system in New York City between March 1 HGNC, 2020 and April 2, 2020, with follow up through April 7, 2020. Primary outcomes were hospitalization and critical illness (intensive care, mechanical ventilation, hospice and/or death MESHD). We conducted multivariable logistic regression to identify risk factors for adverse outcomes, and maximum information gain decision tree classifications to identify key splitters. Results: Among 4,103 Covid-19 MESHD patients, 1,999 (48.7%) were hospitalized, of whom 981/1,999 (49.1%) have been discharged home, and 292/1,999 (14.6%) have died or were discharged to hospice. Of 445 patients requiring mechanical ventilation, 162/445 (36.4%) have died. Strongest hospitalization risks were age [≥]75 years (OR 66.8, 95% CI, 44.7-102.6), age 65-74 (OR 10.9, 95% CI, 8.35-14.34), BMI>40 (OR 6.2, 95% CI, 4.2-9.3), and heart failure MESHD (OR 4.3 95% CI, 1.9-11.2). Strongest critical illness risks were admission oxygen saturation <88% (OR 6.99, 95% CI 4.5-11.0), d-dimer>2500 (OR 6.9, 95% CI, 3.2-15.2), ferritin >2500 (OR 6.9, 95% CI, 3.2-15.2), and C-reactive protein HGNC ( CRP HGNC) >200 (OR 5.78, 95% CI, 2.6-13.8). In the decision tree for admission, the most important features were age >65 and obesity MESHD; for critical illness MESHD, the most important was SpO2<88, followed by procalcitonin >0.5, troponin <0.1 (protective), age >64 and CRP HGNC>200. Conclusions: Age and comorbidities are powerful predictors of hospitalization; however, admission oxygen impairment and markers of inflammation MESHD are most strongly associated with critical illness MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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