Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1492)

ProteinN (428)

NSP5 (315)

ComplexRdRp (187)

ProteinE (102)


SARS-CoV-2 Proteins
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    Estimating the daily trend in the size of COVID-19 MESHD infected population in Wuhan

    Authors: Qiushi Lin; Taojun Hu; Xiao-Hua Zhou

    doi:10.1101/2020.02.12.20022277 Date: 2020-02-13 Source: medRxiv

    There has been an outbreak of coronavirus disease MESHD ( COVID-19 MESHD) in Wuhan city, Hubei province, China since December 2019. Cases have been exported to other parts of China and more than 20 countries. We provide estimates of the daily trend in the size of the epidemic in Wuhan based on detailed information of 10,940 confirmed cases outside Hubei province.

    Multivariate time series approximation by multiple trajectories of a dynamical system. Applications to Internet traffic and COVID-19 MESHD data

    Authors: Victoria Rayskin

    id:2002.05326v2 Date: 2020-02-13 Source: arXiv

    Utilization of multiple trajectories of a dynamical system model provides us with several benefits in approximation of time series. For short term predictions a high accuracy can be achieved via switches to new trajectory at any time. Different long term trends (tendency to different stationary points) of the phase portrait characterize various scenarios of the process realization influenced by externalities. The dynamical system's phase portrait analysis helps to see if the equations properly describe the reality. We also extend the dynamical systems approach (discussed in \cite{R5}) to the dynamical systems with external control. We illustrate these ideas with the help of new examples of the rental properties platform data. We also compare the qualitative properties of and platforms' phase portraits and the corresponding differences of the two platforms' users. In our last example with COVID-19 MESHD data we discuss the high accuracy of the short term prediction of confirmed infection cases, recovery cases and death MESHD cases in various countries.

    ACE2 HGNC Expression in Kidney and Testis May Cause Kidney and Testis Damage After 2019-nCoV Infection MESHD

    Authors: Caibin Fan; Kai Li; Yanhong Ding; Wei Lu Lu; Jianqing Wang

    doi:10.1101/2020.02.12.20022418 Date: 2020-02-13 Source: medRxiv

    In December 2019 and January 2020, novel coronavirus (2019-nCoV) - infected pneumonia MESHD (NCIP) occurred in Wuhan, and has already posed a serious threat to public health. ACE2 HGNC ( Angiotensin Converting Enzyme 2 HGNC) has been shown to be one of the major receptors that mediate the entry of 2019-nCoV into human cells, which also happens in severe acute respiratory syndrome coronavirus MESHD (SARS). Several researches have indicated that some patients have abnormal renal function MESHD or even kidney damage MESHD in addition to injury in respiratory system, and the related mechanism is unknown. This arouses our interest in whether coronavirus infection MESHD will affect the urinary and male reproductive systems. Here in this study, we used the online datasets to analyze ACE2 HGNC expression in different human organs. The results indicate that ACE2 HGNC highly expresses in renal tubular cells, Leydig cells and cells in seminiferous ducts in testis. Therefore, virus might directly bind to such ACE2 HGNC positive cells and damage the kidney and testicular tissue of patients. Our results indicate that renal function evaluation and special care should be performed in 2019-nCoV patients during clinical work, because of the kidney damage MESHD caused by virus and antiviral drugs with certain renal toxicity MESHD. In addition, due to the potential pathogenicity of the virus to testicular tissues, clinicians should pay attention to the risk of testicular lesions MESHD in patients during hospitalization and later clinical follow-up, especially the assessment and appropriate intervention in young patients' fertility.

