Japanese encephalitis virus detections in Australia.

(DOCX)</p

Results of JEV RT-qPCR testing of brain samples.

Results of JEV RT-qPCR testing of brain samples.</p

Maximum clade credibility phylogenetic tree of complete JEV envelope gene sequences, sourced from GenBank.

The phylogeny was reconstructed under a GTR+G+I nucleotide substitution assumption and an uncorrelated relaxed molecular clock model. Genotype V sequences of JEV were excluded from this phylogeny as they were deemed temporal outliers in regression analysis. Posterior probability values of >0.70 are presented adjacent to nodes as indicated by asterisks. The mean time to most recent common ancestor (tMRCA) is presented above major nodes, with error reported as the 95% highest probability density (95% HPD).</p

Primer scheme used for the amplification of JEV 1600bp amplicon sequencing.

(DOCX)</p

Positively selected sites within the JEV/Australia/NT_Tiwi Islands/2021 genome.

(DOCX)</p

Sequence alignment of primers and probes used for the detection of JEV at PWLM and ACDP.

Primer and probe positions are shown according to the sequence of the JEV/Australia/NT_Tiwi Islands/2021 genome (OM867669). JEV RT-PCR assays used at PWLM comprised primers and probes in alignments 1 and 2 [34,35]. JEV RT-PCR assays used at ACDP comprised primers and probes in alignments 3 and 4 [32,33]. (TIF)</p

Maximum likelihood phylogenetic tree of complete JEV genomes available in GenBank.

The TN model with gamma rate heterogeneity was chosen as the most appropriate model by IQ-TREE v.2.0.6. The results from 1000 bootstrap replicates are given on the nodes and the scale represents the number of nucleotide substitutions per site.</p

Maximum likelihood phylogenetic tree of JEV envelope genes available in GenBank.

The TIM2 model with gamma rate heterogeneity was chosen as the most appropriate model by IQ-TREE v.2.0.6. The results from 1000 bootstrap replicates are given on the nodes and the scale represents the number of nucleotide substitutions per site. (TIF)</p

Fig 1 -

Map of the Tiwi Islands showing its proximity to mainland Australia and the Northern Territory. The Tiwi Islands comprise Bathurst Island and Melville Island. The locations of major settlements on these islands are shown. Darwin is the capital city of the Northern Territory. The map was created in QGIS version 3.26.2-Buenos Aires (QGIS Development Team (2022). QGIS Geographic Information System. Open Source Geospatial Foundation Project. http://qgis.osgeo.org). The base layer of the map used to generate this figure was downloaded from https://www.abs.gov.au/statistics/standards/australian-statistical-geography-standard-asgs-edition-3/jul2021-jun2026/access-and-downloads/digital-boundary-files and is licensed under a Creative Commons Attribution 4.0 International licence.</p