Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens

Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely us...

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Autores principales:	Kevin S. Kuchinski, Jason Nguyen, Tracy D. Lee, Rebecca Hickman, Agatha N. Jassem, Linda M.N. Hoang, Natalie A. Prystajecky, John R. Tyson
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2022
Materias:	SARS-CoV-2 Amplicon sequencing COVID-19 Variant of concern Viral genomics Genomic surveillance Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/e140c1b18f2d48e4bead103d6baa45c3
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spelling	oai:doaj.org-article:e140c1b18f2d48e4bead103d6baa45c32021-11-26T04:24:30ZMutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens1201-971210.1016/j.ijid.2021.10.050https://doaj.org/article/e140c1b18f2d48e4bead103d6baa45c32022-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1201971221008389https://doaj.org/toc/1201-9712Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely used sequencing protocols by the ARTIC network and Freed et al. Three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada. We provide laboratory validation of protocol modifications that restored sequencing performance. The study findings indicate that genomic sequencing protocols require immediate updating to address emerging mutations. This work also suggests that routine monitoring and protocol updates will be necessary as SARS-CoV-2 continues to evolve. The bioinformatic and laboratory approaches used here provide guidance for this kind of assay maintenance.Kevin S. KuchinskiJason NguyenTracy D. LeeRebecca HickmanAgatha N. JassemLinda M.N. HoangNatalie A. PrystajeckyJohn R. TysonElsevierarticleSARS-CoV-2Amplicon sequencingCOVID-19Variant of concernViral genomicsGenomic surveillanceInfectious and parasitic diseasesRC109-216ENInternational Journal of Infectious Diseases, Vol 114, Iss , Pp 51-54 (2022)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 Amplicon sequencing COVID-19 Variant of concern Viral genomics Genomic surveillance Infectious and parasitic diseases RC109-216
spellingShingle	SARS-CoV-2 Amplicon sequencing COVID-19 Variant of concern Viral genomics Genomic surveillance Infectious and parasitic diseases RC109-216 Kevin S. Kuchinski Jason Nguyen Tracy D. Lee Rebecca Hickman Agatha N. Jassem Linda M.N. Hoang Natalie A. Prystajecky John R. Tyson Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
description	Mutations in emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages can interfere with laboratory methods used to generate viral genome sequences for public health surveillance. We identified 20 mutations that are widespread in variant of concern lineages and affect widely used sequencing protocols by the ARTIC network and Freed et al. Three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada. We provide laboratory validation of protocol modifications that restored sequencing performance. The study findings indicate that genomic sequencing protocols require immediate updating to address emerging mutations. This work also suggests that routine monitoring and protocol updates will be necessary as SARS-CoV-2 continues to evolve. The bioinformatic and laboratory approaches used here provide guidance for this kind of assay maintenance.
format	article
author	Kevin S. Kuchinski Jason Nguyen Tracy D. Lee Rebecca Hickman Agatha N. Jassem Linda M.N. Hoang Natalie A. Prystajecky John R. Tyson
author_facet	Kevin S. Kuchinski Jason Nguyen Tracy D. Lee Rebecca Hickman Agatha N. Jassem Linda M.N. Hoang Natalie A. Prystajecky John R. Tyson
author_sort	Kevin S. Kuchinski
title	Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
title_short	Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
title_full	Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
title_fullStr	Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
title_full_unstemmed	Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
title_sort	mutations in emerging variant of concern lineages disrupt genomic sequencing of sars-cov-2 clinical specimens
publisher	Elsevier
publishDate	2022
url	https://doaj.org/article/e140c1b18f2d48e4bead103d6baa45c3
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Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens

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