Distinct distribution of HEV-3 subtypes across humans, animals, and environmental waters in Sweden

Abstract

We previously observed a notable discrepancy in the distribution of HEV-3 subtypes between wastewater and clinical samples in Sweden. To confirm this observation and comprehensively elucidate HEV-3 circulation patterns across humans, animals, and environmental waters in Sweden, we analysed the HEV genetic diversity in archived wastewater samples between late 2016 and early 2018, clinical cases between 2012 and 2024, and all available Swedish sequences from the NCBI Virus database. HEV RNA was detected in all archived wastewater samples, with subtype 3c being the only subtype identified. In typed clinical cases, subtypes 3f (45/126) and 3c (44/126) were nearly equally distributed, though regional dominance varied. When incorporating human sequences from other Swedish studies, subtype 3f became dominant (75/168). Analysis of all available sequences revealed that 3f (113/136) was the dominant subtype in Sus scrofa (pigs and wild boars), while 3c (30/33) was dominant in environmental waters. These findings highlight the complex transmission dynamics of HEV-3 in Sweden. The near-absence of 3c in Swedish domestic pigs and wild boars, despite its high proportion in clinical cases, raises the question about the source of human 3c infection. In addition, the near-exclusive detection of 3c in wastewater suggests potential differences in viral shedding, disease severity of HEV-3 subtypes, or alternative host sources. This study emphasizes the importance of integrated One Health surveillance to track HEV circulation across reservoirs.

Keywords: One health; animal reservoir; environmental surveillance; genetic diversity; rat HEV; wastewater; waterborne transmission; zoonotic transmission.

Figure 1.

Distribution of HEV genotypes and subtypes in genotyped clinical samples in Sweden between 2012 and 2024. (A) Distribution of HEV genotypes and HEV-3 subtypes in clinically confirmed cases in Sweden between 2012 and 2024. The proportion of different subtypes is shown. (B) Yearly variation in HEV-3c, 3f, and other HEV genotypes/subtypes between 2012 and 2024.

Figure 2.

The genotype distribution of HEV across humans, animals, and environmental waters in Sweden. This figure shows the distribution of HEV genotypes across humans (A), animals (B), and environmental water (C) in Sweden. The pie charts represent the relative proportions of each identified genotype within each source, with the total number of samples (N) analysed indicated below each chart.

Figure 3.

Phylogenetic tree of HEV partial RdRp region. Phylogenetic tree was constructed based on the 311 nucleotides of partial HEV RdRp region using UPGMA method. Sequences labelled in red represent those isolated from human cases in Sweden. Sequences labelled in green represent those isolated from Swedish animals. Sequences labelled in blue represent those isolated from environmental waters in Sweden. Sequences belonging to subtype 3f, 3e, and 3c/i, are highlighted on the right of the phylogenetic tree.