About: Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

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About: Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation
Creator	Lina, Bruno Valette, Martine Josset, Laurence Bal, Antonin Brun, Solenne Burfin, Gwendolyne Regue, Hadrien Charre, Caroline Destras, Ginevra, Christophe Sabatier, Marina Scholtes, Caroline
source	BioRxiv
abstract	Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialized kits including a hybridization capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP) and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples, with mNGS and RVOP producing the most complete genomes. For mid viral loads, 2/8 and 1/8 genomes were incomplete (<99%) with mNGS and both CleanPlex and RVOP, respectively. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques yielding complete genomes for 7/8 samples. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in two samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34-nt deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a default of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer annealing or probe-hybridizing regions and would require regular updates of the technique according to SARS-CoV-2 evolution.
has issue date	2020-07-15(xsd:dateTime)
bibo:doi	10.1101/2020.07.14.201947
has license	biorxiv
sha1sum (hex)	d9b83fc7f2119e6f0331c01d90b8db71ca6993af
schema:url	https://doi.org/10.1101/2020.07.14.201947
resource representing a document's title	Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation
schema:publication	bioRxiv
resource representing a document's body	covid:d9b83fc7f2119e6f0331c01d90b8db71ca6993af#body_text
is schema:about of	named entity 'whole-genome sequencing' named entity 'Since' named entity 'whole-genome sequencing' named entity 'NGS' named entity 'SARS-CoV-2' named entity 'genome' named entity 'amplicon' named entity 'genome' named entity 'sequenced' named entity 'amplicons' named entity 'Illumina' named entity 'amplicon' named entity 'sequenced' named entity 'mNGS' named entity 'RNA' named entity 'primers' named entity 'primers' named entity 'primers' named entity 'nCoV' named entity 'algorithm' named entity 'amplicon' named entity 'SARS-CoV-2' named entity 'amplicon sequencing' named entity 'Oxford Nanopore Technologies' named entity 'multiplexed' named entity 'DRCI' named entity 'Illumina' named entity 'multiplex PCR' named entity 'library preparation' named entity 'perl' named entity 'consensus sequence' named entity 'SARS-CoV-2' named entity 'multiplex PCR' named entity 'majority rule' named entity 'Philip Robinson' named entity 'annealing' named entity 'Consensus sequences' named entity 'mNGS' named entity 'SARS-CoV-2' named entity 'flow cell' named entity 'genome' named entity 'Wuhan' named entity 'entire genome' named entity 'deletions' named entity 'PCR' named entity 'base pairs' named entity 'database' named entity 'amplicons' named entity 'data analysis' named entity 'genome' named entity 'multiplexed' named entity 'Lyon' named entity 'SARS-CoV-2' named entity 'barcode' named entity 'primers' named entity 'genome' named entity 'FLO' named entity 'cDNA' named entity 'PCR' named entity 'COVID-19 outbreak' named entity 'SARS-CoV-2' named entity 'WGS' named entity 'WORLDWIDE' named entity 'GENOME SEQUENCING' named entity 'OUTBREAK' named entity 'SARS-COV-2' covid:arg/d9b83fc7f2119e6f0331c01d90b8db71ca6993af named entity 'COVID-19' named entity 'WGS' named entity 'performed' named entity 'Evaluation' named entity 'BEGINNING' named entity 'DIVERSE'

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