Encephalitis is inflammation of the parenchyma of the brain, resulting from direct viral invasion or occurring as a postinfectious immunologic complication caused by a hypersensitivity reaction to a virus or another foreign protein. Symptoms include fever, headache, and altered mental status, often accompanied by seizures or focal neurologic deficits. Diagnosis requires cerebrospinal fluid analysis and neuroimaging. Treatment involves antiviral medications when indicated (eg, in herpes simplex virus encephalitis) and is otherwise supportive.
(See also Introduction to Brain Infections.)
Etiology of Encephalitis
Primary viral infection
Viruses causing primary encephalitis directly invade the brain. These infections may be
Epidemic (eg, due to arbovirus, echovirus, coxsackievirus, or poliovirus [in some underdeveloped countries])
Sporadic (eg, due to herpes simplex, varicella-zoster, lymphocytic choriomeningitis, rabies, or mumps virus)
Mosquito-borne arboviral encephalitides infect people during the spring, summer, and early fall when the weather is warm (see table Some Arboviral Encephalitides). Incidence in the United States varies from 150 to > 4000 cases yearly, mostly in children. Most cases occur during epidemics.
Some Arboviral Encephalitides
Virus | Distribution | Mortality Rate | Comments |
|---|---|---|---|
Florida, Puerto Rico, the U. S. Virgin Islands Common in Africa, India, Guam, Southeast Asia, New Guinea, China, Mexico, Central America Reunion Islands, limited areas of Europe | < 1% overall, but in patients > 60, there is increased risk of death for 3 months after symptom onset, including deaths from cerebrovascular diseases, ischemic heart diseases, and diabetes* | Should be considered in US travelers who develop encephalitis after visiting endemic areas Can lead to severe encephalitis and even death, especially in infants and people > 65 | |
Colorado tick fever virus | Western United States and Canada in areas that are 4,000 to 10,000 ft above sea level | Rarely causes death | Causes a nonspecific febrile illness, rarely complicated by meningitis or encephalitis |
Japanese encephalitis virus | Asia and the western Pacific; uncommon in the United States (mainly in travelers returning from endemic areas) | < 1% overall, but up to 30% of severe cases† | Affects mainly children Usually mild and self-limiting, but severe in about 1 in 250 cases Vaccine used in endemic areas and recommended for travelers to these areas |
La Crosse virus (California virus) | Primarily in the north central United States but geographically widespread | Probably < 1% ‡ | Is probably underrecognized Accounts for most cases of arbovirus encephalitis in children |
St. Louis encephalitis virus | Mostly in urban areas of the central and southeastern United States but also in western states | — | Occurs in periodic urban epidemics; otherwise sporadic and rare |
Powassan virus | Primarily in the northeastern states and the Great Lakes region of the United States Southeastern Canada and Russia (southeastern Siberia, northeast of Vladivostok) | About 10 to 15%§ | Although rare, appears to be increasing since 2007; occurs in the late spring to mid-fall, when ticks are most active Should be considered in patients with encephalitis, especially those with a history of tick bite, a lot of time spent outdoors, and/or residence in or recent travel to an endemic area |
Tick-borne encephalitis virus | Northern Asia, Russia, and many parts of Europe | Usually 1–2% but varies based on subtype (0.5–35%)¶ | Occurs from early spring to late summer when ticks are most active Highest incidence and most severe symptoms in people ≥ 50 years Should be suspected in travelers who have a nonspecific febrile illness that progresses to neuroinvasive disease within 4 weeks after arriving from an endemic area and who may have been exposed to ticks |
Venezuelan equine encephalitis | Mainly in parts in South and Central America; only rarely in the United States (mainly in travelers returning from endemic areas) | 0–1%[a], primarily in children | Vaccine available for equines; investigational vaccine used in laboratory workers at risk |
