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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (2227)

ProteinN (575)

NSP5 (418)

ComplexRdRp (253)

ProteinE (148)


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SARS-CoV-2 Proteins
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    Development and utilization of an intelligent application for aiding COVID-19 MESHD diagnosis

    Authors: Zirui Meng; Minjin Wang; Huan Song; Shuo Guo; Yanbing Zhou; Weimin Li; Yongzhao Zhou; Mengjiao Li; Xingbo Song; Yi Zhou; Qingfeng Li; Xiaojun Lu; Binwu Ying

    doi:10.1101/2020.03.18.20035816 Date: 2020-03-21 Source: medRxiv

    On basis of laboratory examinations indicators from a total of 620 samples, a machine learning-based diagnosis model was developed, and subsequently implemented as a COVID-19 MESHD diagnosis aid APP. External validation showed satisfiable model prediction performance (i.e., AUC= 0.872) which guarantees the promising use of this tool for extensive screening.

    Building a COVID-19 MESHD Vulnerability Index

    Authors: Dave DeCaprio; Joseph A Gartner III; Thadeus Burgess; Sarthak Kothari; Shaayaan Sayed; Carol J McCall

    doi:10.1101/2020.03.16.20036723 Date: 2020-03-21 Source: medRxiv

    COVID-19 MESHD is an acute respiratory disease MESHD that has been classified as a pandemic by the World Health Organization. Information regarding this particular disease is limited, however, it is known to have high mortality rates, particularly among individuals with preexisting medical conditions. Creating models to identify individuals who are at the greatest risk for severe complications due to COVID-19 MESHD will be useful to help for outreach campaigns in mitigating the diseases worst effects. While information specific to COVID-19 MESHD is limited, a model using complications due to other upper respiratory infections MESHD can be used as a proxy to help identify those individuals who are at the greatest risk. We present the results for three models predicting such complications, with each model having varying levels of predictive effectiveness at the expense of ease of implementation.

    The reflection on an AIDS patient with asymptomatic COVID-19 MESHD 

    Authors: Rongrong Yang; Xien Gui; Shicheng Gao; Pingzheng Mo; Hengning Ke; Yongxi Zhang; Yong Xiong

    doi:10.21203/rs.3.rs-18738/v1 Date: 2020-03-21 Source: ResearchSquare

    We reported the process of exposure, clinical characteristics, diagnosis and prognosis of an A IDS MESHDpatient with asymptomatic COVID-19 MESHD. In our report, we found the asymptomatic is still shedding virus for at least 29 days. Therefore, we suggested that for individuals who had close contact with diagnosed or suspected COVID-19 MESHD patients, in addition to isolation, medical observation, and further related testing if clinical symptoms appear in the observation period, it is best to collect nasopharyngeal and throat swab specimens and test for COVID-19 MESHD nucleic acid as early as possible. The purpose of this active detection is to screen out COVID-19 MESHD asymptomatic patients, and to avoid further transmission through recessive source of i nfection. MESHD Our findings will facilitate understanding of asymptomatic COVID-19 MESHD and improve prevention strategies against COVID-19 MESHD transmission. 

    A meta-analysis of clinical characteristics and mortality COVID-19 MESHD pneumonia

    Authors: Shangxia Jiang; Yueming Wu; Tianzheng Lou; Junlong Xu; Yu Zhang; Hu Chen; Hewei Xu

