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Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains


Lewandowska, Dagmara W; Zagordi, Osvaldo; Zbinden, Andrea; Schuurmans, Macé M; Schreiber, Peter; Geissberger, Fabienne-Desirée; Huder, Jon B; Böni, Jürg; Benden, Christian; Mueller, Nicolas J; Trkola, Alexandra; Huber, Michael (2015). Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains. Diagnostic Microbiology and Infectious Disease, 83(2):133-138.

Abstract

Multiplex PCR assays for respiratory viruses are widely used in routine diagnostics, as they are highly sensitive, rapid, and cost effective. However, depending on the assay system, cross-reactivity between viruses that share a high sequence homology as well as detection of rare virus isolates with sequence variations can be problematic. Virus sequence-independent metagenomic high-throughput sequencing allows for accurate detection of all virus species in a given sample, as we demonstrate here for human Enterovirus and Rhinovirus in a lung transplant patient. While early in infection a commercial PCR assay recorded Rhinovirus, high-throughput sequencing correctly identified human Enterovirus C104 as the source of infection, highlighting the potential of the technology and the benefit of applying open assay formats in complex diagnostic situations.

Abstract

Multiplex PCR assays for respiratory viruses are widely used in routine diagnostics, as they are highly sensitive, rapid, and cost effective. However, depending on the assay system, cross-reactivity between viruses that share a high sequence homology as well as detection of rare virus isolates with sequence variations can be problematic. Virus sequence-independent metagenomic high-throughput sequencing allows for accurate detection of all virus species in a given sample, as we demonstrate here for human Enterovirus and Rhinovirus in a lung transplant patient. While early in infection a commercial PCR assay recorded Rhinovirus, high-throughput sequencing correctly identified human Enterovirus C104 as the source of infection, highlighting the potential of the technology and the benefit of applying open assay formats in complex diagnostic situations.

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6 citations in Web of Science®
4 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > University Hospital Zurich > Clinic for Pneumology
04 Faculty of Medicine > University Hospital Zurich > Clinic for Infectious Diseases
Dewey Decimal Classification:610 Medicine & health
Language:English
Date:October 2015
Deposited On:20 Nov 2015 13:16
Last Modified:08 Dec 2017 14:53
Publisher:Elsevier
ISSN:0732-8893
Publisher DOI:https://doi.org/10.1016/j.diagmicrobio.2015.06.017
PubMed ID:26231254

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