Corpus overview


MeSH Disease

Human Phenotype

Cough (10)

Fever (8)

Pneumonia (3)

Hypertension (3)

Dyspnea (1)


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    Ruling In and Ruling Out COVID-19: Computing SARS-CoV-2 Infection Risk TRANS Infection Risk TRANS From Symptoms, Imaging and Test Data.

    Authors: Chistopher D'Ambrosia; Henrik Christensen; Eliah Aronoff-Spencer

    doi:10.1101/2020.09.18.20197582 Date: 2020-09-22 Source: medRxiv

    Background: Assigning meaningful probabilities of SARS CoV2 infection risk TRANS infection risk TRANS presents a diagnostic challenge across the continuum of care. Methods: We integrated patient symptom and test data using machine learning and Bayesian inference to quantify individual patient risk of SARS CoV 2 infection MESHD. We trained models with 100,000 simulated patient profiles based on thirteen symptoms, estimated local prevalence SERO, imaging, and molecular diagnostic performance SERO from published reports. We tested these models with consecutive patients who presented with a COVID 19 compatible illness at the University of California San Diego Medical Center over 14 days starting in March 2020. Results: We included 55 consecutive patients with fever HP fever MESHD (78%) or cough HP cough MESHD (77%) presenting for ambulatory (n=11) or hospital care (n=44). 51% (n=28) were female TRANS, 49% were age TRANS <60. Common comorbidities included diabetes MESHD (22%), hypertension HP hypertension MESHD (27%), cancer MESHD (16%) and cardiovascular disease MESHD (13%). 69% of these (n=38) were RT-PCR confirmed positive for SARS CoV2 infection, 11 had repeated negative nucleic acid testing and an alternate diagnosis. Bayesian inference network, distance metric learning, and ensemble models discriminated between patients with SARS CoV2 infection MESHD and alternate diagnoses with sensitivities SERO of 81.6 to 84.2%, specificities of 58.8 to 70.6%, and accuracies of 61.4 to 71.8%. After integrating imaging and laboratory test statistics with the predictions of the Bayesian inference network, changes in diagnostic uncertainty at each step in the simulated clinical evaluation process were highly sensitive to location, symptom, and diagnostic test choices. Conclusions: Decision support models that incorporate symptoms and available test results can help providers diagnose SARS CoV2 infection MESHD in real world settings.

    Risk Factors Analysis of COVID-19 Patients with ARDS MESHD and Prediction Based on Machine Learning

    Authors: Wan Xu; Nan-Nan Sun; Hai-Nv Gao; Zhi-Yuan Chen; Ya Yang; Bin Ju; Ling-Ling Tang

    doi:10.21203/ Date: 2020-09-15 Source: ResearchSquare

    COVID-19 is a newly emerging infectious disease MESHD, which is generally susceptible to human beings and has caused huge losses to people's health. Acute respiratory distress HP respiratory distress MESHD syndrome ( ARDS MESHD) is one of the common clinical manifestations of severe COVID-19 and it is also responsible for the current shortage of ventilators worldwide. This study aims to analyze the clinical characteristics of COVID-19 ARDS MESHD patients and establish a diagnostic system based on artificial intelligence (AI) method to predict the probability of ARDS in COVID-19 patients. We collected clinical data of 659 COVID-19 patients from 11 regions in China. The clinical characteristics of the two groups were elaborately compared and both traditional machine learning algorithms MESHD and deep learning-based methods were used to build the prediction models. Results indicated the median age TRANS of ARDS MESHD patients was 56.5 years old, which was significantly older than those with non-ARDS by 7.5 years. Male TRANS and patients with BMI>25 were more likely to develop ARDS MESHD. The clinical features of ARDS MESHD patients included cough HP (80.3%), polypnea (59.2%), lung consolidation (53.9%), secondary bacterial infection MESHD (30.3%), and comorbidities such as hypertension HP hypertension MESHD (48.7%). Abnormal biochemical indicators such as lymphocyte count, leukocyte counting, CK, NLR, AST, LDH, and CRP were all strongly related to the aggravation of ARDS. Furthermore, through various AI methods for modeling and prediction effect evaluation based on the above risk factors, decision tree achieved the best AUC, sensitivity SERO, and specificity in identifying the mild patients who were easy to develop ARDS MESHD, which undoubtedly helps to optimize the treatment strategy, reduce mortality, and relieve the medical pressure. 

