Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (289)

ProteinN (99)

NSP5 (59)

ComplexRdRp (26)

NSP3 (17)


SARS-CoV-2 Proteins
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    Laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infection MESHDs

    Authors: Yang Yang; Minghui Yang; Chenguang Shen; Fuxiang Wang; Jing Yuan; Jinxiu Li; Mingxia Zhang; Zhaoqin Wang; Li Xing; Jinli Wei; Ling Peng; Gary Wong; Haixia Zheng; Mingfeng Liao; Kai Feng; Jianming Li; Qianting Yang; Juanjuan Zhao; Zheng Zhang; Lei Liu; Yingxia Liu

    doi:10.1101/2020.02.11.20021493 Date: 2020-02-12 Source: medRxiv

    Background: The outbreak of novel coronavirus pneumonia MESHD ( NCP PROTEIN) caused by 2019-nCoV spread rapidly, and elucidation the diagnostic accuracy of different respiratory specimens is crucial for the control and treatment of this diseases. Methods: Respiratory samples including nasal swabs, throat swabs, sputum and bronchoalveolar lavage fluid MESHD ( BALF MESHD) were collected from Guangdong CDC confirmed NCP PROTEIN patients, and viral RNAs were detected using a CFDA approved detection kit. Results were analyzed in combination with sample collection date and clinical information. Finding: Except for BALF MESHD, the sputum possessed the highest positive rate (74.4%~88.9%), followed by nasal swabs (53.6%~73.3%) for both severe and mild cases during the first 14 days after illness onset (d.a.o). For samples collected [≥] 15 d.a.o, sputum and nasal swabs still possessed a high positive rate ranging from 42.9%~61.1%. The positive rate of throat swabs collected [≥] 8 d.a.o was low, especially in samples from mild cases. Viral RNAs could be detected in all the lower respiratory tract of severe cases, but not the mild cases. CT scan of cases 02, 07 and 13 showed typical viral pneumonia MESHD with ground glass opacity, while no viral RNAs were detected in first three or all the upper respiratory samples. Interpretation: Sputum is most accurate for laboratory diagnosis of NCP PROTEIN, followed by nasal swabs. Detection of viral RNAs in BLAF is necessary for diagnosis and monitoring of viruses in severe cases. CT scan could serve as an important make up for the diagnosis of NCP PROTEIN. Funding National Science and Technology Major Project, Sanming Project of Medicine and China Postdoctoral Science Foundation.

    Estimation of the Time-Varying Reproduction Number of 2019-nCoV Outbreak in China

    Authors: Chong You; Yuhao Deng; Wenjie Hu; Jiarui Sun; Qiushi Lin; Feng Zhou; Cheng Heng Pang; Yuan Zhang; Zhengchao Chen; Xiao-Hua Zhou

    doi:10.1101/2020.02.08.20021253 Date: 2020-02-11 Source: medRxiv

    Background: The 2019-nCoV outbreak in Wuhan, China has attracted world-wide attention. As of February 11, 2020, a total of 44730 cases of novel coronavirus-infected pneumonia MESHD associated with COVID-19 MESHD were confirmed by the National Health Commission of China. Methods: Three approaches, namely Poisson likelihood-based method (ML), exponential growth rate-based method (EGR) and stochastic Susceptible-Infected-Removed dynamic model-based method (SIR), were implemented to estimate the basic and controlled reproduction numbers. Results: A total of 71 chains of transmission together with dates of symptoms onset and 67 dates of infections were identified among 5405 confirmed cases outside Hubei as reported by February 2, 2020. Based on this information, we find the serial interval having an average of 4.41 days with a standard deviation of 3.17 days and the infectious period having an average of 10.91 days with a standard deviation of 3.95 days. Conclusions: The controlled reproduction number is declining. It is lower than one in most regions of China, but is still larger than one in Hubei Province. Sustained efforts are needed to further reduce the Rc to below one in order to end the current epidemic.

    The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against 2019-nCoV

    Authors: Bishajit Sarkar; Md. Asad Ullah; Fatema Tuz Johora; Masuma Afrin Taniya; Yusha Araf

    doi:10.1101/2020.02.05.935072 Date: 2020-02-11 Source: bioRxiv

    Wuhan Novel Coronavirus disease MESHD ( COVID-19 MESHD) outbreak has become a global outbreak which has raised the concern of scientific community to design and discover a definitive cure against this deadly virus which has caused deaths of numerous infected people upon infection MESHD and spreading. To date, no antiviral therapy or vaccine is available which can effectively combat the infection caused by this virus. This study was conducted to design possible epitope-based subunit vaccines against the SARS-CoV-2 virus using the approaches of reverse vaccinology and immunoinformatics. Upon continual computational experimentation three possible vaccine constructs were designed and one vaccine construct was selected as the best vaccine based on molecular docking study which is supposed to effectively act against SARS-CoV-2. Later, molecular dynamics simulation and in silico codon adaptation experiments were carried out in order to check biological stability and find effective mass production strategy of the selected vaccine. Hopefully, this study will contribute to uphold the present efforts of the researches to secure a definitive treatment against this lethal virus.