    Data-Based Analysis, Modelling and Forecasting of the novel Coronavirus (2019-nCoV) outbreak

    Authors: Cleo Anastassopoulou; Lucia Russo; Athanasios Tsakris; Constantinos Siettos

    doi:10.1101/2020.02.11.20022186 Date: 2020-02-13 Source: medRxiv

    Since the first suspected case of coronavirus disease-2019 ( COVID-19 MESHD) on December 1st, 2019, in Wuhan, Hubei Province, China, a total of 40,235 confirmed cases and 909 deaths have been reported in China up to February 10, 2020, evoking fear locally and internationally. Here, based on the publicly available epidemiological data for Hubei, China from January 11 to February 10, 2020, we provide estimates of the main epidemiological parameters. In particular, we provide an estimation of the case fatality and case recovery ratios, along with their 90% confidence intervals as the outbreak evolves. On the basis of a Susceptible-Infected-Recovered-Dead (SIDR) model, we provide estimations of the basic reproduction number (R0), and the per day infection mortality and recovery rates. By calibrating the parameters of the SIRD model to the reported data, we also attempt to forecast the evolution of the of the outbreak at the epicenter three weeks ahead, i.e. until February 29. As the number of infected individuals, especially of those with asymptomatic or mild courses, is suspected to be much higher than the official numbers, which can be considered only as a subset of the actual numbers of infected MESHD and recovered cases in the total population, we have repeated the calculations under a second scenario that considers twenty times the number of confirmed infected cases and forty times the number of recovered, leaving the number of deaths unchanged. Based on the reported data, the expected value of R0 as computed considering the period from the 11th of January until the 18th of January, using the official counts of confirmed cases was found to be ~4.6, while the one computed under the second scenario was found to be ~3.2. Thus, based on the SIRD simulations, the estimated average value of R0 was found to be ~2.6 based on confirmed cases and ~2 based on the second scenario. Our forecasting flashes a note of caution for the presently unfolding outbreak in China. Based on the official counts for confirmed cases, the simulations suggest that the cumulative number of infected could reach 180,000 (with lower bound of 45,000) by February 29. Regarding the number of deaths, simulations forecast that on the basis of the up to the 10th of February reported data, the death toll might exceed 2,700 (as a lower bound) by February 29. Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected MESHD and recovered cases in the population most likely are much higher than the reported ones. Thus, in a scenario where we have taken twenty times the confirmed number of infected MESHD and forty times the confirmed number of recovered cases, the case fatality ratio is around 0.15% in the total population. Importantly, based on this scenario, simulations suggest a slow down of the outbreak in Hubei at the end of February.

    Clinical diagnosis of 8274 samples with 2019-novel coronavirus in Wuhan

    Authors: Ming Wang; Qing Wu; Wanzhou Xu; Bin Qiao; Jingwei Wang; Hongyun Zheng; Shupeng Jiang; Junchi Mei; Zegang Wu; Yayun Deng; Fangyuan Zhou; Wei Wu; Yan Zhang; Zhihua Lv; Jingtao Huang; Xiaoqian Guo; Lina Feng; Zunen Xia; Di Li; Zhiliang Xu; Tiangang Liu; Pingan Zhang; Yongqing Tong; Yan Li

    doi:10.1101/2020.02.12.20022327 Date: 2020-02-13 Source: medRxiv

    Background: 2019-Novel coronavirus (2019-nCoV) outbreaks create challenges for hospital laboratories because thousands of samples must be evaluated each day. Sample types, interpretation methods, and corresponding laboratory standards must be established. The possibility of other infections should be assessed to provide a basis for clinical classification, isolation, and treatment. Accordingly, in the present study, we evaluated the testing methods for 2019-nCoV and co-infections MESHD. Methods: We used a fluorescence-based quantitative PCR kit urgently distributed by the Chinese CDC to detect 8274 close contacts in the Wuhan region against two loci on the 2019-nCoV genome. We also analyzed 613 patients with fever MESHD who underwent multiple tests for 13 respiratory pathogens; 316 subjects were also tested for 2019-nCoV. Findings: Among the 8274 subjects, 2745 (33.2%) had 2019-nCoV infection MESHD; 5277 (63.8%) subjects showed negative results in the 2019-nCoV nucleic acid test (non-019-nCoV); and 252 cases (3.0%) because only one target was positive, the diagnosis was not definitive. Sixteen patients who originally had only one positive target were re-examined a few days later; 14 patients (87.5%) were finally defined as 2019-nCoV-positive, and 2 (12.5%) were finally defined as negative. The positive rates of nCoV-NP and nCovORF1ab were 34.7% and 34.7%, respectively. nCoV-NP-positive only and nCovORF1ab-positive cases accounted for 1.5% and 1.5%, respectively. In the 316 patients with multiple respiratory pathogens, 104 were positive for 2019-nCov and 6/104 had co-infection MESHD with coronavirus (3/104), influenza A virus (2/104), rhinovirus (2/104), and influenza A H3N2 (1/104); the remaining 212 patients had influenza A virus (11/202), influenza A H3N2 (11/202), rhinovirus (10/202), respiratory syncytial virus MESHD (7/202), influenza B virus (6/202), metapneumovirus (4/202), and coronavirus (2/202). Interpretation: Clinical testing methods for 2019-nCoV require improvement. Importantly, 5.8% of 2019-nCoV infected and 18.4% of non-2019-nCoV-infected patients had other pathogen infections. It is important to treat combined infections and perform rapid screening to avoid cross-contamination of patients. A test that quickly and simultaneously screens as many pathogens as possible is needed.