Throughout the continental United States and other parts of North America Africa, Europe, the Middle East, and West Asia | About 9% of patients with involvement of the central nervous system (CNS)[b] | As of 2017, spread from the East Coast, where it first appeared in 1999, to all of the western states | |
Eastern equine encephalitis virus | Eastern United States; a few cases in the Great Lakes states | About 50‒70%[c] | Occurs as small epidemics every 10‒20 years, mainly among young children and people > 55 |
Western equine encephalitis virus | — | — | For unknown reasons, has largely disappeared from the United States since 1988 |
Florida South America, Central America, Caribbean Islands, Pacific Islands, Cape Verde (a nation of islands off the northwest coast of Africa), Southeast Asia | — | There have been no cases of local transmission of Zika virus in the continental United States since 2018 ([d]ref) May cause a dengue-like illness and has been implicated in causing Guillain-Barré syndrome, severe brain damage, and microcephaly in infants of infected mothers | |
* Cerqueira-Silva T, Pescarini JM, Cardim CL, et al: Risk of death following chikungunya virus disease in the 100 million Brazilian cohort, 2015–18: A matched cohort study and self-controlled case series. Lancet Infectious Diseases 25(5):504-513, 2024. † LaBeaud AD, Bashir F, King CH: Measuring the burden of arboviral diseases: The spectrum of morbidity and mortality from four prevalent infections. Population Health Metrics 9:1, 2011. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024945/pdf/1478-7954-9-1.pdf ‡ Vahey GV, Lindsey NP, Staples JE, et al:: La Crosse virus disease in the United States, 2003–2019. Am J Trop Med Hyg 105(3):807-812, 2021. doi: 10.4269/ajtmh.21-0294 §Centers for Disease Control and Prevention: Powassan virus. Historic data (2004–2023). Accessed July 5, 2024. ¶ Hills SL, Poehling KA, Chen WH, et alMMWR Recommen Rep 72(5):1-29, 2023. [a]Centers for Disease Control and Prevention: Venezuelan equine encephalitis—Colombia, 1995. MMWR 44(39):721-724, 1995 [b] Fagre AC, Lyons S, Staples JE, et al: West Nile virus and other nationally notifiable arboviral diseases—United States, 2021. MMWR 72(34):901-906, 2023. [c]Centers for Disease Control and Prevention: Eastern Equine Encephalitis Virus. Accessed July 5, 2024. [d] Zika Cases in the United States. Centers for Disease Control and Prevention. Accessed May 31, 2024. | |||
In the United States, the most common sporadic encephalitis is caused by herpes simplex virus (HSV); hundreds to several thousand cases occur yearly. Most are due to HSV-1, but HSV-2 may be more common among immunocompromised patients. HSV encephalitis occurs at any time of the year, tends to affect patients < 20 or > 40 years, and is often fatal if untreated.
Rabies remains a significant cause of encephalitis in developing countries and still causes a few cases of encephalitis in the United States.
Encephalitis can also occur as a late reactivation of latent or subclinical viral infection. The best known types are
Subacute sclerosing panencephalitis (which occurs years after a measles infection and is thought to represent reactivation of the original infection; it is now rare in Western countries)
Progressive multifocal leukoencephalopathy (which is caused by reactivation of JC virus; particularly in patients with end-stage HIV infection or those who are immunosuppressed)
Herpes simplex type 1 and herpes zoster encephalitis
Immunologic reaction
influenza A or B virus, enteroviruses, Epstein-Barr virus (1), herpes viruses (2), hepatitis A or hepatitis B virus, or HIV. Immunologically mediated encephalitis also occurs in patients with cancer and other autoimmune disorders.
Rarely, apparent encephalitis has developed in patients with COVID-19, caused by the novel pandemic severe acute respiratory syndrome coronavirus (SARS-CoV2); the mechanism is not clear, but an immunologic contribution to the mechanism of apparent encephalitis is possible (2).
