Emergence and spread of Japanese encephalitis virus genotype IV in a novel ecosystem: Australia, 2021-2022

An unprecedented outbreak of the mosquito-borne Japanese encephalitis virus (JEV) occurred in south-eastern Australia in 2022. The outbreak was caused by a novel lineage of JEV genotype IV, which first emerged in Northern Australia in 2021, and resulted in 45 human cases, including 7 deaths, and over 80 infected piggeries during 2021 and 2022. We analyzed 166 whole genomes of JEV from field collected mosquitoes (n=9), humans (n=2), and farmed (n=136) and feral pigs (n=19). The majority of outbreak sequences clustered into two genetically distinct lineages (clades A and B), separated by three formative single nucleotide polymorphisms, which were circulating between February 2021 and August 2022. Both lineages were detected in mosquito and pig samples, while only clade A was detected in the human samples sequenced. We conclude that clades A and B were likely to have been circulating prior to the outbreak. A lack of spatial-temporal phylogenetic structure suggests a rapid dispersal of the outbreak lineages in largely JEV naïve vertebrate populations and competent mosquito vector populations. Ongoing surveillance and genomic characterization of new detections is required to monitor the spread of JEV, the emergence of alternative JEV genotypes or lineages, as well as changes in the viral ecology.