Respiratory Treatment and Prevention (Advances in Experimental Medicine and Biology)

Advs Exp. Medicine, Biology - Neuroscience and Respiration (2016) 27: 53–62
DOI 10.1007/5584_2016_42
#Springer International Publishing Switzerland 2017
Published online: 13 July 2016

Sensitivity of Next-Generation Sequencing

Metagenomic Analysis for Detection

of RNA and DNA Viruses in Cerebrospinal

Fluid: The Confounding Effect

of Background Contamination

Iwona Bukowska-Os ́ko, Karol Perlejewski, Shota Nakamura,

Daisuke Motooka, Tomasz Stokowy, Joanna Kosin ́ska,

Marta Popiel, Rafał Płoski, Andrzej Horban, Dariusz Lipowski,

Kamila Caraballo Corte ́s, Agnieszka Pawełczyk,

Urszula Demkow, Adam Ste ̨pien ́, Marek Radkowski,

and 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 immu-

nodeficiency virus (HIV) and herpes simplex virus (HSV) in cerebrospinal

I. Bukowska-Os ́ko, K. Perlejewski (*), M. Popiel,
K. Caraballo Corte ́s, A. Pawełczyk, M. Radkowski, and
T. Laskus
Department of Immunopathology of Infectious and
Parasitic Diseases, Warsaw Medical University, 3C
Pawin ́skiego St, 02-106 Warsaw, Poland
e-mail:[email protected]

S. Nakamura and D. Motooka
Department of Infection Metagenomics, Genome
Information Research Center, Research Institute for
Microbial Diseases, Osaka University, 3-1 Yamadaoka,
Suita, Osaka, Japan

T. Stokowy
Department of Clinical Science, Bergen University, 5021
Bergen, Norway

J. Kosin ́ska and R. Płoski

Department of the Medical Genetics, Warsaw Medical

University, 3C Pawin ́skiego St, 02-106 Warsaw, Poland

A. Horban and D. Lipowski

Municipal Hospital for Infectious Diseases, 37 Wolska St,

01-201 Warsaw, Poland

U. Demkow

Department of Laboratory Medicine and Clinical

Immunology of Developmental Age, Warsaw Medical

University, 24 Marszałkowska St, 00-576 Warsaw,

Poland

A. Ste ̨pien ́

Department of Neurology, Military Institute of Medicine,

128 Szasero ́w St, 04-141 Warsaw, Poland

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