Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
    displaying 641 - 650 records in total 1297
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    Distributions and risks of SARS-CoV-2 in hospital outdoor environment

    Authors: Dayi Zhang; Yunfeng Yang; Xia Huang; Jingkun Jiang; Miao Li; Xian Zhang; Haibo Ling; Jing Li; Yi Liu; Guanghe Li; Weiwei Li; Chuan Yi; Ting Zhang; Yongzhong Jiang; Yan Xiong; Zhenyu Hu; Xinzi Wang; Songqiang Deng; Peng Zhao; Jiuhui Qu

    doi:10.1101/2020.05.12.20097105 Date: 2020-05-18 Source: medRxiv

    The outbreak of coronavirus infectious disease MESHD-2019 (COVID-19) pandemic has rapidly spread throughout over 200 countries, posing a global threat to human health. Till 15th May 2020, there are over 4.5 million confirmed cases TRANS, with roughly 300,000 death1. To date, most studies focus on severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) in indoor environment owing to its main transmission TRANS routes via human respiratory droplets and direct contact2,3. It remains unclear whether SARS-CoV-2 can spill over and impose transmission risks TRANS to outdoor environments despite potential threats to people and communities. Here, we investigated the presence of SARS-CoV-2 by measuring viral RNA in 73 samples from outdoor environment of three hospitals in Wuhan. We detected SARS-CoV-2 in soils (205-550 copies/g), aerosols (285-1,130 copies/m3) and wastewaters (255 to 18,744 copies/L) in locations close to hospital departments receiving COVID-19 patients or in wastewater treatment sectors. These findings reveal significant viral spillover in hospital outdoor environments that was possibly caused by respiratory droplets from patients or aerosolized particles from wastewater containing SARS-CoV-2. In contrast, SARS-CoV-2 was not detected in other areas or on surfaces with regular disinfection implemented. Soils may behave as viral warehouse through deposition and serve as a secondary source spreading SARS-CoV-2 for a prolonged time. For the first time, our findings demonstrate that there are high-risk areas in hospital outdoor environments to spread SARS-CoV-2, calling for sealing of wastewater treatment unit and complete sanitation to prevent COVID-19 transmission risks TRANS.

    Epitope-Based Peptide Vaccine Against Severe Acute Respiratory Syndrome MESHD-Coronavirus-2 Nucleocapsid Protein: An in silico Approach

    Authors: Ahmed Rakib; Saad Ahmed Sami; Md. Ashiqul Islam; Shahriar Ahmed; Farhana Binta Faiz; Bibi Humayra Khanam; Mir Muhammad Nasir Uddin; Dr. Talha Bin Emran

    doi:10.1101/2020.05.16.100206 Date: 2020-05-17 Source: bioRxiv

    With an increasing fatality rate, severe acute respiratory syndrome MESHD-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. SARS-CoV-2 is a member of the Coronaviridae family, which is transmitted from animal to human and because of being contagious, further it transmitted human to human. Recently, the World Health Organization (WHO) has announced the infectious disease MESHD caused by SARS-CoV-2, which is known as coronavirus disease MESHD-2019 (COVID-2019) as a global pandemic. But, no specific medications are available for the treatment of COVID-19 so far. As a corollary, there is a need for a potential vaccine to impede the progression of the disease MESHD. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication as well as interferes with host immune responses. We have comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we have predicted the most immunogenic epitope for T-cell as well as B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.

    predCOVID-19: A Systematic Study of Clinical Predictive Models for Coronavirus Disease MESHD 2019

    Authors: Patrick Schwab; August DuMont Schütte; Benedikt Dietz; Stefan Bauer

    id:2005.08302v1 Date: 2020-05-17 Source: arXiv

    Coronavirus Disease MESHD 2019 (COVID-19) is a rapidly emerging respiratory disease MESHD caused by the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2). Due to the rapid human-to-human transmission TRANS of SARS-CoV-2, many healthcare systems are at risk of exceeding their healthcare capacities, in particular in terms of SARS-CoV-2 tests, hospital and intensive care unit (ICU) beds and mechanical ventilators. Predictive algorithms could potentially ease the strain on healthcare systems by identifying those who are most likely to receive a positive SARS-CoV-2 test, be hospitalised or admitted to the ICU. Here, we study clinical predictive models that estimate, using machine learning and based on routinely collected clinical data, which patients are likely to receive a positive SARS-CoV-2 test, require hospitalisation or intensive care. To evaluate the predictive performance SERO of our models, we perform a retrospective evaluation on clinical and blood SERO analysis data from a cohort of 5644 patients. Our experimental results indicate that our predictive models identify (i) patients that test positive for SARS-CoV-2 a priori at a sensitivity SERO of 75% (95% CI: 67%, 81%) and a specificity of 49% (95% CI: 46%, 51%), (ii) SARS-CoV-2 positive patients that require hospitalisation with 0.92 AUC (95% CI: 0.81, 0.98), and (iii) SARS-CoV-2 positive patients that require critical care with 0.98 AUC (95% CI: 0.95, 1.00). In addition, we determine which clinical features are predictive to what degree for each of the aforementioned clinical tasks. Our results indicate that predictive models trained on routinely collected clinical data could be used to predict clinical pathways for COVID-19, and therefore help inform care and prioritise resources.

