Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (1267)

Fever (752)

Cough (610)

Hypertension (432)

Anxiety (411)


Transmission

age categories (3362)

Transmission (3037)

gender (1549)

fomite (1281)

contact tracing (1116)


Seroprevalence
    displaying 15841 - 15850 records in total 16034
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    Evaluating new evidence in the early dynamics of the novel coronavirus COVID-19 outbreak in Wuhan, China with real time domestic traffic and potential asymptomatic TRANS transmissions TRANS

    Authors: Can Zhou

    doi:10.1101/2020.02.15.20023440 Date: 2020-02-18 Source: medRxiv

    The novel coronavirus (COVID-19), first detected in Wuhan, China in December 2019, has spread to 28 countries/regions with over 43,000 confirmed cases TRANS. Much about this outbreak is still unknown. At this early stage of the epidemic, it is important to investigate alternative sources of information to understand its dynamics and spread. With updated real time domestic traffic, this study aims to integrate recent evidence of international evacuees extracted from Wuhan between Jan. 29 and Feb. 2, 2020 to infer the dynamics of the COVD-19 outbreak in Wuhan. In addition, a modified SEIR model was used to evaluate the empirical support for the presence of asymptomatic TRANS transmissions TRANS. Based on the data examined, this study found little evidence for the presence of asymptomatic TRANS transmissions TRANS. However, it is still too early to rule out its presence conclusively due to sample size and other limitations. The updated basic reproductive number TRANS was found to be 2.12 on average with a 95% credible interval of [2.04, 2.18]. It is smaller than previous estimates probably because the new estimate factors in the social and non-pharmaceutical mitigation implemented in Wuhan through the evacuee dataset. Detailed predictions of infected individuals exported both domestically and internationally were produced. The estimated case confirmation rate has been low but has increased steadily to 23.37% on average. The findings of this study depend on the validity of the underlying assumptions, and continuing work is needed, especially in monitoring the current infection status of Wuhan residents.

    Structure of dimeric full-length human ACE2 in complex with B0AT1

    Authors: Qiang Zhou; Renhong Yan; Yuanyuan Zhang; Yaning Li; Lu Xia

    doi:10.1101/2020.02.17.951848 Date: 2020-02-18 Source: bioRxiv

    Angiotensin-converting enzyme 2 (ACE2) is the surface receptor for SARS coronavirus ( SARS-CoV MESHD), directly interacting with the spike glycoprotein (S protein). ACE2 is also suggested to be the receptor for the new coronavirus (2019-nCoV), which is causing a serious epidemic in China manifested with severe respiratory syndrome MESHD. B0AT1 (SLC6A19) is a neutral amino acid transporter whose surface expression in intestinal cells requires ACE2. Here we present the 2.9 [A] resolution cryo-EM structure of full-length human ACE2 in complex with B0AT1. The complex, assembled as a dimer of ACE2-B0AT1 heterodimers, exhibits open and closed conformations due to the shifts of the peptidase domains (PDs) of ACE2. A newly resolved Collectrin-like domain (CLD) on ACE2 mediates homo-dimerization. Structural modelling suggests that the ACE2-B0AT1 complex can bind two S proteins simultaneously, providing important clues to the molecular basis for coronavirus recognition and infection MESHD.

    Can Search Query Forecast successfully in China's 2019-nCov pneumonia HP pneumonia MESHD?

    Authors: Li Xiaoxuan; Wu Qi; Lv Benfu

    doi:10.1101/2020.02.12.20022400 Date: 2020-02-18 Source: medRxiv

    Recently the novel coronavirus (2019-nCov) pneumonia HP pneumonia MESHD outbreak in China then the world, and the Number of infections MESHD and death MESHD continues to increases. Search Query performs well in forecasting the epidemics. It is still a question whether search engine data can forecast the drift and the inflexion in 2019-nCov pneumonia HP pneumonia MESHD. Based on the Baidu Search Index, we propose three prediction models: composite Index, composite Index with filtering and suspected NCP(Novel Coronavirus Pneumonia HP). The result demonstrates that the predictive model of composite index with filtering performs the best while the model of suspected NCP has the highest forecast error. We further predict the out-of-the-set NCP confirmed cases TRANS and monitor that the next peak of new diagnoses will occur on February 16th and 17th.

