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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2019-06-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-019-45328-3 |
| _version_ | 1818345880215879680 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T17:09:24Z |
| format | Article |
| id | doaj.art-c66d3e8d3a4c4644bab4335348af5faa |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-13T17:09:24Z |
| publishDate | 2019-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-c66d3e8d3a4c4644bab4335348af5faa2022-12-21T23:37:36ZengNature PortfolioScientific Reports2045-23222019-06-019111110.1038/s41598-019-45328-3A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillanceTracy Taylor0Emma R. Lee1Mikaela Nykoluk2Eric Enns3Binhua Liang4Rupert Capina5Marie-Krystel Gauthier6Gary Van Domselaar7Paul Sandstrom8James Brooks9Hezhao Ji10National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaBioinformatics Core, National Microbiology Laboratory, Public Health Agency of CanadaBioinformatics Core, National Microbiology Laboratory, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaBioinformatics Core, National Microbiology Laboratory, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of CanadaAbstract 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.https://doi.org/10.1038/s41598-019-45328-3 |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-019-45328-3 |
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