Metagenomic next-generation sequencing in the diagnosis of viral encephalitis

Table 1 Viral agents associated with encephalitis

Viral agent	Viral family/group	Common clinical context	Main diagnostic methods	Contribution of mNGS
Herpes simplex virus 1	Herpesviridae	Sporadic necrotizing encephalitis in adults, temporal lobe involvement	CSF HSV PCR, MRI, EEG	Complementary evaluation in PCR-negative, equivocal, or atypical cases
Herpes simplex virus 2	Herpesviridae	Neonatal infection, meningoencephalitis, immunosuppression	CSF HSV PCR, serum/CSF tests	Simultaneous detection within broad pathogen screening
Varicella zoster virus	Herpesviridae	Encephalitis, meningoencephalitis, vasculopathy, immunosuppression	CSF VZV PCR, CSF anti-VZV antibodies	Contribution to diagnosis of VZV neuroinfection without rash or with atypical presentation
Enteroviruses	Picornaviridae	Viral meningitis/encephalitis in children, brainstem encephalitis	CSF PCR, respiratory/stool PCR	Typing, genomic characterization, and detection of strains outside standard panels
Parechovirus	Picornaviridae	Sepsis-like illness and encephalitis in neonates and infants	CSF/blood PCR	Diagnostic contribution in cases not covered by conventional panels
West Nile virus	Flaviviridae	Seasonal arboviral encephalitis, neuroinvasive disease in older adults	Serum/CSF IgM, PCR, neutralization tests	Supportive diagnosis in early-stage or geographically unexpected cases
Japanese encephalitis virus	Flaviviridae	Encephalitis in endemic regions, travel-associated infection	CSF/serum IgM, PCR	Detection in travel-associated cases or when targeted testing has not been performed
Tick-borne encephalitis virus	Flaviviridae	Tick exposure, Europe/Asia-associated encephalitis	Serum/CSF IgM, PCR	Contribution in cases with tick exposure and inconclusive PCR/serology
Powassan virus	Flaviviridae	Tick-borne severe encephalitis	Serology, PCR, public health laboratory tests	Detection of rare arboviruses outside routine panels
Chikungunya virus	Togaviridae	Travel-/outbreak-associated fever, arthralgia, rarely encephalitis	PCR, IgM/IgG serology	Diagnostic contribution in atypical cases with neurological complications
Rabies virus	Rhabdoviridae	Fatal encephalitis after animal exposure	Saliva/skin biopsy PCR, serology, antigen tests	May assist in suspected cases not confirmed by conventional tests
JC virus	Polyomaviridae	Progressive multifocal leukoencephalopathy in immunocompromised patients	CSF JC virus PCR, MRI	Detection during broad diagnostic evaluation in immunocompromised patients
Cytomegalovirus	Herpesviridae	Advanced immunosuppression, transplantation, human immunodeficiency virus	CSF/blood CMV PCR	Assessment of opportunistic infection and coinfection
HHV-6	Herpesviridae	Post-transplant encephalitis, limbic encephalitis	CSF HHV-6 PCR, viral load	Requires careful interpretation to distinguish reactivation, chromosomal integration, and true infection
Astrovirus	Astroviridae	Unexplained encephalitis in immunocompromised patients	mNGS, confirmatory PCR	Identification of unexpected neurotropic agents
Bornavirus	Bornaviridae	Rare, severe/fatal encephalitis, zoonotic association	mNGS, PCR, serology, tissue examination	Important contribution to discovery of novel or rare pathogens

mNGS: Metagenomic next-generation sequencing; CSF: Cerebrospinal fluid; HSV: Herpes simplex virus; PCR: Polymerase chain reaction; MRI: Magnetic resonance imaging; EEG: Electroencephalography; VZV: Varicella zoster virus; IgM: Immunoglobulin M; CMV: Cytomegalovirus; HHV-6: Human herpesvirus 6.