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Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations

Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of e...

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Autores principales: Perlejewski, Karol, Bukowska-Ośko, Iwona, Rydzanicz, Małgorzata, Pawełczyk, Agnieszka, Caraballo Cortѐs, Kamila, Osuch, Sylwia, Paciorek, Marcin, Dzieciątkowski, Tomasz, Radkowski, Marek, Laskus, Tomasz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528011/
https://www.ncbi.nlm.nih.gov/pubmed/32999423
http://dx.doi.org/10.1038/s41598-020-73156-3
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author Perlejewski, Karol
Bukowska-Ośko, Iwona
Rydzanicz, Małgorzata
Pawełczyk, Agnieszka
Caraballo Cortѐs, Kamila
Osuch, Sylwia
Paciorek, Marcin
Dzieciątkowski, Tomasz
Radkowski, Marek
Laskus, Tomasz
author_facet Perlejewski, Karol
Bukowska-Ośko, Iwona
Rydzanicz, Małgorzata
Pawełczyk, Agnieszka
Caraballo Cortѐs, Kamila
Osuch, Sylwia
Paciorek, Marcin
Dzieciątkowski, Tomasz
Radkowski, Marek
Laskus, Tomasz
author_sort Perlejewski, Karol
collection PubMed
description Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 10(5) to 10(2) and from 10(5) to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common.
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spelling pubmed-75280112020-10-02 Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations Perlejewski, Karol Bukowska-Ośko, Iwona Rydzanicz, Małgorzata Pawełczyk, Agnieszka Caraballo Cortѐs, Kamila Osuch, Sylwia Paciorek, Marcin Dzieciątkowski, Tomasz Radkowski, Marek Laskus, Tomasz Sci Rep Article Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 10(5) to 10(2) and from 10(5) to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common. Nature Publishing Group UK 2020-09-30 /pmc/articles/PMC7528011/ /pubmed/32999423 http://dx.doi.org/10.1038/s41598-020-73156-3 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Perlejewski, Karol
Bukowska-Ośko, Iwona
Rydzanicz, Małgorzata
Pawełczyk, Agnieszka
Caraballo Cortѐs, Kamila
Osuch, Sylwia
Paciorek, Marcin
Dzieciątkowski, Tomasz
Radkowski, Marek
Laskus, Tomasz
Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
title Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
title_full Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
title_fullStr Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
title_full_unstemmed Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
title_short Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
title_sort next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528011/
https://www.ncbi.nlm.nih.gov/pubmed/32999423
http://dx.doi.org/10.1038/s41598-020-73156-3
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