Japanese Encephalitis Virus
LEVELS: Likely to occur; Severe; Extraordinary biosecurity required; Reference or research laboratory required; Moderate; Significant disruption; Little; Needed but not available
| Register id | japanese_encephalitis_virus |
| Type | virus |
| Scientific name | Japanese encephalitis virus |
| NCBI taxid | 11072 |
| Evidence | 4 document(s) |
| Assigned | 2026-09-06, against criteria version 093366e352a2 |
Overview
Japanese encephalitis virus is a mosquito-borne flavivirus and one of the leading causes of viral encephalitis in people across southern, eastern and southeastern Asia — an estimated 68,000 human cases a year, three-quarters of them in children, with 20-30% of clinical cases fatal and a third to a half of survivors left with lasting neurological damage. Pigs are central to it. They are the major amplifying host, developing high levels of virus in the blood for several days, and they are particularly attractive to the mosquitoes that carry it, so a build- up of virus in pigs typically precedes an epidemic in people. In the pigs themselves the disease is modest: infection in growing and adult pigs is usually a self-limiting fever, but a pregnant sow infected at the wrong time produces abortions, stillbirths and mummified or malformed piglets, and boars can become temporarily infertile. The 2022 Australian outbreak showed what an incursion looks like — more than 80 commercial piggeries across four states affected, with 42 human cases and seven deaths. The United States has competent mosquito species and wading-bird hosts even though the main Asian vector is absent, which is why the virus is watched here. Veterinary vaccines exist and sows are vaccinated annually in some endemic countries, but the emergence of a new genotype has raised real doubts about how well the existing products cross- protect.
C1 Zoonotic potential
Likelihood of transmission from pigs to humans
Likely to occur: Transmission from pigs can occur even when control points are intact, or is prevented only by extraordinary control measures such as respiratory protection or vector control
Basis. ch30 30.2.3: "Humans become infected when bitten by an infected mosquito... An estimated 68,000 human cases of JE occur annually but the number of cases can exceed 100,000 in some years." "Amplification of JEV in pigs is thought to precede epidemic transmission." 30.2.4: "Pigs are the major amplification hosts of JEV, especially in epidemic areas, and maintenance hosts in endemic areas. They develop high levels of viremia, lasting 2-5 days, capable of infecting various species of biting mosquito. Pigs are particularly attractive to the major mosquito vectors as a source of blood meals." 30.2.10: "Targeted vaccination of piggery workers should be considered for immunologically naive populations considered high-risk." shic_2024_jev: "JEV is a zoonotic pathogen." "Amplification of JEV in swine often precedes human epidemics." "humans are incidental (dead-end) hosts."
How this level was decided
Level 4, and it is the framework's own worked example at that level. The pig is not an incidental host here -- it is THE amplifying host, developing viraemia high enough to infect the vectors that prefer to feed on it, and amplification in pigs is what precedes epidemic human transmission. Transmission occurs even with control points intact, because the control point is a mosquito. The chapter's recommendation that piggery workers be vaccinated is the industry conceding the point. Level 4 confirmed. Swine amplification preceding human epidemics is the strongest form of the pig-as-source claim C1 measures.
C2 Zoonotic impact
Severity of human illness caused by the agent
Severe: Infection carries a substantial risk of life-threatening illness, death, or permanent disability, even if human infections are uncommon
Basis. ch30 30.2.3: "Approximately 75% of cases occur in children aged 0-14 years. Most human infections are asymptomatic, with 1 in 50 to 1 in 1000 infections progressing to clinical disease. Approximately 20-30% of JE cases are fatal, 30-50% develop long-term neuropsychological sequelae, and the remaining cases fully recover." 30.2.1: "JEV is a major cause of human viral encephalitis and childhood viral neurological infection and disability in southern, eastern, and southeastern Asia." shic_2024_jev: "It causes an estimated 70,000 cases of viral encephalitis annually, with a 20-30% mortality rate."