    Distinct conformational states of SARS-CoV-2 spike protein

    Authors: Yongfei Cai; Jun Zhang; Tianshu Xiao; Hanqin Peng; Sarah M. Sterling; Richard M. Walsh Jr.; Shaun Rawson; Sophia Rits-Volloch; Bing Chen

    doi:10.1101/2020.05.16.099317 Date: 2020-05-17 Source: bioRxiv

    The ongoing SARS-CoV-2 ( severe acute respiratory syndrome MESHD coronavirus 2) pandemic has created urgent needs for intervention strategies to control the crisis. The spike (S) protein of the virus forms a trimer and catalyzes fusion between viral and target cell membranes - the first key step of viral infection MESHD. Here we report two cryo-EM structures, both derived from a single preparation of the full-length S protein, representing the prefusion (3.1[A] resolution) and postfusion (3.3[A] resolution) conformations, respectively. The spontaneous structural transition to the postfusion state under mild conditions is independent of target cells. The prefusion trimer forms a tightly packed structure with three receptor-binding domains clamped down by a segment adjacent to the fusion peptide, significantly different from recently published structures of a stabilized S ectodomain trimer. The postfusion conformation is a rigid tower-like trimer, but decorated by N-linked glycans along its long axis with almost even spacing, suggesting possible involvement in a mechanism protecting the virus from host immune responses and harsh external conditions. These findings advance our understanding of how SARS-CoV-2 enters a host cell and may guide development of vaccines and therapeutics.

    SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins

    Authors: Marti Cortey; Yanli Li; Ivan Diaz; Hepzibar Clilverd; Laila Darwich; Enric Mateu

    doi:10.1101/2020.05.16.099499 Date: 2020-05-17 Source: bioRxiv

    The Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naive human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%.

    Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2

    Authors: Melle Holwerda; Manon Wider; Volker Thiel; Ronald Dijkman

    doi:10.1101/2020.05.17.100404 Date: 2020-05-17 Source: bioRxiv

    With currently over 4 million confirmed cases TRANS worldwide, including more than 300000 deaths MESHD, the current Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) pandemic has a major impact on the economy and health care system. Currently, a limited amount of prophylactic or therapeutic intervention options are available against SARS-CoV-2. In this study, we screened 400 compounds from the antimicrobial Pandemic Response Box library for inhibiting properties against SARS-CoV-2. We identified sixteen compounds that potently inhibited SARS-CoV-2 replication, of which five compounds displayed equal or even higher antiviral activity compared to Remdesivir. These results show that five compounds should be further investigated for their mode of action, safety and efficacy against SARS-CoV-2. HighlightsO_LI400 compounds from the pandemic response box were tested for antiviral activity against SARS-CoV-2. C_LIO_LI5 compounds had an equal or higher antiviral efficacy towards SARS-CoV-2, compared to the nucleoside analogue Remdesivir. C_LI

    Establishment of an African green monkey model for COVID-19

    Authors: Courtney B. Woolsey; Viktoriya Borisevich; Abhishek N Prasad; Krystle N. Agans; Daniel J. Deer; Natalie S. Dobias; John C. Heymann; Stephanie L. Foster; Corri B. Levine; Liana Medina; Kevin Melody; Joan B. Geisbert; Karla A. Fenton; Thomas W. Geisbert; Robert W. Cross

    doi:10.1101/2020.05.17.100289 Date: 2020-05-17 Source: bioRxiv

    Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is responsible for an unprecedented global pandemic of COVID-19. Animal models are urgently needed to study the pathogenesis of COVID-19 and to screen candidate vaccines and treatments. Nonhuman primates (NHP) are considered the gold standard model for many infectious pathogens as they usually best reflect the human condition. Here, we show that African green monkeys support a high level of SARS-CoV-2 replication and develop pronounced respiratory disease MESHD that may be more substantial than reported for other NHP species including cynomolgus and rhesus macaques. In addition, SARS-CoV-2 was detected in mucosal samples of all animals including feces of several animals as late as 15 days after virus exposure. Importantly, we show that virus replication and respiratory disease MESHD can be produced in African green monkeys using a much lower and more natural dose of SARS-CoV-2 than has been employed in other NHP studies.