    doi:10.21203/rs.3.rs-18723/v2 Date: 2020-03-21 Source: ResearchSquare

    Abstract: Objective To investigate the Corona Virus Disease MESHD 2019( COVID-19 MESHD) clinical characteristics and mortality risk by pooling the open published data. Methods Studies relevant to COVID-19 MESHD published in Pubmed, China Wanfang database, ChinaXiv and medRxiv were systematic screened by using the text word of “ COVID-19 MESHD”, 2019-nCoV, “SARS-CoV-2”, “NCP”. The mortality and clinical characteristic of the COVID-19 MESHD cases such as male/female ratio, mechanical ventilation ratio and top c linical symptom rate of the COVID-19 MESHD cases were pooled. Results Ten clinical studies relevant to COVID-19 MESHD were identified by electronic searching the related databases. The combined mortality was 0.03(95%CI: 0.01-0.04) for COVID-19 MESHD cases by random effect model. The pooled female ratio of the COVID-19 MESHD cases from 10 published data was 0.41(95%CI:0.37-0.46). The pooled invasive and non-invasive ventilation ratio were 0.03(95%CI:0.01-0.05) and 0.06(95%CI:0.02-0.09) respectively for patients with COVID-19 MESHD pneumonia MESHD. The pooled clinical symptom rate of fever MESHD, cough MESHD, headache MESHD and fatigue MESHD were 0.80(95%CI:0.60-1.01), 0.12(95%CI:0.08-0.17), 0.68(95%CI:0.57-0.73) and 0.51(95%CI:0.36-0.67) respectively under random effect model. Conclusion According to the present published data, male was more cline to susceptible to COVID-19 MESHD compared to female. The fever MESHD, cough MESHD and fatigue MESHD were the most common symptom of COVID-19 MESHD cases. About 10% of patients received invasive or noninvasive mechanical ventilation with the overall crude mortality of 3%.

    Window of Opportunity for Mitigation to Prevent Overflow of ICU capacity in Chicago by COVID-19 MESHD

    Authors: Sergei Maslov; Nigel Goldenfeld

    id:2003.09564v1 Date: 2020-03-21 Source: arXiv

    We estimate the growth in demand for ICU beds in Chicago during the emerging COVID-19 MESHD epidemic, using state-of-the-art computer simulations calibrated for the SARS-CoV-2 virus. The questions we address are these: (1) Will the ICU capacity in Chicago be exceeded, and if so by how much? (2) Can strong mitigation strategies, such as lockdown or shelter in place order, prevent the overflow of capacity? (3) When should such strategies be implemented? Our answers are as follows: (1) The ICU capacity may be exceeded by a large amount, probably by a factor of ten. (2) Strong mitigation can avert this emergency situation potentially, but even that will not work if implemented too late. (3) If the strong mitigation precedes April 1st, then the growth of COVID-19 MESHD can be controlled and the ICU capacity could be adequate. The earlier the strong mitigation is implemented, the greater the probability that it will be successful. After around April 1 2020, any strong mitigation will not avert the emergency situation. In Italy, the lockdown occurred too late and the number of deaths is still doubling every 2.3 days. It is difficult to be sure about the precise dates for this window of opportunity, due to the inherent uncertainties in computer simulation. But there is high confidence in the main conclusion that it exists and will soon be closed. Our conclusion is that, being fully cognizant of the societal trade-offs, there is a rapidly closing window of opportunity to avert a worst-case scenario in Chicago, but only with strong mitigation/lockdown implemented in the next week at the latest. If this window is missed, the epidemic will get worse and then strong mitigation/lockdown will be required after all, but it will be too late.

    Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis

    Authors: Rahila Sardar; Deepshikha Satish; Shweta Birla; Dinesh Gupta

    doi:10.1101/2020.03.21.001586 Date: 2020-03-21 Source: bioRxiv

    The ongoing pandemic of the coronavirus disease 2019 MESHD ( COVID-19 MESHD) is an infectious disease MESHD caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). We have performed an integrated sequence-based analysis of SARS-CoV2 genomes from different geographical locations in order to identify its unique features absent in SARS-CoV MESHD and other related coronavirus family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique features of the SARS-CoV2 genome, which includes a unique mutation in the spike surface glycoprotein (A930V (24351C>T)) in the Indian SARS-CoV2, absent in other strains studied here. We have also predicted the impact of the mutations in the spike glycoprotein PROTEIN function and stability, using computational approach. To gain further insights into host responses to viral infection MESHD, we predict that antiviral host-miRNAs may be controlling the viral pathogenesis. Our analysis reveals nine host miRNAs which can potentially target SARS-CoV2 genes. Interestingly, the nine miRNAs do not have targets in SARS and MERS genomes. Also, hsa- miR-27b HGNC is the only unique miRNA which has a target gene in the Indian SARS-CoV2 genome. We also predicted immune epitopes in the genomes

    RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWAB USING QIAGEN RNEASY KITS OR DIRECTLY VIA OMISSION OF AN RNA EXTRACTION STEP

    Authors: Emily A Bruce; Meei-Li Huang; Garrett A Perchetti; Scott Tighe; Jessica J Hoffman; Pheobe Laaguiby; Diana L Gerrard; Arun Nalla; Yulun Wei; Alexander L Greninger; Sean A. Diehl; David J Shirley; Debra G. B. Leonard; Christopher D. Huston; Beth D. Kirkpatrick; Julie Dragon; Jessica W Crothers; Keith R Jerome; Jason W Botten

    doi:10.1101/2020.03.20.001008 Date: 2020-03-21 Source: bioRxiv

    The ongoing COVID-19 MESHD COVID-19 MESHD pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 MESHD testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 MESHD patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 MESHD testing and should be applicable throughout the world.