    Insights from early mathematical models of 2019-nCoV acute respiratory disease ( COVID-19 MESHD) dynamics

    Authors: Jomar F. Rabajante

    id:2002.05296v3 Date: 2020-02-13 Source: arXiv

    In December 2019, a novel coronavirus (SARS-CoV-2) has been identified to cause acute respiratory disease MESHD in humans. An outbreak of this disease has been reported in mainland China with the city of Wuhan as the recognized epicenter. The disease has also been exported to other countries, including the Philippines, but the level of spread is still under control (as of 08 February 2020). To describe and predict the dynamics of the disease, several preliminary mathematical models are formulated by various international study groups. Here, the insights that can be drawn from these models are discussed, especially as inputs for designing strategies to control the epidemics. Proposed model-based strategies on how to prevent the spread of the disease in local setting, such as during large social gatherings, are also presented. The model shows that the exposure time is a significant factor in spreading the disease. With a basic reproduction number equal to 2, and 14-day infectious period, an infected person staying more than 9 hours in the event could infect other people. Assuming the exposure time is 18 hours, the model recommends that attendees of the social gathering should have a protection with more than 70 percent effectiveness.

    Epidemic size of novel coronavirus-infected pneumonia in the Epicenter Wuhan: using data of five-countries' evacuation action

    Authors: Hongxin Zhao; Sailimai Man; Bo Wang; Yi Ning

    doi:10.1101/2020.02.12.20022285 Date: 2020-02-13 Source: medRxiv

    Background: Since late December 2019, novel coronavirus-infected pneumonia MESHD ( NCP PROTEIN) emerged in Wuhan, Hubei province, China. Meanwhile, NCP PROTEIN rapidly spread from China to other countries, and several countries' government rush to evacuate their citizens from Wuhan. We analyzed the infection rate of the evacuees and extrapolated the results in Wuhan's NCP PROTEIN incidence estimation. Methods: We collected the total number and confirmed cases of 2019-nCov infection MESHD in the evacuation of Korea, Japan, Germany, Singapore, and France and estimated the infection rate of the 2019 novel coronavirus (2019-nCov) among people who were evacuated from Wuhan with a meta-analysis. NCP PROTEIN incidence of Wuhan was indirectly estimated based on data of evacuation. Results: From Jan 29 to Feb 2, 2020, 1916 people have been evacuated from Wuhan, among them 17 have been confirmed 2019-nCov infected. The infection rate is estimated to be 1.1% (95% CI 0.4%-3.1%) using one group meta-analysis method with random effect model. We then estimated that almost 110,000 (95% CI: 40,000-310,000) people were infected with 2019-nCov in Wuhan around Feb 2, 2020, assuming the infection risk of evacuees is close to Chinese citizens in Wuhan. Conclusions: At the beginning of the outbreak, incidence of NCP PROTEIN may be vastly underestimated. Our result emphasizes that 2019-nCov has proposed a huge public health threats in Wuhan. We need to respond more rapidly, take large-scale public health interventions and draconian measures to limiting population mobility and control the epidemic.

