Results of JEV RT-qPCR testing of brain samples.

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

Japanese encephalitis virus detections in Australia.

(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

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

Serogroup (Panel A) and clonal complex (Panel B) distribution per annum from 2000–2014.

<p>(A) Serogroup was reported for 436 IMD cases. (B) Clonal complex was reported for 278 cultured isolates. The category “Other” indicates clonal complexes with rare frequency (less than 5 isolates) and represents cc8, cc22, cc35, cc60, cc162, cc167, cc212, cc461, cc1157 and no assigned cc.</p

BEXSERO^® antigen sequence type diversity within WA meningococcal population.

<p>BEXSERO^® antigen sequence type diversity within WA meningococcal population.</p