Viral Metagenomics on Cerebrospinal Fluid.

Edridge Edridge,Deijs Deijs,Brouwer Brouwer,Jebbink Jebbink,Van Der Hoek Van Der Hoek,Bakker Bakker,Kinsella Kinsella,Van Zeggeren Van Zeggeren,Van De Beek Van De Beek

doi:10.3390/genes10050332

Abstract

Identifying the causative pathogen in central nervous system (CNS) infections is crucial for patient management and prognosis. Many viruses can cause CNS infections, yet screening for each individually is costly and time-consuming. Most metagenomic assays can theoretically detect all pathogens, but often fail to detect viruses because of their small genome and low viral load. Viral metagenomics overcomes this by enrichment of the viral genomic content in a sample. VIDISCA-NGS is one of the available workflows for viral metagenomics, which requires only a small input volume and allows multiplexing of multiple samples per run. The performance of VIDISCA-NGS was tested on 45 cerebrospinal fluid (CSF) samples from patients with suspected CNS infections in which a virus was identified and quantified by polymerase chain reaction. Eighteen were positive for an RNA virus, and 34 for a herpesvirus. VIDISCA-NGS detected all RNA viruses with a viral load >2 × 104 RNA copies/mL (n = 6) and 8 of 12 of the remaining low load samples. Only one herpesvirus was identified by VIDISCA-NGS, however, when withholding a DNase treatment, 11 of 18 samples with a herpesvirus load >104 DNA copies/mL were detected. Our results indicate that VIDISCA-NGS has the capacity to detect low load RNA viruses in CSF. Herpesvirus DNA in clinical samples is probably non-encapsidated and therefore difficult to detect by VIDISCA-NGS.

Highlights

For patients with a suspected central nervous system (CNS) infection, rapid and accurate diagnosis is vital to determine treatment and improve prognosis [1]
Samples had been tested by routine diagnostic for enterovirus, human immunodeficiency virus 1 (HIV-1, in case the patients were HIV-1 seropositive), parechovirus, and herpesviruses
We examined the number of putative VIDISCA-NGS fragments in the human herpesvirus genomes

Summary

Introduction

For patients with a suspected central nervous system (CNS) infection, rapid and accurate diagnosis is vital to determine treatment and improve prognosis [1]. The differential diagnosis of such patients includes infectious etiologies, of which viruses are the most common [2], and non-infectious etiologies, such as auto-immune diseases [3]. When differentiating between an auto-immune and viral origin, immune suppression could lead to deleterious outcomes when caused by an unidentified virus [5]. During the last two decades, conventional diagnostics for viral CNS infections have shifted from non-specific culturing techniques towards highly-specific viral nucleic acid amplification tests, like. RNA virus virus not not found found by VIDISCA-NGS. U test between the positive and negative samples. The Mann-Whitney positive and negative VIDISCA-NGS samples.

Methods

Results

Conclusion