    Caution on Kidney Dysfunctions of 2019-nCoV Patients

    Authors: - Anti-2019-nCoV Volunteers; Zhen Li; Ming Wu; Jiwei Yao; Jie Guo; Xiang Liao; Siji Song; Jiali Li; Guangjie Duan; Yuanxiu Zhou; Xiaojun Wu; Zhansong Zhou; Taojiao Wang; Ming Hu; Xianxiang Chen; Yu Fu; Chong Lei; Hailong Dong; Chuou Xu; Yahua Hu; Min Han; Yi Zhou; Hongbo Jia; Xiaowei Chen; Junan Yan

    doi:10.1101/2020.02.08.20021212 Date: 2020-02-12 Source: medRxiv

    Summary Background: To date, large amounts of epidemiological and case study data have been available for the Coronavirus Disease 2019 MESHD ( COVID-19 MESHD), which suggested that the mortality was related to not just respiratory complications. Here, we specifically analyzed kidney functions in COVID-19 MESHD patients and their relations to mortality. Methods: In this multi-centered, retrospective, observational study, we included 193 adult patients with laboratory-confirmed COVID-19 MESHD from 2 hospitals in Wuhan, 1 hospital in Huangshi (Hubei province, 83 km from Wuhan) and 1 hospital in Chongqing (754 km from Wuhan). Demographic data, symptoms, laboratory values, comorbidities, treatments, and clinical outcomes were all collected, including data regarding to kidney functions. Data were compared among three groups: non-severe COVID-19 MESHD patients (128), severe COVID-19 MESHD patients (65) and a control group of other pneumonia MESHD (28). For the data from computed tomographic (CT) scans, we also included a control group of healthy subjects (110 cases, without abnormalities in the lung MESHD and without kidney diseases MESHD). The primary outcome was a common presence of kidney dysfunctions MESHD in COVID-19 MESHD patients and the occurrence of acute kidney injury MESHD ( AKI MESHD) in a fraction of COVID-19 MESHD patients. Secondary outcomes included a survival analysis of COVID-19 MESHD patients in conditions of AKI MESHD or comorbid chronic illnesses. Findings: We included 193 COVID-19 MESHD patients (128 non-severe, 65 severe (including 32 non-survivors), between January 6th and February 21th,2020; the final date of follow-up was March 4th, 2020) and 28 patients of other pneumonia MESHD (15 of viral pneumonia MESHD, 13 of mycoplasma pneumonia MESHD) before the COVID-19 MESHD outbreak. On hospital admission, a remarkable fraction of patients had signs of kidney dysfunctions MESHD, including 59% with proteinuria MESHD, 44% with hematuria MESHD, 14% with increased levels of blood urea nitrogen, and 10% with increased levels of serum creatinine, although mild but worse than that in cases with other pneumonia MESHD. While these kidney dysfunctions MESHD might not be readily diagnosed as AKI MESHD at admission, over the progress during hospitalization they could be gradually worsened and diagnosed as AKI MESHD. A univariate Cox regression analysis showed that proteinuria MESHD, hematuria MESHD, and elevated levels of blood urea nitrogen, serum creatinine, uric acid as well as D-dimer were significantly associated with the death of COVID-19 MESHD patients respectively. Importantly, the Cox regression analysis also suggested that COVID-19 MESHD patients that developed AKI MESHD had a ~5.3-times mortality risk of those without AKI MESHD, much higher than that of comorbid chronic illnesses (~1.5 times risk of those without comorbid chronic illnesses). Interpretation: To prevent fatality in such conditions, we suggested a high degree of caution in monitoring the kidney functions of severe COVID-19 MESHD patients regardless of the past disease history. In addition, upon day-by-day monitoring, clinicians should consider any potential interventions to protect kidney functions at the early stage of the disease and renal replacement therapies in severely ill patients, particularly for those with strong inflammatory reactions or a cytokine storm. Funding: None.