    Two-week global trends on 2019-nCoV fatality and virulence rates: a cross-sectional study

    Authors: Jorge Arroz

    doi:10.21203/rs.2.23981/v1 Date: 2020-02-18 Source: ResearchSquare

    BackgroundThe recent Public Health Emergency of International Concern, caused by a novel coronavirus (2019-nCoV) is fast spreading, and contribution for the increase of knowledge about this outbreak is desired. The aim of this study is to analyse the global trend of 2019-nCoV fatality and virulence rates from 24 January to 06 February 2020.MethodsA cross-sectional study was carried out. Data from 2019-nCoV, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome coronavirus MESHD (MERS CoV) were obtained from World Health Organization. Only confirmed cases TRANS and deaths directly attributed to these viruses were considered. For 2019-nCoV, severe illness was also considered. Two endpoints of interest were analysed: trends in fatality rate (death among confirmed cases TRANS x 100) and virulence rate (severe illness MESHD among confirmed cases TRANS x 100).ResultsThe 2019-nCoV fatality and virulence rate decreased 1.0 and 7.3 percent points during the analysed time-frame, respectively. The SARS-CoV and MERS-CoV fatality MESHD rate are five and 17 times higher than the current 2019-nCoV fatality rate. The current cumulative 2019-nCoV confirmed cases TRANS exceeded 3.5 and 11.3 times the SARS-CoV MESHD and MERS-CoV confirmed cases TRANS, respectivelly.ConclusionsA reduction in fatality and virulence rate associated with the novel coronavirus was observed in the analyzed time-frame. The novel coronavirus is spreading at higher rates than SARS-CoV MESHD and MERS-CoV, although with comparative lower fatality rates. Continuous surveillance using additional indicators such as virulence rate (in addition to the fatality rate) may contribute to broaden and deepen the knowledge about the novel coronavirus.

    Assessing the impact of reduced travel TRANS on exportation dynamics of novel coronavirus infection MESHD (COVID-19)

    Authors: Asami Anzai; Tetsuro Kobayashi; Natalie M. Linton; Ryo Kinoshita; Katsuma Hayashi; Ayako Suzuki; Yichi Yang; Sungmok Jung; Takeshi Miyama; Andrei R. Akhmetzhanov; Hiroshi Nishiura

    doi:10.1101/2020.02.14.20022897 Date: 2020-02-17 Source: medRxiv

    The impact of the drastic reduction in travel TRANS volume within mainland China in January and February 2020 was quantified with respect to reports of novel coronavirus (COVID-19) infections outside China. Data on confirmed cases TRANS diagnosed outside China were analyzed using statistical models to estimate the impact of travel TRANS reduction on three epidemiological outcome measures: (i) the number of exported cases, (ii) the probability of a major epidemic, and (iii) the time delay to a major epidemic. From 28 January to 7 February 2020, we estimated that 226 exported cases (95% confidence interval: 86, 449) were prevented, corresponding to a 70.4% reduction in incidence compared to the counterfactual scenario. The reduced probability of a major epidemic ranged from 7% to 20% in Japan, which resulted in a median time delay to a major epidemic of two days. Depending on the scenario, the estimated delay may be less than one day. As the delay is small, the decision to control travel TRANS volume through restrictions on freedom of movement should be balanced between the resulting estimated epidemiological impact and predicted economic fallout.