    Molecular characterization of SARS-CoV-2 in the first COVID-19 MESHD cluster in France reveals an amino-acid deletion in nsp2 HGNC (Asp268Del)

    Authors: Antonin Bal; Gregory Destras; Alexandre Gaymard; Maude Bouscambert-Duchamp; Martine Valette; Vanessa Escuret; Emilie Frobert; Genevieve Billaud; Sophie Trouillet-Assant; Valerie Cheynet; Karen Brengel-Pesce; Florence Morfin; Bruno Lina; Laurence Josset

    doi:10.1101/2020.03.19.998179 Date: 2020-03-21 Source: bioRxiv

    We present the first genetic characterization of a COVID-19 MESHD cluster in Europe using metagenomic next-generation sequencing (mNGS). Despite low viral loads, the mNGS workflow used herein allowed to characterize the whole genome sequences of SARS-CoV2 isolated from an asymptomatic patient, in 2 clinical samples collected 1 day apart. Comparison of these sequences suggests viral evolution with development of quasispecies. In addition, the present workflow identified a new deletion in nsp2 HGNC (Asp268Del) which was found in all 3 samples originating from this cluster as well as in 37 other viruses collected in England and in Netherlands, suggesting the spread of this deletion in Europe. The impact of Asp268Del on SARS-CoV-2 transmission and pathogenicity, as well as on PCR performances and anti-viral strategy should be rapidly evaluated in further studies.

    All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus

    Authors: Xiong Ding; Kun Yin; Ziyue Li; Changchun Liu

    doi:10.1101/2020.03.19.998724 Date: 2020-03-21 Source: bioRxiv

    A recent outbreak of novel coronavirus (SARS-CoV-2), the causative agent of COVID-19 MESHD, has spread rapidly all over the world. Human immunodeficiency MESHD virus ( HIV MESHD) is another deadly virus and causes acquired immunodeficiency syndrome MESHD ( AIDS MESHD). Rapid and early detection of these viruses will facilitate early intervention and reduce disease transmission risk. Here, we present an All-In-One Dual CRISPR-Cas12a (termed "AIOD-CRISPR") assay method for simple, rapid, ultrasensitive, one-pot, and visual detection of coronavirus SARS-CoV-2 and HIV virus MESHD. In our AIOD CRISPR assay, a pair of crRNAs was introduced to initiate dual CRISPR-Cas12a detection and improve detection sensitivity. The AIOD-CRISPR assay system was successfully utilized to detect nucleic acids (DNA and RNA) of SARS-CoV-2 and HIV with a sensitivity of few copies. Also, it was evaluated by detecting HIV-1 RNA extracted from human plasma samples, achieving a comparable sensitivity with real-time RT-PCR method. Thus, our method has a great potential for developing next-generation point-of-care molecular diagnostics.

    Network structure of COVID-19 MESHD spread and the lacuna in India's testing strategy

    Authors: Anand Sahasranaman; Nishanth Kumar

    id:2003.09715v1 Date: 2020-03-21 Source: arXiv

    We characterize the network of COVID-19 MESHD spread in India and find that the transmission rate is 0.43, with daily case growth driven by individuals who contracted the virus abroad. We explore the question of whether this represents exponentially decaying dynamics or is simply an artefact of India's testing strategy. Testing has largely been limited to individuals travelling from high-risk countries and their immediate contacts, meaning that the network reflects positive identifications from a biased testing sample. Given generally low levels of testing and an almost complete absence of testing for community spread, there is significant risk that we may be missing out on the actual nature of outbreak. India still has an apparently low current caseload, with possibly a small window of time to act, and should therefore aggressively and systematically expand random testing for community spread, including for asymptomatic cases. This will help understand true transmission characteristics and plan appropriately for the immediate future.

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MeSH Disease
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SARS-CoV-2 Proteins


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