Hepatitis E virus (HEV) along the food chain: Investigations into spread, genetic diversity and molecular tracing of HEV in Switzerland

Dr.med.vet Thesis by Isabelle Vonlanthen-Specker

Hepatitis E virus is a zoonosis and can be the causative agent of acute hepatitis in humans. HEV-3, the most important genotype in Europe, is transmitted from the reservoir hosts (pigs, wild boars, more rarely deer) to humans mainly via the consumption of raw or undercooked meat and meat products.
The study aims at investigating the genetic diversity of HEV in Switzerland in different host species and along the food chain with the final goal to establish a sequence repository that supports molecular epidemiology of human HEV cases in Switzerland. Especially the confirmation of a proposed Swiss-specific HEV subtype 3s is of interest. 
In the first part of the project, pig livers from slaughtered pigs, perished pigs (carcass collection points) and wild boar livers from two cantonal hunting grounds were screened for Hepatitis E virus and the detected viral genomes were sequenced. Antibody prevalence was determined using meat juice. In addition, we received HEV positive pork products from different food safety diagnostic labs and determined the viral genomic sequence using Sanger and next generation sequencing (NGS). In a second part, individual and collective faecal samples and manure from different farms are tested for HEV in order to i) enlarge the sequence collection and ii) determine an efficient screening tool to determine the HEV status of pig herds. 
The project is still ongoing but for the first part data are already available: Viral RNA was detected in 5 % of the wild boars, 0.5 % of the fattening pigs and 13 % of the pigs from the carcass collection points which were mostly younger than the fattening pigs. So far 32 samples were successfully subtyped, 25 of which could be assigned to the proposed Swiss-specific subtype 3s. Antibodies were detected in 18 % of the wild boars and 59 % of the fattening pigs. Four almost complete sequences from three wild boars and one pig could be generated by NGS using our in-house ViroScreen protocol. Other interesting viruses such as the newly described porcine circovirus type 3 were detected in the wild boar livers by virome analysis.
The results obtained so far support the hypothesis of a Swiss specific HEV subtype. The proposed HEV 3s subgroup seems to prevail in the Swiss swine and wild boar population, possibly due to pig movements predominantly occurring within Swiss boundaries. Comparison of our sequences from animals and pork products to the ones gained from human patients at the University hospital in Lausanne (curtesy to Dr. Roland Sahli) shows that HEV 3s is also the predominant subtype in humans. Hence, HEV in Switzerland is mainly of the proposed new 3s subgroup and infections in humans are primarily of domestic nature.