Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (1295)

Fever (190)

Cough (154)

Respiratory distress (95)

Hypertension (79)


Transmission

Seroprevalence
    displaying 61 - 70 records in total 1295
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    Authors: Zhe Wang; Chenhao Jiang; Xuxuan Zhang; Yingna Zhang; Yan Ren; Xiangting Gao

    doi:10.21203/rs.3.rs-72821/v1 Date: 2020-09-05 Source: ResearchSquare

    Background: Coronavirus disease 2019 (COVID-19) is a disease that causes fatal disorders MESHD including severe pneumonia HP pneumonia MESHD. Our study aimed to utilize bioinformatics method to analyze the expression profiling by high throughput sequencing in human bronchial organoids/primary human airway epithelial infected MESHD with SARS-CoV-2 to identify the potentially crucial genes and pathways associated with COVID-19.Methods: We analyzed microarray datasets GSE153970 and GSE150819 derived from the GEO database. Firstly, the Differentially expressed genes (DEGs) in human bronchial organoids/primary human airway epithelial infected MESHD with SARS-CoV-2. Next, the DEGs were used for GO and KEGG pathway enrichment analysis. Then, the PPI network was constructed and Cytoscape was used to find the key genes.Results: Gene expression profiles of GSE153970 and GSE150819, in all 12 samples were analyzed. A total of 145 DEGs and 5 hub genes were identified in SARS-CoV-2. Meanwhile, we found that the 145 genes are associated with immune responses and the top 5 hub genes including CXCL8, CXCL1, CXCL2, CCL20, and CSF2 were mainly related to leukocyte migration, endoplasmic reticulum lumen, receptor ligand activity. In addition, the results also showed that the hub genes were associated with Cytokine−cytokine receptor interaction, IL−17 signaling pathway, and Rheumatoid arthritis HP Rheumatoid arthritis MESHD in SARS-CoV-2 infection MESHD.Conclusion: The five crucial genes consisting of CXCL8, CXCL1, CXCL2, CCL20, and CSF2 were considered as hub genes of SARS-CoV-2, which may be used as diagnostic biomarkers or molecular targets for the treatment of SARS-CoV-2. It is evidenced that bioinformatics analyses in SARS-CoV-2 can be useful for understanding the underlying molecular mechanism and exploring effective therapeutic targets.

    Clustering COVID-19 Lung Scans

    Authors: Jacob Householder; Andrew Householder; John Paul Gomez-Reed; Fredrick Park; Shuai Zhang

    id:2009.09899v1 Date: 2020-09-05 Source: arXiv

    With the recent outbreak of COVID-19, creating a means to stop it's spread and eventually develop a vaccine are the most important and challenging tasks that the scientific community is facing right now. The first step towards these goals is to correctly identify a patient that is infected with the virus. Our group applied an unsupervised machine learning technique to identify COVID-19 cases. This is an important topic as COVID-19 is a novel disease currently being studied in detail and our methodology has the potential to reveal important differences between it and other viral pneumonia MESHD pneumonia HP. This could then, in turn, enable doctors to more confidently help each patient. Our experiments utilize Principal Component Analysis (PCA), t-distributed Stochastic Neighbor Embedding (t-SNE), and the recently developed Robust Continuous Clustering algorithm (RCC). We display the performance SERO of RCC in identifying COVID-19 patients and its ability to compete with other unsupervised algorithms, namely K-Means++ (KM++). Using a COVID-19 Radiography dataset, we found that RCC outperformed KM++; we used the Adjusted Mutual Information Score (AMI) in order to measure the effectiveness of both algorithms. The AMI for the two and three class cases of KM++ were 0.0250 and 0.054, respectively. In comparison, RCC scored 0.5044 in the two class case and 0.267 in the three class case, clearly showing RCC as the superior algorithm. This not only opens new possible applications of RCC, but it could potentially aid in the creation of a new tool for COVID-19 identification.

    Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients

    Authors: Anthony Levasseur; Jeremy Delerce; Aurelia Caputo; Ludivine Brechard; Philippe Colson; Jean-Christophe Lagier; Pierre-Edouard Fournier; Didier Raoult

    doi:10.1101/2020.09.04.282616 Date: 2020-09-04 Source: bioRxiv

    The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia MESHD pneumonia HP. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility TRANS, infectivity, severity of symptoms and mortality associated to this infectious disease MESHD. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5/3 UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

    Combined lymphocyte/monocyte count, D-dimer and iron status predict COVID-19 course and outcome in a long-term care facility

    Authors: Flavia Biamonte; Cirino Botta; Maria Mazzitelli; Salvatore Rotundo; Enrico Maria Trecarichi; Daniela Foti; Carlo Torti; Giuseppe Viglietto; Daniele Torella; Francesco Costanzo

    doi:10.21203/rs.3.rs-72047/v1 Date: 2020-09-04 Source: ResearchSquare

    Background: The Sars-CoV-2 can cause severe pneumonia HP pneumonia MESHD with multiorgan disease, which created an urgent need for the identification of clinical and laboratory predictors of the progression towards severe and fatal forms of this illness. In the present study, we retrospectively evaluated and integrated laboratory parameters/variables of 45 elderly TRANS subjects from a long-term care facility with Sars-CoV-2 outbreak and spread, to identify potential common patterns of systemic response able to better stratify patients’ clinical course and outcome.Methods: Baseline white blood SERO cells, granulocytes’, lymphocytes’, and platelets’ counts, hemoglobin, total iron, ferritin, D-dimer, and interleukin 6 (IL-6) concentration were used to generate a principal component analysis (PCA). Statistical analysis was performed by using R statistical package version 4.0.Results: Of the 45 patients, 19 were male TRANS and 26 were female TRANS, with a median age TRANS of 81 years. The overall mortality rate was 26.67%. By PCA and clustering approach we identified 3 laboratory patterns of response, renamed as low-risk, intermediate-risk, and high-risk, strongly associated with patients’ survival (p<0.01). D-dimer, iron status, lymphocyte/monocyte count represented the main markers discriminating high- and low-risk groups. Furthermore, patients belonging to the high-risk group presented a significantly longer time to ferritin decrease (p:0.047). Iron-to-ferritin-ratio (IFR) significantly segregated recovered and dead patients in the intermediate-risk group (p:0.012).Conclusions: Our data generate the hypothesis that a combination of few laboratory parameters, and in particular iron status, D-dimer and lymphocyte/monocyte count at admission and during the hospital stay, can predict clinical progression in COVID-19.

    Performance SERO of serum SERO apolipoprotein-A1 as a sentinel of Covid-19

    Authors: Thierry Poynard; Olivier Deckmyn; Marika Rudler; Valentina Peta; Yen Ngo; Mathieu Vautier; Sepideh Akhavan; Vincent Calvez; Clemence Franc; Jean Marie Castille; Fabienne Drane; Mehdi Sakka; Dominique Bonnefont-Rousselot; Jean Marc Lacorte; David Saadoun; Yves Allenbach; Olivier Benveniste; Frederique Gandjbakhch; Julien Mayaux; Olivier Lucidarme; Bruno Fautrel; Vlad Ratziu; Chantal Housset; Dominique Thabut; Patrice Cacoub; Fredrik Nyberg; Jose D Posada; Christian G Reich; Lisa M Schilling; Karishma Shah; Nigham H Shah; Vignesh Subbian; Lin Zhang; Hong Zhu; Patrick Ryan; Daniel Prieto-Alhambra; Kristin Kostka; Talita Duarte-Salles

