Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.

Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long...

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Autores principales:	Broňa Brejová, Kristína Boršová, Viktória Hodorová, Viktória Čabanová, Askar Gafurov, Dominika Fričová, Martina Neboháčová, Tomáš Vinař, Boris Klempa, Jozef Nosek
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ecd116393eff4c7e8b10110ed224fbb9
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spelling	oai:doaj.org-article:ecd116393eff4c7e8b10110ed224fbb92021-12-02T20:16:26ZNanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.1932-620310.1371/journal.pone.0259277https://doaj.org/article/ecd116393eff4c7e8b10110ed224fbb92021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0259277https://doaj.org/toc/1932-6203Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.Broňa BrejováKristína BoršováViktória HodorováViktória ČabanováAskar GafurovDominika FričováMartina NeboháčováTomáš VinařBoris KlempaJozef NosekPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0259277 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Broňa Brejová Kristína Boršová Viktória Hodorová Viktória Čabanová Askar Gafurov Dominika Fričová Martina Neboháčová Tomáš Vinař Boris Klempa Jozef Nosek Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
description	Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
format	article
author	Broňa Brejová Kristína Boršová Viktória Hodorová Viktória Čabanová Askar Gafurov Dominika Fričová Martina Neboháčová Tomáš Vinař Boris Klempa Jozef Nosek
author_facet	Broňa Brejová Kristína Boršová Viktória Hodorová Viktória Čabanová Askar Gafurov Dominika Fričová Martina Neboháčová Tomáš Vinař Boris Klempa Jozef Nosek
author_sort	Broňa Brejová
title	Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
title_short	Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
title_full	Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
title_fullStr	Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
title_full_unstemmed	Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
title_sort	nanopore sequencing of sars-cov-2: comparison of short and long pcr-tiling amplicon protocols.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/ecd116393eff4c7e8b10110ed224fbb9
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Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.

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