Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.

<h4>Objectives</h4>The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of n...

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Autores principales:	Nick P G Gauthier, Cassidy Nelson, Michael B Bonsall, Kerstin Locher, Marthe Charles, Clayton MacDonald, Mel Krajden, Samuel D Chorlton, Amee R Manges
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d103ed76e80a48a6bc28800a8f6ce736
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spelling	oai:doaj.org-article:d103ed76e80a48a6bc28800a8f6ce7362021-12-02T20:19:09ZNanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.1932-620310.1371/journal.pone.0259712https://doaj.org/article/d103ed76e80a48a6bc28800a8f6ce7362021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0259712https://doaj.org/toc/1932-6203<h4>Objectives</h4>The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2.<h4>Methods</h4>We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies.<h4>Results</h4>Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia.<h4>Conclusions</h4>This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.Nick P G GauthierCassidy NelsonMichael B BonsallKerstin LocherMarthe CharlesClayton MacDonaldMel KrajdenSamuel D ChorltonAmee R MangesPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11, p e0259712 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nick P G Gauthier Cassidy Nelson Michael B Bonsall Kerstin Locher Marthe Charles Clayton MacDonald Mel Krajden Samuel D Chorlton Amee R Manges Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
description	<h4>Objectives</h4>The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2.<h4>Methods</h4>We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies.<h4>Results</h4>Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia.<h4>Conclusions</h4>This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.
format	article
author	Nick P G Gauthier Cassidy Nelson Michael B Bonsall Kerstin Locher Marthe Charles Clayton MacDonald Mel Krajden Samuel D Chorlton Amee R Manges
author_facet	Nick P G Gauthier Cassidy Nelson Michael B Bonsall Kerstin Locher Marthe Charles Clayton MacDonald Mel Krajden Samuel D Chorlton Amee R Manges
author_sort	Nick P G Gauthier
title	Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
title_short	Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
title_full	Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
title_fullStr	Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
title_full_unstemmed	Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
title_sort	nanopore metagenomic sequencing for detection and characterization of sars-cov-2 in clinical samples.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/d103ed76e80a48a6bc28800a8f6ce736
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Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.

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