Corpus overview


MeSH Disease

Human Phenotype

Pneumonia (1057)

Fever (656)

Cough (529)

Hypertension (364)

Anxiety (297)


age categories (2683)

Transmission (2461)

gender (1247)

fomite (1117)

contact tracing (884)

    displaying 1 - 10 records in total 13107
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    Prediction and Analysis of SARS-CoV-2-Targeting microRNA in Human Lung Epithelium

    Authors: Jonathan Tak-Sum Chow; Leonardo Salmena

    id:10.20944/preprints202008.0253.v1 Date: 2020-08-11 Source:

    Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2), an RNA virus, is responsible for coronavirus disease MESHD 2019 (COVID-19) pandemic of 2020. Experimental evidence suggests that microRNA can mediate an intracellular defence mechanism against some RNA viruses. The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection MESHD. We hypothesize that high expression of specific coronavirus-targeting microRNA in lung epithelia may protect against infection MESHD and viral propagation, conversely low expression may confer susceptibility to infection MESHD. We have identified 128 human microRNA with potential to target the SARS-CoV-2 genome, most of which have very low expression in lung epithelia. Six of these 128 microRNA are differentially expressed upon in vitro infection MESHD of SARS-CoV-2. Twenty-eight and 23 microRNA also target the SARS-CoV and MERS-CoV, respectively. In addition, 48 and 32 microRNA are commonly identified in two other studies. Further research into identifying bona fide coronavirus targeting microRNA will be useful in understanding the importance of microRNA as cellular defence mechanism against pathogenic coronavirus infections MESHD.

    Impact of COVID-19 on Urology Practice in Saudi Arabia

    Authors: Meshari Alzahrani; Mohammad Alkhamees; Sulaiman Almutairi; Ahmed Aljuhayman; Sultan Alkhateeb

    id:10.20944/preprints202008.0261.v1 Date: 2020-08-11 Source:

    From the moment the World Health Organization (WHO) declared COVID-19 to be a pandemic disease MESHD, COVID-19 began to affect the lives of many healthcare providers worldwide. In response to this pandemic, urology departments and training residency programs implemented urgent measures to reduce outpatient clinics, adopted the use of telemedicine, regulated emergency MESHD and outpatient urological procedures, promoted the use of operating theatres, and developed the use of sustainable e-learning alternatives to traditional urology resident/staff educational activities. Here, we review the response of urologists in Saudi Arabia to the COVID-19 pandemic and how they applied both for the patients and for the healthcare of urologist personnel.

    The Spectrum of Cardiovascular Complications in COVID-19- A Comprehensive Literature Review

    Authors: Raja Shakeel Mushtaque; Rabia Mushtaque; Shahbano Baloch; Aadil Raza; Haseeb Bhatti; Zohaib Khan

    id:10.20944/preprints202008.0257.v1 Date: 2020-08-11 Source:

    A newly identified novel coronavirus named as severe acute respiratory syndrome MESHD-related coronavirus2 (SARS‐CoV 2) has given rise to the global pandemic. SARS-CoV2 which causes coronavirus disease MESHD 2019 (COVID-19), is a positive-stranded RNA virus with nucleocapsid. It binds to host angiotensin-converting enzyme2 (ACE2) receptor through surface glycoprotein (S protein). These ACE 2 receptors are attached to the cell membranes of many organs. Thus, COVID-19 does not only result in acute respiratory distress HP syndrome MESHD but also affects multiple organ systems, requiring a multidisciplinary approach to manage this disease MESHD. COVID-19 can damage the myocardial cells and result in fulminant myocarditis MESHD myocarditis HP, acute cardiac injury, cardiomyopathy MESHD cardiomyopathy HP, heart failure MESHD, cardiogenic shock MESHD cardiogenic shock HP, or arrhythmia HP. COVID-19 seeds harmful immune response through cytokine storm leading to indirect organ damage. In this literature review, the available data is comprehended regarding cardiovascular complications in COVID-19, and the correlation of biomarkers with the disease MESHD activity is discussed. This literature review also highlights the important treatment options and outcomes of the individual study.

    Recognition of Potential COVID-19 Drug Treatments Through the Study of Existing Protein-Drug and Protein-Protein Structures: An Analysis of Kinetically Active Residues

    Authors: Ognjen Perišić

    id:202008.0248/v1 Date: 2020-08-11 Source:

    We report the results of our study of approved drugs as potential treatments for COVID 19, based on the application of various bioinformatics predictive methods. The drugs studied include chloroquine, ivermectin, remdesivir, sofosbuvir, boceprevir, and α-difluoromethylornithine (DMFO). Our results indicate that these small molecules selectively bind to stable, kinetically active residues and residues adjoining them on the surface of proteins and inside protein pockets, and that some prefer hydrophobic over other active sites. Our approach is not restricted to viruses and can facilitate rational drug design, as well as improve our understanding of molecular interactions, in general.