    Anti-SARS and anti-HCV drugs repurposing against the Papain-like protease PROTEIN of the newly emerged coronavirus (2019-nCoV)

    Authors: Abdo Elfiky; Noha S Ibrahim

    doi:10.21203/rs.2.23280/v1 Date: 2020-02-10 Source: ResearchSquare

    A new mysterious coronavirus outbreak started last month in China. The World Health Organization (WHO) termed the new virus strain 2019-nCoV to be the seventh reported human coronaviruses (HCoV). A seafood market in Wuhan city, central China was the starting point of the emergence with unknown animal causes the first animal to human infection. Until today 904 confirmed deaths MESHD and more than 40000 cases confirmed in China and 28 countries. There is a massive fear of the human to human transmission of 2019-nCoV that reported last week by the Chinese government. The most famous two strains of HCoV are the Severe Acute Respiratory Syndrome coronavirus (SARS CoV) and the Middle East Respiratory Syndrome coronavirus (MERS CoV) MESHD. The former had emerged in China in 2002 while the latter emerged in the Middle East region in 2012 and south Korea in 2015. In this study, the newly emerged 2019-nCoV papain-like protease PROTEIN ( PLpro PROTEIN) is targeted by anti-SARS PLpro PROTEIN drugs and the anti- Hepatitis C Virus MESHD (HCV) Non-structural protein 3 PROTEIN (NS3) serine protease drugs. Sequence analysis, modeling, and docking are used to get a valid model for 2019-nCoV PLpro PROTEIN. The results suggest the effectiveness of the anti-SARS drugs (GRL-0667, GRL-0617, and Mycophenolic acid) and the anti-HCV drugs (Grazoprevir, Telaprevir, and Boceprevir) as potent inhibitors against the newly emerged coronavirus.  

    Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication

    Authors: Linlin Zhang; Daizong Lin; Yuri Kusov; Yong Nian; Qingjun Ma; Jiang Wang; Albrecht von Brunn; Pieter Leyssen; Kristina Lanko; Johan Neyts; Adriaan de Wilde; Eric J. Snijder; Hong Liu; Rolf Hilgenfeld

    doi:10.1101/2020.02.10.936898 Date: 2020-02-10 Source: bioRxiv

    The main protease PROTEIN of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued structure-based design of peptidomimetic -ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease:inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected MESHD cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the -ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against Middle East Respiratory Syndrome coronavirus MESHD.

    The fiscal value of human lives lost from coronavirus disease ( COVID-19 MESHD) in China

    Authors: Joses M. Kirigia; Rosenabi Deborah Karimi Muthuri

    doi:10.21203/rs.2.23296/v2 Date: 2020-02-10 Source: ResearchSquare

    Objective: According to the WHO coronavirus disease MESHD ( COVID-19 MESHD) situation report 35, as of 24 th February 2020, there was a total of 77,262 confirmed COVID-19 MESHD cases in China. That included 2,595 deaths. The specific objective of this study was to estimate the fiscal value of human lives lost due to COVID-19 MESHD in China as of 24 th February 2020. Results:   The deaths from COVID-19 MESHD had a discounted (at 3%) total fiscal value of Int$ 924,346,795 in China. Out of which, 63.2% was borne by people aged 25-49 years, 27.8% by people aged 50-64 years, and 9.0% by people aged 65 years and above. The average fiscal value per death was Int$ 356,203. Re-estimation of the economic model alternately with 5% and 10 discount rates led to a reduction in the expected total fiscal value by 21.3% and 50.4%, respectively. Furthermore, the re-estimation of the economic model using the world’s highest average life expectancy of 87.1 years (which is that of Japanese females), instead of the national life expectancy of 76.4 years, increased the total fiscal value by Int$ 229,456,430 (24.8%).