    doi:10.1101/2020.09.01.20186213 Date: 2020-09-03 Source: medRxiv

    Background Since 1920, a decrease in serum SERO cholesterol has been identified as a marker of severe pneumonia HP pneumonia MESHD. We have assessed the performance SERO of serum SERO apolipoprotein-A1, the main transporter of HDL-cholesterol, to identify the early spread of coronavirus disease MESHD 2019 (Covid-19) in the general population and its diagnostic performance SERO for the Covid-19. Methods We compared the daily mean serum SERO apolipoprotein-A1 during the first 34 weeks of 2020 in a population that is routinely followed for a risk of liver fibrosis MESHD risk in the USA (212,297 sera) and in France (20,652 sera) in relation to a local increase in confirmed cases TRANS, and in comparison to the same period in 2019 (266,976 and 28,452 sera, respectively). We prospectively assessed the sensitivity SERO of this marker in an observational study of 136 consecutive hospitalized cases and retrospectively evaluated its specificity in 7,481 controls representing the general population. Results The mean serum SERO apolipoprotein-A1 levels in the survey populations began decreasing in January 2020, compared to the same period in 2019. This decrease was highly correlated with the daily increase in confirmed Covid-19 cases in the following 34 weeks, both in France and USA, including the June and mid-July recovery periods in France. Apolipoprotein-A1 at the 1.25 g/L cutoff had a sensitivity SERO of 90.6% (95%CI84.2-95.1) and a specificity of 96.1% (95.7-96.6%) for the diagnosis of Covid-19. The area under the characteristics curve was 0.978 (0.957-0.988), and outperformed haptoglobin and liver function tests. The adjusted risk ratio of apolipoprotein-A1 for survival without transfer to intensive care unit was 5.61 (95%CI 1.02-31.0;P=0.04). Conclusion Apolipoprotein-A1 could be a sentinel of the pandemic in existing routine surveillance of the general population. NCT01927133, CER-2020-14.

    Deep-learning convolutional neural networks with transfer learning accurately classify COVID19 lung infection MESHD on portable chest radiographs

    Authors: Shreeja Kikkisetti; Jocelyn Zhu; Beiyi Shen; Haifang Li; Tim Duong; Peng Wang; Xu Zhang; Kangli Cui; Tingting Tao; Zhongyu Li; Wenwen Chen; Yongtang Zheng; Jianhua Qin; Zhiqiang Ku; Zhiqiang An; Birte Kalveram; Alexander N Freiberg; Vineet D Menachery; Xuping Xie; Kenneth S Plante; Scott C Weaver; Pei-Yong Shi; Pieter S. Hiemstra; Bruce A. Ponder; Mika J Makela; Kristiina Malmstrom; Robert C. Rintoul; Paul A. Reyfman; Fabian J. Theis; Corry-A Brandsma; Ian Adcock; Wim Timens; Cheng J. Xu; Maarten van den Berge; Roland F. Schwarz; Gerard H. Koppelman; Martijn C. Nawijn; Alen Faiz

    doi:10.1101/2020.09.02.20186759 Date: 2020-09-02 Source: medRxiv

    Portable chest x-ray (pCXR) has become an indispensable tool in the management of Coronavirus Disease MESHD 2019 (COVID-19) lung infection MESHD. This study employed deep-learning convolutional neural networks to classify COVID-19 lung infections on pCXR from normal and related lung infections MESHD to potentially enable more timely and accurate diagnosis. This retrospect study employed deep-learning convolutional neural network (CNN) with transfer learning to classify based on pCXRs COVID-19 pneumonia HP pneumonia MESHD (N=455) on pCXR from normal (N=532), bacterial pneumonia MESHD pneumonia HP (N=492), and non-COVID viral pneumonia MESHD pneumonia HP (N=552). The data was split into 75% training and 25% testing. A five-fold cross-validation was used. Performance SERO was evaluated using receiver-operating curve analysis. Comparison was made with CNN operated on the whole pCXR and segmented lungs. CNN accurately classified COVID-19 pCXR from those of normal, bacterial pneumonia MESHD pneumonia HP, and non-COVID-19 viral pneumonia MESHD pneumonia HP patients in a multiclass model. The overall sensitivity SERO, specificity, accuracy, and AUC were 0.79, 0.93, and 0.79, 0.85 respectively (whole pCXR), and were 0.91, 0.93, 0.88, and 0.89 (CXR of segmented lung). The performance SERO was generally better using segmented lungs. Heatmaps showed that CNN accurately localized areas of hazy appearance, ground glass opacity and/or consolidation on the pCXR. Deep-learning convolutional neural network with transfer learning accurately classifies COVID-19 on portable chest x-ray against normal, bacterial pneumonia MESHD pneumonia HP or non-COVID viral pneumonia MESHD pneumonia HP. This approach has the potential to help radiologists and frontline physicians by providing more timely and accurate diagnosis.

