Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (465)

Fever (273)

Cough (217)

Hypertension (192)

Respiratory distress (119)


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    Clinical Characteristics of SARS-CoV-2 Pneumonia MESHD Pneumonia HP Compared to Controls in Chinese Han Population

    Authors: Yang Xu; Yi-rong Li; Qiang Zeng; Zhi-bing Lu; Yong-zhe Li; Wei Wu; Sheng-yong Dong; Gang Huang; Xing-huan Wang

    doi:10.1101/2020.03.08.20031658 Date: 2020-03-10

    Background In December 2019, novel coronavirus (SARS-CoV-2) infected pneumonia MESHD pneumonia HP occurred in Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of SARS-CoV-2 pneumonia MESHD pneumonia HP without comorbidities compared to normal controls in Chinese Han population is limited. Our objective is to describe the epidemiological and clinical characteristics of SARS-CoV-2 pneumonia MESHD pneumonia HP without comorbidities compared to normal controls in the Chinese Han population. Methods Retrospective, multi-center case series of the 69 consecutive hospitalized patients with confirmed SARS-CoV-2 pneumonia MESHD pneumonia HP, from February 7 to February 28, 2020; final date of follow-up was February 29, 2020. Results The study population included 69 hospitalized patients with confirmed SARS-CoV-2 pneumonia MESHD pneumonia HP without comorbidities and 14,117 normal controls. 50.7% patients were male TRANS and 49.3% were female TRANS; 1.5% patients were asymptomatic TRANS cases, 63.8% patients were mild cases, and 36.2% patients were severe or critical cases. Compared with mild patients (n = 44), severe or critical patients (n = 25) were significantly older (median age TRANS, 67 years [IQR, 58-79] vs. 49 years [IQR, 36-60]; P < 0.01). Fever MESHD Fever HP was present in 98.6% of the patients. The second most common symptom was cough MESHD cough HP (62.3%), fatigue MESHD fatigue HP (58.0%), sputum (39.1%), and headache MESHD headache HP (33.3%). The median incubation period TRANS was 4 days (IQR, 2 to 7). Leukocyte count was 74.1% of normal controls and lymphocyte count was 45.9% of normal controls. The phenomenon of lymphocyte depletion (PLD) observed in severe or critical cases in 100%. Levels of lactate dehydrogenase, D-dimer, procalcitonin, and interleukin-6 were showed significant differences between mild and severe or critical cases. Chest computed tomographic scans showed bilateral patchy patterns (49.3%), local patchy shadowing (29.0%), and ground glass opacity (21.7%). 7.3% patients were diagnosed ARDS, 7.3% patients were diagnosed acute cardiac injury (troponin I >28 pg/mL) and 4.4% patients were diagnosed fungal infections MESHD or shock MESHD shock HP. 4.3% patients have been discharged; 1.5% patient had died; 1.5% patient had recovery. Conclusions In this multicenter case series of 69 patients without comorbidities, the full spectrum of asymptomatic TRANS, mild, severe, and critical cases is described. 50.7% patients were male TRANS and 49.3% were female TRANS; 1.5% patients were asymptomatic TRANS cases, 63.8% patients were mild cases, and 36.2% patients were severe or critical cases. 4.3% patients have been discharged; 1.5% patient had died; 1.5% patient had recovery. Among the 25 patients with severe or critical disease MESHD, 12.0% patients were underwent non-invasive mechanical ventilation, 8.0% patients underwent invasive mechanical ventilation, and 4.0% patients died.

    Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay

    Authors: James P Broughton; Xianding Deng; Guixia Yu; Clare L Fasching; Jasmeet Singh; Jessica Streithorst; Andrea Granados; Alicia Sotomayor-Gonzalez; Kelsey Zorn; Allan Gopez; Elaine Hsu; Wei Gu; Steven Miller; Chao-Yang Pan; Hugo Guevara; Debra Wadford; Janice Chen; Charles Y Chiu

    doi:10.1101/2020.03.06.20032334 Date: 2020-03-10

    An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease MESHD associated with infection MESHD has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (~30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance SERO to the US CDC SARS-CoV-2 real-time RT-PCR assay.

    Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak

    Authors: Yuan Liu; Zhi Ning; Yu Chen; Ming Guo; Yingle Liu; Nirmal Kumar Gali; Li Sun; Yusen Duan; Jing Cai; Dane Westerdahl; Xinjin Liu; Kin-fai Ho; Haidong Kan; Qingyan Fu; Ke Lan

    doi:10.1101/2020.03.08.982637 Date: 2020-03-10

    BackgroundThe ongoing outbreak of COVID-19 has spread rapidly and sparked global concern. While the transmission TRANS of SARS-CoV-2 through human respiratory droplets and contact with infected persons is clear, the aerosol transmission TRANS of SARS-CoV-2 has been little studied. MethodsThirty-five aerosol samples of three different types (total suspended particle, size segregated and deposition aerosol) were collected in Patient Areas (PAA) and Medical Staff Areas (MSA) of Renmin Hospital of Wuhan University (Renmin) and Wuchang Fangcang Field Hospital (Fangcang), and Public Areas (PUA) in Wuhan, China during COVID-19 outbreak. A robust droplet digital polymerase chain reaction (ddPCR) method was employed to quantitate the viral SARS-CoV-2 RNA genome and determine aerosol RNA concentration. ResultsThe ICU, CCU and general patient rooms inside Renmin, patient hall inside Fangcang had undetectable or low airborne SARS-CoV-2 concentration but deposition samples inside ICU and air sample in Fangcang patient toilet tested positive. The airborne SARS-CoV-2 in Fangcang MSA had bimodal distribution with higher concentration than those in Renmin during the outbreak but turned negative after patients number reduced and rigorous sanitization implemented. PUA had undetectable airborne SARS-CoV-2 concentration but obviously increased with accumulating crowd flow. ConclusionsRoom ventilation, open space, proper use and disinfection of toilet can effectively limit aerosol transmission TRANS of SARS-CoV-2. Gathering of crowds with asymptomatic TRANS carriers TRANS is a potential source of airborne SARS-CoV-2. The virus aerosol deposition on protective apparel or floor surface and their subsequent resuspension is a potential transmission TRANS pathway and effective sanitization is critical in minimizing aerosol transmission TRANS of SARS-CoV-2.

    Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1

    Authors: Neeltje van Doremalen; Trenton Bushmaker; Dylan Morris; Myndi Holbrook; Amandine Gamble; Brandi Williamson; Azaibi Tamin; Jennifer Harcourt; Natalie Thornburg; Susan Gerber; Jamie Lloyd-Smith; Emmie de Wit; Vincent Munster

    doi:10.1101/2020.03.09.20033217 Date: 2020-03-10

    A novel human coronavirus, now named severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2, referred to as HCoV-19 here) that emerged in Wuhan, China in late 2019 is now causing a pandemic. Here, we analyze the aerosol and surface stability of HCoV-19 and compare it with SARS-CoV-1, the most closely related human coronavirus.2 We evaluated the stability of HCoV-19 and SARS-CoV-1 in aerosols and on different surfaces and estimated their decay rates using a Bayesian regression model

    The epidemiological characteristics of 2019 novel coronavirus diseases MESHD (COVID-19) in Jingmen,Hubei,China

    Authors: Qijun Gao; yingfu hu; zhiguo dai Sr.; Jing wu; Feng Xiao; Jing wang

    doi:10.1101/2020.03.07.20031393 Date: 2020-03-10

    Abstract Background:There is currently a global outbreak of coronavirus disease MESHD 2019 (COVID-19),and its epidemic characteristics in the areas where the outbreak has been successfully controlled are rarely reported. Objective: Describe the epidemic characteristics of COVID-19 in Jingmen,Hubei,introduce the local prevention and control experience,and observe the impact of various prevention and control measures on the number of new cases. Methods: All the COVID-19 patients diagnosed in the municipal districts of Jingmen from January 12 to February 29,2020 were enrolled in this study. We described epidemiological data and observed the impact of control measures on the epidemic. Findings: Of the 219 cases (110 men and 109 women), 88 (40%) had exposure to Wuhan. The median age TRANS was 48 years ( range,2-88 years;IQR,35-60). Thirty-three severe patients with a median age TRANS of 66 years(range,33-82 years,IQR,57-76) were treated in intensive care units; out of these patients, 66.7 %(22) were men and 19 (57.5%) had chronic diseases MESHD, including hypertension MESHD hypertension HP, diabetes, heart failure MESHD, stroke MESHD stroke HP, and renal insufficiency MESHD renal insufficiency HP. Under the control measures, the number of new patients gradually decreased and nearly disappeared after 18 days. Wearing masks in all kinds of situations prevents most infections MESHD and is one of the most effective prevention and control measures. Interpretation: In conclusion,all people are susceptible to COVID-19, and older males TRANS and those with comorbid conditions are more likely to become severe cases. Even though COVID-19 is highly contagious,control measures have proven to be very effective, particularly wearing masks,which could prevent most infections MESHD.

