Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (720)

ProteinN (158)

NSP5 (76)

ComplexRdRp (47)

ProteinE (44)


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SARS-CoV-2 Proteins
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    Evidence for gastrointestinal infection of SARS-CoV-2

    Authors: Fei Xiao; Meiwen Tang; Xiaobin Zheng; Chunna Li; Jianzhong He; Zhongsi Hong; Siwen Huang; Zhenyi Zhang; Xianqi Lin; Zhaoxiong Fang; Renxu Lai; Shoudeng Chen; Jing Liu; Jin Huang; Jinyu Xia; Zhonghe Li; Guanmin Jiang; Ye Liu; Xiaofeng Li; Hong Shan

    doi:10.1101/2020.02.17.20023721 Date: 2020-02-20 Source: medRxiv

    The new coronavirus (SARS-CoV-2) outbreak originating from Wuhan, China, poses a threat to global health. While it's evident that the virus invades respiratory tract and transmits from human to human through airway, other viral tropisms and transmission routes remain unknown. We tested viral RNA in stool from 73 SARS-CoV-2-infected MESHD hospitalized patients using rRT-PCR. 53.42% of the patients tested positive in stool. 23.29% of the patients remained positive in feces even after the viral RNA decreased to undetectable level in respiratory tract. The viral RNA was also detected in gastrointestinal tissues. Furthermore, gastric, duodenal and rectal epithelia showed positive immunofluorescent staining of viral host receptor ACE2 HGNC and viral nucleocapsid protein PROTEIN in a case of SARS-CoV-2 infection MESHD. Our results provide evidence for gastrointestinal infection of SARS-CoV-2 MESHD, highlighting its potential fecal-oral transmission route.

    Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 MESHD outbreak in China: a population based cross-sectional survey

    Authors: Mengcen Qian; Qianhui Wu; Peng Wu; Zhiyuan Hou; Yuxia Liang; Benjamin J Cowling; Hongjie Yu

    doi:10.1101/2020.02.18.20024448 Date: 2020-02-20 Source: medRxiv

    Objective: To investigate psychological MESHD and behavioral responses to the threat of SARS-CoV-2 infections MESHD and their associations with public perceptions in China Design: Cross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020 Setting: Wuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan) Participants: Random sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18 Main outcome measures: Anxiety MESHD (measured by the 7-item generalized anxiety disorder MESHD [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out). Results: The prevalence rates of moderate or severe anxiety MESHD (score [≥]10 on GAD-7) were 32.7% (n=167) among Wuhan participants and 20.4% (n=102) among Shanghai participants. 78.6% (n=401) of Wuhan participants and 63.9% (n=320) of Shanghai participants had carried out all six precautionary behaviors. For both measures, Wuhan participants were more responsive to the outbreak (p<0.001). Controlling for personal characteristics, logistic regression results suggested that risks of moderate or severe anxiety MESHD were positively associated with perceived susceptibility (odds ratio 1.6, 95% confidence interval 1.3-1.8) and severity of the disease (1.6, 1.4-1.9) and confusion MESHD about information reliability (1.6, 1.5-1.9). Having confidence in taking measures to protect oneself against the disease was associated with a lower risk (0.6, 0.5-0.7). The strongest predictor of behavioral change was perceived severity (1.2, 1.1-1.4), followed by confusion MESHD about information reliability (1.1, 1.0-1.3). Conclusions: Psychological and behavioral responses to COVID-19 MESHD have been dramatic during the rising phase of the outbreak. Our results support efforts for timely dissemination of accurate and reliable information to address the high anxiety MESHD level.

    Structural basis for the recognition of the 2019-nCoV by human ACE2

    Authors: Renhong Yan; Yuanyuan Zhang; Yingying Guo; Lu Xia; Qiang Zhou

    doi:10.1101/2020.02.19.956946 Date: 2020-02-20 Source: bioRxiv

    Angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) has been suggested to be the cellular receptor for the new coronavirus (2019-nCoV) that is causing the coronavirus disease 2019 MESHD ( COVID-19 MESHD). Like other coronaviruses such as the SARS-CoV, the 2019-nCoV uses the receptor binding domain (RBD) of the surface spike glycoprotein PROTEIN ( S protein PROTEIN S protein HGNC) to engage ACE2 HGNC. We most recently determined the structure of the full-length human ACE2 HGNC in complex with a neutral amino acid transporter B0AT1 HGNC. Here we report the cryo-EM structure of the full-length human ACE2 HGNC bound to the RBD of the 2019-nCoV at an overall resolution of 2.9 [A] in the presence of B0AT1 HGNC. The local resolution at the ACE2 HGNC-RBD interface is 3.5 [A], allowing analysis of the detailed interactions between the RBD and the receptor. Similar to that for the SARS-CoV MESHD, the RBD of the 2019-nCoV is recognized by the extracellular peptidase domain (PD) of ACE2 HGNC mainly through polar residues. Pairwise comparison reveals a number of variations that may determine the different affinities between ACE2 HGNC and the RBDs from these two related viruses.

    Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins

    Authors: Kangpeng Xiao Sr.; Junqiong Zhai; Yaoyu Feng; Niu Zhou; Xu Zhang; Jie-Jian Zou; Na Li; Yaqiong Guo; Xiaobing Li; Xuejuan Shen; Zhipeng Zhang; Fanfan Shu; Wanyi Huang; Yu Li; Ziding Zhang; Rui-Ai Chen; Ya-Jiang Wu; Shi-Ming Peng; Mian Huang; Wei-Jun Xie; Qin-Hui Cai; Fang-Hui Hou; Yahong Liu; Wu Chen; Lihua Xiao; Yongyi Shen

    doi:10.1101/2020.02.17.951335 Date: 2020-02-20 Source: bioRxiv

    The outbreak of 2019-nCoV in the central Chinese city of Wuhan at the end of 2019 poses unprecedent public health challenges to both China and the rest world1. The new coronavirus shares high sequence identity to SARS-CoV MESHD and a newly identified bat coronavirus2. While bats may be the reservoir host for various coronaviruses, whether 2019-nCoV has other hosts is still ambiguous. In this study, one coronavirus isolated from Malayan pangolins showed 100%, 98.2%, 96.7% and 90.4% amino acid identity with 2019-nCoV in the E, M, N and S genes, respectively. In particular, the receptor-binding domain of the S protein PROTEIN of the Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference. Comparison of available genomes suggests 2019-nCoV might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. Infected pangolins showed clinical signs and histopathological changes, and the circulating antibodies reacted with the S protein PROTEIN of 2019-nCoV. The isolation of a coronavirus that is highly related to 2019-nCoV in the pangolins suggests that these animals have the potential to act as the intermediate host of 2019-nCoV. The newly identified coronavirus in the most-trafficked mammal could represent a continuous threat to public health if wildlife trade is not effectively controlled.

    Estimating the case fatality ratio of the COVID-19 MESHD epidemic in China

    Authors: Xing Wang; Zihui Ma; Yi Ning; Chen Chen; Rujin Chen; Qiwen Chen; Heng Zhang; Chunming Li; Yan He; Tao Wang; Cheng Tong; Junqing Wu; Yuyan Li; Handong Ma; Shaodian Zhang; Hongxin Zhao

    doi:10.1101/2020.02.17.20023630 Date: 2020-02-20 Source: medRxiv

    Background: Corona Virus Disease MESHD 2019 ( COVID-19 MESHD) due to severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) emerged in Wuhan city and rapidly spread throughout China since late December 2019. Crude case fatality ratio (CFR) with dividing the number of known deaths MESHD by the number of confirmed cases does not represent the true CFR and might be off by orders of magnitude. We aim to provide a precise estimate of the CFR of COVID-19 MESHD using statistical models at the early stage of the epidemic. Methods: We extracted data from the daily released epidemic report published by the National Health Commission P. R. China from 20 Jan 2020, to 1 March 2020. Competing risk model was used to obtain the cumulative hazards for death MESHD, cure, and cure-death hazard ratio. Then the CFR was estimated based on the slope of the last piece in joinpoint regression model, which reflected the most recent trend of the epidemic. Results: As of 1 March 2020, totally 80,369 cases were diagnosed as COVID-19 MESHD in China. The CFR of COVID-19 MESHD were estimated to be 70.9% (95% CI: 66.8%-75.6%) during Jan 20-Feb 2, 20.2% (18.6%-22.1%) during Feb 3 HGNC-14, 6.9% (6.4%-7.4%) during Feb 15-23, 1.5% (1.4%-1.6%) during Feb 24- March 1 HGNC in Hubei province, and 20.3% (17.0%-25.3%) during Jan 20-28, 1.9% (1.8%-2.1%) during Jan 29-Feb 12, 0.9% (0.8%-1.1%) during Feb 13-18, 0.4% (0.4%-0.5%) during Feb 19- March 1 HGNC in other areas of China, respectively. Conclusions: Based on analyses of public data, we found that the CFR in Hubei was much higher than that of other regions in China, over 3 times in all estimation. The CFR would follow a downwards trend based on our estimation from recently released data. Nevertheless, at early stage of outbreak, CFR estimates should be viewed cautiously because of limited data source on true onset and recovery time.