    Who should we test for COVID-19?A triage model built from national symptom surveys

    Authors: Saar Shoer; Tal Karady; Ayya Keshet; Smadar Shilo; Hagai Rossman; Amir Gavrieli; Tomer Meir; Amit Lavon; Dmitry Kolobkov; Iris Kalka; Anastasia Godneva; Ori Cohen; Adam Kariv; Ori Hoch; Mushon Zer-Aviv; Noam Castel; Carole Sudre; Anat Ekka Zohar; Angela Irony; Timothy Spector; Benjamin Geiger; Dorit Hizi; Varda Shalev; Ran Balicer; Eran Segal

    doi:10.1101/2020.05.18.20105569 Date: 2020-05-21 Source: medRxiv

    The gold standard for COVID-19 diagnosis is detection of viral RNA in a reverse transcription PCR test. Due to global limitations in testing capacity, effective prioritization of individuals for testing is essential. Here, we devised a model that estimates the probability of an individual to test positive for COVID-19 based on answers to 9 simple questions regarding age TRANS, gender TRANS, presence of prior medical conditions, general feeling, and the symptoms fever HP fever MESHD, cough HP cough MESHD, shortness of breath MESHD, sore throat and loss of taste MESHD or smell, all of which have been associated with COVID-19 infection MESHD. Our model was devised from a subsample of a national symptom survey that was answered over 2 million times in Israel over the past 2 months and a targeted survey distributed to all residents of several cities in Israel. Overall, 43,752 adults TRANS were included, from which 498 self-reported as being COVID-19 positive. We successfully validated the model on held-out individuals from Israel where it achieved a positive predictive value SERO (PPV) of 46.3% at a 10% sensitivity SERO and demonstrated its applicability outside of Israel by further validating it on an independently collected symptom survey dataset from the U.K., U.S. and Sweden, where it achieved a PPV of 34.7% at 10% sensitivity SERO. Moreover, evaluating the model's performance SERO on this latter independent dataset on entries collected one week prior to the PCR test and up to the day of the test we found the highest performance SERO on the day of the test. As our tool can be used online and without the need of exposure to suspected patients, it may have worldwide utility in combating COVID-19 by better directing the limited testing resources through prioritization of individuals for testing, thereby increasing the rate at which positive individuals can be identified and isolated.

    Key predictors of attending hospital with COVID19: An association study from the COVID Symptom Tracker App in 2,618,948 individuals

    Authors: Mary Ni Lochlainn; Karla A Lee; Carole H Sudre; Thomas Varsavsky; M. Jorge Cardoso; Cristina Menni; Ruth C. E. Bowyer; Long H. Nguyen; David Alden Drew; Sajaysurya Ganesh; Julien Lavigne du Cadet; Alessia Visconti; Maxim B Freydin; Marc Modat; Mark S Graham; Joan Capdevila Pujol; Benjamin Murray; Julia S El-Sayed Moustafa; Xinyuan Zhang; Richard Davies; Mario Falchi; Timothy D Spector; Andrew T Chan; Sebastien Ourselin; Claire J Steves