How this level was decided
Level 4. Of those who become clinically ill, a fifth to a third die and half of the survivors are left with permanent neuropsychological damage -- that is the level 4 test met twice over, and mostly in children. NOTE ON THE DENOMINATOR, because it is the one argument against: only 1 in 50 to 1 in 1000 infections becomes clinical, so most infected people are unharmed. The criterion scores the illness rather than the infection, and JE is one of the great causes of childhood neurological disability in Asia, so the rare-extreme-outcome caution in C2 does not apply. Level 4 confirmed.
C3 Herd introduction risk
Effort required to keep the agent out of the herd
Extraordinary biosecurity required: Exclusion needs measures beyond the routine, such as air filtration, thermally treated feed and bedding, or repeated costly testing to find carriers, and may still fail
Standing note. GUIDANCE for whoever scores this entry -- it has no assignment yet, so it cannot carry a correction. NOT a bat-type case. Culex tritaeniorhynchus is absent from the US but other competent Culex species and ardeid birds are present -- Eric: competent vectors, "even if they are not ideal vectors". L4 stands.
Basis. ch30 30.2.4 and Eric's standing note on this entry: competent Culex species and ardeid birds are present in the US even though Culex tritaeniorhynchus is not. Mansfield 2025 makes the identical argument for a second continent: "Since appropriate vertebrate host and mosquito vector species are present in Europe and average European summer temperatures continue to increase, JEV introduction could lead to the establishment of the pathogen in native mosquito species and wild birds and disease outbreaks among humans, pigs, and horses. Incursions could occur through movements of infected pigs and mosquitoes but also via migratory birds that act as reservoirs. Introduction and establishment of JEV in these populations may not be apparent at first, providing time for virus spread before spillover to the human population." shic_2024_jev: "JEV is transmitted by mosquitoes. The main vector in Asia is Culex tritaeniorhynchus." "Mosquito control is essential... Recommended practices include removing stagnant water around pig enclosures, using insecticides, installing insect screens, and using fans inside buildings where pigs are housed to disrupt mosquito activity." "JEV emergence in the United States is concerning due to the presence of competent mosquito vectors and susceptible hosts." "Artificial insemination practices could facilitate JEV spread since infected boars shed virus in the semen."
How this level was decided
RENUMBERED L5 -> L4 on 2026-09-03, when C3 was reduced from five levels to four and level 4 absorbed level 5. THE JUDGMENT IS UNCHANGED and this one really is a renumber: the merged level 4 label carries what level 5 said, ending "and may still fail". IT WAS STILL CHECKED rather than assumed, because the last renumber on 2026-09-01 was mechanical and moved twenty-one entries past a level they should have been judged against. The check is the exclusion test -- does housing close the route? For this entry it does not.
EARLIER REASONING, kept because it is the evidence read: Level 5 unchanged, the framework's worked example, and now supported by two independent preparedness assessments reaching the same conclusion about two different continents. The clause that matters most for this level is the last one: establishment may not be apparent at first. Australia found that out retrospectively -- the virus had been circulating for months or years before the 2022 outbreak was detected. An incursion that establishes silently in native mosquitoes and wild birds is one nobody can subsequently remove. Level 4 confirmed, and the recommended controls are the extraordinary list almost verbatim -- insect screens and fans to disrupt mosquito activity inside the building. A semen route through AI is on top of that.
C4 Detection difficulty
Difficulty of recognizing and confirming infection
Reference or research laboratory required: A validated assay exists, but only at a national reference or research laboratory rather than at local or regional level
Basis. Mansfield 2025 is an alignment exercise between FIVE European veterinary NATIONAL REFERENCE laboratories, built on JEV-positive pig sera supplied by the WOAH Reference Laboratory for JEV in South Korea, an EU Reference Laboratory proficiency panel, and plaque reduction neutralisation on Vero C1008 cells. It names both obstacles the chapter names: "Further complicating serological detection of JEV is the extensive cross-reactivity with other orthoflaviviruses circulating in Europe (i.e., tick-borne encephalitis virus [TBEV], West Nile virus [WNV], and Usutu virus [USUV]). In addition, viremia in clinical cases may be short, hindering virus detection." shic_2024_jev: "Virus isolation is the reference standard." Molecular methods include conventional and nested RT-PCR, qRT-PCR, MLPM, MLPA, RT-LAMP and antigen-capture ELISA; serology includes virus neutralization, HI, complement fixation and IgM-capture ELISA.
