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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (2072)

ProteinN (547)

NSP5 (412)

ComplexRdRp (249)

ProteinE (144)


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SARS-CoV-2 Proteins
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    The transmembrane serine protease inhibitors are potential antiviral drugs for 2019-nCoV targeting the insertion sequence-induced viral infectivity enhancement

    Authors: Tong Meng; Hao Cao; Hao Zhang; Zijian Kang; Da Xu; Haiyi Gong; Jing Wang; Zifu Li; Xingang Cui; Huji Xu; Haifeng Wei; Xiuwu Pan; Rongrong Zhu; Jianru Xiao; Wang Zhou; Liming Cheng; Jianmin Liu

    doi:10.1101/2020.02.08.926006 Date: 2020-02-11 Source: bioRxiv

    At the end of 2019, the SARS-CoV-2 induces an ongoing outbreak of pneumonia MESHD in China1, even more spread than SARS-CoV infection2. The entry of SARS-CoV into host cells mainly depends on the cell receptor ( ACE2 HGNC) recognition and spike protein PROTEIN cleavage-induced cell membrane fusion3,4. The spike protein PROTEIN of SARS-CoV-2 also binds to ACE2 HGNC with a similar affinity, whereas its spike protein PROTEIN cleavage remains unclear5,6. Here we show that an insertion sequence in the spike protein PROTEIN of SARS-CoV-2 enhances the cleavage efficiency, and besides pulmonary alveoli MESHD, intestinal and esophagus epithelium were also the target tissues of SARS-CoV-2. Compared with SARS-CoV MESHD, we found a SPRR insertion in the S1/S2 protease cleavage sites of SARS-CoV-2 spike PROTEIN protein increasing the cleavage efficiency by the protein sequence aligment and furin score calculation. Additionally, the insertion sequence facilitates the formation of an extended loop which was more suitable for protease recognition by the homology modeling and molicular docking. Furthermore, the single-cell transcriptomes identified that ACE2 HGNC and TMPRSSs are highly coexpressed in AT2 cells of lung, along with esophageal MESHD upper epithelial cells and absorptive enterocytes. Our results provide the bioinformatics evidence for the increased spike protein PROTEIN cleavage of SARS-CoV-2 and indicate its potential target cells.

    The Pathogenicity of 2019 Novel Coronavirus in hACE2 HGNC Transgenic Mice

    Authors: Linlin Bao; Wei Deng; Baoying Huang; Hong Gao; Jiangning Liu; Lili Ren; Qiang Wei; Pin Yu; Yanfeng Xu; Feifei Qi; Yajin Qu; Fengdi Li; Qi Lv; Wenling Wang; Jing Xue; Shuran Gong; Mingya Liu; Guanpeng Wang; Shunyi Wang; Zhiqi Song; Linna Zhao; Peipei Liu; Li Zhao; Fei Ye; Huijuan Wang; Weimin Zhou; Na Zhu; Wei Zhen; Haisheng Yu; Xiaojuan Zhang; Li Guo; Lan Chen; Conghui Wang; Ying Wang; Xinmin Wang; Yan Xiao; Qiangming Sun; Hongqi Liu; Fanli Zhu; Chunxia Ma; Lingmei Yan; Mengli Yang; Jun Han; Wenbo Xu; Wenjie Tan; Xiaozhong Peng; Qi Jin; Guizhen Wu; Chuan Qin