    doi:10.1101/2020.04.25.20079251 Date: 2020-04-29 Source: medRxiv

    Objectives: We aimed to identify key demographic risk factors for hospital attendance with COVID-19 infection MESHD. Design: Community survey Setting: The COVID Symptom Tracker mobile application co-developed by physicians and scientists at Kings College London, Massachusetts General Hospital, Boston and Zoe Global Limited was launched in the UK and US on 24th and 29th March 2020 respectively. It captured self-reported information related to COVID-19 symptoms and testing. Participants: 2,618,948 users of the COVID Symptom Tracker App. UK (95.7%) and US (4.3%) population. Data cut-off for this analysis was 21st April 2020. Main outcome measures: Visit to hospital and for those who attended hospital, the need for respiratory support in three subgroups (i) self-reported COVID-19 infection MESHD with classical symptoms (SR-COVID-19), (ii) self-reported positive COVID-19 test results (T-COVID-19), and (iii) imputed/predicted COVID-19 infection based on symptomatology (I-COVID-19). Multivariate logistic regressions for each outcome and each subgroup were adjusted for age TRANS and gender TRANS, with sensitivity SERO analyses adjusted for comorbidities. Classical symptoms were defined as high fever HP fever MESHD and persistent cough HP for several days. Results: Older age TRANS and all comorbidities tested were found to be associated with increased odds of requiring hospital care for COVID-19. Obesity HP (BMI >30) predicted hospital care in all models, with odds ratios (OR) varying from 1.20 [1.11; 1.31] to 1.40 [1.23; 1.60] across population groups. Pre-existing lung disease MESHD and diabetes MESHD were consistently found to be associated with hospital visit with a maximum OR of 1.79 [1.64,1.95] and 1.72 [1.27; 2.31]) respectively. Findings were similar when assessing the need for respiratory support, for which age TRANS and male TRANS gender TRANS played an additional role. Conclusions: Being older, obese MESHD, diabetic MESHD or suffering from pre-existing lung, heart or renal disease MESHD placed participants at increased risk of visiting hospital with COVID-19. It is of utmost importance for governments and the scientific and medical communities to work together to find evidence-based means of protecting those deemed most vulnerable from COVID-19. Trial registration: The App Ethics have been approved by KCL ethics Committee REMAS ID 18210, review reference LRS-19/20-18210

    SARS-COV-2 comorbidity network and outcome in hospitalized patients in Crema, Italy

    Authors: Gianpaolo Benelli; Elisabetta Buscarini; Ciro Canetta; Giuseppe La Piana; Guido Merli; Alessandro Scartabellati; Giovanni Vigano; Roberto Sfogliarini; Giovanni Melilli; Roberto Assandri; Daniele Cazzato; Davide Sebastiano Rossi; Susanna Usai; Guido Caldarelli; Tommaso Gili; Irene Tramacere; Germano Pellegata; Giuseppe Lauria

    doi:10.1101/2020.04.14.20053090 Date: 2020-04-20 Source: medRxiv

    No systematic data on hospitalized SARS-COV-2 patients from Western countries are available. We report onset, course, correlations with comorbidities, and diagnostic accuracy of nasopharyngeal swab in 539 individuals suspected to carry SARS-COV-2 admitted to the hospital of Crema, Italy. All individuals underwent clinical and laboratory exams, SARS-COV-2 reverse transcriptase-polymerase chain reaction on nasopharyngeal swab, and chest X-ray and/or computed tomography (CT). Data on onset, course, comorbidities, number of drugs including angiotensin converting enzyme (ACE) inhibitors and angiotensin-II-receptor antagonists (sartans), follow-up swab, pharmacological treatments, non-invasive respiratory support, ICU admission, and deaths MESHD were recorded. Among 411 SARS-COV-2 patients (66.6% males TRANS) median age TRANS was 70.5 years (range 1-99). Chest CT was performed in 317 (77.2%) and showed interstitial pneumonia MESHD pneumonia HP in 304 (96%). Fatality rate was 17.5% (74% males TRANS), with 6.6% in 60-69 years old, 21.1% in 70-79 years old, 38.8% in 80-89 years old, and 83.3% above 90 years. No death occurred below 60 years. Non-invasive respiratory support rate was 27.2% and ICU admission 6.8%. Older age TRANS, cough HP and dyspnea HP dyspnea MESHD at onset, hypertension HP hypertension MESHD, cardiovascular diseases MESHD, diabetes MESHD, renal insufficiency HP renal insufficiency MESHD, >7 drugs intake and positive X-ray, low lymphocyte count, high C-reactive protein, aspartate aminotransferase and lactate dehydrogenase values, and low PO2 partial pressure with high lactate at arterial blood SERO gas analysis at admission were significantly associated with death MESHD. Use of ACE inhibitors or sartans was not associated with outcomes. Comorbidity network analysis revealed homogenous distribution of deceased and 60-80 aged TRANS SARS-COV-2 patients across diseases. Among 128 swab negative patients at admission (63.3% males TRANS) median age TRANS was 67.7 years (range 1-98). Chest CT was performed in 87 (68%) and showed interstitial pneumonia MESHD pneumonia HP in 76 (87.3%). Follow-up swab turned positive in 13 of 32 patients. Using chest CT at admission as gold standard on the entire study population of 539 patients, nasopharyngeal swab had 80% sensitivity SERO. SARS-CoV-2 caused high mortality among patients older than 60 years and correlated with pre-existing multiorgan impairment. ACE inhibitors and sartans did not influence patients' outcome.