    Impact of seasonal forcing on a potential SARS-CoV-2 pandemic

    Authors: Richard A Neher; Robert Dyrdak; Valentin Druelle; Emma B Hodcroft; Jan Albert

    doi:10.1101/2020.02.13.20022806 Date: 2020-02-17 Source: medRxiv

    A novel coronavirus (SARS-CoV-2) first detected in Wuhan, China, has spread rapidly since December 2019, causing more than 80,000 confirmed infections TRANS infections MESHD and 2,700 fatalities (as of Feb 27, 2020). Imported cases and transmission TRANS clusters of various sizes have been reported globally suggesting a pandemic is likely. Here, we explore how seasonal variation in transmissibility TRANS could modulate a SARS-CoV-2 pandemic. Data from routine diagnostics show a strong and consistent seasonal variation of the four endemic coronaviruses (229E, HKU1, NL63, OC43) and we parameterize our model for SARS-CoV-2 using these data. The model allows for many subpopulations of different size with variable parameters. Simulations of different scenarios show that plausible parameters result in a small peak in early 2020 in temperate regions of the Northern Hemisphere and a larger peak in winter 2020/2021. Variation in transmission TRANS and migration rates can result in substantial variation in prevalence SERO between regions. While the uncertainty in parameters is large, the scenarios we explore show that transient reductions in the incidence rate might be due to a combination of seasonal variation and infection MESHD control efforts but do not necessarily mean the epidemic is contained. Seasonal forcing on SARS-CoV-2 should thus be taken into account in the further monitoring of the global transmission TRANS. The likely aggregated effect of seasonal variation, infection control measures and transmission TRANS rate variation is a prolonged pandemic wave with lower prevalence SERO at any given time, thereby providing a window of opportunity for better preparation of health care systems.

    Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like Protease (3CLpro) Structure: Virtual Screening Reveals Velpatasvir, Ledipasvir, and Other Drug Repurposing Candidates

    Authors: Yu Wai Chen; Chin-Pang Yiu; Kwok-Yin Wong

    doi:10.26434/chemrxiv.11831103.v2 Date: 2020-02-17 Source: ChemRxiv

    We prepared the three-dimensional model of the 2019-nCoV 3C-like protease (3CLpro) using the crystal structure of the highly-similar (96% identity) ortholog from the SARS-CoV MESHD. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are in the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV MESHD enzyme can be conferred on its 2019-nCoV counterpart. With the 3CLpro molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the 2019-nCoV with minimal side effects, commonly fatigue HP fatigue MESHD and headache HP headache MESHD. The drugs Epclusa (velpatasvir / sofosbuvir) and Harvoni (ledipasvir / sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.

    Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (COVID-19)

    Authors: Ruiyun Li; Sen Pei; Bin Chen; Yimeng Song; Tao Zhang; Wan Yang; Jeffrey Shaman

    doi:10.1101/2020.02.14.20023127 Date: 2020-02-17 Source: medRxiv

    Background Estimation of the fraction and contagiousness of undocumented novel coronavirus (COVID-19) infections is critical for understanding the overall prevalence SERO and pandemic potential of this disease. Many mild infections MESHD are typically not reported and, depending on their contagiousness, may support stealth transmission TRANS and the spread of documented infection MESHD. Methods Here we use observations of reported infection MESHD and spread within China in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with the emerging coronavirus, including the fraction of undocumented infections and their contagiousness. Results We estimate 86% of all infections MESHD were undocumented (95% CI: [82%-90%]) prior to the Wuhan travel TRANS shutdown (January 23, 2020). Per person, these undocumented infections MESHD were 52% as contagious as documented infections ([44%-69%]) and were the source of infection for two-thirds of documented cases. Our estimate of the reproductive number TRANS (2.23; [1.77-3.00]) aligns with earlier findings; however, after travel TRANS restrictions and control measures were imposed this number falls HP considerably. Conclusions A majority of COVID-19 infections were undocumented prior to implementation of control measures on January 23, and these undocumented infections substantially contributed to virus transmission TRANS. These findings explain the rapid geographic spread of COVID-19 and indicate containment of this virus will be particularly challenging. Our findings also indicate that heightened awareness of the outbreak, increased use of personal protective measures, and travel TRANS restriction have been associated with reductions of the overall force of infection MESHD; however, it is unclear whether this reduction will be sufficient to stem the virus spread.

