Japanese encephalitis virus: an emerging and re-emerging virus in Australia

Keywords: ardeid birds, Culex sp. mosquitoes, domestic piggeries, feral pigs, flaviviruses, Japanese encephalitis, Japanese encephalitis virus, JEV genotype IV, malformed and stillborn pigs, Torres Strait.

Japanese encephalitis virus (JEV) is the major vaccine-preventable cause of human encephalitis in Asia,¹ with a geographic range extending from eastern, south-eastern and southern Asia. In 1995, it moved into Oceania for the first time, causing infections in Papua New Guinea (PNG) and the Torres Strait (TS) of northern Australia.² It is a vector-borne flavivirus, and a member of the Japanese encephalitis serological complex, that includes West Nile (Kunjin subtype) and Murray Valley encephalitis viruses in Australia.³ JEV exists in zoonotic transmission cycles between ardeid birds (maintenance or reservoir hosts), such as herons and egrets, and pigs (amplifying hosts) and Culex sp. mosquitoes, particularly Culex tritaeniorhynchus, although other species such as Cx. gelidus, Cx. vishnui and Cx. fuscocephala are also important vectors in specific areas, with Cx. annulirostris the probable major vector species in Australia (Fig. 1).⁴

Fig. 1.  The amplification cycle of Japanese encephalitis virus (JEV). The major vertebrate species are ardeid birds (maintenance or reservoir host) and pigs (amplifying host). Feral pigs are also expected to be an important reservoir and amplifier. Other vertebrate species, such as possums, bats and ducks, may also play a role in the JEV amplification cycle. Culex species mosquitoes are the main vectors. Direct transmission between pigs can also occur. Humans, horses and other livestock species do not develop viraemia of sufficient magnitude to infect biting mosquito vectors and are therefore dead-end hosts (Possum image: Flaticon.com).

JEV causes occasional disease in humans, horses and pigs,⁵ and rare cases of fatal disease in other species. Infection in horses is generally asymptomatic, but very occasionally it can lead to a severe neurological disease. Horses and humans are recognised as ‘dead-end’ hosts as viraemia levels are not high enough to infect mosquitoes. JEV is an important disease of pigs. Although infection of adult pigs is generally asymptomatic but with a measurable viraemia, it is an important cause of reproductive disease resulting in still-births, malformations and mummified foetuses (Fig. 2), and surviving piglets often display fatal neurological symptoms. Vector-free transmission between pigs has also been demonstrated through virus shedding in oro-nasal secretions.⁶ In humans, most cases are asymptomatic, but between 1:30 and 1:300 cases depending on endemicity and past exposures, can lead to clinical disease, usually a severe meningomyeloencephaltitis with 25% mortality and 50% of survivors suffering neuropsychiatric sequelae.⁷ Some patients present with a poliovirus-like flaccid paralysis.⁷ Where JEV reaches a new geographic area, adults and children are affected, but adults over 60 years of age are more likely to have severe symptomatic disease.⁷

Fig. 2.  Aborted foetuses caused by JEV infection of a pregnant sow from an affected Australian piggery in 2022. Piglets ranged from well-preserved carcasses (left) to fragmented foetal mummies (right). Credit: Dr Willy Suen, Australian Centre for Disease Preparedness.

It is believed that JEV evolved from an ancestral virus in the Indonesia-Malaysia region,^8,9 and subsequently diverged into five genotypes I, II, III, IV, and V.^8–12 Genotype I has been further divided into Ia and Ib.¹³ Phylogenetic studies showed that genotype V is the oldest genotype, followed by IV, III, II, and I as the youngest. In general, GIb, and GIII are considered to be largely associated with seasonal, epidemic disease in temperate areas, whereas GIa, GII and GIV are associated with endemic disease in tropical areas of south-east Asia.^14,15 Over the past 2–3 decades, GIb has replaced GIII in temperate areas.^13–16 The two most rarely detected genotypes have been GIV and GV. GV was isolated initially in Singapore in 1952,¹² but not seen again for 57 years until 2009 when an isolate was reported from Tibet, China,¹⁷ and further isolates reported from Korea.¹⁸ GIV was first described from mosquitoes trapped in various parts of Indonesia between 1980 and 1981,^11,19 but was not seen again for 36 years until isolated in Bali from pigs in 2017²⁰ and Cx. vishnui mosquitoes in 2019.²¹ Also in 2019, an Australian tourist became infected with JEV GIV in Bali and later died in Brisbane.²² Thus, the geographic range of GIV viruses was previously considered to be confined to Indonesia.

