Viral Metagenomics on Cerebrospinal Fluid

Area of Science:

• Virology
• Infectious Diseases
• Genomics

Background:

• Accurate identification of pathogens in central nervous system (CNS) infections is vital for patient outcomes.
• Traditional methods for detecting viruses in CNS infections are often costly and time-consuming.
• Metagenomic approaches offer a comprehensive solution but face challenges with low viral loads and small viral genomes.

Purpose of the Study:

• To evaluate the performance of the VIDISCA-NGS workflow for viral metagenomics in cerebrospinal fluid (CSF) samples.
• To assess the workflow's ability to detect and quantify viral pathogens, particularly RNA viruses and herpesviruses, in suspected CNS infections.

Main Methods:

• The VIDISCA-NGS workflow was applied to 45 CSF samples previously characterized by polymerase chain reaction (PCR).
• Samples included those positive for RNA viruses and herpesviruses with varying viral loads.
• Performance was assessed by comparing VIDISCA-NGS results with PCR quantification, including experiments with and without DNase treatment.

Main Results:

• VIDISCA-NGS successfully detected all RNA viruses with viral loads exceeding 2 × 10^4 copies/mL and 8 out of 12 lower-load samples.
• Detection of herpesviruses was limited (one positive) unless DNase treatment was omitted, which improved detection to 11 out of 18 high-load samples.
• The workflow demonstrated a strong capacity for identifying low-load RNA viruses in CSF.

Conclusions:

• VIDISCA-NGS is a promising tool for detecting RNA viruses in CSF, even at low concentrations.
• The detection of herpesviruses by VIDISCA-NGS is challenging, likely due to non-encapsidated viral DNA in clinical samples.
• Further optimization, particularly regarding DNA extraction and treatment steps, may be necessary to improve herpesvirus detection using this workflow.