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Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases

Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of...

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Autores principales: Kufner, Verena, Plate, Andreas, Schmutz, Stefan, Braun, Dominique L., Günthard, Huldrych F., Capaul, Riccarda, Zbinden, Andrea, Mueller, Nicolas J., Trkola, Alexandra, Huber, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770117/
https://www.ncbi.nlm.nih.gov/pubmed/31470675
http://dx.doi.org/10.3390/genes10090661
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author Kufner, Verena
Plate, Andreas
Schmutz, Stefan
Braun, Dominique L.
Günthard, Huldrych F.
Capaul, Riccarda
Zbinden, Andrea
Mueller, Nicolas J.
Trkola, Alexandra
Huber, Michael
author_facet Kufner, Verena
Plate, Andreas
Schmutz, Stefan
Braun, Dominique L.
Günthard, Huldrych F.
Capaul, Riccarda
Zbinden, Andrea
Mueller, Nicolas J.
Trkola, Alexandra
Huber, Michael
author_sort Kufner, Verena
collection PubMed
description Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests.
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spelling pubmed-67701172019-10-30 Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases Kufner, Verena Plate, Andreas Schmutz, Stefan Braun, Dominique L. Günthard, Huldrych F. Capaul, Riccarda Zbinden, Andrea Mueller, Nicolas J. Trkola, Alexandra Huber, Michael Genes (Basel) Article Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests. MDPI 2019-08-29 /pmc/articles/PMC6770117/ /pubmed/31470675 http://dx.doi.org/10.3390/genes10090661 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kufner, Verena
Plate, Andreas
Schmutz, Stefan
Braun, Dominique L.
Günthard, Huldrych F.
Capaul, Riccarda
Zbinden, Andrea
Mueller, Nicolas J.
Trkola, Alexandra
Huber, Michael
Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases
title Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases
title_full Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases
title_fullStr Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases
title_full_unstemmed Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases
title_short Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases
title_sort two years of viral metagenomics in a tertiary diagnostics unit: evaluation of the first 105 cases
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770117/
https://www.ncbi.nlm.nih.gov/pubmed/31470675
http://dx.doi.org/10.3390/genes10090661
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