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Japanese Encephalitis

Queensland Health Guidelines for Public Health Units

Revision History

Version Date Changes



March 2010 

April 2011

Full revision of guideline

Change to Notification Criteria and Notification Procedure 

Infectious Agent

The infectious agent is the Japanese encephalitis (JE) virus, a flavivirus.

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Notification Criteria

Clinical evidence [1],[2] 
Non-encephalitic disease: acute febrile illness with headache, myalgia and/or rash
Encephalitic disease: acute febrile meningoencephalitis characterised by one or more of the following:

  • focal neurological disease or clearly impaired level of consciousness
  • an abnormal computerised tomogram (CT) or magnetic resonance image (MRI) or electroencephalogram (EEG)
  • presence of pleocytosis in CSF.

Poliomyelitis-like disease: an acute flaccid paralysis.

NB: Asymptomatic infections occur, and are usually detected through serosurveys.

Laboratory definitive evidence

  1. Isolation of JE virus
  2. detection of JE virus by nucleic acid testing
  3. lgG seroconversion or a significant increase in antibody level (in qualitative assays) or a fourfold or greater rise in titre in paired sera to JE virus-specific lgG proven by neutralisation or another specific test, with no history of recent JE vaccination
  4. detection of JE virus-specific lgM in cerebrospinal fluid, in the absence of lgM to Murray Valley encephalitis (MVE), Kunjin and dengue viruses
  5. detection of JE virus-specific lgM in serum in the absence of lgM to MVE, Kunjin and dengue viruses, with no history of recent JE vaccination.

Confirmation of laboratory result by a second arbovirus reference laboratory is required if the case appears to have been acquired in mainland Australia, to meet national case definition requirements.  However public health management of the outbreak should not be delayed.

Community Outbreak Criteria 
Torres Strait islands: More than one case of locally acquired (symptomatic) JE, with the cases linked in time and place.

Mainland Australia: One or more confirmed cases of locally acquired (symptomatic) JE.

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Notification Procedure

To notify (i) on receipt of request for examination by telephone or facsimile and (ii) upon confirmation of diagnosis by telephone.

Reporting to NOCS

Report only confirmed cases. Do not notify asymptomatic cases detected through serosurveys.

Confirmed case

A confirmed case requires laboratory definitive evidence AND clinical evidence.

Objectives of surveillance         

1. To monitor for the emergence of JE virus in Queensland.
2. To identify cases and outbreaks so that appropriate public health action can be taken.

Public Health Significance and Occurence

JE is a mosquito-borne disease. It is the leading cause of childhood encephalitis in Asia.
The JE virus (and therefore JE) is widely distributed in southeast and southern Asia extending from China and India east to Japan and south into Indonesia and Papua New Guinea. There are between 30,000 and 50,000 cases reported annually worldwide with a case fatality rate of between 20 and 30%. A further 50-60% of survivors experience long term neurological sequelae. 

In 1995 JE emerged as a public health concern in northern Australia, with an outbreak in the Torres Strait. Three cases of JE, two of which were fatal, occurred in residents of Badu Island. Two further human cases, one in the Torres Strait and one on the west coast of Cape York were identified following a second outbreak in 1998.  Although the JE virus remains exotic to Australia, seasonal incursions of the JE virus have been detected (usually in sentinel pigs) in the Torres Strait every year (with the exception of 1999) since 1995. Sentinel pig surveillance for JE virus in the outer islands of the Torres Strait ceased in 2005. JE vaccination of the residents of the outer Torres Strait islands commenced in the latter part of 1995, and has continued since then, albeit a more restricted program in recent years.

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Clinical Features

The majority of JE virus infections are either asymptomatic or present as a mild febrile illness with or without headache. JE typically has a prodromal phase characterised by fever, headache and gastrointestinal symptoms which can rapidly progress to a reduced level of consciousness and coma. Seizures may occur. JE virus is also an occasional cause of polio-like acute flaccid paralysis. The encephalitis cannot be distinguished clinically from other central nervous system infections; it is associated with a high likelihood of neurological sequelae (up to 60%), particularly in infants.


