Metagenomic next-generation sequencing in the diagnosis of viral encephalitis

Table 3 Comparative summary of key clinical evidence on cerebrospinal fluid metagenomic next-generation sequencing for central nervous system infection

Ref.	Population/workflow	Main findings	Key limitations	Clinical interpretation
Wilson et al[22]; prospective, multicenter	204 patients with meningitis/encephalitis; clinical adjudication against conventional testing	58 infections in 57 patients; 13/58 (22%) identified only by mNGS; 8/13 likely clinical effect; 7/13 guided treatment	Missed 11 serology-only, 7 non-CSF/tissue, and 8 low-titer infections	Adds actionable diagnoses but cannot replace serology, tissue testing, or targeted assays
Xing et al[25]; prospective, multicenter	213 patients with suspected infectious encephalitis/meningitis	mNGS positivity 57% in definite CNS infection and 42.6% in definite viral disease; AUC 0.659 at SSRN ≥ 2	Performance depends on threshold, case definition, and pathogen spectrum	Useful in selected unresolved cases; yield is not uniform across disease groups
Qu et al[27]; systematic review and meta-analysis	12 studies; heterogeneous populations, assays, reference standards, and thresholds	Pooled sensitivity 77% (95%CI: 70%-82%); specificity 96% (95%CI: 93%-98%); AUC 0.91; viral subgroup 82%/97%	Specificity heterogeneity I2 = 72.07%; too few non-Illumina studies for platform comparison	Pooled accuracy is promising but should not be applied as a universal assay estimate
Benoit et al[28]; seven-year clinical performance	4828 CSF samples; adjudicated subset included 220 CNS infections	14.4% of samples positive; mNGS alone identified 48/220 infections (21.8%); sensitivity 63.1%, specificity 99.6%, accuracy 92.9%	Sensitivity rose to 86% against CSF direct detection alone, illustrating reference-standard effects	High specificity and meaningful incremental yield, with persistent sensitivity gaps

mNGS: Metagenomic next-generation sequencing; CSF: Cerebrospinal fluid; CNS: Central nervous system; AUC: Area under the receiver operating characteristic curve; SSRN: Strictly mapped read number; CI: Confidence interval.