    Occurrence of Pneumothorax HP and Pneumomediastinum HP in Covid-19 patients during non-invasive ventilation with Continuous Positive Airway Pressure

    Authors: Antonio Gidaro; Federica Samartin; Anna Maria Brambilla; Chiara Cogliati; Stella Ingrassia; Francesco Banfi; Viola Cupiraggi; Cecilia Bonino; Marco Schiuma; Andrea Giacomelli; Stefano Rusconi; Emanuele Salvi

    doi:10.1101/2020.08.31.20185348 Date: 2020-09-02 Source: medRxiv

    Background: Acute Hypoxemic Respiratory Failure MESHD Respiratory Failure HP ( AHRF MESHD) is a common complication of Covid-19 related pneumonia HP pneumonia MESHD, for which non-invasive ventilation (NIV) with Helmet Continuous Positive Airway Pressure (CPAP) is widely used. During past epidemics of SARS and MERS pneumomediastinum HP (PNM) and pneumothorax HP (PNX) were common complications (respectively 1.7-12% and 16,4%) either spontaneous or associated to ventilation. Methods: Aim of our retrospective study was to investigate the incidence of PNX/PNM in COVID-19 pneumonia HP pneumonia MESHD patients treated with CPAP. Moreover, we examined the correlation between PNX/PNM and Positive end-expiratory pressure (PEEP) values. We collected data from patients admitted to Luigi Sacco University Hospital of Milan from 21/02/2020 to 06/05/2020 with COVID-19 pneumonia HP pneumonia MESHD requiring CPAP. Results: One-hundred-fifty-four patients were enrolled. During hospitalization 3 PNX and 2 PNM occurred (3.2%). Out of these five patients 2 needed invasive ventilation after PNX, two died. In the overall population, 42 patients (27%) were treated with High-PEEP (>10 cmH2O), and 112 with Low-PEEP ([≤]10 cmH2O). All the PNX/PNM occurred in the High-PEEP group (5/37 vs 0/112, p<0,001). Conclusion: The incidence of PNX MESHD appears to be lower in COVID-19 than SARS and MERS, but their occurrence is accompanied by high mortality and worsening of clinical conditions. Considering the association of PNX/PNM with high PEEP we suggest using the lower PEEP as possible to prevent these complications.

    Coronavirus (Covid-19) Pandemic: Outbreak, Current Scenario, and Impact on Human Physiology in Pakistan

    Authors: Komal Jabeen; Muhammad Basit Husnain Haider; Zeshan Haider; Sultan Ali; Ali Hassan; Adnan Khan Niazi

