Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (193)

Fever (160)

Cough (132)

Hypertension (91)

Respiratory distress (61)


Transmission

Transmission (527)

age categories (494)

fomite (226)

gender (223)

asymptotic cases (186)


Seroprevalence
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    K18-hACE2 Mice for Studies of COVID-19 Treatments and Pathogenesis Including Anosmia HP

    Authors: Stanley Perlman; Jian Zheng; LOK YIN ROY WONG; Kun Li; Abhishek K Verma; Miguel E Ortiz Bezara; Christine Wohlford-Lenane; Mariah R. Leidinger; Michael C. Kundson; David K. Meyerholz; Paul B McCray Jr.

    doi:10.1101/2020.08.07.242073 Date: 2020-08-10 Source: bioRxiv

    The ongoing COVID-19 pandemic is associated with substantial morbidity and mortality. While much has been learned in the first months of the pandemic, many features of COVID-19 pathogenesis remain to be determined. For example, anosmia HP is a common presentation and many patients with this finding show no or only minor respiratory signs. Studies in animals experimentally infected with SARS-CoV-2, the cause of COVID-19, provide opportunities to study aspects of the disease MESHD not easily investigated in human patients. COVID-19 severity ranges from asymptomatic TRANS to lethal. Most experimental infections MESHD provide insights into mild disease MESHD. Here, using K18-hACE2 mice that we originally developed for SARS studies, we show that infection MESHD with SARS-CoV-2 causes severe disease in the lung MESHD, and in some mice, the brain. Evidence of thrombosis MESHD and vasculitis MESHD vasculitis HP was detected in mice with severe pneumonia MESHD pneumonia HP. Further, we show that infusion of convalescent plasma SERO (CP) from a recovered COVID-19 patient provided protection against lethal disease MESHD. Mice developed anosmia HP at early times after infection MESHD. Notably, while treatment with CP prevented significant clinical disease MESHD, it did not prevent anosmia HP. Thus K18-hACE2 mice provide a useful model for studying the pathological underpinnings of both mild and lethal COVID-19 and for assessing therapeutic interventions.

    Comparative analyses of SARS-CoV-2 binding (IgG, IgM, IgA) and neutralizing antibodies SERO from human serum samples SERO

    Authors: Livia Mazzini; Donata Martinuzzi; Inesa Hyseni; Giulia Lapini; Linda Benincasa; Pietro Piu; Claudia Maria Trombetta; Serena Marchi; Ilaria Razzano; Alessandro Manenti; Emanuele Montomoli

    doi:10.1101/2020.08.10.243717 Date: 2020-08-10 Source: bioRxiv

    A newly identified coronavirus, named SARS-CoV-2, emerged in December 2019 in Hubei Province, China, and quickly spread throughout the world; so far, it has caused more than 18 million cases of disease MESHD and 700,000 deaths MESHD. The diagnosis of SARS-CoV-2 infection MESHD is currently based on the detection of viral RNA in nasopharyngeal swabs by means of molecular-based assays, such as real-time RT-PCR. Furthermore, serological assays SERO aimed at detecting different classes of antibodies SERO constitute the best surveillance strategy for gathering information on the humoral immune response to infection MESHD and the spread of the virus through the population, in order to evaluate the immunogenicity of novel future vaccines and medicines for the treatment and prevention of COVID-19 disease MESHD. The aim of this study was to determine SARS-CoV-2-specific antibodies SERO in human serum samples SERO by means of different commercial and in-house ELISA SERO kits, in order to evaluate and compare their results first with one another and then with those yielded by functional assays using wild-type virus. It is important to know the level of SARS-CoV-2-specific IgM, IgG and IgA antibodies SERO in order to predict population immunity and possible cross-reactivity with other coronaviruses and to identify potentially infectious subjects. In addition, in a small sub-group of samples, we performed a subtyping Immunoglobulin G ELISA SERO. Our data showed an excellent statistical correlation between the neutralization titer and the IgG, IgM and IgA ELISA SERO response against the receptor-binding domain of the spike protein, confirming that antibodies SERO against this portion of the virus spike protein are highly neutralizing and that the ELISA SERO Receptor-Binding Domain-based assay can be used as a valid surrogate for the neutralization assay in laboratories which do not have Biosecurity level-3 facilities.

    Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

    Authors: Gregory Queromes; Gregory Destras; Antonin Bal; Hadrien Regue; Gwendolyne Burfin; Solenne Brun; Remi Fanget; Florence Morfin; Martine Valette; Bruno Lina; Emilie Frobert; Laurence Josset

    doi:10.1101/2020.08.07.241653 Date: 2020-08-10 Source: bioRxiv

    Through routine genomic surveillance of the novel SARS-CoV-2 virus (n=229 whole genome sequences), 2 different frameshifting deletions were newly detected in the open reading frame (ORF) 6, starting at the same position (27267). While the 26-nucleotide deletion variant was only found in one sample in March 2020, the 34-nucleotide deletion variant was found within a single geriatric hospital unit in 5/9 patients sequenced and one health care worker with samples collected between April 2nd and 9th, 2020. Both the presence of the 34-nucleotide deletion variant limited to this unit and the clustering of the corresponding whole genome sequences by phylogeny analysis strongly suggested a nosocomial transmission TRANS between patients. Interestingly, prolonged viral excretion of the 34-nucleotide deletion variant was identified in a stool sample 14 days after initial diagnosis for one patient. Clinical data revealed no significant difference in disease MESHD severity between patients harboring the wild-type or the 34-nucleotide deletion variants. The in vitro infection MESHD of the two deletion variants on primate endothelial kidney cells (BGM) and human lung adenocarcinoma MESHD lung adenocarcinoma HP cells (Calu-3) yielded comparable replication kinetics with the wild-type strain. Furthermore, high viral loads were found in vivo regardless of the presence or absence of the ORF6 deletion. Our study highlights the transmission TRANS and replication capacity of two newly described deletion variants in the same ORF6 region.

    Individualized Prediction of COVID-19 Adverse outcomes with MLHO

    Authors: Hossein Estiri; Zachary H. Strasser; Shawn N. Murphy

    id:2008.03869v1 Date: 2020-08-10 Source: arXiv

    The COVID-19 pandemic has devastated the world with health and economic wreckage. Precise estimates of the COVID-19 adverse outcomes on individual patients could have led to better allocation of healthcare resources and more efficient targeted preventive measures. We developed MLHO (pronounced as melo) for predicting patient-level risk of hospitalization, ICU admission, need for mechanical ventilation, and death MESHD from patients' past (before COVID-19 infection MESHD) medical records. MLHO is an end-to-end Machine Learning pipeline that implements iterative sequential representation mining and feature and model selection to predict health outcomes. MLHO's architecture enables a parallel and outcome-oriented calibration, in which different statistical learning algorithms and vectors of features are simultaneously tested and leveraged to improve prediction of health outcomes. Using clinical data from a large cohort of over 14,000 patients, we modeled the four adverse outcomes utilizing about 600 features representing patients' before-COVID health records. Overall, the best predictions were obtained from extreme and gradient boosting models. The median AUC ROC for mortality prediction was 0.91, while the prediction performance SERO ranged between 0.79 and 0.83 for ICU, hospitalization, and ventilation. We broadly describe the clusters of features that were utilized in modeling and their relative influence on predicting each outcome. As COVID-19 cases are re-surging in the U.S. and around the world, a Machine Learning pipeline like MLHO is crucial to improve our readiness for confronting the potential future waves of COVID-19, as well as other novel infectious diseases MESHD that may emerge in the near future.

    Prediction of Covid-19 Infections MESHD Through December 2020 for 10 US States Using a Two Parameter Transmission TRANS Model Incorporating Outdoor Temperature and School Re-Opening Effects

    Authors: Ty A Newell

    doi:10.1101/2020.08.06.20169896 Date: 2020-08-07 Source: medRxiv

    Covid-19 infection MESHD case predictions (total cases) are made for August through December 2020 for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, and NC). A two-parameter model based on social distance index (SDI) and disease MESHD transmission TRANS efficiency (G) parameters is used to characterize SARS-CoV-2 disease MESHD disease spread TRANS spread. Current lack of coherent and coordinated US policy causes the US to follow a linear infection MESHD growth path with a limit cycle behavior that modulates the US between accelerating and decaying infection MESHD growth on either side of a linear growth path boundary. Four prediction cases are presented: 1) No school re-openings; fall HP season temperature effect 2) No school re-openings; no fall HP season temperature effect 3) School re-openings; fall HP season temperature effect 4) School re-openings; no fall HP season temperature effect Fall HP outdoor temperatures, in contrast to the 1918 pandemic, are predicted to be beneficial for dampening SARS-CoV-2 transmission TRANS in States as they pass through swing season temperature range of 70F to 50F. Physical re-opening of schools in September are predicted to accelerate infections MESHD. States with low current infectious case numbers (eg, NY) are predicted to be minimally impacted while States with high current infectious case numbers (eg, CA and FL) will be significantly impacted by school re-openings. Updated infection MESHD predictions will be posted monthly (Sept, Oct, Nov, Dec) with adjustments based on actual trends in SDI and G. Assessments related to outdoor temperature impact, school re-openings, and other public gathering re-openings will be discussed in updated reports.

