Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics

Abstract

Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.

Human herpesvirus 6 infection as a trigger of multiple sclerosis: an update of recent literature

“…It revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%) [ 37 ].…”

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

“…Although all these methods solve the problem of insufficient material for sequencing in low-biomass samples, they neither reduce nor distinguish contaminants from true signals. Moreover, as previously mentioned, there is some evidence that these kits can be the source of extra genetic background themselves ( Thoendel et al, 2017 ; Oechslin et al, 2018 ; Perlejewski et al, 2020a ).…”

“…Such contamination effects are common, as several studies have found contaminant microbial DNA in laboratory reagents and laboratory surfaces ( Salter et al, 2014 ; Eisenhofer et al, 2019 ; Stinson et al, 2019 ). While several groups have also reported on the presence of genomic contaminants in viral SM data, there are no established criteria for examination and/or reporting of contamination in virome-focused studies ( Moustafa et al, 2017 ; Zolfo et al, 2019 ; Perlejewski et al, 2020a ). The current review emphasizes the impact of contaminants on viral studies, especially when using low-biomass samples, and proposes recommendations to minimize its effect.…”