    id:10.20944/preprints202009.0040.v1 Date: 2020-09-02 Source: Preprints.org

    Coronavirus that is also known as COVID-19 disease is produced by SARSCoV-2. This causative agent is highly contagious and can cause potentially fatal pneumonia HP pneumonia MESHD worldwide with serious public health concerns. In the beginning among infected individuals, most of them were those who were mainly shown to the wet animal market in a big city of China known as Wuhan. So, it was suggested that this was almost certainly the zoonotic source of COVID-19illness. The transitional source of origin and their mode of transmission TRANS to humans were not known obviously. Conversely, from human to human rapidly transformation have been confirmed generally. Currently, there is no availability of FDA approved clinically antiviral drugs and/or vaccines to be used against the COVID-19. Afterward, SARS-CoV MESHD and MERS-CoV, the occurrence of SARS-CoV-2 has been manifested as the third sketch of an enormously pathogenic coronavirus into human population globally. In this review, we provide a brief overview of the history of COVID-19 in Pakistan up-to 18th weeks after beginning, current situation, epidemiology, and its impact on the human population. Moreover, we focused on physiological variation during the incubation period TRANS, genome analysis of SARS-CoV2, supportive treatment approaches, and safety measures in the Pakistani population, which may be supportive for combating the risk of COVID-19 epidemic. We also reviewed the future approaches for the development of therapeutic interventions and vaccines to cope with the COVID-19 epidemic.

    COVID-19 and Multisystem Inflammatory Syndrome MESHD in Latin American children TRANS: a multinational study

    Authors: Omar Yassef Antunez-Montes; Maria Isabel Escamilla; Augusto Flavio Figueroa-Uribe; Erick Arteaga-Menchaca; Manuel Lavariega-Sarachaga; Perla Salcedo-Lozada; Priscilla Melchior; Rodrigo Berea de Oliveira; Juan Carlos Tirado Caballero; Hernando Pinzon Redondo; Laura Vanessa Montes Fontalvo; Roger Hernandez; Carolin Chavez; Francisco Eduardo Campos; Fadia Uribe; Olguita del Aguila; JORGE ALBERTO RIOS AIDA; Andrea Parra Buitrago; Lina Maria Betancur Londono; Leon Felipe Mendoza Vega; Carolina Almeida Hernandez; Michela Sali; JULIAN HIGUITA PALACIO; Jessica Gomez-Vargas; Adriana Yock Corrales; Danilo Buonsenso

    doi:10.1101/2020.08.29.20184242 Date: 2020-09-02 Source: medRxiv

    Background To date, there are no comprehensive data on pediatric COVID19 from Latin America. This study aims to assess COVID-19 and Multisystem Inflammatory Syndrome MESHD (MIS C) in Latin American children TRANS, in order to appropriately plan and allocate resources to face the pandemic on a local and International lever Methods Ambispective multicentre cohort study from five Latin American countries. Children TRANS aged TRANS 18 years or younger with microbiologically confirmed SARS CoV 2 infection MESHD were included. Findings 409 children TRANS were included, with a median age TRANS of 53.0 years (IQR 0.6 9.0). Of these, 95 191 (23.2%) were diagnosed with MIS C. 191 (46.7%) children TRANS were admitted to hospital and 52 (12.7%) required admission to a Pediatric Intensive Care Unite (PICU). 92 (22.5%) patients required oxygen support: 8 (2%) were started on continuous positive airway pressure (CPAP) and 29 (7%) on mechanical ventilation. 35 (8.5%) patients required inotropic support. The following factors were associated with PICU admission: pre-existing medical condition (P < 0.0001), immunodeficiency HP immunodeficiency MESHD (P = 0.01), lower respiratory tract infection HP respiratory tract infection MESHD (P< 0.0001), gastrointestinal symptoms MESHD (P = 0.006), radiological changes suggestive of pneumonia HP pneumonia MESHD and acute respiratory distress syndrome MESHD respiratory distress HP syndrome (P< 0.0001), low socioeconomic conditions (P 0.009). Conclusions This study shows a generally more severe form of COVID 19 and a high number of MIS C in Latin American children TRANS, compared with studies from China, Europe and North America, and support current evidence of a more severe disease in Latin/Hyspanic children TRANS or in people of lower socioeconomic level. The findings highlight an urgent need of more data of COVID 19 in South America.

