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


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Article Info

DATE

2020-09-30

AUTHORS

Karol Perlejewski, Iwona Bukowska-Ośko, Małgorzata Rydzanicz, Agnieszka Pawełczyk, Kamila Caraballo Cortѐs, Sylwia Osuch, Marcin Paciorek, Tomasz Dzieciątkowski, Marek Radkowski, Tomasz Laskus

ABSTRACT

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 105 to 102 and from 105 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. More... »

PAGES

16173

References to SciGraph publications

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  • 2007-06-08. Comparison of two methods used for monitoring low-copy cytomegalovirus infection in a patient with chronic myeloid leukemia after unrelated umbilical cord blood transplantation in ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS
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  • 2017-08-08. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples in MICROBIOME
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41598-020-73156-3

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    33 schema: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<sup>5</sup> to 10<sup>2</sup> and from 10<sup>5</sup> 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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