    The Anomalous Nature of the Fecal Swab Sample Used for RaTG13 Genome Assembly as Revealed by NGS Data Analysis

    Authors: Monali Rahalkar; Rahul Bahulikar

    id:202008.0205/v2 Date: 2020-08-11 Source:

    RaTG13 beta coronavirus, which exists in the form of a genome sequence, is the closest relative TRANS of SARS-CoV-2 reported till date. The sample from which RaTG13 virus was sequenced was a bat fecal swab collected in 2013 from Tongguan, Mojiang, Yunnan province, China. The genome data for RaTG13, MN996532.1, was deposited on 27th Jan 2020 and the raw data (Illumina reads) was deposited a fortnight later on 13th Feb 2020[accn]. Comparison of the RNA Seq data of RaTG13 fecal swab sample to the corresponding data from the bat fecal swabs deposited by the same working group indicated that the raw data seemed to be anomalous in several aspects. Thirty percent of the reads did not match with anything. From the rest of the 70%, an abnormal high proportion was contributed by reads derived from eukaryotes (~68%). These matched with the sequences of not one but various bat species (round leaf bats, fruit bats and other bats) and animal species (squirrels, foxes, etc.) as per Krona analysis included with the SRA data. The proportion of the bacterial reads in the swab was exceptionally low, i.e. 0.7%, which is abnormal, compared to the 70-90% bacterial abundance in other bat fecal swabs. Furthermore, we also found another set of raw data associated with RaTG13, amplicon sequencing of the genome (SRX8357956), which was submitted in May 2020. Analysis of the amplicons by BLAST showed that these collectively do not cover the whole genome (MN996532.1). On closer inspection, the dates mentioned in the files of the sequenced amplicons were also found to be older (2017, 2018). Collectively, the anomalies in the raw data of RaTG13 pose an important question about the overall authenticity of the RaTG13 genome sequence.

    Petabase-scale sequence alignment catalyses viral discovery

    Authors: Robert C Edgar; Jeff Taylor; Tomer Altman; Pierre Barbera; Dmitry Meleshko; Victor Lin; Dan Lohr; Gherman Novakovsky; Basem Al-Shayeb; Jill Banfield; Anton Korobeynikov; Rayan Chikhi; Artem Babaian

    doi:10.1101/2020.08.07.241729 Date: 2020-08-10 Source: bioRxiv

    Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome MESHD Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, `Serratus`, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community ( Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones.

    Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site

    Authors: Emre Aktas

    doi:10.1101/2020.08.10.244632 Date: 2020-08-10 Source: bioRxiv

    There are some mutations are known related to SARS-CoV-2. Together with these mutations known, we tried to show other newly mutations regionally. According to our results which 4326 whole sequences are used, we found that some mutations occur only in a certain region, while some other mutations are found in each regions. Especially in Asia, more than one mutation (three different mutations are found in QLA46612 isolated from South Korea) was seen in the same sequence. Although we detected a huge number of mutations (we found more than seventy in Asia) by regions, some of them were predicted that damage spike's protein structure by using bioinformatic tools. The predicted results are G75V (isolated from North America), T95I (isolated from South Korea), G143V (isolated from North America), M177I (isolated Asia), L293M (isolated from Asia), P295H (isolated from Asia), T393P (isolated from Europe), P507S (isolated from Asia), D614G (isolated from all regions) respectively. Also, in this study, we tried to show how possible binding sites of ligands change if the spike protein structure is damaged and whether more than one mutation affects ligand binding was estimated using bioinformatics tools. Interestingly, mutations that predicted to damage the structure do not affect ligand binding sites, whereas ligands' binding sites were affected in those with multiple mutations. Focusing on mutations may opens up the window to exploit new future therapeutic targets.

    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.

    High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing

    Authors: Rahul C. Bhoyar; Abhinav Jain; Paras Sehgal; Mohit Kumar Divakar; Disha Sharma; Mohamed Imran; Bani Jolly; Gyan Ranjan; Mercy Rophina; Sumit Sharma; Sanjay Siwach; Kavita Pandhare; Swayamprabha Sahoo; Maheswata Sahoo; Ananya Nayak; Jatindra Nath Mohanty; Jayashankar Das; Sudhir Bhandari; Sandeep K Mathur; Anshul Kumar; Rahul Sahlot; Pallavali Rojarani; Juturu Vijaya Lakshmi; Araveti Surekha; Pulala Chandra Sekhar; Shelly Mahajan; Shet Masih; Pawan Singh; Vipin Kumar; Blessy Jose; Vidur Mahajan; Vivek Gupta; Rakesh Gupta; Prabhakar Arumugam; Anjali Singh; Ananya Nandy; Raghavendran P.V.; Rakesh Mohan Jha; Anupama Kumari; Sheetal Gandotra; Vivek Rao; Mohammed Faruq; Sanjeev Kumar; Betsy Reshma G; Narendra G Varma; Shuvra Shekhar Roy; Antara Sengupta; Sabyasachi Chattopadhyay; Khushboo Singhal; Shalini Pradhan; Nishu Tyagi; Saruchi Wadhwa; Diksha Jha; Salwa Naushin; Mukta Poojary; Vinod Scaria; Sridhar Sivasubbu

    doi:10.1101/2020.08.10.242677 Date: 2020-08-10 Source: bioRxiv

    The rapid emergence of coronavirus disease MESHD 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity SERO assay for the detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.

    DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans- infection MESHD and can be inhibited by a glycomimetic antagonist

    Authors: Michel Thepaut; Joanna Luczkowiak; Corinne Vives; Nuria Labiod; Isabelle Bally; Fatima Lasala; Yasmina Grimoire; Daphna Fenel; Sara Sattin; Nicole Thielens; Guy Schoehn; Anna Bernardi; Rafael Delgado; Franck Fieschi

    doi:10.1101/2020.08.09.242917 Date: 2020-08-10 Source: bioRxiv

    The efficient spread of SARS-CoV-2 resulted in a pandemic that is unique in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in air mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection MESHD, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. Thus, we described a mechanism potentiating viral capture and spreading of infection MESHD. Early involvement of APCs opens new avenues for understanding and treating the imbalanced innate immune response observed in COVID-19 pathogenesis.

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MeSH Disease
Human Phenotype

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