A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance

Abstract Conventional HIV drug resistance (HIVDR) genotyping utilizes Sanger sequencing (SS) methods, which are limited by low data throughput and the inability of detecting low abundant drug resistant variants (LADRVs). Here we present a next generation sequencing (NGS)-based HIVDR typing platform...

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Autores principales:	Tracy Taylor, Emma R. Lee, Mikaela Nykoluk, Eric Enns, Binhua Liang, Rupert Capina, Marie-Krystel Gauthier, Gary Van Domselaar, Paul Sandstrom, James Brooks, Hezhao Ji
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c66d3e8d3a4c4644bab4335348af5faa
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spelling	oai:doaj.org-article:c66d3e8d3a4c4644bab4335348af5faa2021-12-02T15:09:14ZA MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance10.1038/s41598-019-45328-32045-2322https://doaj.org/article/c66d3e8d3a4c4644bab4335348af5faa2019-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-45328-3https://doaj.org/toc/2045-2322Abstract Conventional HIV drug resistance (HIVDR) genotyping utilizes Sanger sequencing (SS) methods, which are limited by low data throughput and the inability of detecting low abundant drug resistant variants (LADRVs). Here we present a next generation sequencing (NGS)-based HIVDR typing platform that leverages the advantages of Illumina MiSeq and HyDRA Web. The platform consists of a fully validated sample processing protocol and HyDRA web, an open web portal that allows automated customizable NGS-based HIVDR data processing. This platform was characterized and validated using a panel of HIV-spiked plasma representing all major HIV-1 subtypes, pedigreed plasmids, HIVDR proficiency specimens and clinical specimens. All examined major HIV-1 subtypes were consistently amplified at viral loads of ≥1,000 copies/ml. The gross error rate of this platform was determined at 0.21%, and minor variations were reliably detected down to 0.50% in plasmid mixtures. All HIVDR mutations identifiable by SS were detected by the MiSeq-HyDRA protocol, while LADRVs at frequencies of 1~15% were detected by MiSeq-HyDRA only. As compared to SS approaches, the MiSeq-HyDRA platform has several notable advantages including reduced cost and labour, and increased sensitivity for LADRVs, making it suitable for routine HIVDR monitoring for both patient care and surveillance purposes.Tracy TaylorEmma R. LeeMikaela NykolukEric EnnsBinhua LiangRupert CapinaMarie-Krystel GauthierGary Van DomselaarPaul SandstromJames BrooksHezhao JiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-11 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tracy Taylor Emma R. Lee Mikaela Nykoluk Eric Enns Binhua Liang Rupert Capina Marie-Krystel Gauthier Gary Van Domselaar Paul Sandstrom James Brooks Hezhao Ji A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
description	Abstract Conventional HIV drug resistance (HIVDR) genotyping utilizes Sanger sequencing (SS) methods, which are limited by low data throughput and the inability of detecting low abundant drug resistant variants (LADRVs). Here we present a next generation sequencing (NGS)-based HIVDR typing platform that leverages the advantages of Illumina MiSeq and HyDRA Web. The platform consists of a fully validated sample processing protocol and HyDRA web, an open web portal that allows automated customizable NGS-based HIVDR data processing. This platform was characterized and validated using a panel of HIV-spiked plasma representing all major HIV-1 subtypes, pedigreed plasmids, HIVDR proficiency specimens and clinical specimens. All examined major HIV-1 subtypes were consistently amplified at viral loads of ≥1,000 copies/ml. The gross error rate of this platform was determined at 0.21%, and minor variations were reliably detected down to 0.50% in plasmid mixtures. All HIVDR mutations identifiable by SS were detected by the MiSeq-HyDRA protocol, while LADRVs at frequencies of 1~15% were detected by MiSeq-HyDRA only. As compared to SS approaches, the MiSeq-HyDRA platform has several notable advantages including reduced cost and labour, and increased sensitivity for LADRVs, making it suitable for routine HIVDR monitoring for both patient care and surveillance purposes.
format	article
author	Tracy Taylor Emma R. Lee Mikaela Nykoluk Eric Enns Binhua Liang Rupert Capina Marie-Krystel Gauthier Gary Van Domselaar Paul Sandstrom James Brooks Hezhao Ji
author_facet	Tracy Taylor Emma R. Lee Mikaela Nykoluk Eric Enns Binhua Liang Rupert Capina Marie-Krystel Gauthier Gary Van Domselaar Paul Sandstrom James Brooks Hezhao Ji
author_sort	Tracy Taylor
title	A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
title_short	A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
title_full	A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
title_fullStr	A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
title_full_unstemmed	A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance
title_sort	miseq-hydra platform for enhanced hiv drug resistance genotyping and surveillance
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/c66d3e8d3a4c4644bab4335348af5faa
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A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance

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