    REMBRANDT: A high-throughput barcoded sequencing approach for COVID-19 screening.

    Authors: Dario Palmieri; Jalal K Siddiqui; Anne Gardner; Richard Fishel; Wayne Miles

    doi:10.1101/2020.05.16.099747 Date: 2020-05-17 Source: bioRxiv

    The Severe Acute Respiratory Syndrome MESHD Coronavirus-2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), is a highly infectious RNA virus. A still-debated percentage of patients develop coronavirus disease MESHD 2019 (COVID-19) after infection MESHD, whose symptoms include fever MESHD fever HP, cough MESHD cough HP, shortness of breath and fatigue MESHD fatigue HP. Acute and life-threatening respiratory symptoms are experienced by 10-20% of symptomatic patients, particularly those with underlying medical conditions that includes diabetes, COPD and pregnancy. One of the main challenges in the containment of COVID-19 is the identification and isolation of asymptomatic TRANS/pre-symptomatic individuals. As communities re-open, large numbers of people will need to be tested and contact-tracing TRANS of positive patients will be required to prevent additional waves of infections MESHD and enable the continuous monitoring of the viral loads COVID-19 positive patients. A number of molecular assays are currently in clinical use to detect SARS-CoV-2. Many of them can accurately test hundreds or even thousands of patients every day. However, there are presently no testing platforms that enable more than 10,000 tests per day. Here, we describe the foundation for the REcombinase Mediated BaRcoding and AmplificatioN Diagnostic Tool (REMBRANDT), a high-throughput Next Generation Sequencing-based approach for the simultaneous screening of over 100,000 samples per day. The REMBRANDT protocol includes direct two-barcoded amplification of SARS-CoV-2 and control amplicons using an isothermal reaction, and the downstream library preparation for Illumina sequencing and bioinformatics analysis. This protocol represents a potentially powerful approach for community screening, a major bottleneck for testing samples from a large patient population for COVID-19.

    Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel

    Authors: Yipeng Cao; Rui Yang; Wei Wang; Imshik Lee; Ruiping Zhang; Wenwen Zhang; Jiana Sun; Bo Xu; Xiangfei Meng

    doi:10.1101/2020.05.17.099143 Date: 2020-05-17 Source: bioRxiv

    Coronavirus disease MESHD 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease MESHD that is of public health emergency MESHD of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 has high homology with that of severe acute respiratory syndrome MESHD coronavirus. (SARS-CoV) In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms on the basis of combined in silico methods. Our results suggest that the pentameric E protein promotes the penetration of monovalent ions through the channel. Analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore demonstrated a clear wetting/dewetting transition with monovalent cation selectivity under transmembrane voltage, which indicates that it is a hydrophobic voltage-dependent channel. Overall, these results provide structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel.

    Immunoinformatics-Guided Designing of an Epitope-Based Vaccine against Severe Acute Respiratory Syndrome MESHD-Coronavirus-2 Spike Glycoprotein

    Authors: Ahmed Rakib; Saad Ahmed Sami; Arkajyoti Paul; Asif Shahriar; Abu Montakim Tareq; Nazim Uddin Emon; Nusrat Jahan Mimi; Md. Mustafiz Chowdhury; Taslima Akter Eva; Sajal Chakraborty; Sagar Shil; Sabrina Jahan Mily; Talha Bin Emran

    id:10.20944/preprints202005.0271.v1 Date: 2020-05-16 Source: Preprints.org

    Currently, with a large number of fatality rates, coronavirus disease MESHD-2019 (COVID-19) has emerged as a potential threat to human health worldwide. It has been well-known that severe acute respiratory syndrome MESHD-coronavirus-2 (SARS-CoV-2) is responsible for COVID-19 and World Health Organization (WHO) proclaimed the contagious disease MESHD as a global pandemic. Researchers from different parts of the world amalgamate together inquest of remedies for this deadly virus. Recently, it has been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator behind the entrance into the host cells. Our group has comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis along with the phylogenetic analysis. Further, this research work predicted the most immunogenic epitopes for both B-cell and T-cell. Notably, we focused mainly on major histocompatibility complex (MHC) class I potential peptides and predicted two epitopes; WTAGAAAYY and GAAAYYVGY, that bind with the MHC class I alleles which are further validated by molecular docking analysis. Furthermore, this study also proposed that the selected epitopes were shown availability in a greater range of the population. Hence, our study comes up with a strong base for the implementation of designing novel vaccine candidates against SARS-CoV-2, however adequate laboratory works will need to be conducted for the appropriate application.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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