    Prognostic value of NT-proBNP in patients with severe COVID-19

    Authors: Lei Gao; Dan Jiang; Xuesong Wen; Xiaocheng Cheng; Min Sun; Bin He; Lin-na You; Peng Lei; Xiao-wei Tan; Shu Qin; Guoqiang Cai; Dongying Zhang

    doi:10.1101/2020.03.07.20031575 Date: 2020-03-10

    The outbreak of coronavirus disease MESHD 2019 (COVID-19) caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) in China has been declared a public health emergency MESHD of international concern. The cardiac injury was dominate in the process. However, whether N terminal pro B type natriuretic peptide (NT-proBNP) predicted outcome of COVID-19 patients was unknown. The study initially enrolled 102 patients with severe COVID-19 pneumonia MESHD pneumonia HP from a continuous sample. After screening out the ineligible cases, 54 patients were analyzed in this study. Results found that patients with higher NT-proBNP (above 88.64 pg/mL) level had more risks of in-hospital death MESHD. After adjusting for potential cofounders in separate modes, NT-proBNP presented as an independent risk factor of in-hospital death MESHD in patients with severe COVID-19.

    Prevalence SERO and Risk Factors of Acute Posttraumatic Stress Symptoms during the COVID-19 Outbreak in Wuhan, China

    Authors: Luna Sun; Zhuoer Sun; Lili Wu; Zhenwen Zhu; Fan Zhang; Zhilei Shang; Yanpu Jia; Jingwen Gu; Yaoguang Zhou; Yan Wang; Nianqi Liu; Weizhi Liu

    doi:10.1101/2020.03.06.20032425 Date: 2020-03-10

    Background A novel coronavirus (SARA-CoV-2) emerged in Wuhan, China, in December 2019. Within a few weeks, the disease MESHD caused by SARA-CoV-2, which is named COVID-19, has escalated into an unprecedented ongoing outbreak with frightening speed, becoming a global health emergency MESHD. This study aimed to exam the prevalence SERO and risk factors of acute posttraumatic stress symptoms (PTSS) in Chinese people shortly after the massive outbreak of COVID-19. Method An online anonymous questionnaire survey was conducted in mainland China between 30 January and 3 February, 2020. The survey consisted of two self-administered questionnaires: one was designed to require personal information ( gender TRANS, age TRANS, education background), current location, recent exposure history of Wuhan, the classification of population, and subjective sleep quality; the other was the PTSD Checklist for DSM-5 (PCL-5), which was to assess PTSS referring to the outbreak. Results A total of 2091 Chinese participated in the current study. The prevalence SERO of PTSS among the public in mainland China 1 month after the COVID-19 outbreak was 4.6%. Multiple linear regression analysis revealed that gender TRANS (p < 0.001), exposure history of Wuhan (p = 0.047), classification of population (p < 0.001), and subjective sleep quality (p < 0.001) could be regarded as predictor factors for PTSS. Conclusions The results showed that some Chinese showed acute PTSS during the COVID-19 outbreak. Therefore, comprehensive psychological intervention needs further implementation. Furthermore, females TRANS, people who having recent exposure history of Wuhan, those at high risk of infection TRANS risk of infection TRANS infection MESHD or with poor sleep quality deserve special attention.

    Clinical Characteristics of Two Human to Human Transmitted Coronaviruses: Corona Virus Disease MESHD 2019 versus Middle East Respiratory Syndrome MESHD Coronavirus.