    Aberrant pathogenic GM-CSF HGNC+ T cells and inflammatory CD14 HGNC+ CD16 HGNC+ monocytes in severe pulmonary syndrome patients of a new coronavirus

    Authors: Yonggang Zhou; Binqing Fu; Xiaohu Zheng; Dongsheng Wang; Changcheng Zhao; Yingjie Qi; Rui Sun; Zhigang Tian; Xiaoling Xu; Haiming Wei

    doi:10.1101/2020.02.12.945576 Date: 2020-02-20 Source: bioRxiv

    Pathogenic human coronavirus infections MESHD, such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) MESHD, cause high morbidity and mortality 1,2. Recently, a severe pneumonia-associated respiratory syndrome MESHD caused by a new coronavirus was reported at December 2019 (2019-nCoV) in the city Wuhan, Hubei province, China3-5, which was also named as pneumonia-associated respiratory syndrome MESHD (PARS)6. Up to 9th of February 2020, at least 37, 251 cases have been reported with 812 fatal cases according to the report from China CDC. However, the immune mechanism that potential orchestrated acute mortality from patients of 2019-nCoV is still unknown. Here we show that after the 2019-nCoV infection MESHD, CD4+T lymphocytes are rapidly activated to become pathogenic T helper (Th) 1 cells and generate GM-CSF HGNC etc. The cytokines environment induces inflammatory CD14 HGNC+ CD16 HGNC+ monocytes with high expression of IL-6 HGNC and accelerates the inflammation MESHD. These aberrant and excessive immune cells may enter the pulmonary circulation in huge numbers and play an immune damaging role to causing lung functional disability and quick mortality. Our results demonstrate that excessive non-effective host immune responses by pathogenic T cells and inflammatory monocytes may associate with severe lung pathology. Therefore, we suggest that monoclonal antibody that targets the GM-CSF HGNC or interleukin 6 receptor HGNC may potentially curb immunopathology caused by 2019-nCoV and consequently win more time for virus clearance.

    Risk management-based security evaluation model for telemedicine systems

    Authors: Dong-won Kim; Jin-young Choi; Keun-hee Han

    doi:10.21203/rs.2.24146/v2 Date: 2020-02-20 Source: ResearchSquare

    Background: Infectious diseases that can cause epidemics, such as COVID-19 MESHD, SARS-CoV MESHD, and MERS-CoV MESHD, constitute a major social issue, with healthcare providers fearing secondary, tertiary, and even quaternary infections. To alleviate this problem, telemedicine is increasingly being viewed as an effective means through which patients can be diagnosed and medications prescribed by doctors via untact (i.e., non-face-to-facemedical services. Thus, concomitant with developments in information and communication technology (ICT), medical institutions have actively analyzed and applied ICT to medical systems to provide optimal medical services. However, with the convergence of these diverse technologies, various risks and security threats have emerged. To protect patients and improve telemedicine quality for patient safety, it is necessary to analyze these risks and security threats comprehensively and institute appropriate countermeasures. Methods: The security threats likely to be encountered in each of seven telemedicine service areas were analyzed, and related data were collected directly through on-site surveys by a medical institution. Subsequently, an attack tree, the most popular reliability and risk modeling approach for systematically characterizing the potential risks of telemedicine systems, was examined and utilized with the attack occurrence probability and attack success probability as variables to provide a comprehensive risk assessment method. Results: In this study, the most popular modelling method, an attack tree, was applied to the telemedicine environment, and the security concerns for telemedicine systems were found to be very large. Risk management and evaluation methods suitable for the telemedicine environment were identified, and their benefits and potential limitations were assessed. Conclusion: This research should be beneficial to security experts who wish to investigate the impacts of cybersecurity threats on remote healthcare and researchers who wish to identify new modeling opportunities to apply security risk modeling techniques.

    Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions

    Authors: Alba Grifoni; John Sidney; Yun Zhang; Richard H. Scheuermann; Bjoern H. Peters; Alessandro Sette

    doi:10.1101/2020.02.12.946087 Date: 2020-02-20 Source: bioRxiv

    Effective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (2019-nCoV) require the development of data and tools to understand and monitor viral spread and immune responses. However, little information about the targets of immune responses to 2019-nCoV is available. We used the Immune Epitope Database and Analysis Resource (IEDB) resource to catalog available data related to other coronaviruses, including SARS-CoV MESHD, which has high sequence similarity to 2019-nCoV, and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in 2019-nCoV that have high homology to SARS virus. Parallel bionformatic predictions identified a priori potential B and T cell epitopes for 2019-nCoV. The independent identification of the same regions using two approaches reflects the high probability that these regions are targets for immune recognition of 2019-nCoV. ONE SENTENCE SUMMARYWe identified potential targets for immune responses to 2019-nCoV and provide essential information for understanding human immune responses to this virus and evaluation of diagnostic and vaccine candidates.

