Next-generation sequencing for cytomegalovirus antiviral resistance genotyping in a clinical virology laboratory
Copyright © 2021 Elsevier B.V. All rights reserved..
INTRODUCTION: The identification of CMV antiviral drug resistance (AVDR) is a critical diagnostic test for immunocompromised patients with CMV infection and a failure of virologic response on optimal antiviral treatment. We developed a next-generation sequencing (NGS) assay for CMV AVDR testing and compared the AVDR mutations identified by NGS to Sanger sequencing.
METHODS: Retrospective review of CMV AVDR testing requests for UL97 and UL54 at our laboratory from 2014 to 2019 was conducted. NGS was performed on the MinION and compared to Sanger sequencing performed at the national reference laboratory. Analysis of the sequences was completed with a novel cloud bioinformatics platform (BugSeq).
RESULTS: Twenty patient samples previously characterized were included for study on the MinION. NGS captured all of the CMV AVDR mutations identified by Sanger, and identified additional mutations in UL97 and/or UL54 in 8/13 (62%) of the samples. An analysis of the depth of coverage at which we no longer detected minority single nucleotide variants (SNVs) detected in the original data was conducted, estimating a recall of 95% at 1800 fold coverage.
CONCLUSION: NGS utilizing MinION technology for the detection of CMV AVDR mutations identified additional minority variants in UL97 and UL54 as compared with Sanger sequencing. Through the application of a bioinformatics pipeline available online, our NGS process eliminates barriers associated with the use of the MinION and NGS in clinical laboratories.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:192 |
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| Enthalten in: |
Antiviral research - 192(2021) vom: 25. Aug., Seite 105123 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chorlton, Samuel D [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 03.12.2021 Date Revised 14.12.2021 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.antiviral.2021.105123 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM327213280 |
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| 100 | 1 | |a Chorlton, Samuel D |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Next-generation sequencing for cytomegalovirus antiviral resistance genotyping in a clinical virology laboratory |
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| 500 | |a Date Revised 14.12.2021 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2021 Elsevier B.V. All rights reserved. | ||
| 520 | |a INTRODUCTION: The identification of CMV antiviral drug resistance (AVDR) is a critical diagnostic test for immunocompromised patients with CMV infection and a failure of virologic response on optimal antiviral treatment. We developed a next-generation sequencing (NGS) assay for CMV AVDR testing and compared the AVDR mutations identified by NGS to Sanger sequencing | ||
| 520 | |a METHODS: Retrospective review of CMV AVDR testing requests for UL97 and UL54 at our laboratory from 2014 to 2019 was conducted. NGS was performed on the MinION and compared to Sanger sequencing performed at the national reference laboratory. Analysis of the sequences was completed with a novel cloud bioinformatics platform (BugSeq) | ||
| 520 | |a RESULTS: Twenty patient samples previously characterized were included for study on the MinION. NGS captured all of the CMV AVDR mutations identified by Sanger, and identified additional mutations in UL97 and/or UL54 in 8/13 (62%) of the samples. An analysis of the depth of coverage at which we no longer detected minority single nucleotide variants (SNVs) detected in the original data was conducted, estimating a recall of 95% at 1800 fold coverage | ||
| 520 | |a CONCLUSION: NGS utilizing MinION technology for the detection of CMV AVDR mutations identified additional minority variants in UL97 and UL54 as compared with Sanger sequencing. Through the application of a bioinformatics pipeline available online, our NGS process eliminates barriers associated with the use of the MinION and NGS in clinical laboratories | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a CMV | |
| 650 | 4 | |a Sequencing | |
| 650 | 4 | |a UL54 | |
| 650 | 4 | |a UL97 | |
| 650 | 7 | |a Antiviral Agents |2 NLM | |
| 650 | 7 | |a DNA, Viral |2 NLM | |
| 650 | 7 | |a UL54 protein, Human herpesvirus 5 |2 NLM | |
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| 650 | 7 | |a Phosphotransferases (Alcohol Group Acceptor) |2 NLM | |
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| 700 | 1 | |a Ritchie, Gordon |e verfasserin |4 aut | |
| 700 | 1 | |a Lawson, Tanya |e verfasserin |4 aut | |
| 700 | 1 | |a McLachlan, Elizabeth |e verfasserin |4 aut | |
| 700 | 1 | |a Romney, Marc G |e verfasserin |4 aut | |
| 700 | 1 | |a Matic, Nancy |e verfasserin |4 aut | |
| 700 | 1 | |a Lowe, Christopher F |e verfasserin |4 aut | |
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