    doi:10.1101/2020.02.07.939389 Date: 2020-02-11 Source: bioRxiv

    Severe acute respiratory syndrome CoV-2 MESHD (SARS-CoV-2) caused the Corona Virus Disease MESHD 2019 ( COVID-19 MESHD) cases in China has become a public health emergency of international concern (PHEIC). Based on angiotensin converting enzyme 2 (ACE2) as cell entry receptor of SARS-CoV, we used the hACE2 HGNC transgenic mice infected with SARS-CoV-2 to study the pathogenicity of the virus. Weight loss MESHD and virus replication in lung were observed in hACE2 HGNC mice infected with SARS-CoV-2. The typical histopathology was interstitial pneumonia MESHD with infiltration of significant lymphocytes and monocytes in alveolar MESHD interstitium, and accumulation of macrophages in alveolar cavities MESHD. Viral antigens were observed in the bronchial epithelial cells, alveolar MESHD macrophages and alveolar epithelia MESHD. The phenomenon was not found in wild type mice with SARS-CoV-2 infection MESHD. The pathogenicity of SARS-CoV-2 in hACE2 HGNC mice was clarified and the Kochs postulates were fulfilled as well, and the mouse model may facilitate the development of therapeutics and vaccines against SARS-CoV-2.

    Design of multi epitope-based peptide vaccine against E protein PROTEIN of human 2019-nCoV: An immunoinformatics approach

    Authors: Miyssa I. Abdelmageed; Abdelrahman Hamza Abdelmoneim Sr.; Mujahed Ibrahim Mustafa Sr.; Nafisa M. Elfadol; Naseem S. Murshed; Shaza W. Shantier; Abdelrafie M. Makhawi

    doi:10.1101/2020.02.04.934232 Date: 2020-02-11 Source: bioRxiv

    BackgroundNew endemic disease has been spread across Wuhan City, China on December 2019. Within few weeks, the World Health Organization (WHO) announced a novel coronavirus designated as coronavirus disease 2019 MESHD ( COVID-19 MESHD). In late January 2020, WHO declared the outbreak of a "public-health emergency of international concern" due to the rapid and increasing spread of the disease worldwide. Currently, there is no vaccine or approved treatment for this emerging infection MESHD; thus the objective of this study is to design a multi epitope peptide vaccine against COVID-19 MESHD using immunoinformatics approach. MethodSeveral techniques facilitating the combination of immunoinformatics approach and comparative genomic approach were used in order to determine the potential peptides for designing the T cell epitopes-based peptide vaccine using the envelope protein PROTEIN of 2019-nCoV as a target. ResultsExtensive mutations, insertion and deletion were discovered with comparative sequencing in COVID-19 MESHD strain. Additionally, ten peptides binding to MHC class I and MHC class II were found to be promising candidates for vaccine design with adequate world population coverage of 88.5% and 99.99%, respectively. ConclusionT cell epitopes-based peptide vaccine was designed for COVID-19 MESHD using envelope protein PROTEIN as an immunogenic target. Nevertheless, the proposed vaccine is rapidly needed to be validated clinically in order to ensure its safety, immunogenic profile and to help on stopping this epidemic before it leads to devastating global outbreaks.

    EPIDEMIC TRENDS ANALYSIS AND RISK ESTIMATION OF 2019-NCOV OUTBREAK

    Authors: Qinghe Liu; Zhicheng Liu; Deqiang Li; Zefei Gao; Junkai Zhu; Junyan Yang; Qiao Wang

    doi:10.1101/2020.02.09.20021444 Date: 2020-02-11 Source: medRxiv

    Since December 8, 2019, the spread of COVID-19 MESHD is increasing every day. It is particularly important to predict the trend of the epidemic for the timely adjustment of the economy and industries. We proposed a Flow-SEHIR model, based on which we performed the trends of 2019-nCoV ( COVID-19 MESHD) in China. The results show the basic reproductive numbers R0 of COVID-19 MESHD is 3.56 (95% CI: 2.31 - 4.81). The number of daily confirmed new cases reaches the inflection point on Feb. 6 - 10 outside Hubei. For the maximum of infected cases number, the predicted peak value in China except Hubei was estimated to be 13806 (95% CI: 11926 - 15845). The peak arrival time is on March 3 - 9. The peak cumulative number of patients in Hubei was estimated to be 63800 (95% CI: 59300 - 76500). The temporal number of patients in most areas of China outside Hubei will peak from March 12th to March 15th, 2020. The peak values of more than 73.5% provinces or regions in China will be controlled within 1000.

