Diagnostic accuracy of VIDISCA-NGS in patients with suspected central nervous system infections

Abstract

Objectives: Confirming the diagnosis in viral central nervous system (CNS) infections can be difficult with the currently available diagnostic tools. Virus discovery cDNA amplified fragment length polymorphism next generation sequencing (VIDISCA NGS) is a promising viral metagenomic technique that enables the detection of all viruses in a single assay. We performed a retrospective study on the diagnostic accuracy of VIDISCA NGS in cerebrospinal fluid (CSF) of individuals with suspected CNS infections. Methods: Consecutive adult patients presenting to the Emergency Department or inpatients, who un derwent a lumbar puncture for the suspicion of a CNS infection, were included if they were diagnosed with a viral CNS infection, or if a viral CNS infection was initially suspected but eventually a different diagnosis was made. A quantitative PCR panel of the most common causative viruses was performed on CSF of these patients as reference standard and compared with the results of VIDISCA NGS, the index test.Results: We included 38 individuals with viral CNS infections and 35 presenting with suspected CNS infection for whom an alternative aetiology was finally established. Overall sensitivity and specificity were 52% (95% CI 31% 73%) and 100% (95% CI 91% 100%), respectively. One enterovirus, detected by VIDISCA NGS, was only identified by quantitative PCR upon retesting. Additional viruses identified by VIDISCA NGS consisted of GB virus C, human papillomavirus, human mastadenovirus C, Merkel cell polyoma virus and anelloviruses. Conclusion:In patients for whom routine diagnostics do not yield a causative pathogen, VIDISCA NGS can be of additional value as it can detect a broader range of viruses, but it does not perform well enough to replace quantitativePCR.

Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach

“…Subsequently, data were unblinded for optimization of threshold parameters. For controls, previously generated [ 22 ] sequencing data from 74 patient CSF samples tested negative in culture for bacteria were included in analysis, approved by a separate decision of the Medical Ethics Committee of the Amsterdam UMC (METC2014_290). These samples were from patients undergoing lumbar puncture for suspected CNS infection, and either viral CNS infection was diagnosed or CNS infection was eventually ruled out.…”

High-throughput sequencing technology facilitates the discovery of novel biomarkers for antiphospholipid syndrome

“…In recent years, the continuous development and innovation of NGS (next-generation sequencing) technology has greatly promoted the integration and development of all fields of genome research (18). NGS technology mainly obtains DNA sequence data by library construction, cross-linking amplification between library and vector, synthesis and sequencing on top of vector (19).…”

Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome

“…Viral metagenomics using unbiased next generation sequencing is a suitable technology to identify such virome changes, allowing us to increase our knowledge of virosphere diversity and providing us with a tool to elucidate the etiology of diseases the cause of which is yet unknown [7,8]. One of these unbiased virus discovery methods is VIDISCA, virus discovery cDNA-AFLP (amplified fragment length polymorphism) [9], which has been successfully used to detect a large number of novel human and animal viruses in cell culture supernatants [10], sera [11,12], feces [11,12], respiratory clinical samples [9], cerebrospinal fluid [13,14], and multiple solid tissues [15].…”