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Authors: Iwona BukowskaOśko 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
Publish Date: 2016
Volume: , Issue: , Pages: 53-62
Abstract
Nextgeneration 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 RiboSPIA 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 59 and 214 of all reads in water samples and 23 in the control CSF sample The bacterial sequences corresponded mainly to Psychrobacter Acinetobacter and Corynebacterium genera In conclusion RiboSPIA 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 RTPCR and PCR Despite these reservations NGS seems to be a promising method for the diagnosis of viral infections
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