Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of ... View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2016-07-13

AUTHORS

Iwona Bukowska-Ośko , Karol Perlejewski , Shota Nakamura , Daisuke Motooka , Tomasz Stokowy , Joanna Kosińska , Marta Popiel , Rafał Płoski , Andrzej Horban , Dariusz Lipowski , Kamila Caraballo Cortés , Agnieszka Pawełczyk , Urszula Demkow , Adam Stępień , Marek Radkowski , Tomasz Laskus

ABSTRACT

Next-generation sequencing (NGS) followed by metagenomic analysis enables the detection and identification of known as well as novel pathogens. It could be potentially useful in the diagnosis of encephalitis, caused by a variety of microorganisms. The aim of the present study was to evaluate the sensitivity of isothermal RNA amplification (Ribo-SPIA) followed by NGS metagenomic analysis in the detection of human immunodeficiency virus (HIV) and herpes simplex virus (HSV) in cerebrospinal fluid (CSF). Moreover, we analyzed the contamination background. We detected 102 HIV copies and 103 HSV copies. The analysis of control samples (two water samples and one CSF sample from an uninfected patient) revealed the presence of human DNA in the CSF sample (91 % of all reads), while the dominating sequences in water were qualified as ‘other’, related to plants, plant viruses, and synthetic constructs, and constituted 31 % and 60 % of all reads. Bacterial sequences represented 5.9 % and 21.4 % of all reads in water samples and 2.3 % in the control CSF sample. The bacterial sequences corresponded mainly to Psychrobacter, Acinetobacter, and Corynebacterium genera. In conclusion, Ribo-SPIA amplification followed by NGS metagenomic analysis is sensitive for detection of RNA and DNA viruses. Contamination seems common and thus the results should be confirmed by other independent methods such as RT-PCR and PCR. Despite these reservations, NGS seems to be a promising method for the diagnosis of viral infections. More... »

PAGES

53-62

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/5584_2016_42

DOI

http://dx.doi.org/10.1007/5584_2016_42

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007541069

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27405447


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