Metagenomic next-generation sequencing in the diagnosis of viral encephalitis

Table 2 Representative viral findings detected or investigated by metagenomic next-generation sequencing and their clinical interpretation

Agent identified/investigated by mNGS	Specimen type	Clinical context	Contribution of mNGS	Points to consider in clinical interpretation
HSV-1/HSV-2	CSF	Acute necrotizing encephalitis, temporal lobe involvement	Complementary diagnosis together with targeted PCR or in PCR-negative/equivocal cases	Empirical acyclovir should not be delayed while awaiting mNGS results
VZV	CSF	Encephalitis without rash, vasculopathy, immunosuppression	Detection of atypical VZV neuroinfection	CSF antibody testing may be more sensitive than PCR in some cases
Enterovirus	CSF, stool, respiratory sample	Pediatric encephalitis, brainstem involvement	Detection of the causative agent and genomic typing	Alternative specimens may be useful if CSF viral load is low
West Nile virus	CSF, serum/plasma	Arboviral encephalitis, seasonal neuroinvasive disease	Detection of viral RNA in early infection or unexpected cases	Should be interpreted together with serology
Chikungunya virus	CSF, serum	Travel-/outbreak-associated neurological disease	Diagnosis in atypical cases without targeted testing	Should be supported by clinical and epidemiological history
Powassan virus	CSF, serum	Severe encephalitis after tick exposure	Identification of a rare arbovirus	Confirmation by a public health laboratory may be required
Astrovirus	CSF, brain tissue	Undiagnosed encephalitis in immunocompromised patients	Discovery of a neurotropic agent not included in conventional panels	Contamination, systemic infection, and true CNS invasion should be distinguished
Bornavirus	CSF, brain tissue	Severe/fatal encephalitis, zoonotic exposure	Discovery of a novel/rare pathogen and genomic characterization	Tissue-level confirmation and epidemiological investigation are important
JC virus	CSF	Leukoencephalopathy in immunocompromised patients	Detection of an opportunistic viral agent during broad screening	Should be evaluated together with clinical and MRI findings
HHV-6	CSF	Post-transplant limbic encephalitis	Detection of an opportunistic viral agent or reactivation	Chromosomal integration and latent reactivation should be considered
CMV	CSF, blood	Advanced immunosuppression, transplantation	Assessment of systemic and CNS involvement	Should be interpreted together with blood viral load and clinical presentation
Unknown/novel virus	CSF, brain tissue	Undiagnosed encephalitis, outbreak or zoonotic suspicion	Novel pathogen discovery, phylogenetic analysis	Independent confirmation, negative controls, and epidemiological assessment are required

mNGS: Metagenomic next-generation sequencing; HSV: Herpes simplex virus; CSF: Cerebrospinal fluid; PCR: Polymerase chain reaction; VZV: Varicella zoster virus; MRI: Magnetic resonance imaging; CNS: Central nervous system; HHV-6: Human herpesvirus 6; CMV: Cytomegalovirus.