The following is a summary of “Validation of an automated, end-to-end metagenomic sequencing assay for agnostic detection of respiratory viruses,” published in the May 2024 issue of Infectious Disease by Gauthier et al.
Traditional tests need help identifying all possible pathogens, while metagenomic next-generation sequencing (NGS) offers a promising yet underutilized solution due to practical challenges in clinical settings.
Researchers conducted a retrospective study to evaluate an optimized end-to-end mNGS assay for detecting respiratory viruses with faster turnaround times, lower costs, and improved data analysis.
They validated the assay with 359 residual nasopharyngeal swab specimens from Vancouver General Hospital, comprising RT-PCR-positive or negative cases for Influenza, SARS-CoV-2, and RSV. Quantification was done for sample stability, assay precision, impact of background nucleic acid levels, and analytical detection limits. Estimations were made for diagnostic performance metrics.
The results showed that the mNGS assay demonstrated high precision and semi-quantitative capabilities, with analytical limits of detection ranging from 103 to 104 copies/mL. The assay exhibited high specificity (100%) and sensitivity (61.9% Overall: 86.8%; RT-PCR Ct < 30). Which simultaneously processes up to 55 specimens on an Oxford Nanopore GridION device, with results reported within 12 hours.
Investigators concluded that optimized mNGS assay effectively diagnosed respiratory viruses while demonstrating feasibility for clinical use in diagnostics, infection control, and public health surveillance.
Source: academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiae226/7663232