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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (144)

ProteinS (39)

ProteinN (33)

ComplexRdRp (17)

ProteinM (17)


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SARS-CoV-2 Proteins
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    The multi-epitope vaccine prediction to combat Pandemic SARS-CoV-2, an immunoinformatic approach

    Authors: K. M. Kaderi Kibria; Md. Shaid bin Islam; Hedayet Ullah; Mojnu Miah

    doi:10.21203/rs.3.rs-21853/v1 Date: 2020-04-07 Source: ResearchSquare

    Novel coronavirus (SARS-CoV-2) leads to coronavirus disease MESHD 19 ( COVID-19 MESHD) recently declared as a pandemic for its outbreak within almost 190 countries worldwide. No effective drugs and/or vaccines authenticated against this rapidly spreading virus till now. This study aims to establish an efficient multi-epitope vaccine that could elicit both T-cell and B-cell responses sufficient to recognize confirmed surface proteins of the virus. The sequences of the viral surface proteins, e PROTEIN.g. envelope protein (E PROTEIN), membrane glycoprotein (M PROTEIN), and S1 and S2 domain of spike surface glycoprotein (S PROTEIN) collected from the NCBI database. We adopted an immunoinformatic strategy to identify the immunogenic region of the proteins and assessed their affinity with MHC class-I and MHC class-II by various bioinformatics tools. Top epitopes have been selected and assessed for population coverage and conservancy among 180 SARS-CoV-2 genomes. Along with the above analyses, and results of Antigenicity, Allergenicity, and transmembrane location prediction, we selected top epitopes from these four proteins. The epitopes were assembled by the AAY linker to form a multi-epitope vaccine is 70 aa long, can be synthesized commercially. This should be processed by Antigen-presenting cells; consequently, the surface proteins might be recognized by the helper and cytotoxic T-cells as well as by B-cells. We also assessed the structural and various physicochemical properties of the novel chimeric peptide for its suitability as a multi-epitope vaccine. This in-silico study leads to a rationally designed potential vaccine candidate that could be assessed by wet-lab experiments driving towards efficient combat of the novel coronavirus outbreak.

    Coronavirus hemagglutinin-esterase and spike proteins PROTEIN co-evolve for functional balance and optimal virion avidity

    Authors: Yifei Lang; Wentao Li; Zeshi Li; Danielle Koerhuis; Arthur C.S. van den Burg; Erik Rozemuller; Berend-Jan Bosch; Frank J.M. van Kuppeveld; Geert-Jan P.H. Boons; Eric G. Huizinga; Hilde M. van der Schaar; Raoul J. de Groot

    doi:10.1101/2020.04.03.003699 Date: 2020-04-05 Source: bioRxiv

    Human coronaviruses OC43 and HKU1 are respiratory pathogen of zoonotic origin that have gained worldwide distribution. OC43 apparently emerged from a bovine coronavirus (BCoV) spill-over. All three viruses attach to 9-O-acetylated sialoglycans via spike protein S PROTEIN with hemagglutinin-esterase HE acting as a receptor-destroying enzyme. In BCoV, an HE lectin domain promotes esterase activity towards clustered substrates. OC43 and HKU1, however, lost HE lectin function as an adaptation to humans. Replaying OC43 evolution, we knocked-out BCoV HE lectin function and performed forced evolution-population dynamics analysis. Loss of HE receptor-binding selected for second-site mutations in S, decreasing S binding affinity by orders of magnitude. Irreversible HE mutations selected for cooperativity in virus swarms with low-affinity S minority variants sustaining propagation of high-affinity majority phenotypes. Salvageable HE mutations induced successive second-site substitutions in both S and HE. Apparently, S and HE are functionally interdependent and co-evolve to optimize the balance between attachment and release. This mechanism of glycan-based receptor usage, entailing a concerted, fine-tuned activity of two envelope protein PROTEIN species, is unique among CoVs, but reminiscent of that of influenza A viruses (IAVs). Apparently, general principles fundamental to virion-sialoglycan interactions prompted convergent evolution of two important groups of human and animal pathogens.