    Authors: Ping Xu; Guo-Dong Sun; Zhi-Zhong Li

    doi:10.1101/2020.03.08.20032821 Date: 2020-03-10

    After the outbreak of the middle east respiratory syndrome MESHD (MERS) worldwide in 2012. Currently, a novel human coronavirus has caused a major disease MESHD outbreak, and named corona virus disease MESHD 2019 (COVID-19). The emergency MESHD of MRES-COV and COVID-19 has caused global panic and threatened health security. Unfortunately, the similarities and differences between the two coronavirus diseases MESHD remain to be unknown. The aim of this study, therefore, is to perform a systematic review to compare epidemiological, clinical and laboratory features of COVID-19 and MERS-COV population. We searched PubMed, EMBASE and Cochrane Register of Controlled Trials database to identify potential studies reported COVID-19 or MERS-COV. Epidemiological, clinical and laboratory outcomes, the admission rate of intensive cure unit (ICU), discharge rate and fatality rate were evaluated using GraphPad Prism software. Thirty-two studies involving 3770 patients (COVID-19 = 1062, MERS-COV = 2708) were included in this study. The present study revealed that compared with COVID-19 population, MERS-COV population had a higher rate of ICU admission, discharge and fatality and longer incubation time. It pointed out that fever MESHD fever HP, cough MESHD cough HP and generalised weakness and myalgia MESHD myalgia HP were main clinical manifestations of both COVID-19 and MERS-COV, whereas ARDS was main complication. The most effective drug for MERS-COV is ribavirin and interferon.

    In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19

    Authors: Ben Orsburn; Conor Jenkins; Sierra D Miller; Benjamin A Neely; Namandje M Bumpus

    doi:10.1101/2020.03.08.980383 Date: 2020-03-10

    We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity and false positives we remove peptides from consideration that have sequence homology or similar chemical characteristics using a progressively larger database of background peptides. Using this pipeline, we can remove 47 peptides from consideration as diagnostic due to the presence of peptides derived from the human proteome. To address the complexity of the human microbiome, we describe a method to create a database of all proteins of relevant abundance in the saliva microbiome. By utilizing a protein-based approach to the microbiome we can more accurately identify peptides that will be problematic in COVID-19 studies which removes 12 peptides from consideration. To identify diagnostic peptides, another 7 peptides are flagged for removal following comparison to the proteome backgrounds of viral and bacterial pathogens of similar clinical presentation. By aligning the protein sequences of SARS-CoV-2 field isolates deposited to date we can identify peptides for removal due to their presence in highly variable regions that may lead to false negatives as the pathogen evolves. We provide maps of these regions and highlight 3 peptides that should be avoided as potential diagnostic or vaccine targets. Finally, we leverage publicly deposited proteomics data from human cells infected with SARS-CoV-2, as well as a second study with the closely related MERS-CoV to identify the two proteins of highest abundance in human infections MESHD. The resulting final list contains the 24 peptides most unique and diagnostic of SARS-CoV-2 infections MESHD. These peptides represent the best targets for the development of antibodies SERO are clinical diagnostics. To demonstrate one application of this we model peptide fragmentation using a deep learning tool to rapidly generate targeted LCMS assays and data processing method for detecting CoVID-19 infected patient samples. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC="FIGDIR/small/980383v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1d7fd4borg.highwire.dtl.DTLVardef@136563borg.highwire.dtl.DTLVardef@57641dorg.highwire.dtl.DTLVardef@16de9a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

    A deterministic epidemic model for the emergence of COVID-19 in China

    Authors: Meng Wang; Jingtao Qi

    doi:10.1101/2020.03.08.20032854 Date: 2020-03-10

    Coronavirus disease MESHD (COVID-19) broke out in Wuhan, Hubei province,China, in December 2019 and soon after Chinese health authorities tookunprecedented prevention and control measures to curb the spreading ofthe novel coronavirus-related pneumonia MESHD pneumonia HP. We develop a mathematicalmodel based on daily updates of reported cases to study the evolutionof the epidemic. With the model, on 95% confidence level, we estimatethe basic reproduction number TRANS, R0 TRANS = 2.82 {+/-} 0.11, time between March19 and March 21 when the effective reproduction number TRANS becoming lessthan one, the epidemic ending after April 2 and the total number ofconfirmed cases approaching 14408 {+/-} 429 on the Chinese mainlandexcluding Hubei province.

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MeSH Disease
Human Phenotype

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