    Expression of ACE2, TMPRSS2, and CTSL in human airway epithelial cells under physiological and pathological conditions: Implications for SARS-CoV2 infection MESHD

    Authors: Junping Yin; Brigitte Kasper; Frank Petersen; Xinhua Yu

    doi:10.1101/2020.08.06.240796 Date: 2020-08-07 Source: bioRxiv

    SARS-CoV-2 enters into human airway epithelial cells via membrane fusion or endocytosis, and this process is dependent on ACE2, TMPRSS2, and cathepsin L. In this study, we examined the expression profiles of the three SARS-CoV-2 entry-related genes in primary human airway epithelial cells isolated from donors with different physiological and pathological backgrounds such as smoking, COPD, asthma MESHD asthma HP, lung cancer, allergic rhinitis MESHD allergic rhinitis HP, cystic fibrosis MESHD, or viral infections MESHD. By reanalyzing 54 GEO datasets comprising transcriptomic data of 3428 samples, this study revealed that i) smoking is associated with an increased expression of ACE2 and TMPRSS2 and a decreased expression of cathepsin L; ii) infection MESHD of rhinovirus as well as poly(I:C) stimulation leads to high expression of all three SARS-CoV-2 entry-related genes; iii) expression of ACE2 and cathepsin L in nasal epithelial cells are decreased in patients with asthma MESHD asthma HP and allergic rhinitis MESHD allergic rhinitis HP. In conclusion, this study implicates that infection MESHD of respiratory viruses, cigarette smoking and allergic respiratory diseases MESHD might affect the susceptibility to and the development of COVID-19.

    Single-cell RNA-seq reveals profound monocyte changes in Paediatric Inflammatory Multisystem Syndrome MESHD Temporally associated with SARS-CoV-2 infection MESHD (PIMS-TS)

    Authors: Eleni Syrimi; Eanna Fennell; Alex Richter; Pavle Vrljicak; Richard Stark; Sascha Ott; Paul G Murray; Eslam Al-abadi; Ashish Chikermane; Pamela Dawson; Scott Hackett; Deepthi Jyothish; Hari Krishnan Kanthimathinathan; Sean Monaghan; Prasad Nagakumar; Barnaby R Scholefield; Steven Welch; Pamela Kearns; Graham Taylor

    doi:10.1101/2020.08.06.20164848 Date: 2020-08-07 Source: medRxiv

    Paediatric inflammatory multisystem inflammatory syndrome MESHD temporally associated with SARS-CoV-2 infection MESHD (PIMS-TS) is a new disease MESHD with overlapping features of Kawasaki disease MESHD (KD) and toxic shock MESHD shock HP syndrome MESHD. Unbiased single cell RNA sequencing analysis of peripheral blood SERO mononuclear cells from PIMS-TS and KD patients shows monocytes are the main source of pro-inflammatory cytokines and large changes in the frequency of classical, intermediate and non-classical monocytes occur in both diseases MESHD.

    Dynamics of neutralizing antibody SERO titers in the months after SARS-CoV-2 infection MESHD

    Authors: Katharine HD Crawford; Adam S Dingens; Rachel Eguia; Caitlin R Wolf; Naomi Wilcox; Jennifer K Logue; Kiel Shuey; Amanda M Casto; Brooke Fiala; Samuel Wrenn; Deleah Pettie; Neil P King; Helen Y Chu; Jesse D Bloom

    doi:10.1101/2020.08.06.20169367 Date: 2020-08-07 Source: medRxiv

    Most individuals infected with SARS-CoV-2 develop neutralizing antibodies SERO that target the viral spike protein. Here we quantify how levels of these antibodies SERO change in the months following SARS-CoV-2 infection MESHD by examining longitudinal samples collected between {approx}30 and 152 days post- symptom onset TRANS from a prospective cohort of 34 recovered individuals with asymptomatic TRANS, mild, or moderate-severe disease MESHD. Neutralizing antibody SERO titers declined an average of about four-fold from one to four months post- symptom onset TRANS. Importantly, our data are consistent with the expected early immune response to viral infection MESHD, where an initial peak in antibody SERO levels is followed by a decline to a lower plateau. Additional studies of long-lived B-cells and antibody SERO titers over longer time frames are necessary to determine the durability of immunity to SARS-CoV-2.

