Japanese encephalitis virus detections in Australia.

(DOCX)</p

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

(DOCX)</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

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

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

(DOCX)</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

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

Results of JEV RT-qPCR testing of brain samples.

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

Image_5_H7N9 bearing a mutation in the nucleoprotein leads to increased pathology in chickens.jpeg

The zoonotic H7N9 avian influenza (AI) virus first emerged in 2013 as a low pathogenic (LPAI) strain, and has repeatedly caused human infection resulting in severe respiratory illness and a mortality of ~39% (>600 deaths) across five epidemic waves. This virus has circulated in poultry with little to no discernible clinical signs, making detection and control difficult. Contrary to published data, our group has observed a subset of specific pathogen free chickens infected with the H7N9 virus succumb to disease, showing clinical signs consistent with highly pathogenic AI (HPAI). Viral genome sequencing revealed two key mutations had occurred following infection in the haemagglutinin (HA 226 L>Q) and nucleoprotein (NP 373 A>T) proteins. We further investigated the impact of the NP mutation and demonstrated that only chickens bearing a single nucleotide polymorphism (SNP) in their IFITM1 gene were susceptible to the H7N9 virus. Susceptible chickens demonstrated a distinct loss of CD8+ T cells from the periphery as well as a dysregulation of IFNγ that was not observed for resistant chickens, suggesting a role for the NP mutation in altered T cell activation. Alternatively, it is possible that this mutation led to altered polymerase activity, as the mutation occurs in the NP 360-373 loop which has been previously show to be important in RNA binding. These data have broad ramifications for our understanding of the pathobiology of AI in chickens and humans and provide an excellent model for investigating the role of antiviral genes in a natural host species.</p