    Preliminary study to identify severe from moderate cases of COVID-19 using NLR&RDW-SD combination parameter

    Authors: changzheng wang; Chengbin Li

    doi:10.1101/2020.04.09.20058594 Date: 2020-04-14 Source: medRxiv

    Objectives: Investigate the characteristics and rules of hematology changes in patients with COVID-19, and explore the possibility to identify moderate and severe patients using conventional hematology parameters or combined parameters. Methods: The clinical data of 45 moderate and severe type patients with SARS-CoV-2 infections MESHD in Jingzhou Central Hospital from January 23 to February 13, 2020 were collected. The epidemiological indexes, clinical symptoms and laboratory test results of the patients were retrospectively analyzed. Those parameters with significant differences between the two groups were analyzed, and the combination parameters with best diagnostic performance SERO were selected using the LDA method. Results: Of the 45 patients with COVID-19 (35 moderate and 10 severe cases), 23 were male TRANS and 22 female TRANS, aged TRANS 16-62 years. The most common clinical symptoms were fever HP fever MESHD (89%) and dry cough MESHD cough HP (60%). As the disease progressed, WBC, Neu#, NLR, PLR, RDW-CV and RDW-SD parameters in the severe group were significantly higher than that in the moderate group (P<0.05); meanwhile, Lym#, Eos#, HFC%, RBC, HGB and HCT parameters in the severe group were significantly lower than that in the moderate group (P<0.05). For NLR, the AUC, the best cut-off value, the sensitivity SERO and the specificity were 0.890, 13.39, 83.3% and 82.4% respectively, and for PLR , the AUC, the best cut-off, the sensitivity SERO and the specificity were 0.842, 267.03, 83.3% and 74.0% respectively. The combined parameter NLR&RDW-SD had the best diagnostic efficiency (AUC was 0.938) and when the cut-off value was 1.046, the sensitivity SERO and the specificity were 90.0% and 84.7% respectively, followed by the fitting parameter NLR&RDW-CV (AUC = 0.923). When the cut-off value was 0.62, the sensitivity SERO and the specificity for distinguishing severe type from moderate cases of COVID-19 were 90.0% and 82.4% respectively. Conclusions: The combined parameter NLR&RDW-SD is the best hematology index and can help clinicians to predict the severity of COVID-19 patients, and it can be used as a useful indicator to help prevent and control the epidemic.

    Clinical features and outcomes of 197 adult TRANS discharged patients with COIVD-19 in Yichang, Hubei

    Authors: Fating Zhou; Xiaogang Yu; Xiaowei Tong; Rong Zhang

    doi:10.1101/2020.03.26.20041426 Date: 2020-03-30 Source: medRxiv

    Purpose To investigate the epidemiology and clinical features of discharged adult TRANS patients with COVID-19 in Yichang. Method The retrospective study recruited 197 cases of COVID-19 discharged from Yichang Central People's Hospital and Yichang Third People's Hospital from Jan 17 to Feb 26, 2020. All cases were confirmed TRANS by real-time RT-PCR or chest computer tomography (CT).The survivors were followed up until March 4,2020. Clinical data, including demographic characteristic, presentation, exposure history, laboratory examination, radiology and prognosis were enrolled and analyzed by SPSS 19.0 software. Results There were 197 adult TRANS discharged patients with COVID-19 in this study. Statistical analysis indicated that the average age TRANS was 55.94 years, and female TRANS patients were 50.3%. Those patients mainly resided in urban with exposure history in 2 weeks. Fever HP Fever MESHD, cough HP cough MESHD and weakness MESHD were the common symptoms. Leucocytes were mainly normal or decreased in 185 patents, both lymphocytes and eosinophils reduced, the ratios were 56.9% and 50.3%, respectively. On the contrary, lactate dehydrogenases raised in 65 patients. C-reactive protein elevated in the most of patients. The sensitivity SERO of RT-PCR was 63.5%. Chest CT indicated that bilateral patchy shadows were the most common imaging manifestations.169 patients recovered and transferred to a designated hospital for observation, and the others turned worst and died of acute respiratory failure MESHD respiratory failure HP. Conclusion COIVD-19 infection MESHD have become a life-threaten public health problem, the sensitivity SERO of RT-PCR was limited. Chest CT scan was recommended for the suspected patients. Moreover, lymphocytopenia MESHD and eosinophils declining without leukocytes increasing may be considered as a useful evidence for the diagnosis.