    Abnormal respiratory patterns classifier may contribute to large-scale screening of people infected with COVID-19 MESHD in an accurate and unobtrusive manner

    Authors: Yunlu Wang; Menghan Hu; Qingli Li; Xiao-Ping Zhang; Guangtao Zhai; Nan Yao

    id:2002.05534v1 Date: 2020-02-12 Source: arXiv

    Research significance: During the epidemic prevention and control period, our study can be helpful in prognosis, diagnosis and screening for the patients infected with COVID-19 MESHD (the novel coronavirus) based on breathing characteristics. According to the latest clinical research, the respiratory pattern of COVID-19 MESHD is different from the respiratory patterns of flu and the common cold. One significant symptom that occurs in the COVID-19 MESHD is Tachypnea MESHD. People infected MESHD with COVID-19 MESHD have more rapid respiration. Our study can be utilized to distinguish various respiratory patterns and our device can be preliminarily put to practical use. Demo videos of this method working in situations of one subject and two subjects can be downloaded online. Research details: Accurate detection of the unexpected abnormal respiratory pattern of people in a remote and unobtrusive manner has great significance. In this work, we innovatively capitalize on depth camera and deep learning to achieve this goal. The challenges in this task are twofold: the amount of real-world data is not enough for training to get the deep model; and the intra-class variation of different types of respiratory patterns is large and the outer-class variation is small. In this paper, considering the characteristics of actual respiratory signals, a novel and efficient Respiratory Simulation Model (RSM) is first proposed to fill the gap between the large amount of training data and scarce real-world data. Subsequently, we first apply a GRU neural network with bidirectional and attentional mechanisms (BI-AT-GRU) to classify 6 clinically significant respiratory patterns ( Eupnea, Tachypnea, Bradypnea MESHD, Biots, Cheyne-Stokes MESHD and Central-Apnea MESHD). The proposed deep model and the modeling ideas have the great potential to be extended to large scale applications such as public places, sleep scenario, and office environment.

    Traditional Chinese herbal medicine for treating novel coronavirus ( COVID-19 MESHD) pneumonia: protocol for a systematic review and meta-analysis

    Authors: Yuxi Li; Xiaobo Liu; Liuxue Guo; Juan Li; Dongling Zhong; Mike Clarke; Yonggang Zhang; Rongjiang Jin

    doi:10.21203/rs.2.23447/v2 Date: 2020-02-12 Source: ResearchSquare

    Background A new type of coronavirus, novel coronavirus ( COVID-19 MESHD), is causing an increasing number of cases of pneumonia MESHD and was declared a Public Health Emergency of International Concern by the World Health Organization on 30 January 2020. The virus first appeared in Wuhan, China in late December 2019 and traditional Chinese herbal medicine is being used for its treatment. This systematic review and meta-analysis will assess studies of the effects of traditional Chinese herbal medicine in COVID-19 MESHD pneumonia MESHD. Methods We will search electronic databases including PubMed, Embase, the Cochrane Central Register of Controlled Trials (CENTRAL), Chinese Biomedical Literature Database (CBM), China National Knowledge Infrastructure (CNKI), Chinese Science and Technology Periodical Database (VIP) and Wanfang database using keywords related to COVID-19 MESHD and traditional Chinese herbal medicine. Reference lists of relevant trials and reviews will be searched. We will manually search grey literature, such as conference proceedings and academic degree dissertations, and trial registries. Two independent reviewers will screen studies (XL and DZ), extract data (YL and LG) and evaluate risk of bias (YL and DZ). Data analysis will be conducted using Review Manager software (version 5.3.5) and R software (version 3.6.1). Statistical heterogeneity will be assessed using a standard Chi-square test with a significance level of P < 0.10. Biases associated with study size (e.g. publication bias MESHD) will be investigated using funnel plots, the Egger 's test and Begg 's test and Trim and Fill analysis. Discussion This study will provide a high-quality synthesis of the effects of traditional Chinese herbal medicine for COVID-19 MESHD. The use of traditional Chinese herbal medicine for treatment or prevention of these novel viral infections affecting the pneumonia MESHD will be investigated. Systematic review registration PROSPERO registration number: CRD42020168004

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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