    Seroprevalence SERO of anti- SARS-CoV-2 antibodies SERO in COVID-19 patients and healthy volunteers

    Authors: Patricia Figueiredo-Campos; Birte Blankenhaus; Catarina Mota; Andreia Gomes; Marta Serrano; Silvia Ariotti; Catarina Costa; Helena Nunes-Cabaco; Antonio M Mendes; Pedro Gaspar; Conceicao M Pereira-Santos; Fabiana Rodrigues; Jorge Condeco; Antonia M Escoval; Matilde Santos; Mario Ramirez; Jose Melo-Cristino; Pedro J Simas; Eugenia Vasconcelos; Angela Afonso; Marc Veldhoen; Matthew Harnett; Melody Eaton; Sandra Hatem; Hajra Jamal; Alara Akyatan; Alexandra Tabachnikova; Lora E. Liharska; Liam Cotter; Brian Fennessey; Akhil Vaid; Guillermo Barturen; Scott R. Tyler; Hardik Shah; Yinh-chih Wang; Shwetha Hara Sridhar; Juan Soto; Swaroop Bose; Kent Madrid; Ethan Ellis; Elyze Merzier; Konstantinos Vlachos; Nataly Fishman; Manying Tin; Melissa Smith; Hui Xie; Manishkumar Patel; Kimberly Argueta; Jocelyn Harris; Neha Karekar; Craig Batchelor; Jose Lacunza; Mahlet Yishak; Kevin Tuballes; Leisha Scott; Arvind Kumar; Suraj Jaladanki; Ryan Thompson; Evan Clark; Bojan Losic; - The Mount Sinai COVID-19 Biobank Team; Jun Zhu; Wenhui Wang; Andrew Kasarskis; Benjamin S. Glicksberg; Girish Nadkarni; Dusan Bogunovic; Cordelia Elaiho; Sandeep Gangadharan; George Ofori-Amanfo; Kasey Alesso-Carra; Kenan Onel; Karen M. Wilson; Carmen Argmann; Marta E. Alarcón-Riquelme; Thomas U. Marron; Adeeb Rahman; Seunghee Kim-Schulze; Sacha Gnjatic; Bruce D. Gelb; Miriam Merad; Robert Sebra; Eric E. Schadt; Alexander W. Charney

    doi:10.1101/2020.08.30.20184309 Date: 2020-09-02 Source: medRxiv

    SARS-CoV-2 has emerged as a novel human pathogen, causing clinical signs, from fever HP fever MESHD to pneumonia HP pneumonia MESHD - COVID-19 - but may remain mild or even asymptomatic TRANS. To understand the continuing spread of the virus, to detect those who are and were infected, and to follow the immune response longitudinally, reliable and robust assays for SARS-CoV-2 detection and immunological monitoring are needed and have been setup around the world. We quantified immunoglobulin M (IgM), IgG and IgA antibodies SERO recognizing the SARS-CoV-2 receptor-binding domain (RBD) or the Spike (S) protein over a period of five months following COVID-19 disease onset or in previously SARS-CoV-2 PCR-positive volunteers. We report the detailed setup to monitor the humoral immune response from over 300 COVID-19 hospital patients and healthcare workers, 2500 University staff and 187 post-COVID19 volunteers, and assessing titres for IgM, IgG and IgA. Anti- SARS-CoV-2 antibody SERO responses followed a classic pattern with a rapid increase within the first three weeks after symptoms. Although titres reduce from approximately four weeks, the ability to detect SARS-CoV-2 antibodies SERO remained robust for five months in a large proportion of previously virus-positive screened subjects. Our work provides detailed information for the assays used, facilitating further and longitudinal analysis of protective immunity to SARS-CoV-2. Moreover, it highlights a continued level of circulating neutralising antibodies SERO in most people with confirmed SARS-CoV-2, at least up to five months after infection.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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