    Machine learning-based analysis of genomes suggests associations between Wuhan 2019-nCoV and bat Betacoronaviruses

    Authors: Gurjit S Randhawa; Maximillian P.M. Soltysiak; Hadi El Roz; Camila P.E. de Souza; Kathleen A. Hill; Lila Kari

    doi:10.1101/2020.02.03.932350 Date: 2020-02-04 Source: bioRxiv

    As of February 20, 2020, the 2019 novel coronavirus (renamed to COVID-19 MESHD) spread to 30 countries with 2130 deaths MESHD and more than 75500 confirmed cases. COVID-19 MESHD is being compared to the infamous SARS coronavirus MESHD, which resulted, between November 2002 and July 2003, in 8098 confirmed cases worldwide with a 9.6% death rate and 774 deaths MESHD. Though COVID-19 MESHD has a death rate of 2.8% as of 20 February, the 75752 confirmed cases in a few weeks (December 8, 2019 to February 20, 2020) are alarming, with cases likely being under-reported given the comparatively longer incubation period. Such outbreaks demand elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 MESHD genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 MESHD genomes. The proposed method combines supervised machine learning with digital signal processing for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearmans rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp. Our results support a hypothesis of a bat origin and classify COVID-19 MESHD as Sarbecovirus, within Betacoronavirus. Our method achieves high levels of classification accuracy and discovers the most relevant relationships among over 5,000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.

    Fast assessment of human receptor-binding capability of 2019 novel coronavirus (2019-nCoV)

    Authors: Qiang Huang; Andreas Herrmann

    doi:10.1101/2020.02.01.930537 Date: 2020-02-03 Source: bioRxiv

    The outbreaks of 2002/2003 SARS, 2012/2015 MERS and 2019/2020 Wuhan respiratory syndrome MESHD clearly indicate that genome evolution of an animal coronavirus (CoV) may enable it to acquire human transmission ability, and thereby to cause serious threats to global public health. It is widely accepted that CoV human transmission is driven by the interactions of its spike protein (S PROTEIN S-protein HGNC) with human receptor on host cell surface; so, quantitative evaluation of these interactions may be used to assess the human transmission capability of CoVs. However, quantitative methods directly using viral genome data are still lacking. Here, we perform large-scale protein-protein docking to quantify the interactions of 2019-nCoV S-protein HGNC S-protein PROTEIN receptor-binding domain (S-RBD) with human receptor ACE2 HGNC, based on experimental SARS-CoV S-RBD MESHD- ACE2 HGNC complex structure. By sampling a large number of thermodynamically probable binding conformations with Monte Carlo algorithm, this approach successfully identified the experimental complex structure as the lowest-energy receptor-binding conformations, and hence established an experiment-based strength reference for evaluating the receptor-binding affinity of 2019-nCoV via comparison with SARS-CoV MESHD. Our results show that this binding affinity is about 73% of that of SARS-CoV MESHD, supporting that 2019-nCoV may cause human transmission similar to that of SARS-CoV MESHD. Thus, this study presents a method for rapidly assessing the human transmission capability of a newly emerged CoV and its mutant strains, and demonstrates that post-genome analysis of protein-protein interactions may provide early scientific guidance for viral prevention and control.

    Direct Measurement of Rates of Asymptomatic Infection and Clinical Care-Seeking for Seasonal Coronavirus

    Authors: Jeffrey Shaman; Marta Galanti

    doi:10.1101/2020.01.30.20019612 Date: 2020-02-03 Source: medRxiv

    The pandemic potential of the novel coronavirus (nCoV) that emerged in Wuhan, China, during December 2019 is strongly tied to the number and contagiousness of undocumented human infections. Here we present findings from a proactive longitudinal sampling study of acute viral respiratory infections MESHD that documents rates of asymptomatic infection and clinical care seeking for seasonal coronavirus. We find that the majority of infections are asymptomatic by most symptom definitions and that only 4% of individuals experiencing a seasonal coronavirus infection MESHD episode sought medical care for their symptoms. These numbers indicate that a very high percentage of seasonal coronavirus infections MESHD are undocumented and provide a reference for understanding the spread of the emergent nCoV.

    Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

    Authors: Sara Cleemput; Wim Dumon; Vagner Fonseca; Wasim Abdool Karim; Marta Giovanetti; Luiz C. J. Alcantara; Koen Deforche; Tulio de Oliveira

    doi:10.1101/2020.01.31.928796 Date: 2020-02-02 Source: bioRxiv

    SummaryGenome Detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus MESHD in Brazil. Here, we present The Genome Detective Coronavirus Typing Tool that can accurately identify novel coronavirus (2019-nCoV) sequences isolated in China and around the world. The tool can accept up to 2,000 sequences per submission and the analysis of a new whole genome sequence will take approximately one minute. The tool has been tested and validated with hundreds of whole genomes from ten coronavirus species, and correctly classified all of the SARS-related coronavirus ( SARSr-CoV MESHD) and all of the available public data for 2019-nCoV. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines. AvailabilityAvailable online: * and Supplementary informationSupplementary data is available online.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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