    Quickly And Simply Detection For Coronavirus Including SARS-CoV-2 On The Mobile Real-Time PCR Device And Without RNA Extraction

    Authors: Masaaki Muraoka; Yukiko Tanoi; Tetsutaro Tada; MIkio Mizukoshi; Osamu Kawaguchi

    doi:10.1101/2020.08.06.20168294 Date: 2020-08-07 Source: medRxiv

    Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) was reported to WHO as an outbreak in Wuhan City, Hubei Province, China on end of 2019, afterwards epidemic in many countries, and pandemic on the worldwide in 2020. Usually detection of coronavirus including SARS-CoV-2 was detected by real-time RT-PCR method, but it must be long time that RNA is treated by extraction, concentration and purification, and detected by RT-PCR method. We modified various methods, of which evaluated if each method is short and simple enough. In one point of the evaluations, real-time RT-PCR could be finished in very short time with using mobile real-time PCR device PCR1100 (Nippon Sheet Glass Co. Ltd.). It was able to detect positive control RNA for 20 minutes by each method according to the National Institute of Infections MESHD Disease MESHD in Japan (NIID), and less than 13.5 minutes according to the Centers for Disease MESHD Control and Prevention in USA (CDC). In another point of the evaluations, surprisingly, Human coronavirus 229E, which was substituted for SARS-CoV-2, could be detected in crude state without treatment in advance of RNA. As that was, it was possible to detect coronavirus with direct RT-PCR. Therefore, it might eliminate wasteful time, avoid secondary infection MESHD infection and risk TRANS infection and risk TRANS and risk of contamination. In light of the above two points, SARS-CoV-2 might be detected more quickly and more simply. With using this mobile real-time PCR, these methods should be suitable for not only SARS-CoV-2 but also other various viruses and might save time compared to earlier detection methods.

    Clinical and intestinal histopathological findings in SARS-CoV-2/COVID-19 patients with hematochezia HP

    Authors: Margaret Cho; Weiguo Liu; Sophie Balzora; Yvelisse Suarez; Deepthi Hoskoppal; Neil D Theise; Wenqing Cao; Suparna A Sarkar

    doi:10.1101/2020.07.29.20164558 Date: 2020-08-07 Source: medRxiv

    Gastrointestinal (GI) symptoms of SARS-CoV2/COVID-19 in the form of anorexia MESHD anorexia HP, nausea MESHD nausea, vomiting HP, vomiting MESHD, abdominal pain MESHD abdominal pain HP and diarrhea MESHD diarrhea HP are usually preceeded by respiratory manifestations and are associated with a poor prognosis. Hematochezia HP is an uncommon clinical presentation of COVID-19 disease MESHD and we hypothesize that older patients with significant comorbidites ( obesity MESHD obesity HP and cardiovascular) and prolonged hospitalization are suspectible to ischemic injury to the bowel. We reviewed the clinical course, key laboratory data including acute phase reactants, drug/medication history in two elderly TRANS male TRANS patients admitted for COVID-19 respiratory failure HP. Both patients had a complicated clinical course and suffered from hematochezia HP and acute blood SERO loss anemia MESHD anemia HP requiring blood SERO transfusion around day 40 of their hospitalization. Colonoscopic impressions were correlated with the histopathological findings in the colonic biopies and changes compatible with ischemia MESHD to nonspecific acute inflammation MESHD, edema MESHD edema HP and increased eosinophils in the lamina propria were noted.Both patients were on anticoagulants, multiple antibiotics and antifungal agents due to respiratory infections MESHD at the time of lower GI bleeding. Hematochezia HP resolved spontaneously with supportive care. Both patients eventually recovered and were discharged. Elderly TRANS patients with significant comorbid conditions are uniquely at risk for ischemic injury to the bowel. Hypoxic conditions due to COVID-19 pneumonia MESHD pneumonia HP and respiratory failure HP, compounded by preexisting cardiovascular complications, and/or cytokine storm orchestrated by the viral infection MESHD leading to alteration in coagulation profile and/or drug/medication injury can be difficult to distinguish in these critically ill patients. Presentation of hematochezia HP may further increase the mortality and morbidity of COVID-19 patients, and prompt consultation and management by gastroenterology is therefore warranted.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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