    Epitope-based chimeric peptide vaccine design against S, M and E proteins PROTEIN of SARS-CoV-2 etiologic agent of global pandemic COVID-19 MESHD: an in silico approach

    Authors: M. Shaminur Rahman; M. Nazmul Hoque; M. Rafiul Islam; Salma Akter; A. S. M. Rubayet-Ul-Alam; Mohammad Anwar Siddique; Otun Saha; Md. Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain

    doi:10.1101/2020.03.30.015164 Date: 2020-03-31 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing pandemic of coronavirus disease 2019 MESHD ( COVID-19 MESHD), a public health emergency of international concern declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomic was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M and E proteins PROTEIN. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of [≥] 90.0% world population coverage for different ethnic groups. Molecular docking of the chimeric vaccine peptide with the immune receptors ( TLR3 HGNC and TLR4 HGNC) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased INF-{gamma} and IL-2 HGNC cytokines. The codon optimization and mRNA secondary structure prediction revealed the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19 MESHD.

    Presence of SARS-Coronavirus-2 in sewage

    Authors: Gertjan Medema; Leo Heijnen; Goffe Elsinga; Ronald Italiaander; Anke Brouwer

    doi:10.1101/2020.03.29.20045880 Date: 2020-03-30 Source: medRxiv

    In the current COVID-19 MESHD COVID-19 MESHD pandemic, a significant proportion of cases shed SARS-Coronavirus-2 (SARS-CoV-2) with their faeces. To determine if SARS-CoV-2 is present in sewage during the emergence of COVID-19 MESHD in the Netherlands, sewage samples of 7 cities and the airport were tested using RT-PCR against three fragments of the nucleocapsid protein PROTEIN gene (N1-3) and one fragment of the envelope protein PROTEIN gene (E PROTEIN). No SARS-CoV-2 was detected in samples of February 6, three weeks before the first case was reported in the Netherlands on February 27. On March 5, the N1 fragment was detected in sewage of five sites. On March 15/16, the N1 fragment was detected in sewage of six sites, and the N3 and E fragment were detected at 5 and 4 sites respectively. This is the first report of detection of SARS-CoV-2 in sewage. The detection of the virus in sewage, even when the COVID-19 MESHD incidence is low, indicates that sewage surveillance could be a sensitive tool to monitor the circulation of the virus in the population.

    Structural Basis for Potent Neutralization of Betacoronaviruses by Single-domain Camelid Antibodies

    Authors: Daniel Wrapp; Dorien De Vlieger; Kizzmekia S Corbett; Gretel M Torres; Wander Van Breedam; Kenny Roose; Loes van Schie; - VIB-CMB COVID-19 Response Team; Markus Hoffmann; Stefan Pöhlmann; Barney S Graham; Nico Callewaert; Bert Schepens; Xavier Saelens; Jason S McLellan

    doi:10.1101/2020.03.26.010165 Date: 2020-03-28 Source: bioRxiv

    The pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV) MESHD, severe acute respiratory syndrome coronavirus (SARS-CoV-1) MESHD and COVID-19 MESHD coronavirus (SARS-CoV-2) have all emerged into the human population with devastating consequences. These viruses make use of a large envelope protein PROTEIN called spike (S) to engage host cell receptors and catalyze membrane fusion. Because of the vital role that these S proteins PROTEIN play, they represent a vulnerable target for the development of therapeutics to combat these highly pathogenic coronaviruses. Here, we describe the isolation and characterization of single-domain antibodies (VHHs) from a llama immunized with prefusion-stabilized coronavirus spikes. These VHHs are capable of potently neutralizing MERS-CoV MESHD or SARS-CoV-1 S pseudotyped viruses. The crystal structures of these VHHs bound to their respective viral targets reveal two distinct epitopes, but both VHHs block MESHD receptor binding. We also show cross-reactivity between the SARS-CoV-1 S-directed VHH and SARS-CoV-2 S MESHD, and demonstrate that this cross-reactive VHH is capable of neutralizing SARS-CoV-2 S pseudotyped viruses as a bivalent human IgG Fc-fusion. These data provide a molecular basis for the neutralization of pathogenic betacoronaviruses by VHHs and suggest that these molecules may serve as useful therapeutics during coronavirus outbreaks.