Encephalopathies caused by autoantibodies to neuronal membrane proteins (eg, N-methyl-d-aspartate receptors [NMDAR]) may mimic viral encephalitis. Studies indicate that anti-NMDAR encephalitis is more common than viral encephalitides. Anti-NMDAR encephalitis was first described in young women with ovarian teratomas but can occur in both sexes and at any age. Anti-NMDAR encephalitis also occurs as a postinfectious complication of HSV encephalitis, resulting in clinical decline within weeks of the HSV infection.
Etiology references
1. Schwenkenbecher P, Skripuletz T, Lange P, et al; German Network for Research on Autoimmune Encephalitis: Intrathecal antibody production against Epstein-Barr, herpes simplex, and other neurotropic viruses in autoimmune encephalitis. Neurol Neuroimmunol Neuroinflamm 8(6):e1062, 2021. doi: 10.1212/NXI.0000000000001062
2. Meinhardt J, Streit S, Dittmayer C, et al: The neurobiology of SARS-CoV-2 infection. Nat Rev Neurosci 25(1):30-42, 2024. doi: 10.1038/s41583-023-00769-8
Pathophysiology of Encephalitis
In acute encephalitis, inflammation and edema occur in infected areas throughout the cerebral hemispheres, brain stem, cerebellum, and, occasionally, spinal cord. Petechial hemorrhages may be present in severe infections. Direct viral invasion of the brain usually damages neurons, sometimes producing microscopically visible inclusion bodies, and triggers inflammation that may persist after clearance of virus (1). Severe infection, particularly untreated herpes simplex virus (HSV) encephalitis, can cause brain hemorrhagic necrosis.
Acute disseminated encephalomyelitis is characterized by multifocal areas of perivenous demyelination and absence of virus in the brain.
Pathophysiology reference
1. Godinho-Silva C, Cardoso F, Veiga-Fernandes H: Neuro-immune cell units: A new paradigm in physiology. Annu Rev Immunol 237:19-46, 2019. doi: 10.1146/annurev-immunol-042718-041812
Symptoms and Signs of Encephalitis
Symptoms of encephalitis include fever, headache, and altered mental status, often accompanied by seizures and focal neurologic deficits. A gastrointestinal (GI) or respiratory prodrome may precede these symptoms. Meningeal signs are typically mild and less prominent than other manifestations.
Status epilepticus, particularly convulsive status epilepticus, or coma suggests severe brain inflammation and a poor prognosis.
Olfactory seizures, manifested as an aura of foul smells (rotten eggs, burnt meat), indicate temporal lobe involvement and suggest HSV encephalitis.
Diagnosis of Encephalitis
MRI
Cerebrospinal fluid (CSF) testing
Encephalitis is suspected in patients with unexplained alterations in mental status. Clinical presentation and differential diagnoses may suggest certain diagnostic tests, but MRI and CSF analysis (including polymerase chain reaction [PCR] for HSV and other viruses) are usually done, typically with other tests (eg, serologic tests) to identify the causative virus. Despite extensive testing, the cause of many cases of encephalitis remains unknown.
Cytomegalovirus encephalitis should be considered in patients with HIV/AIDS or other immunocompromised conditions and can be diagnosed by PCR.
MRI
Contrast-enhanced MRI is sensitive for early HSV encephalitis, showing edema in the orbitofrontal and temporal areas, which HSV typically infects. MRI shows demyelination in progressive multifocal leukoencephalopathy and may show basal ganglia and thalamic abnormalities in West Nile and eastern equine encephalitis. MRI can also exclude lesions that mimic viral encephalitis (eg, brain abscess, sagittal sinus thrombosis).
CT is much less sensitive than MRI for HSV encephalitis but can help because it is rapidly available and can exclude disorders that make lumbar puncture risky (eg, mass lesions, hydrocephalus, cerebral edema).