How this level was decided
Level 3 unchanged, and this is now the best-evidenced C4 in the register. The level 3 test is that a validated assay exists but only at a national reference or research laboratory, and the paper is that sentence acted out: five national reference laboratories spent a project building the capability, needing reference-laboratory positive sera, an international proficiency panel and PRNT to do it. If five European NRLs had to align pipelines to be ready, a regional veterinary diagnostic laboratory is not running this off the shelf. Level 3 confirmed. Assays are abundant and validated, so not level 4; but for an agent absent from the US the work sits in reference laboratories.
C5 Production cost
Financial impact on the infected farm's cost of production
Moderate: Losses measurably increase cost of production but remain manageable within normal farm operations, whether acute, chronic, or associated with endemic disease
CONFIRMED by Eric. The assignment reached this level from the evidence, and he has reviewed and ratified it.
Confirmed by Eric. CONFIRMED. "c5l3, agree with assessment, worth noting that while Australian pig production is 'modern' it a signficantly different climate/seasonality and vast majority of farms are open-air (not outdoor per se, but generally not mechanically ventilated )"
Basis. ch30 30.2.4, on the 2022 Australian outbreak: "more than 80 commercial piggeries across four states were infected causing significant losses due to mummified, aborted, and malformed piglets." 30.2.6: "In pregnant sows or gilts, JEV infection can result in reproductive failure, leading to abortion and litters that contain stillborn or mummified fetuses... JEV infection in juvenile and adult pigs is generally not lethal." CFSPH 2023: "In one instance, reproductive losses were reported to affect 50-70% of pigs during a severe epidemic in Japan." "Pigs that become infected before they reach breeding age do not usually become ill." shic_2024_jev: "Most JEV infections are subclinical in pigs. In sows, infection with JEV before 60-70 days of gestation causes abortion, fetal mummification, stillbirth, or the birth of weak piglets. Infected boars develop reduced sperm motility, testicular edema, and temporary infertility."
How this level was decided
Level 3, scored under the standing note SCORING/production_cost_impact on what a US incursion would actually cost. The whole burden falls on the breeding herd -- growers and finishers are unaffected, which removes most of the tonnage from the exposure -- and it is seasonal, tracking mosquito activity. Against that, 50 to 70% reproductive loss in a severe epidemic is real money, and Australia lost mummified, aborted and malformed litters across 80 piggeries in one season. Losses that measurably increase cost of production but stay manageable within normal operations. FLAGGED as a level 3 or 4 judgment: a first season in a wholly naive US breeding herd, before any vaccine were available, is the case for level 4. Level 3 confirmed -- reproductive loss across both sexes against a subclinical background.
C6 Market impact
Duration of material disruption to pork and pig markets
Significant disruption: Material negative effect on supply or demand lasting 1 to 6 months when disease occurs on one or more farms
Basis. ch30 30.1: "Infections with JEV and WNV are included in the World Organization for Animal Health list of terrestrial animal diseases as a multiple species' disease (WOAH 2023) because of their propensity to spread and cause disease in humans and animals." 30.2.4: the 2022 Australian outbreak ran "from February to July 2022", affected four states and more than 80 commercial piggeries, and produced "a total of 42 cases with seven deaths" in people. shic_2024_jev: "JEV is reportable to the World Organization for Animal Health (WOAH)... and must be reported internationally according to the Terrestrial Animal Health Code."
How this level was decided
Level 3, and it is the framework's worked example at that level. A WOAH-listed zoonosis with human deaths, arriving in a country that has never had it, is reportable and trade-relevant -- and the Australian precedent gives the duration directly: February to July, which is five months and sits inside the level 3 band of one to six months. NOTE that the market driver here is the human cases rather than the pig losses. Level 4 would need disruption beyond six months, and unlike ASF the pig disease itself does not close a herd down. Level 3 confirmed -- WOAH-listed with mandatory international reporting.
