Japanese Encephalitis Virus: Japanese Encephalitis (JE) is a mosquito borne zoonotic viral disease caused by arbovirus (flavivirus), involving the Central Nervous System. Japanese encephalitis is the leading viral cause of Acute Encephalitis Syndrome (AES) in Asia. The disease primarily affects children under the age of fifteen years. Seventy percent of those who develop illness either die or survive with a long-term neurological disability. Japanese encephalitis is caused by the Japanese encephalitis virus, an arbovirus. Arbovirus is short for arthropod-borne virus. Arboviruses are a large group of viruses that are spread by certain invertebrate animals (arthropods), most commonly blood-sucking insects. Like most arboviruses, Japanese encephalitis is spread by infected mosquitoes. Japanese encephalitis is a potentially severe viral disease that is spread by infected mosquitoes in the agricultural regions of Asia. It is one of several mosquito-borne virus diseases that can affect the central nervous system and cause severe complications and death. Japanese encephalitis can be a risk to travelers to rural areas where the disease is common. There is no specific treatment for Japanese encephalitis. The Japanese encephalitis virus has a complex life cycle involving domestic pigs and a specific type of mosquito, Culex tritaeniorhynchus that lives in rural rice-growing and pig-farming regions. The mosquito breeds in flooded rice fields, marshes, and standing water around planted fields. The virus can infect humans, most domestic animals, birds, bats, snakes, and frogs. The incubation period in man, following mosquito bite varies from 5 to 15 days. After infection; the virus invades the central nervous system, including the brain and spinal cord. The virus initially propagates at the site of the bite and in regional lymph nodes. Subsequently, viremia develops, leading to inflammatory changes in the heart, lungs, liver, and reticuloendothelial system. Most infections are cleared before the virus can invade the central nervous system (CNS), leading to subclinical disease. Japanese encephalitis usually starts as a flu-like illness, with fever, chills, tiredness, headache, nausea, and vomiting. Confusion and agitation can also occur in the early stage. The illness can progress to a serious infection of the brain (encephalitis) and can be fatal in 30% of cases. Among the survivors, another 30% will have serious brain damage, including paralysis. The transmission of the JE virus has been widespread in India. The first evidence of presence of the presence of the JE virus dates back to 1952 in the Nagpur subdivision of Maharashtra. JE was clinically diagnosed for the first time in 1955 at Vellore in the North Arcot district of Tamil Nadu. In subsequent years, outbreaks have occurred in various States. The first major JE epidemic was reported from the Burdwan and Bankura districts of West Bengal in 1973 followed by another outbreak in 1976. Outbreaks have been reported from states like Uttar Pradesh, West Bengal, Assam, Andhra Pradesh, Karnataka, Bihar, Tamil Nadu, Haryana and other states through the years.


Methodology: Taqman Real time PCR assay

Clinical Use:

  • Routine blood examination: To detect any significant changes in the blood cell and its associated components.
  • Assess viral measured by changes in the JEV RNA levels
  • Assess prognosis and early diagnosis for better patient cure
  • Confirm active Japanese Encephalitis (JEV) infection In patient


  • Elevation of the levels of CSF protein in about 50% of cases
  •    suspected  patient with evidence of a neurologic infection (such as encephalitis, meningitis, or

Acute flaccid paralysis persons

  • residing in areas where extended community outbreaks exist
  • international travelers to regions of the world where JEV is endemic
  • Vaccinated patient



Performed:  Every day
Reported: 2-3 days

Specimen Required: Blood, serum, plasma, Collect in: Lavender (EDTA), pink (K2EDTA), or serum separator tube. Cerebrospinal fluid (CSF) Stability collection to initiation of testing On Cells: Ambient: 4 hours; after separation from cells: Refrigerated: 48 hours; Frozen at -20°C: 72 hours; Frozen at -70°C: 4 months. Do not thaw avoid repeated freezing and thawing.

NOTE: Collect CSF specimen in sterile screw capped bottles under all aseptic precautions for attempting isolation of virus minimum 0.5ml of CSF is required for acceptance of standard diagnosis.

Specimen Preparation: CSF, Separate serum or plasma from cells within 24 hours.


Storage/Transport Temperature: Frozen-20 0C. Refrigerate specimens at 2°C-4°C.

Unacceptable Conditions:  Heparinized specimens, Hemolysis sample, Quantity not sufficient for analysis, specimen grossly contaminated, specimen too old, frozen whole blood specimen, specimen leaky or tube broken.


Interpretation: This test can quantitate/detect Japanese Encephalitis RNA Virus over the linear range 80-107 copies/mL. However this does not mean that lower copies or higher copies cannot be detected. The lower copies can be detected in some cases. This is a limitation of the currently available extraction systems. A negative result does not preclude the presence of JEV infection because results depend on adequate/proper patient sample storage and transportation as RNA is fragile and thermo labile, absence of inhibitors and sufficient RNA to be detected. Japanese Encephalitis is a viral disease, and as such, antibiotics are of no value in the treatment of the infection. There is no hyperimmune E globulin available for pre- or post-exposure prophylaxis. Humans may be infected by direct contact of infectious material with broken skin or mucous membranes, accidental parenteral inoculation or aerosol. Diagnosticians collecting samples should also take the appropriate precautions.

The result of this test must always be correlated with clinical status and history of the patient and other relevant data and   should not be used alone for the interpretation.   

Note: The test is intended for use in conjunction with clinical presentation and other laboratory markers as an indicator of disease prognosis.

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