    Personalized workflow to identify optimal T-cell epitopes for peptide-based vaccines against COVID-19 MESHD

    Authors: Rui Qiao; Ngoc Hieu Tran; Baozhen Shan; Ali Ghodsi; Ming Li

    id:2003.10650v1 Date: 2020-03-24 Source: arXiv

    Traditional vaccines against viruses are designed to target their surface proteins, i.e PROTEIN., antigens, which can trigger the immune system to produce specific antibodies to capture and neutralize the viruses. However, viruses often evolve quickly, and their antigens are prone to mutations to avoid recognition by the antibodies (antigenic drift). This limitation of the antibody-mediated immunity could be addressed by the T-cell mediated immunity, which is able to recognize conserved viral HLA peptides presented on virus-infected cells. Thus, by targeting conserved regions on the genome of a virus, T-cell epitope-based vaccines are less subjected to mutations and may work effectively on different strains of the virus. Here we propose a personalized workflow to identify an optimal set of T-cell epitopes based on the HLA alleles and the immunopeptidome of an individual person. Specifically, our workflow trains a machine learning model on the immunopeptidome and then predicts HLA peptides from conserved regions of a virus that are most likely to trigger responses from the person T cells. We applied the workflow to identify T-cell epitopes for the SARS-COV-2 virus, which has caused the recent COVID-19 MESHD COVID-19 MESHD pandemic in more than 100 countries across the globe.

    Scope of Natural Plant Extract to Deactivate COVID-19 MESHD

    Authors: Md Abdus Shahid; Mohammad Asaduzzaman Chowdhury; Mohammod Abul Kashem

    doi:10.21203/rs.3.rs-19240/v1 Date: 2020-03-24 Source: ResearchSquare

    The outbreak of coronavirus disease 2019 MESHD ( COVID-19 MESHD) has emerged as a severe threat for public health and economy throughout the world. The structure of corona virus is composed of RNA based proteins that contains amino (-NH2) and carboxyl (-COOH) groups.  It includes nucleocapsid protein (N PROTEIN- protein), spike PROTEIN protein (S PROTEIN S-protein HGNC protein), envelope PROTEIN and hemagglutinin-esterase dimer (HE). These proteins affect adversely on human gastrointestinal system, heart, kidney, liver, and central nervous system leading to several organ damages. This investigation reveals that the extracted components of natural plants, especially hydroxyl (-OH) groups react chemically to deactivate the active components of the virus by esterification   process. As a case study, using one of the natural resources, as for example, licorice (Glycyrrhiza glabra) which has the components of glycyrrhizin, glycyrrhetic acid, liquiritin and isoliquiritin that can be used to neutralize the activeness of COVID-19 MESHD and it can be used as an antiviral drug. The extracted licorice is further processed with PVA solution to form antiviral nano-membrane for potential application as wound dressing materials, musk, gloves and against skin infection MESHD by electrospinning.  The morphology of the membrane is characterized using scanning electron microscope (SEM). The research suggests that the other plants having deactivate components against virus can be applicable to resolve the human health crisis of the globe. 

    Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR

    Authors: Lianhua Dong; Junbo Zhou; Chunyan Niu; Quanyi Wang; Yang Pan; Sitong Sheng; Xia Wang; Yongzhuo Zhang; Jiayi Yang; Manqing Liu; Yang Zhao; Xiaoying Zhang; Tao Zhu; Tao Peng; Jie Xie; Yunhua Gao; Di Wang; Yun Zhao; Xinhua Dai; Xiang Fang

