About: Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

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About: Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions
Creator	Xu, Dong Mason, Christopher Ruggiero, Phyllis Tanner, Nathan Danko, David Meleshko, Dmitry Rennert, Hanna Tatonetti, Nicholas Zietz, Michael Afshinnekoo, Ebrahim Westover, Craig Meydan, Cem Ramlall, Vijendra Young, Benjamin Steel, Peter Bhattacharya, Chandrima Ryon, Krista Sierra, Maria Foox, Gawrys, Imielinski, Marcin Ivanov, Nikolay Langhorst, Bradley Mackay, Matthew Mozsary, Christopher Pohle, Diana Rosiene, Joel Sedlazeck, Shaiber, Alon Shemesh, Amos
Source	BioRxiv; Medline
abstract	The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
has issue date	2020-05-01(xsd:dateTime)
bibo:doi	10.1101/2020.04.20.048066
bibo:pmid	32511352
has license	biorxiv
sha1sum (hex)	0f21544beb39b29181bbf366393f8d071c7e2f2f
schema:url	https://doi.org/10.1101/2020.04.20.048066
resource representing a document's title	Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions
has PubMed identifier	32511352
schema:publication	bioRxiv
resource representing a document's body	covid:0f21544beb39b29181bbf366393f8d071c7e2f2f#body_text
is schema:about of	named entity 'Severe Acute Respiratory Syndrome Coronavirus 2' named entity 'COVID-19' named entity 'biomarkers' named entity 'ACE inhibitors' named entity 'SARS' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'angiotensin receptor blockers' named entity 'oropharyngeal' named entity 'interferon' named entity 'co-infection' named entity 'hypertension' named entity 'SARS-CoV-2' named entity 'Reproducibility' named entity 'Wuhan' named entity 'coronary heart diseases' named entity 'GISAID' named entity 'probability' named entity 'New York' named entity 'boxplots' named entity 'RNA' named entity 'protein' named entity 'Supp' named entity 'allele frequencies' named entity 'inflammation' named entity 'RNA-seq' named entity 'genome' named entity 'viral load' named entity 'antigen processing' named entity 'alleles' named entity 'IL6' named entity 'heme' named entity 'ARBs' named entity 'RFU' named entity 'gene expression' named entity 'SARS-CoV-2' named entity 'CXCL10' named entity 'enzyme inhibition' named entity 'Wuhan' named entity 'commensal' named entity 'up-regulated' named entity 'viral species' named entity 'SNV' named entity 'risk factors' named entity 'pathogen' named entity 'intubation' named entity 'primers' named entity 'survival analysis' named entity 'ACE2' named entity 'gene' named entity 'protein' named entity 'viral infections' named entity 'coronavirus'

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