    Optimizing diagnostic strategy for novel coronavirus pneumonia MESHD pneumonia HP, a multi-center study in Eastern China

    Authors: Jing-Wen Ai; Hao-Cheng Zhang; Teng Xu; Jing Wu; Mengqi Zhu; Yi-Qi Yu; Han-Yue Zhang; Zhongliang Shen; Yang Li; Xian Zhou; Guo-Qing Zang; Jie Xu; Wen-Jing Chen; Yong-Jun Li; De-Sheng Xie; Ming-Zhe Zhou; Jing-Ying Sun; Jia-Zhen Chen; Wen-Hong Zhang

    doi:10.1101/2020.02.13.20022673 Date: 2020-02-17 Source: medRxiv

    COVID-19 caused by a novel coronavirus SARS-CoV-2 emerged in Wuhan, Hubei province since December 2019, and caused a rapid outbreak throughout China and globally. Cities outside Hubei are also facing great challenge and require implementing of effective and feasible strategy in precision diagnosing novel coronavirus pneumonia MESHD pneumonia HP (NCP). We described a multicenter prospective study on diagnostic strategy of suspected NCP patients from January 22nd to February 9th, 2020 in Eastern China cities. Nasopharyngeal swabs were collected from the patients. The epidemiological characteristics, clinical symptoms, laboratory assessments, and computed tomographic (CT) scans were obtained. Pathogen screen were performed including RT-PCR, multiplex PCR, rapid flu antigen tests and mNGS. We enrolled 53 suspected NCP patients, among whom 20 were laboratory-confirmed. Fourteen (70%) and 3 (15%) patients were positive for the first and second SARS-CoV-2 RT-PCR test, respectively. All NCP patients were positive for mNGS. Chest CT images and the symptoms of early stage NCP patients were similar to other viral pneumonia MESHD pneumonia HP patients. We identified 11 of 20 co-infections MESHD in NCP cases, including regular respiratory virus, fungi and bacteria synchronously. Genomic analysis showed that 8 of 10 cases had no mutation in virus genome, while 2 cases had only one single mutation in N gene. Our study discovered that a combination of chest CT, SARS-CoV-2 RT-PCR and multi-plex PCR is recommended in regions outside Hubei province. Co-infection MESHD of other pathogens with SARS-CoV-2 exists and should be acknowledged. Repeated sampling, change of specimen type or metagenomics sequencing could further facilitate during critical clinical cases.

    A simple laboratory parameter facilitates early identification of COVID-19 patients

    Authors: Qilin Li; Xiuli Ding; Geqing Xia; Zhi Geng; Fenghua Chen; Lin Wang; Zheng Wang

    doi:10.1101/2020.02.13.20022830 Date: 2020-02-17 Source: medRxiv

    The total number of COVID-19 patients since the outbreak of this infection in Wuhan, China has reached 40000 and are still growing. To facilitate triage or identification of the large number of COVID-19 patients from other patients with similar symptoms in designated fever HP clinics, we set to identify a practical marker that could be conveniently utilized by first-line health-care workers in clinics. To do so, we performed a case-control study by analyzing clinical and laboratory findings between PCR-confirmed SARS-CoV-2 positive patients (n=52) and SARS-CoV-2 negative patients (n=53). The patients in two cohorts all had similar symptoms, mainly fever HP fever MESHD and respiratory symptoms. The rates of patients with leukocyte counts (normal or decreased number) or lymphopenia HP lymphopenia MESHD (two parameters suggested by current National and WHO COVID-19 guidelines) had no differences between these two cohorts, while the rate of eosinopenia (decreased number of eosinophils) in SARS-CoV-2 positive patients (79%) was much higher than that in SARS-CoV-2 negative patients (36%). When the symptoms were combined with eosinopenia, this combination led to a diagnosis sensitivity SERO and specificity of 79% and 64%, respectively, much higher than 48% and 53% when symptoms were combined with leukocyte counts (normal or decreased number) and/ or lymphopenia HP lymphopenia MESHD. Thus, our analysis reveals that eosinopenia may be a potentially more reliable laboratory predictor for SARS-CoV-2 infection MESHD than leukocyte counts and lymphopenia HP lymphopenia MESHD recommended by the current guidelines.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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