    Clinical Characteristics of 34 Children TRANS with Coronavirus Disease MESHD-2019 in the West of China: a Multiple-center Case Series

    Authors: Che Zhang; Jiaowei Gu; Quanjing Chen; Na Deng; Jingfeng Li; Li Huang; Xihui Zhou

    doi:10.1101/2020.03.12.20034686 Date: 2020-03-16 Source: medRxiv

    BACKGROUND Up to 9 March, 2020, 109577 patients were diagnosed with coronavirus disease MESHD-2019 (COVID-19) globally. The clinical and epidemiological characteristics of adult TRANS patients have been revealed recently. However, the information of paediatric patients remains unclear. We describe the clinical and epidemiological characteristics of paediatric patients to provide valuable insight into early diagnosis of COVID-19 in children TRANS, as well as epidemic control policy making. METHODS and FINDINGS This retrospective, observational study was a case series performed at 4 hospitals in the west of China. Thirty-four paediatric patients with COVID-19 were included from January 1 to February 25, 2020. And the final follow-up visit was completed by February 28, 2020. Clinical and epidemiological characteristics were analyzed on the basis of demographic data, medical history, laboratory tests, radiological findings, and treatment information. Data analysis was performed on 34 paediatrics patients with COVID-19 aged TRANS from 1 to 144 months (median 33.00, IQR 10.00 - 94.25), among whom 14 males TRANS (41.18%) were included. 47.60% of patients were noticed without any exposure history. The median incubation period TRANS was 10.50 (7.75 - 25.25) days. Infections of other respiratory pathogens were reported in 16 patients (47.06%). The most common initial symptoms were fever HP fever MESHD (76.47%), cough HP (58.82%), and expectoration (20.59%). Vomiting HP Vomiting MESHD (11.76%) and diarrhea HP diarrhea MESHD (11.76%) were also reported in a considerable portion of cases. A remarkable increase was detected in serum SERO amyloid A for 17 patients (85.00%) and high- sensitivity SERO C-reactive protein for 17 patients (58.62%), while a decrease of prealbumin was noticed in 25 patients (78.13%). In addition, the levels of lactate dehydrogenase was increased significantly in 28 patients (82.35%), as well as -hydroxybutyrate dehydrogenase in 25 patients (73.53%). Patchy lesions in lobules were detected by chest computed tomographic scans in 28 patients (82.36%). The typical feature of ground-glass opacity for adults TRANS was rare in paediatric patients (2.94%). A late-onset pattern of lesions in lobules were also noticed. Stratified analysis of the clinical features were not performed due to relatively limited samples. CONCLUSIONS Our data presented the clinical and epidemiological features of paediatric patients systemically. The findings offer new insight into the early identification and intervention of paediatric patients with COVID-19.

    Chest CT Could Be Used to Diagnose 2019 Novel Coronavirus Pneumonia HP Clinically in Hubei Province