    doi:10.1101/2020.03.14.20036129 Date: 2020-03-18 Source: medRxiv

    BACKGROUND: The outbreak of COVID-19 MESHD caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 140 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnostics of SARS-CoV-2. However, the positive rate of RT-qPCR assay of pharyngeal swab samples are reported to vary from 30~60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach. METHODSWe established a reverse transcription digital PCR (RT-dPCR) protocol to detect SARS-CoV-2 on 194 clinical pharyngeal swab samples, including 103 suspected patients, 75 close contacts and 16 supposed convalescents. RESULTS: The limit of blanks (LoBs) of the RT-dPCR assays were ~1.6, ~1.6 and ~0.8 copies/reaction for ORF 1ab, N and E genes PROTEIN, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever MESHD suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients. CONCLUSION: RT-dPCR could be a confirmatory method for suspected patients diagnosed by RT-qPCR. Furthermore, RT-dPCR was more sensitive and suitable for low viral load specimens from the both patients under isolation and those under observation who may not be exhibiting clinical symptoms.

    Comparative Performance of SARS-CoV-2 Detection Assays using Seven Different Primer/Probe Sets and One Assay Kit

    Authors: Amanda M. Casto; Meei-Li Huang; Arun Nalla; Garrett A. Perchetti; Reigran Sampoleo; Lasata Shrestha; Yulun Wei; Haiying Zhu; Alexander L. Greninger; Keith R. Jerome

    doi:10.1101/2020.03.13.20035618 Date: 2020-03-17 Source: medRxiv

    More than 100,000 people worldwide are known to have been infected with SARS-CoV-2 beginning in December 2019. The virus has now spread to over 93 countries including the United States, with the largest cluster of US cases to date in the Seattle metropolitan area in Washington. Given the rapid increase in the number of local cases, the availability of accurate, high-throughput SARS-CoV-2 testing is vital to efforts to manage the current public health crisis. In the course of optimizing SARS-CoV-2 testing performed by the University of Washington Clinical Virology Lab (UW Virology Lab), we tested assays using seven different primer/probe sets and one assay kit HGNC. We found that the most sensitive assays were those the used the E-gene PROTEIN primer/probe set described by Corman et al. (Eurosurveillance 25(3), 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045) and the N2 set described by the CDC (Division of Viral Diseases MESHD, Centers for Disease Control and Prevention, 2020, https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf). All assays tested were found to be highly specific for SARS-CoV-2, with no cross-reactivity with other respiratory viruses observed in our analyses regardless of the primer/probe set or kit HGNC used. These results will provide invaluable information to other clinical laboratories who are actively developing SARS-CoV-2 testing protocols at a time when increased testing capacity is urgently needed worldwide.

    Predicting COVID-19 MESHD distribution in Mexico through a discrete and time-dependent Markov chain and an SIR-like model

    Authors: Alfonso Vivanco-Lira

    id:2003.06758v1 Date: 2020-03-15 Source: arXiv

    COVID-19 MESHD is an emergent viral infection which rose in December 2019 in a city in the Chinese province of Hubei, Wuhan; the viral aetiology of this infection is now known as COVID-19 MESHD virus, which belongs to the Betacoronavirus genus. This virus produces the syndrome of acute respiratory stress MESHD that h as been witnessed in other coronaviruses, such as that MERS-CoV in Middle East countries or SARS-CoV which was seen in 2002 and 2003 in China. This virus mediates its entry through its spike (S) proteins PROTEIN interacting with ACE2 receptors in lung epithelial cells, and may promote an inflammatory response by means of inflammasome NLRP3 activation and unfolded protein response (these are possibly consequence of the envelope E protein PROTEIN of COVID-19 MESHD virus). Efforts have been made worldwide to prevent further spread of the disease, but in March 2020 the WHO declared it a pandemic emergency and Mexico started to report its first cases. In this paper we attempt to summarize the biological features of the virus and the possible pathophysiological mechanisms of its disease, as well as a stochastic model characterizing the probability distribution of cases in Mexico by states and the estimated number of cases in Mexico through a differential equation model (modified SIR model), thus will we be able to characterize the disease and its course in Mexico in order to display more preparedness and promote more logical actions by both the policy makers as well as the general population.

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MeSH Disease
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SARS-CoV-2 Proteins


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