Hepatitis E virus strains infecting Swedish domestic pigs are unique for each pig farm and remain in the farm for at least 2 years

Abstract

Hepatitis E virus (HEV) genotype 3 (HEV3) is distributed globally and infects both humans and animals, mainly domestic pigs and wild boars, which are the major reservoirs. In this study, the prevalence of HEV among Swedish pigs was investigated by HEV RNA analysis in 363 faecal samples from 3-month-old piglets sampled twice (2013 and 2014) in 30 Swedish pig farms. Four different types of farms were investigated; organic, conventional closed (keeping the sow), satellites in a sow pool (conventional farms sharing sows) and conventional non-closed farms (purchasing gilts). More than two-thirds (77%) of the farms had HEV-infected pigs. HEV RNA was found in faeces from 79 pigs (22%). Partial ORF1 could be sequenced in 46 strains. Phylogenetic analysis revealed a unique HEV3 strain for each farm. Strains sampled more than a year apart from the same farm were closely related, indicating that the same HEV strain is present for several years on the farm. Despite that only 4% of the Swedish pig farms were investigated, two farms had strains similar to those from humans, another had strains similar to wild boar HEV. The uniqueness of strains from each farm indicates a possibility to identify a source of infection down to farm level. This knowledge may be used by the farms to investigate the effectiveness of good hygiene routines to reduce the amount of HEV and thus the infection risk in the farm, and for Swedish public health authorities to identify cases of HEV transmissions from consumption of uncooked pork.

Keywords: HEV; HEV RNA; anti-HEV; zoonosis.

Figure 1

Map of Sweden showing the counties and number of farms per county (in red) where samples were collected for this study in 2013/2014 and from farm 12A in 2007. The figures in parentheses depict the number of farms with positive piglets, the number of farms with strains that could be sequenced. The number and region of hunting of 289 sampled wild boars shot in Sweden between 2007 and 2016 and previously published are shown in green (Roth et al., 2016; Widén et al., 2010). The figures in parenthesis depict the number of PCR positive wild boars

Figure 2

The enlarged branch of HEV3 subtype 3f strains in a UPGMA phylogenetic tree based on 325 nucleotides of partial ORF1 for genotype 3. Bootstrap values from 1,000 replicas are given below the branches. The strains from pigs are given in red, those from wild boars in green and those from humans in blue. The farm designations where the strains were collected are given on the branches and the region of origin of the farms are given at the nodes. The farms in which samples were collected in 2007 and 2009 are indicated with year after the name of the farm. Farms marked with an asterisk indicate farms with strains collected more than a year apart. Accession number and origin of the strains are given at the nodes