About: Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping

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About: Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping
Creator	Pekosz, Andrew Hardick, Justin Rothman, Richard Robinson, Matthew Larman, H Hansen, Kasper Monaco, Daniel Shaw-Saliba, Kathryn Credle, Joel Eshleman, Susan Gunn, Jonathan Mostafa, Heba Sie, Brandon Steinegger, Martin Tchir, Alexandra Zheng, Xuwen
source	BioRxiv; Medline; PMC; WHO
abstract	The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq (“cRASL-seq”), which enables analysis of any targeted pathogen- (and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ~1–100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
has issue date	2020-06-03(xsd:dateTime)
bibo:doi	10.1101/2020.06.03.130591
bibo:pmid	32577648
has license	cc-by-nc-nd
sha1sum (hex)	bad2a9bd3f7309193ac6ccfd819f2169db587ae0
schema:url	https://doi.org/10.1101/2020.06.03.130591
resource representing a document's title	Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping
has PubMed Central identifier	PMC7302202
has PubMed identifier	32577648
schema:publication	bioRxiv
resource representing a document's body	covid:bad2a9bd3f7309193ac6ccfd819f2169db587ae0#body_text
is schema:about of	named entity 'ITS' named entity 'TARGET' named entity 'SARS-COV-2' named entity 'SAMPLE' named entity 'OLIGONUCLEOTIDE' named entity 'SENSITIVE' named entity 'NASOPHARYNGEAL' named entity 'HIGHLY SENSITIVE' named entity 'PROTOCOL' named entity 'SURVEILLANCE' named entity 'IMPACT' named entity 'ANALYSIS' named entity 'PATIENT' named entity 'GENOTYPING' named entity 'CURRENT' named entity 'DOES NOT' named entity 'LIGATION' named entity 'METHOD' named entity 'POLYMORPHISMS' named entity 'public health' named entity 'virulence' named entity 'target sequences' named entity 'RASL' named entity 'oligonucleotide' named entity 'DNA sequencing' named entity 'oligonucleotide' named entity 'nasopharyngeal' named entity 'genotypes' named entity 'RefSeq' named entity 'DTT' named entity 'GAPDH' named entity 'Hilden' named entity 'reagent' named entity 'Illumina' named entity 'brucellosis' named entity 'molecular diagnostics' named entity 'DNA testing' named entity 'ligation' named entity 'RT-PCR' named entity 'unemployment' named entity 'ligation' named entity 'next-generation sequencing' named entity 'gene expression' named entity 'PCR' named entity 'RASL' named entity 'ligation' named entity 'oligonucleotide' named entity 'organism' named entity 'SNPs' named entity 'RNA molecules' named entity 'qPCR' named entity 'hybridization' named entity 'PCR' named entity 'nucleic acid' named entity 'H3N2' named entity 'Oligo' named entity 'RNA sequences' named entity 'polyadenylated' named entity 'gene expression' named entity 'enzyme' named entity 'SNPs' named entity 'speci' named entity 'PCR' named entity 'RASL' named entity 'RNA' named entity 'SARS-CoV-2'

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