The primary maintenance hosts of JE virus in endemic areas are thought to be wading (ardeid) birds and pigs, both of which act as reservoirs for infection. 

Pigs play a major role as amplifying hosts in both endemic and epidemic areas. Other vertebrate species such as horses, cattle, buffalo and goats may be infected, but do not appear to be amplifying or maintenance hosts. Indeed these other animals may serve as ‘dampers’ to impede transmission by attracting infected mosquitoes which might otherwise feed on pigs. Macropods such as wallabies and kangaroos are also unlikely to be amplifying hosts and almost certainly act as ‘dampers’ in, for example, Cape York.

Human cases have very low levels of viraemia, ie. humans are essentially ‘dead end’ hosts and highly unlikely to initiate local transmission.

Mode of Transmission

The JE virus has been isolated from a wide range of mosquito species, but not all are believed to be able or competent to transmit the virus.

In those areas of Australia affected to date, the primary vector has been the fresh water breeding mosquito Cx. annulirostris (the common banded mosquito). Cx. annulirostris belongs to the Cx. sitiens subgroup, whose members are morphologically difficult to distinguish. Some of these other members (eg. Cx. sitiens and Cx. gelidus ) could be significant vectors in other areas in future outbreaks.

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Incubation Period

Usually 5-15 days.

Period of Communicability

No direct human to human transmission.

Susceptibility and Resistance

Susceptibility to clinical disease is usually highest in infancy and old age; inapparent or undiagnosed infection is more common at other ages. Infection confers life-long immunity.

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Investigation: Determine possible source of infection.
Management: If considered to be locally acquired, refer to outbreak section below. 
Contact Tracing: Not routinely required.  If case considered to be locally acquired, refer to outbreak section below.

Community Outbreaks/epidemics

An outbreak of JE in mainland Australia requires the constitution of an outbreak management team (OMT) consisting of essential stakeholders (including disease control, epidemiology, medical entomology, vector control, environmental health, animal health, infectious diseases, primary health care, laboratory, health promotion and communications personnel). The involvement of a communications officer is essential, as briefings and a communication strategy will need to be developed quickly.

If (after excluding recent travel to Asia, Papua New Guinea or the outer islands of the Torres Strait) it is apparent that a JE case acquired the infection in mainland Australia, the OMT should consider the following:

• Assessment of the case’s possible exposures during the apparent exposure period. These include places where the case stayed overnight, recent evening/overnight outdoor activities (eg. camping) and the proximity to water sources, recall of the presence of significant numbers of mosquitoes, any mosquito precautions used etc.

• Assessment of any companions or contacts of the case during the apparent exposure period (mild febrile illness may be indicative of JE virus infection).

• Local health care providers (GPs, community health centres, hospitals) should be promptly informed of the outbreak and requested to notify any apparent encephalitis cases immediately (prior to any diagnostic test results being available).

• The communication strategy should be implemented, to make the local community aware of the outbreak and measures that will minimise risk of infection. Relevant local media should be used, and health promotion expertise should be used to ensure information is disseminated in an appropriate way at the local level.

• A serosurvey should be considered, to ascertain whether there have been any asymptomatic or mild human infections, and if so the extent of these infections.

Mosquito vectors
• An environmental survey of possible culicine mosquito breeding sites should be made. The PHU medical entomologist should be able to advise on the types of likely sites in the locality where the infection may have been acquired.

• Larval surveys using dippers should be undertaken in possible mosquito breeding sites.  Samples should be kept in 70% alcohol for subsequent identification. Data should be mapped and placed into a database.

• Where feasible, larviciding of breeding sites, particularly those close to people’s residences (eg. septic tanks, drains), should be undertaken.

• Adult mosquitoes should be collected using CO2-baited light traps. Adult mosquitoes should be retrieved early in the morning, and adults identified and sorted to species on a cold table or by immobilising with triethylamine.  Pooled specimens should be frozen and transported in either dry ice or a nitrogen dry shipper, and virological studies should be conducted on the pooled mosquitoes. 