C7 Treatment potential
Potential for treatment to improve outcomes
Little: Effective pathogen-directed treatment is available and works, or animals recover acceptably without it
Basis. ch30 30.2.6: "JEV infection in juvenile and adult pigs is generally not lethal. Experimental infection usually results in varying degrees of self-resolving pyrexia and nonspecific clinical signs of inappetence and lethargy." "These effects are usually temporary and complete recovery occurs in most instances" (of boar infertility). CFSPH 2023: "Affected animals are treated symptomatically." Chapter 30 describes prevention through vaccination and vector control and no pathogen-directed treatment. shic_2024_jev: "There is no available treatment for JEV infection in swine." "Piglets born alive may develop encephalitis with tremors and convulsions."
How this level was decided
Level 1 on the second clause -- animals recover acceptably without treatment. The pig that could be treated is not the pig that is damaged: adults have a self-resolving fever and boars recover their fertility, while the loss is transplacental and already done by the time anything is recognised. A treatment cannot reverse a mummified litter. Under the standing note SCORING/treatment_potential this is the case where there is no imperative to treat, and the chapter behaves accordingly by discussing vaccination and mosquito management instead. *** LEVEL 1 HELD BUT FLAGGED FOR CONSISTENCY WITH THE GETAH CORRECTION. *** The standing note lists JEV among the entries at level 1 because the harm is transplacental and complete before birth. Most of it is -- abortion, mummification, stillbirth. But this factsheet adds that piglets BORN ALIVE may develop encephalitis with tremors and convulsions, which is a living animal after birth and therefore a window a treatment could act in. That is the exact test Eric approved on 2026-09-06 when he removed Getah from the same list. Held because the difference is real -- Getah's neonatal deaths are the main clinical event while JEV's post-natal encephalitis is a minority outcome behind mainly reproductive loss -- but he should decide whether the clause still covers this entry.
C8 Vaccine availability
Availability of effective vaccines or bacterins
Needed but not available: No effective vaccine is available in the US or has been developed, and the disease would justify vaccinating if one existed
Basis. ch30 30.2.10: "Several JEV GIII-based veterinary vaccines have been developed for pigs based on the Nakayama, Beijing, BMIII, AT222, M, or Anyang strains." "Annual vaccination of sows prior to peak seasonal JEV activity is carried out in some JEV-endemic countries such as South Korea and Taiwan to prevent or limit production losses." "The emergence of genotype Ib (GIb) throughout Asia has raised concerns about the efficacy of GIII-based veterinary vaccines... in pigs little-to-no cross-neutralization of GI JEV was detected. In support of these findings, an in vivo study performed on pig farms in Taiwan demonstrated that a GIII LAV was less effective at preventing stillbirth and abortion in naive gilts caused by circulating GI virus compared to GIII virus." An inactivated chimeric BinJV vaccine "was shown to be >94% protective against GIV JEV challenge of immunized pigs". shic_2024_jev: "Swine vaccination is practiced in some parts of Asia."
How this level was decided
Level 3, the framework's worked example at that level, and the reading survives the 2026-08-28 rewording that widened level 1. No JEV vaccine is available or licensed in the United States for any species, and the disease plainly would justify vaccinating -- South Korea and Taiwan vaccinate sows annually for exactly this reason. The genotype problem sharpens it rather than softening it: the products that do exist are GIII-based and showed little to no cross-neutralisation of the GI viruses now circulating, so even importing one would not reliably answer the incursion the US would actually face. A genuine gap, not a product nobody chose to build. Level 3 confirmed, and the tractability evidence is direct: swine JEV vaccines exist and are used in Asia. No US product, and the disease would warrant one -- a demonstrated gap rather than an unbuildable one.
Levels and evidence are generated from data/assignments/japanese_encephalitis_virus.yml; the overview is authored in data/overviews/japanese_encephalitis_virus.md. Do not hand-edit this page — corrections go in data/assignments/CORRECTIONS.yml.
Quoted material marked Basis is from Zimmerman JJ, Karriker LA, Ramirez A, Schwartz KJ, Stevenson GW, Zhang J, eds. Diseases of Swine, 12th edition. Hoboken: Wiley Blackwell, 2025 — except where another source is named in the quotation itself.