    Tobacco-use disparity in gene expression of ACE2, the receptor of 2019-nCov

    Authors: Guoshuai Cai

    doi:10.1101/2020.02.05.20020107 Date: 2020-02-11 Source: medRxiv

    In current severe global emergency situation of 2019-nCov outbreak, it is imperative to identify vulnerable and susceptible groups for effective protection and care. Recently, studies found that 2019-nCov and SARS-nCov share the same receptor, ACE2. In this study, we analyzed five large-scale bulk transcriptomic datasets of normal lung tissue and two single-cell transcriptomic datasets to investigate the disparities related to race, age, gender and smoking status in ACE2 gene expression and its distribution among cell types. We didn't find significant disparities in ACE2 gene expression between racial groups (Asian vs Caucasian), age groups (>60 vs <60) or gender groups (male vs female). However, we observed significantly higher ACE2 gene expression in former smoker's lung compared to non-smoker's lung. Also, we found higher ACE2 gene expression in Asian current smokers compared to non-smokers but not in Caucasian current smokers, which may indicate an existence of gene-smoking interaction. In addition, we found that ACE2 gene is expressed in specific cell types related to smoking history and location. In bronchial epithelium, ACE2 is actively expressed in goblet cells of current smokers and club cells of non-smokers. In alveoli, ACE2 is actively expressed in remodelled AT2 cells of former smokers. Together, this study indicates that smokers especially former smokers may be more susceptible to 2019-nCov and have infection paths different with non-smokers. Thus, smoking history may provide valuable information in identifying susceptible population and standardizing treatment regimen.

    Diarrhea may be underestimated: a missing link in 2019 novel coronavirus

    Authors: Weicheng Liang; Zhijie Feng; Shitao Rao; Cuicui Xiao; Zexiao Lin; Qi Zhang; Wei Qi

    doi:10.1101/2020.02.03.20020289 Date: 2020-02-11 Source: medRxiv

    The outbreak of pneumonia MESHD caused by the 2019 Novel Coronavirus (2019-nCoV) was reported in Wuhan City, China. However, the clinical symptoms varied in different reports. Based on the results of inter-group difference test, we found that the incidence of diarrhea MESHD differed in three recent reports. As 2019-nCoV utilizes the same cell entry receptor ACE2 HGNC as severe acute respiratory syndrome coronavirus (SARS-CoV) MESHD and ACE2 HGNC tightly controls intestinal inflammation MESHD, to trace the route of infection mediated by 2019-nCoV, we used the single-cell RNA sequencing data for analysis. We found that the ACE2 HGNC mRNA was highly expressed in the healthy human small intestine rather than the lung. Besides, single-cell RNA sequencing data showed that ACE2 HGNC was significantly elevated in the proximal and distal enterocytes, where the small intestinal epithelium is exposed to the foreign pathogen. Thus, we suspect that ACE2 HGNC-expressing small intestinal epithelium cells might be vulnerable to 2019-nCoV infection MESHD when people eat infected wild animals and diarrhea MESHD may serve as an indicator for infection, suggesting that clinicians should pay more attention to patients with diarrhea MESHD during the outbreak of pneumonia MESHD.

    Networks of information token recurrences derived from genomic sequences may reveal hidden patterns in epidemic outbreaks: A case study of the 2019-nCoV coronavirus.

    Authors: Markus Luczak-Roesch

    doi:10.1101/2020.02.07.20021139 Date: 2020-02-11 Source: medRxiv

    Profiling the genetic evolution and dynamic spreading of viruses is a crucial task when responding to epidemic outbreaks. We aim to devise novel ways to model, visualise and analyse the temporal dynamics of epidemic outbreaks in order to help researchers and other people involved in crisis response to make well-informed and targeted decisions about from which geographical locations and time periods more genetic samples may be required to fully understand the outbreak. Our approach relies on the application of Transcendental Information Cascades to a set of temporally ordered nucleotide sequences and we apply it to real-world data that was collected during the currently ongoing outbreak of the novel 2019-nCoV coronavirus. We assess information-theoretic and network-theoretic measures that characterise the resulting complex network and suggest touching points and temporal pathways that are of interest for deeper investigation by geneticists and epidemiologists.

    Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

    Authors: Joel Hellewell; Sam Abbott; Amy Gimma; Nikos I Bosse; Christopher I Jarvis; Timothy W Russell; James D Munday; Adam J Kucharski; W John Edmunds; CMMID nCoV working group; Sebastian Funk; Rosalind M Eggo

    doi:10.1101/2020.02.08.20021162 Date: 2020-02-11 Source: medRxiv

    Background: To assess the viability of isolation and contact tracing to control onwards transmission from imported cases of 2019-nCoV. Methods: We developed a stochastic transmission model, parameterised to the 2019-nCoV outbreak. We used the model to quantify the potential effectiveness of contact tracing and isolation of cases at controlling a 2019 nCoV-like pathogen. We considered scenarios that varied in: the number of initial cases; the basic reproduction number R0; the delay from symptom onset to isolation; the probability contacts were traced; the proportion of transmission that occurred before symptom onset, and the proportion of subclinical infections. We assumed isolation prevented all further transmission in the model. Outbreaks were deemed controlled if transmission ended within 12 weeks or before 5000 cases in total. We measured the success of controlling outbreaks using isolation and contact tracing, and quantified the weekly maximum number of cases traced to measure feasibility of public health effort. Findings: While simulated outbreaks starting with only 5 initial cases, R0 of 1.5 and little transmission before symptom onset could be controlled even with low contact tracing probability, the prospects of controlling an outbreak dramatically dropped with the number of initial cases, with higher R0, and with more transmission before symptom onset. Across different initial numbers of cases, the majority of scenarios with an R0 of 1.5 were controllable with under 50% of contacts successfully traced. For R0 of 2.5 and 3.5, more than 70% and 90% of contacts respectively had to be traced to control the majority of outbreaks. The delay between symptom onset and isolation played the largest role in determining whether an outbreak was controllable for lower values of R0. For higher values of R0 and a large initial number of cases, contact tracing and isolation was only potentially feasible when less than 1% of transmission occurred before symptom onset. Interpretation: We found that in most scenarios contact tracing and case isolation alone is unlikely to control a new outbreak of 2019-nCov within three months. The probability of control decreases with longer delays from symptom onset to isolation, fewer cases ascertained by contact tracing, and increasing transmission before symptoms. This model can be modified to reflect updated transmission characteristics and more specific definitions of outbreak control to assess the potential success of local response efforts.

    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.

    Exploring the coronavirus epidemic using the new WashU Virus Genome Browser

    Authors: Jennifer Flynn; Deepak Purushotham; Mayank NK Choudhary; Xiaoyu Zhuo; Changxu Fan; Gavriel Matt; Daofeng Li; Ting Wang

    doi:10.1101/2020.02.07.939124 Date: 2020-02-11 Source: bioRxiv

    Since its debut in mid-December, 2019, the novel coronavirus (2019-nCoV) has rapidly spread from its origin in Wuhan, China, to several countries across the globe, leading to a global health crisis. As of February 7, 2020, 44 strains of the virus have been sequenced and uploaded to NCBIs GenBank [1], providing insight into the viruss evolutionary history and pathogenesis. Here, we present the WashU Virus Genome Browser, a web-based portal for viewing virus genomic data. The browser is home to 16 complete 2019-nCoV genome sequences, together with hundreds of related viral sequences including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) MESHD, and Ebola virus MESHD. In addition, the browser features unique customizability, supporting user-provided upload of novel viral sequences in various formats. Sequences can be viewed in both a track-based representation as well as a phylogenetic tree-based view, allowing the user to easily compare sequence features across multiple strains. The WashU Virus Genome Browser inherited many features and track types from the WashU Epigenome Browser, and additionally incorporated a new type of SNV track to address the specific needs of viral research. Our Virus Browser portal can be accessed at https://virusgateway.wustl.edu, and documentation is available at https://virusgateway.readthedocs.io/.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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