Flaviviruses for health professionals


Flaviviruses are arthropod-borne positive-strand RNA viruses. Murray Valley encephalitis virus (MVEV), Dengue virus, Kunjin strain of West Nile virus (KUNV) and Japanese encephalitis virus (JEV) are known to be transmitted in Australia and are of major significance to human health. Other flaviviruses known to be transmitted in Australia include Alfuy, Kokobera, Edge Hill, Stratford and New Mapoon viruses, although only Kokobera virus has been shown to cause human disease (very rarely)1.

MVEV and KUNV are endemic in birds in northern Australia with occasional cases occurring in humans. MVEV and KUNV rarely occur in southern Australia. JEV is endemic in the Torres Strait, but until February 2022 had not been acquired in southern Australia.

Clinical presentation

Many people infected with MVEV/KUNV/JEV are asymptomatic or have mild symptoms such as fever, headache, nausea, vomiting, myalgia and arthralgia.

Less than 1% of people develop meningitis or encephalitis and symptoms may include: increasing confusion, headaches, neck stiffness, tremors, drowsiness and seizures. Other patients may present with aseptic meningitis or acute flaccid paralysis and have no encephalopathic features. Patients may present with a syndrome similar to Parkinson's disease, with dull faces that are mask-like and wide unblinking eyes, tremor, and cogwheel rigidity. In infants and young children meningitis or encephalitis may present as irritability or floppiness.

If infection occurs during pregnancy there may be a risk of miscarriage and other complications,

Modes of transmission

These flaviviruses are transmitted to humans by a bite from an infected mosquito. Mosquitoes acquire infection from biting infected animals such as water birds or pigs. Humans are a dead-end host. Pigs are an amplifying host for JEV.

Incubation period

  • MVEV and KUNV 5 to 28 days
  • JEV 5 to 15 days


Consider flavivirus infection in persons with encephalitis/meningoencephalitis and discuss suspected cases with an infectious disease physician. Undertake usual testing to evaluate for other causes of encephalitis/meningoencephalitis (e.g., HSV, VZV, enteroviruses).

Test for flaviviruses in persons with suspected encephalitis/meningoencephalitis without identified cause. Flaviviruses can be diagnosed on PCR of CSF, blood or urine, or by serology. Flaviviruses IgM antibodies can cross-react, especially between MVEV and JEV. 

Send the following to SA Pathology requesting “Flavivirus investigation” on the form.

  • Serum (2 mL in children, 5-8 mL in adults) including both acute and convalescent specimens (3-4 weeks post onset) for flavivirus/JEV IgM, IgG and total antibody.
  • Blood (whole blood [EDTA] 5-8 mL) for flavivirus culture and flavivirus PCR.
  • CSF (at least 1 mL) for flavivirus/JEV PCR and culture, and IgM, IgG and total antibody.
  • Urine (2-5 mL in sterile urine container) for flaviviruses/JEV PCR and culture.

It is suggested any positive results are discussed with a virologist or infectious diseases physician.

Tests for flaviviruses often need to go to reference laboratories interstate, so results can take time.


There is no specific treatment for flaviviruses. Cases who become severely unwell may need supportive treatment in ICU. 

Notify suspected and confirmed cases of flavivirus infection to the Communicable Disease Control Branch on 1300 232 272.



Immunisation plays an important role in protecting against JEV. Two JEV vaccines with different modes of action are available for use in Australia. Imojev (live vaccine) is recommended for use in people aged ≥ 9 months and is given as a single dose. JEspect (inactivated vaccine) is recommended for use in people ≥ 2 months and is given as a two-dose schedule, 28 days apart. It can be used when live vaccine is contraindicated e.g. pregnancy and immunocompromise. As at March 2022, there is a limited supply of JEV vaccines in Australia, so populations at higher risk will be prioritised Communicable Disease Network Australia for vaccination.

There are no available vaccines for MVEV/KUNV.

Personal protection

  • Wearing loose-fitting, light-coloured clothing covering as much as the body as possible
  • Using an insect repellent containing DEET (diethyl toluamide) or picaridin on uncovered skin
  • Protecting rest and sleep areas with mosquito nets
  • Avoiding times of peak mosquito activity – some mosquito species will bite during the day but many are particularly active for two to three hours around sunrise and sunset
  • All people who work with potentially infected animals, work in areas in which infected mosquitoes may be present should wear appropriate personal protective equipment (PPE). The PPE should be chosen based on the assessed level of risk and the task.

Household protection

  • Ensuring pot plant drip trays are emptied at least once a week or are filled with sand
  • Ensuring all windows and openings of houses, boats, caravans and tents are fitted with fine (1mm) insect screens
  • Ensuring rainwater and septic tank openings, wells or other large water containers are covered with wire mesh no coarser than 1mm
  • Appropriate disposal of rubbish: emptying, then covering or puncturing containers that may hold water
  • Stocking ornamental ponds and other man-made water bodies with small Australian native fish to eat any wrigglers
  • Appropriately disinfecting swimming pools and ensuring unused swimming pools are emptied or stocked with small Australian native fish
  • Emptying wading pools at the end of each day
  • Ensuring roof gutters are kept in good repair and that leaves and debris are removed regularly so that pools of water do not form
  • Ensuring bird baths, stock troughs and pets’ drinking water are emptied and refilled at least once a week

Useful resources for health professionals

  • Australian Immunisation Handbook for Japanese encephalitis (JE) vaccine recommend doses
  • Japanese encephalitis virus (JEV) health alert (Australian Government Department for Health)


1 https://www.qld.gov.au/health/condition/infections-and-parasites/viral-infections/flaviviruses-unspecified

2 South Australian Integrated Mosquito Management Resource Package (2006)