CSF testing
Lumbar puncture (spinal tap) is done (1, 2). If encephalitis is present, CSF is characterized by lymphocytic pleocytosis, normal glucose, mildly elevated protein, and an absence of pathogens after Gram staining and culture (similar to CSF in aseptic meningitis). Pleocytosis may be polymorphonuclear in severe infections. CSF abnormalities may not develop until 8 to 24 hours after onset of symptoms. Hemorrhagic necrosis can introduce red blood cells (RBCs) into CSF and elevate protein. CSF glucose levels may be low when the cause is varicella-zoster virus, mumps, or lymphocytic choriomeningitis virus.
CSF samples should be sent for viral identification using PCR or, in suspected cases of arboviral infection, detection of antiviral antibodies in CSF. PCR testing of CSF is the diagnostic test of choice for HSV-1, HSV-2, varicella-zoster virus, cytomegalovirus, enteroviruses, and JC virus. PCR for HSV in CSF is particularly sensitive and specific. However, results may not be available rapidly, and despite advances in technology, false-negative and false-positive results may still occur because of a variety of conditions; not all are technical failures (eg, the blood in a mildly traumatic CSF tap may inhibit the PCR amplification step). False-negative results can occur early in HSV-1 encephalitis; if a false-negative result is suspected based on clinical findings, testing should be repeated in 48 to 72 hours. A recently developed multiplex PCR process, which can detect multiple viral and other infectious agents simultaneously, provides diagnostic information within a few hours. Multiplex PCR results may need to be confirmed by conventional PCR.
CSF viral cultures grow enteroviruses but not most other viruses. For this reason, CSF viral cultures have been superseded by PCR and are rarely used in diagnosis.
CSF viral IgM titers are often useful for diagnosing acute infection, especially West Nile encephalitis, for which they are more reliable than PCR. CSF IgG and IgM titers may be more sensitive than PCR for encephalitis due to reactivated varicella-zoster virus infection. Paired acute and convalescent serologic tests of CSF and blood must be drawn several weeks apart; they can detect an increase in viral titers specific for certain viral infections.
Brain biopsy
Brain biopsy may be indicated for patients who
Are worsening
Have a lesion that is still undiagnosed
However, brain biopsy has a low yield unless it targets an abnormality seen on MRI or CT.
Diagnosis references
1. Venkatesan AR, Tunkel KC, Bloch AS, et al: Case definitions, diagnostic algorithms, and priorities in encephalitis: Consensus statement of the International Encephalitis Consortium. Clin Infect Dis 57(8):1114–1128, 2013. doi.org/10.1093/cid/cit458
2. Funk S, Knapp JK, Lebo E, et al: Combining serological and contact data to derive target immunity levels for achieving and maintaining measles elimination. BMC Med 17(1):180, 2109. doi: 10.1186/s12916-019-1413-7
Treatment of Encephalitis
Supportive care
Supportive therapy for encephalitis includes treatment of fever, dehydration, electrolyte disorders, and seizures. Euvolemia should be maintained.
Because a bacterial CNS infection is often difficult to exclude when patients who appear seriously ill present, empiric antibiotics are often given until bacterial meningitis is excluded.
Prognosis for Encephalitis
Recovery from viral encephalitis may take a very long time. Mortality rate varies with cause, but severity of epidemics due to the same virus varies during different years. Permanent neurologic deficits are common among patients who survive severe infection. Patients may also develop postviral memory impairments (1).
Prognosis reference
1. Kvam KA, Stahl JP, Chow FC, et al: Outcome and sequelae of infectious encephalitis. J Clin Neurol 20(1):23-36, 2024. doi: 10.3988/jcn.2023.0240
Key Points
Viruses that cause epidemic or sporadic infections can invade and infect brain parenchyma (causing encephalitis) and/or trigger postinfectious inflammatory demyelination (acute disseminated encephalomyelitis).
Encephalitis causes fever, headache, and altered mental status, often accompanied by seizures and focal neurologic deficits.
Do contrast-enhanced MRI and CSF testing.
Treat encephalitis due to an immunologic reaction with corticosteroids and plasma exchange or IV immune globulin.
