Methods: Whole genome sequencing (WGS) was performed using target-enrichment and compared with ORF2 sequencing using samples collected from two study cohorts. Cohort A consisted of recent clinical specimens collected from patients with acute HEV (n=30, Oct 2022-Mar 2024). Cohort B consisted of archived clinical specimens (n=21, Jan 2013 to Sep 2022) with robust epidemiological data. We analysed HEV relatedness (phylogeny, mutual nearest-neighbour clustering), subtyping and vaccine amino acid mapping, to explore the concordance between ORF2-490bp, full-length ORF2 and whole-genome analyses. In addition, we assessed the HEV-3 SNP distance threshold appropriate for cluster assignment.