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Encephalitic Flaviviruses - Update for Clinicians

What’s new in this Safety Alert?

This Safety Alert is an update of SA:008/22 Japanese Encephalitis Virus – Update for Clinicians (now rescinded) to include expanded information about Murray Valley Encephalitis Virus (MVEV) and Kunjin Virus (KUNV).


Flaviviruses are a type of arbovirus. Some flaviviruses including Japanese Encephalitis Virus (JEV), Murray Valley Encephalitis Virus (MVEV) and Kunjin Virus (KUNV) (a type of West Nile Virus) are a rare but potentially fatal cause of viral encephalitis.

In early 2022, JEV was found for the first time in people, pigs, other animals and mosquitoes in NSW, Queensland, Victoria and South Australia. During the 2021/22 mosquito season, 13 people in NSW developed severe infections and two of whom died.

During the 2022/23 mosquito season there have been a high number of detections of MVEV in mosquitoes and sentinel chickens in regional NSW. There have also been some detections of KUNV. The NSW Arbovirus Surveillance and Mosquito Monitoring Program weekly reports can be found on the NSW Health website. There has been one confirmed case of JEV notified in NSW during the 2022/23 mosquito season.

On 22 February 2023, the first confirmed human case of MVEV of this mosquito season was identified in a person who lives and works in Murrumbidgee LHD.


•The incubation period after being bitten by an infected mosquito is as follows:

  • JEV: 5-15 days
  • MVEV: typically 7-12 days (occasionally 5-28 days)
  • KUNV: 5-26 days

•Less than 1% of people develop a clinically significant illness.

•Those at increased risk include individuals engaged in outdoor activities duringperiods of heightened mosquito activity.

•Symptoms may include fever, headache, myalgia, rash and diarrhoea.

•Severe disease is associated with acute encephalitis/meningoencephalitis(although particularly rare for KUNV). Neurological sequelae include focal deficitssuch as paresis, cranial nerve pathology and movement disorders. Seizures arecommon, particularly in children.

•Permanent neurological or psychiatric complications occur in 30-50% of caseswith severe disease. The fatality rate can be as high as 30%.

•Supportive care is the mainstay of treatment for JEV/MVEV/KUNV

Diagnostic Recommendations

All patients presenting with suspected viral encephalitis/meningoencephalitis should have the usual investigations conducted, including cerebrospinal fluid (CSF) sampling, if safe and clinically appropriate to do so.

Where CSF is obtained, it should be tested for Herpes Simplex Virus (HSV), varicella-zoster virus (VZV), enteroviruses and other common causes of meningo-encephalitis by multiplex PCR and culture. Flavivirus testing should be considered in the appropriate clinical context.

It is especially important to exclude bacterial meningitis and HSV as they are treatable conditions.

For both adults and children, in cases of suspected viral encephalitis/ meningoencephalitis where the causative agent remains unidentified, especially with acute and clinically consistent MRI/CT1,2 brain changes, the following samples should be sent for analysis (serology/ PCR/ viral culture and sequencing) at the Institute of Clinical Pathology and Medical Research (NSW Health Pathology - ICPMR) at Westmead Hospital:


  • Serum – (2-5 mL from children, 5-8 mL from adults) for acute and convalescent (3-4 weeks post onset) testing for JEV/MVEV/KUNV-specific IgM and total antibodies
  • Whole blood (EDTA tube) for JEV/MVEV/KUNV PCR and virus culture on an acute sample AND

CSF (at least 1-3 mL)

  • JEV/MVEV/KUNV PCR and culture
  • JEV/MVEV/KUNV-specific IgM and total antibodies AND

Urine (2-5 mL in sterile urine jar)

  • JEV/MVEV/KUNV PCR and viral culture.

Transport specimens at 4°C without delay to NSWHP – ICRMR Westmead and enclose an appropriate request form with relevant clinical and epidemiological history including symptom onset, vaccination, travel history and country of birth, to guide laboratory interpretation. Send urgently (same/next day) to ICPMR. Viral culture requires a Biosafety Level 3 laboratory.

Clinical Escalation

Please discuss any suspected cases with your local Infectious Disease service. Infectious Disease services can seek further specialist advice by contacting the Clinical Microbiologist on call at NSWHP-ICPMR through the Westmead Hospital Switchboard (02 8890 5555).

Encourage prevention where practicable

1. Preventing mosquito bites

This includes the use of mosquito repellents, flyscreens, bed-nets, vapour dispensing units (indoors) and mosquito coils (outdoors), wearing long, loose or permethrin impregnated clothing and removing any water-holding containers where mosquitoes may breed. Preventing mosquito bites also helps prevent against other mosquito-borne illnesses.

2. Vaccination for Japanese encephalitis virus.

There is no vaccination for MVEV or KUNV. There are two JEV vaccines registered for use in Australia: Imojev® a live attenuated vaccine (single dose) for people 9 months and older, and JEspect® an inactivated vaccine (2 doses) for those who are unable to receive live vaccines (immunocompromised or pregnant) or aged between 2 to 9 months of age. Due to supply constraints, the vaccine is currently prioritised to those at highest risk of exposure to the virus. For more information visit: Japanese encephalitis vaccination

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