JEV, like many other flaviviruses, has a propensity to spread and establish in new areas. In the 1990s, JEV emerged in parts of Oceania and South-Western Asia, with virus isolations from PNG, Papua Province (Indonesia), the TS of northern Australia, and Pakistan.²³ More recently, JEV has been detected in the bone marrow of passerine birds²⁴ and in Cx. pipiens mosquitoes²⁵ in Italy and in a patient who was co-infected with yellow fever in Angola.²⁶ There is considerable concern that JEV might spread further in Europe²⁷ and into the west coast of North America.²⁸

JEV first appeared in the TS in 1995, where it caused three human cases on Badu, an island in the central TS.²⁹ JEV belonging to GIV was isolated from two asymptomatic human cases. In addition, pigs were found to have seroconverted on at least nine other central and northern TS islands.²⁹ Cx. annulirostris mosquitoes were shown to be the major vector in the outbreak, from which eight isolates of JEV were obtained.³⁰ JE vaccine was offered to the inhabitants of the TS islands.³¹ Later studies showed that the virus had originated from PNG; identical strains of JEV were isolated from Cx. sitiens subgroup mosquitoes trapped in Western Province,³² and human cases of JE were observed at a mission hospital near Kiunga in 1997–98,³³ and Port Moresby in 2004.³⁴ The first case of JE was also reported from Irian Jaya (now Papua) in 1997,³⁵ and several local inhabitants of Timika were found to be seropositive to JEV.³⁶ JEV GII occurred again in 1998 in an unvaccinated child on Badu and the first clinical case on mainland Australia at the mouth of the Mitchell River in Cape York.³⁷ Sentinel pigs on Badu and Cape York seroconverted, and JEV GII was isolated from 3 pigs at Seisa in the Northern Peninsula Area (NPA) at the tip of Cape York.^37,38 A total of 42 JEV isolations were obtained from mosquitoes on Badu, 41 of which were isolated from Cx. annulirostris and one from Aedes vigilax, but no isolate was obtained from mosquitoes trapped on Cape York.³⁹ It has been postulated that the movement of JEV from PNG into Badu and Cape York may have been due to wind-borne mosquitoes during cyclonic weather patterns.⁴⁰

JEV re-emerged in 2000, but virus isolates from mosquitoes and pigs belonged to a different genotype, GI,^39,41 later confirmed as GIa.¹⁴ Further incursions were observed annually between 2001 and 2005 on Badu through sentinel pig seroconversions and mosquito trapping, and JEV was detected on mainland Australia in Cape York again in 2004, with sentinel pig seroconversions and virus isolation from mosquitoes.^38,42 Sentinel pigs were discontinued in the TS at the end 2005, largely for safety reasons, and from the NPA in 2012.³⁸ Sporadic or opportunistic surveillance activities have been carried out by Northern Australian Quarantine Service (NAQS) over the past decade and a half, and serological evidence of JEV activity was reported in pigs and horses in the TS (2005, 2010, 2012, 2013, 2014, 2016, 2017 and 2019) and the NPA (2020 and 2021) (data collected from the NAQS reports in the Australian Animal Health Quarterly, Quarterly Statistics), but no human infections have been reported. It should be noted that testing was performed on single samples only, and serological data cannot distinguish viral genotypes. Nevertheless, they indicate that JEV was either endemic in the TS, or frequently re-introduced from PNG. These results indicate the ongoing risk of JEV to northern Australia.

A fatal case of JE occurred in March 2021 in an inhabitant from the Tiwi Islands.^43,44 Sequence studies confirmed that it was JEV belonging to genotype IV, the first time this genotype was acquired outside Indonesia. It was also the second known fatal human infection due to GIV, the first having been reported in an Australian tourist to Bali.²² The Tiwi Island case was the sentinel case for a subsequent outbreak in early 2022 that was initially detected by the appearance of mummified or malformed foetuses, still births (Fig. 2) and liveborn piglets with neurological signs in piggeries in Queensland, New South Wales, and Victoria.⁴⁵ A human case of encephalitis was confirmed in Queensland, and with other possible cases under investigation, Australia’s Acting Chief Medical Officer formally declared the JE outbreak ‘A Communicable Disease Incident of National Significance’ on 4 March 2022.⁴⁶ The outbreak spread widely in pig farms in Queensland, New South Wales, Victoria and South Australia, affecting over 80 piggeries,⁴⁷ and 42 human cases were reported, seven of which were fatal.⁴⁸ JEV GIV was detected in feral pigs from Northern Territory,^49,50 Queensland⁵⁰ and South Australia⁵¹ either by serology or virus isolation.