• Where feasible, adulticides, such as bioresmethrin and pyrethrins, can be used in Ultra Low Volume (ULV) or thermal foggers to treat residences and discrete communities.  Fogging should be conducted at dusk and dawn.  The public should be advised to close windows before fogging.

• The relative numbers and population densities of putative vector species at and near the apparent exposure site should be estimated.

Animal hosts
• The location of any domestic pigs near the apparent exposure site should be identified and mapped.

• The opportunity should be taken to explain to the pigs’ owners the desirability of relocating pigs away from residences/communities so as to lower the risk of future outbreaks.

• A serosurvey including domestic pigs and (young) feral pigs, to ascertain the extent of porcine infection, should be considered.

• The location of wading bird populations near the apparent exposure site should be identified and mapped.

Other control measures

JE Vaccine: Recommendations for the use of JE vaccine are detailed in the 9th edition (2008) of the Australian Immunisation Handbook. However, the vaccine listed, a mouse-brain derived inactivated JE vaccine which was in use until very recently, is now obsolete and no longer being produced. In 2009, a new JE vaccine, a cell-culture derived vaccine consisting of an inactivated attenuated (SA 14-14-2 strain) JE virus, was registered for use in Australia. It requires a two-dose (days 0, 28) primary vaccine series, and as of February 2010 was only registered for those ≥18 years of age.

Role of JE vaccine in controlling an outbreak of JE in Australia: When an outbreak of JE is recognised in Australia, it is crucial that mosquito control and avoidance measures are implemented immediately in the communities and households in the immediate vicinity of the JE virus activity.

JE vaccination does not currently have a role in the control of incursions of JE virus or outbreaks of JE within Australia, for the following reasons:
(i) there are intrinsic delays in recognising an incursion or outbreak
(ii) it takes time for JE vaccines to induce adequate immunity and
(iii) the JE virus may have already infected all the pigs (amplifying hosts) in the vicinity by the time the incursion or outbreak is recognised, with further amplification thus unlikely.

Role of JE vaccine in preventing disease in future incursions or outbreaks of JE in Australia: JE vaccination should be considered if there is a risk of further incursions or outbreaks. For this reason the investigation into an outbreak should also be viewed as a risk-assessment exercise.

Questions that need to be answered are:

• What was the likelihood of exposure during the incursion or outbreak? This requires information on mosquito densities, pig populations, whether people live in unscreened dwellings close to pigs etc.

• How many people were infected during the outbreak? A serosurvey should be considered to ascertain extent of asymptomatic or mild infection.

• Is another incursion or outbreak likely in the same location? This will require an understanding of the likely source of introduction of the JE virus, weather patterns etc.

• Can the risk of a future incursion or outbreak be minimised through measures such as relocating pigs away from communities, draining mosquito breeding sites, screening dwellings etc?

Risk assessment will inform the decision whether to recommend vaccination. If vaccination is recommended, consideration must be given to how new arrivals (eg. through birth or migration) will be vaccinated, and how any recommended booster doses will be delivered. Consideration should also be given to criteria that might be used to recommend cessation of vaccination programs in the future, should the risk subsequently be reassessed as insignificant.

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Preventive Measures

Public education about personal protection against mosquitoes, especially during the wet season in northern Australia (see MVE protocol).

JE vaccination, especially for travellers to, and expatriates in, PNG and endemic and epidemic countries in Asia. Risk is dependent on season and duration of travel, regions visited, and extent of outdoor activity and mosquito avoidance measures. See current edition of Australian Immunisation Handbook for recommendations.


Report to notifying agency.


Prepare a report of any investigation for the Communicable Diseases Branch, Queensland Health.


Heymann, D. (Ed). 2008. Control of Communicable Diseases Manual, 19th edition. American Public Health Association: Washington .

Solomon T. Flavivirus encephalitis. New Engl J Med,2004; 351: 370-378.

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Last updated: 7 April 2011