    Evaluation of the Efficacy and Safety of Intravenous Remdesivir in Adult Patients with Severe Pneumonia caused by COVID-19 virus Infection MESHD: study protocol for a Phase 3 Randomized, Double-blind, Placebo-controlled, Multicentre trial

    Authors: Peter W Horby; Bin Cao; Yeming Wang; Chen Wang

    doi:10.21203/rs.2.24058/v2 Date: 2020-02-19 Source: ResearchSquare

    Background: A novel coronavirus emerged in Wuhan, Hubei Province, China towards the end of 2019 (SARS-CoV-2 or COVID-19 MESHD virus). Large scale spread within China and internationally led the World Health Organisation to declare a Public Health Emergency of International Concern on 30th January 2020. The clinical manifestations of COVID-19 virus infection MESHD include asymptomatic infection, mild upper respiratory symptoms MESHD, severe viral pneumonia MESHD with respiratory failure MESHD and even death. There are no antivirals of proven clinical efficacy in coronavirus infections MESHD. Remdesivir (GS-5734), a nucleoside analogue, has inhibitory effects on animal and human highly pathogenic coronaviruses, including MERS-CoV and SARS-CoV MESHD, in in-vitro and in-vivo experiments. It is also inhibitory against the COVID-19 MESHD virus in-vitro. The aim of this study is to assess the efficacy and safety of remdesivir in adult patients with severe pneumonia MESHD caused by COVID-19 virus infection MESHD.Methods: The protocol is prepared in accordance with the SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) guidelines. This is a phase 3, randomized, double-blind, placebo-controlled, multicentre trial. Adults (≥18 years) with laboratory confirmed COVID-19 virus infection MESHD, and severe pneumonia signs MESHD or symptoms, and radiologically confirmed severe pneumonia MESHD are randomly assigned in a 2:1 ratio to intravenous remdesivir or placebo for 10 days. The primary endpoint is time to clinical improvement (censored at Day 28), defined as the time (in days) from randomization of study treatment (remdesivir or placebo) until a decline of two categories on a six-category ordinal scale of clinical status (1 ꞊ discharged; 6 ꞊ death MESHD) or live discharge from hospital. One interim analysis for efficacy and futility will be conducted once half of the total number of events required had been observed.Discussion: This is the first randomized, placebo-controlled trial in 2019-nCoV. Enrolment began in sites in Wuhan, Hubei Province, China on 6th February 2020.Trial registration: ClinicalTrials.gov, NCT04257656, 6th February 2020.

    Characterization of spike glycoprotein PROTEIN of 2019-nCoV on virus entry and its immune cross-reactivity with spike glycoprotein PROTEIN of SARS-CoV  

    Authors: Xiuyuan Ou; Yan Liu; Xiaobo Lei; Pei Li; Dan Mi; Lili Ren; Li Guo; Ting Chen; Jiaxing Hu; Zichun Xiang; Zhixia Mu; Xing Chen; Jieyong Chen; Keping Hu; Qi Jin; Jianwei Wang; Zhaohui Qian

    doi:10.21203/rs.2.24016/v1 Date: 2020-02-18 Source: ResearchSquare

    Since beginning of this century, there have already been three zoonotic outbreaks caused by beta coronaviruses (CoV), SA RS-CoV i MESHDn 2002-2003, MERS-CoV in 2012, and the newly identified 2019-nCoV in late 2019, Wuhan, China. As to Feb 10th, 2020, there are over 40,000 confirmed cases and over 900 deaths. However, little is known about the biology of this newly emerged virus. Here we developed a lentiviral based pseudovirus system for S protein PROTEIN of 2019-nCoV to study virus entry in BSL2 settings. First, we confirmed that human an giotensin converting enzyme 2 ( HGNChA CE2) HGNCis the main entry receptor for 2019-nCoV. Second, we found that 2019-nCoV S protein PROTEIN mediated entry on 293/hA CE2 c HGNCells was mainly through endocytosis, and PIKfyve, TP C2, HGNCand ca thepsin L a HGNCre critical for virus entry. Third, 2019-nCoV S protein PROTEIN is less stable than SARS-CoV, and it could trigger protease-independent and receptor dependent cell-cell fusion, which might help virus rapidly spread from cell to cell. Finally and more importantly, polyclonal anti-SARS S1 antibodies T62 effectively inhibited entry of SA RS-CoV S pseudovirions, MESHDbut almost had no effect on entry of 2019-nCoV S pseudovirions. Further studies using sera from one recovered SA RS-CoV p MESHDatient and five 2019-nCoV patients showed that there was only limited cross-neutralization activities between SA RS-CoV a MESHDnd 2019-nCoV sera, suggesting that recovery from one infection might not protect against the other. Our results present potential targets for development of drugs and vaccines for 2019-nCoV. 

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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