Two successful vaccines are available for human use; IMOJEV, a live attenuated chimeric vaccine comprising the yellow fever virus 17D vaccine strain as the backbone, and the pre-membrane and envelope genes of the GIII Chinese live attenuated JEV vaccine virus, SA-14-14-2 strain⁵² and JESPECT, an adjuvanted inactivated Vero cell-grown SA-14-14-2 virus.⁵³ Both vaccines have been shown to protect against the different JEV genotypes. In Australia, those most at risk of infection and for whom vaccination is recommneded include piggery workers, abattoir workers, laboratory workers, hunters of feral pigs, people living nearby to piggeries or wetlands, certain remote Aboriginal communities in northern Australia, and campers and fishers and others involved in outdoor activities near lakes, lagoons and wetlands. There are no vaccines currently available in Australia for pigs or horses. However, inactivated and live attenuated veterinary vaccines based on GIII strains produced by overseas manufacturers may have application in Australia following assessment and regulatory approval. In piggeries, it is expected that vaccination will focus on sows to reduce reproductive losses, rather than pork production animals. Vaccination has not been widely used for the latter due to the costs associated with immunising large numbers of young pigs, high turnover of animals, and the short period for effective immunisation.⁵⁴

JEV GIV was the third genotype to emerge in Australia, but unlike the earlier GII and GIa incursions between 1995 and 2004, little is known about the properties and pathogenesis of JEV GIV viruses. From knowledge gained over many years in Asia with the more common JEV GI, GII and GIII genotypes, and more limited knowledge from the TS, it is assumed the major mosquito vector in Australia is Culex annulirostris, although a number of other vector species may also be involved.⁵⁵ Similarly, the vertebrate hosts in Australia are expected to include ardeid birds as maintenance hosts, and feral and domestic pigs as amplifying hosts, but it is possible other hosts could play a role, such as magpie geese, ducks, and flying foxes. Marsupials appear to be less likely to be involved, although viraemia levels suggested possums could play a role in urban and peri-urban environments.⁵⁶ Feral pigs are expected to be a major vertebrate host because of their abundance and wide distribution (Fig. 3). A number of other questions related to the properties of GIV viruses remain to be determined, including their virulence and neuro-invasiveness compared to other genotypes; their antigenic profile and the sensitivity and specificity of current diagnostic tests; and the sensitivity of current surveillance methods and the need for improved surveillance systems.

Fig. 3.  Map of Australia showing the occurrence, distribution and abundance of feral pigs (Sus scrofa) in Australia. Map generously provided by Invasive Animals Ltd/Centre for Invasive Species Solutions.

The geographic extent of the outbreak is still not fully understood, and is based largely on the location of infected piggeries, human cases and some limited feral pig studies in New South Wales, Queensland, Northern Territory, and South Australia. Further information has recently come from a relatively small human serological survey carried out in five towns in NSW, all of which had evidence of JEV-infected mosquitoes earlier in the year. There was evidence of JEV infection in approximately one in 11 of the 1048 participants, indicating that JEV was prevalent in those areas and suggesting that a relatively large number of people may have been infected.⁵⁷

The close antigenic relationships between flaviviruses can make serology-based diagnostic interpretation complex and difficult.⁵⁸ Improved surveillance methods and procedures are needed to provide early warning of possible virus activity. The origin and route by which the JEV GIV virus reached Australia and where it entered northern Australia remains to be determined, although it may be difficult to obtain an absolute answer. Most evidence would suggest that the virus probably came from a focus of activity in the Indonesian archipelago or PNG through either wind-blown mosquitoes or vagrant or migratory birds. It is probable that the 2022 outbreak was driven in part by the increased rainfall and flooding due to the La Niña weather patterns in 2020–21 and 2021–22 providing conditions for increased mosquito breeding and attracting waterbirds to many additional feeding grounds. There is ongoing concern that JEV GIV will become endemic in Australia, and evidence from the widespread nature of the outbreak suggests that the virus may already be endemic, but this may become clearer as we enter the summer months of 2022–23. The current third year of La Niña weather pattern is therefore of considerable concern.

Data sharing is not applicable as no new data were generated or analysed during this study.

The authors declare no conflicts of interest.

This research did not receive any specific funding.