Japanese Encephalitis detected in pigs in Queensland, NSW and Victoria

28 Feb 2022

Key points:

  • Japanese Encephalitis (JE) has been identified on a number of Australian pig farms. It is considered an emergency animal disease, has an AUSVETPLAN  and is notifiable.  
  • Japanese Encephalitis is most commonly spread through mosquito  vectors. The virus is amplified in pigs and causes clinical signs in this species. It should be included on differential diagnoses list  when clinical signs in pigs  include abortions, foetal malformations, foetal mummification or stillbirths; nervous signs  in neonates; and (rarely) encephalitis in pigs to 6 months of age. 
  • Horses and humans can be infected by JEV  and it can cause a severe encephalitis.  To our knowledge there are no confirmed reports of JE in horses in Australia, however there are implications for live horse export.  JE should be included on differential diagnoses lists  when clinical signs of horses include fever, jaundice and neurological signs.  
  • Please refer to your local Government authorities for the preferred samples and transport methods to make a diagnosis.

Japanese Encephalitis (JE) has been identified on a number of Australian pig farms, eight in total in the last week, one each in  southern QLD and VIC and six in NSW 

Japanese Encephalitis has not been previously found in mainland Australia and as such has been considered exotic and notifiable to the OIE. So far the pig herds affected are in the Murray Darling Basin, however as the main vector of transmission is mosquitos the affected area may increase significantly.   

Japanese Encephalitis is a notifiable disease, if you suspect JE please notify the relevant authority in your state: 

  • Queensland - Biosecurity Queensland on 13 25 23 or phone the all-hours Emergency Animal Disease Watch Hotline (1800 675 888) 
  • New South Wales - Emergency Animal Disease Watch Hotline on 1800 675 888. 
  • Victoria - Emergency Animal Disease Watch Hotline on 1800 675 888  

There is an AUSVETPLAN1 for JE, which provides detailed information on the nature of the disease to assist with recognition and diagnosis.  

We have summarised pertinent points from the AUSVETPLAN1 to provide an overview to assist your understanding of the disease. 

  • Japanese Encephalitis is caused by infection with JE virus (JEV), which is a member of the Flavivirus genus of the family Flaviviridae 
  • Although JEV has been detected in numerous species, few species are thought to play a significant role in the natural transmission of JEV – most commonly waterbirds and pigs (see Section 2.4.2). A few species show clinical signs of disease – most commonly equids, pigs and humans (see Section 2.5.1). Humans are incidental hosts, but JE in humans may cause severe and fatal encephalitis. 


  • In pigs and waterbirds, viraemia, which is associated with a febrile response, can commence as soon as 24 hours after inoculation of virus and may persist for up to 6 days.  
  • Pigs (feral and domestic) develop high levels of viraemia (and are also major amplifiers of the virus. Vector-free transmission between pigs has been demonstrated but is thought to play a less important role in outbreaks than mosquito-borne transmission. 
  • In horses, reported incubation periods from experimental infection range from 4 to 14 days. In humans the incubation period is reported to be 4-14 days. 
  • JEV is relatively unstable and deactivated with heat, UV light and common chemicals used in cleaning. It does not survive well in the environment. 
  • The primary mechanism of spread of JEV between hosts is by bites from infected mosquito vectors. Transmission is believed to be maintained in mosquito–waterbird or mosquito–waterbird–pig cycles. 
  • Although they may be severely clinically affected, horses are considered dead-end hosts that do not develop viraemia of sufficient titre to infect mosquitoes 
  • Transmission to humans is usually by a bite from an infected mosquito. As in horses, it is believed that the low-titre viraemia that develops in humans is insufficient to infect mosquitoes. 
  • JEV is transmitted by mosquito vectors in the Culex, Aedes and Anopheles genera. 
  • In temperate endemic areas, infection builds up in waterbirds and then in pigs in late spring and early summer, spilling over to humans and horses in summer and autumn. In tropical areas, JEV circulates more or less continuously between mosquitoes, birds and pigs. It has been proposed that high rainfall will lead to an increase in mosquito populations, however, this may not occur in areas where torrential rains wash away developing mosquito larvae. 

Diagnostic criteria 

  • Clinical signs - Most infections with JEV are asymptomatic. Clinical disease in animals is most commonly associated with pigs and horses; reports of disease in other species are rare. 
  • Pigs : JE is associated with reproductive failure in pigs, with 50–70% losses reported in affected populations. Pregnant sows and gilts may abort, produce mummified or malformed fetuses, or give birth to stillborn or weak piglets at term. Central nervous system (CNS) signs such as tremors and convulsions, indicative of encephalitis, are occasionally seen in pigs up to 6 months of age.  
  • Horses: Disease in most symptomatic horses is mild, with recovery after 2–3 days. In these cases, affected horses have transient fever, anorexia, lethargy, and congested and jaundiced mucous membranes. Some infected horses develop encephalitis. This may be mild, with the same clinical signs described above accompanied by neurological signs such as difficulty swallowing, ataxia, incoordination and transient neck rigidity. Most of these horses recover within a week. When more severe encephalitis occurs, horses may be hyperexcitable, with high fever, aimless wandering, violent and ‘demented’ behaviour, profuse sweating, muscle tremors and occasional blindness. Some horses with severe encephalitis recover, but many collapse and die within 1–2 days. 

Differential diagnosis 

  • JEV should be included on a DDx list in pigs with signs characterised by abortions, fetal malformations, fetal mummification or stillbirths; nervous signs in neonates; and (rarely) encephalitis in pigs to 6 months of age 
  • JEV should be included on a DDx list in horses with signs characterised by fever, jaundice and neurological signs. 

Diagnostic testing 

  • Diagnostic testing relies on detection and characterisation of the virus via PCR from fresh tissue and blood, as well as serology. Please refer to the AUsvet plan (2.54, pg 13- 15) and your local Government authorities on the preferred samples and transport methods. Blood samples should be collected into serum and heparinised tubes. 


  • There is no specific treatment for viral encephalitis in horses or other livestock, and therapy is primarily supportive 

Minimisation of disease risk 

  • Pigs - Early detection of infection in a piggery near a town or city could be followed by mosquito control measures over an area to suppress infected mosquito populations that might enter the town or city. 
  • Horses - In an outbreak situation, horse owners should reduce the risk of exposure of their horses to mosquitoes, where possible. E.g housing horses in mosquito-screened stables during peak periods of mosquito activity (between dusk and dawn, using fogging, fans and automatic overhead misting systems to eliminate mosquitoes in stables, using physical barriers – for example, rugging and hooding horses in lightweight permethrin-treated material (if climatically appropriate), eliminating mosquito breeding sites on the premises  

Biosafety for humans 

  • Exposure to both infected mosquitos and infectious biological materials from pigs pose a risk to humans and personal protection of staff around pigs is important. (section 4.35 pg 26 Ausvetplan) 
  • Further information relevant to humans can be found here 

We expect that over the coming days and weeks there will be increased information especially if more infected pig herds are identified. We will keep you informed.