    Authors: Xin Wang; Peng Wen; Zhi-Gang Sun; Chun-Yan Xing; Yun Li

    doi:10.21203/ Date: 2020-03-12 Source: ResearchSquare

    Background: In December 2019, novel coronavirus pneumonia MESHD pneumonia HP-19 (COVID-19) was discovered in the viral pneumonia MESHD pneumonia HP cases that occurred in Wuhan, Hubei Province, China; and then quickly spread inside and outside of Wuhan and even other countries. This report describes the clinical course of two patients who had COVID-19.Case presentation: The first case was a typical COVID-19 case. A 66-year-old female TRANS presented to our hospital with a 3-day history of fever HP fever MESHD with coughing HP, white sputum, runny nose and dizziness MESHD. She had contacted with a COVID-19 patient, her daughter-in-law who was diagnosed with COVID-19 two days before. Chest CT showed typical COVID-19 CT imaging. She was diagnosed with COVID-19 by positive nucleic acid test. The second case was a 50-year-old male TRANS with a 2-day history of fever HP fever MESHD and dry coughing HP. He denied having been to Wuhan. Chest CT also showed typical COVID-19 CT imaging. He accepted COVID-19 nucleic acid test using reverse-transcription polymerase chain reaction of his throat swab sampling 7 times and the test results remained controversial. Eventually, he was diagnosed with COVID-19 after 5 days.Conclusions: Chest CT examination has high sensitivity SERO for diagnosis of COVID-19 clinically, particularly when nucleic acid test is negative. Chest CT should be considered for the COVID-19 screening, comprehensive evaluation and following-up and patients could benefit from effective treatment in time.

    Clinical and immunologic features in severe and moderate forms of Coronavirus Disease MESHD 2019

    Authors: Guang Chen; Di Wu; Wei Guo; Yong Cao; Da Huang; Hongwu Wang; Tao Wang; Xiaoyun Zhang; Huilong Chen; Haijing Yu; Xiaoping Zhang; Minxia Zhang; Shiji Wu; Jianxin Song; Tao Chen; Meifang Han; Shusheng Li; Xiaoping Luo; Jianping Zhao; Qin Ning

    doi:10.1101/2020.02.16.20023903 Date: 2020-02-19 Source: medRxiv

    Background Since late December, 2019, an outbreak of pneumonia HP pneumonia MESHD cases caused by the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) emerged in Wuhan, and continued to spread throughout China and across the globe. To date, few data on immunologic features of Coronavirus Disease MESHD 2019 (COVID-19) have been reported. Methods In this single-centre retrospective study, a total of 21 patients with pneumonia HP pneumonia MESHD who were laboratory-confirmed to be infected with SARS-CoV-2 in Wuhan Tongji hospital were included from Dec 19, 2019 to Jan 27, 2020. The immunologic characteristics as well as their clinical, laboratory, radiological features were compared between 11 severe cases and 10 moderate cases. Results Of the 21 patients with COVID-19, only 4 (19%) had a history of exposure to the Huanan seafood market. 7 (33.3%) patients had underlying conditions. The average age TRANS of severe and moderate cases was 63.9 and 51.4 years, 10 (90.9%) severe cases and 7 (70.0%) moderate cases were male TRANS. Common clinical manifestations including fever HP fever MESHD (100%, 100%), cough HP (70%, 90%), fatigue HP fatigue MESHD (100%, 70%) and myalgia HP myalgia MESHD (50%, 30%) in severe cases and moderate cases. PaO2/FiO2 ratio was significantly lower in severe cases (122.9) than moderate cases (366.2). Lymphocyte counts were significantly lower in severe cases (7000 million/L) than moderate cases (11000 million/L). Alanine aminotransferase, lactate dehydrogenase levels, high- sensitivity SERO C-reactive protein and ferritin were significantly higher in severe cases (41.4 U/L, 567.2 U/L, 135.2 mg/L and 1734.4 ug/L) than moderate cases (17.6 U/L, 234.4 U/L, 51.4 mg/L and 880.2 ug /L). IL-2R, TNF- and IL-10 concentrations on admission were significantly higher in severe cases (1202.4 pg/mL, 10.9 pg/mL and 10.9 pg/mL) than moderate cases (441.7 pg/mL, 7.5 pg/mL and 6.6 pg/mL). Absolute number of total T lymphocytes, CD4+T cells and CD8+T cells decreased in nearly all the patients, and were significantly lower in severe cases (332.5, 185.6 and 124.3 million/L) than moderate cases (676.5, 359.2 and 272.0 million/L). The expressions of IFN-{gamma} by CD4+T cells tended to be lower in severe cases (14.6%) than moderate cases (23.6%). Conclusion The SARS-CoV-2 infection MESHD may affect primarily T lymphocytes, particularly CD4+T cells, resulting in significant decrease in number as well as IFN-{gamma} production, which may be associated with disease severity. Together with clinical characteristics, early immunologic indicators including diminished T lymphocytes and elevated cytokines may serve as potential markers for prognosis in COVID-19.

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MeSH Disease
Human Phenotype

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