Genetic Diversity of Hepatitis E Virus Type 3 in Switzerland—From Stable to Table

Abstract

Hepatitis E caused by hepatitis E viruses of the genotype 3 (HEV-3) is a major health concern in industrialized countries and due to its zoonotic character requires a “One Health” approach to unravel routes and sources of transmission. Knowing the viral diversity present in reservoir hosts, i.e., pigs but also wild boars, is an important prerequisite for molecular epidemiology. The aim of this study was to gain primary information on the diversity of HEV-3 subtypes present along the food chain in Switzerland, as well as the diversity within these subtypes. To this end, samples of domestic pigs from slaughterhouses and carcass collection points, as well as from hunted wild boars, were tested for HEV RNA and antibodies. HEV positive meat products were provided by food testing labs. The HEV subtypes were determined using Sanger and next generation sequencing. The genetic analyses confirmed the predominance of a Swiss-specific cluster within subtype HEV-3h in pigs, meat products, and wild boars. This cluster, which may result from local virus evolution due to the isolated Swiss pig industry, supports fast differentiation of domestic and imported infections with HEV.

Frequent Occurrence of Simultaneous Infection with Multiple Rotaviruses in Swiss Pigs

“…The most frequent type of co-infections were triple infections with RVA, RVB, and RVC and double infections with RVA and RVC, while RVB and RVC co-infections were rare. This finding is comparable to other studies, where triple infections were reported most frequently (12–21.1%), followed by AC (6.7–24%), BC (3–8%), and AB (5–16%) double infections [ 14 , 17 , 42 , 43 ]. As also reported previously, single infections were mainly caused by RVA, while RVC and, particularly, RVB were rarely observed alone [ 15 ].…”

“…Due to the low number of samples, it is difficult to conclude on the presence of Swiss subcluster within RV genotypes. However, except for NSP1, NSP2, VP2, and VP3, where most Swiss sequences are closely related, the phylogenetic trees provide no evidence for Swiss-specific subclusters of RVA, as previously observed for other porcine viruses such as hepatitis E virus (HEV) or atypical porcine pestivirus (APPV) [ 43 , 44 ]. In those cases, the high restrictions for the import of living pigs into Switzerland are thought to have favored virus evolution independent from neighboring countries.…”

“…For VP4, four different genotypes were found: P[13] was most frequent ( n = 5), followed by P[6] ( n = 4), P[7], and P[32] ( n = 2 for both). While P[13], P[6], and P[7] are also present in well-known porcine reference genomes, P[32] has so far only been described in pigs from Ireland, UK, Denmark, and Germany [ 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 ].…”

Hepatitis A Virus and Hepatitis E Virus as Food- and Waterborne Pathogens—Transmission Routes and Methods for Detection in Food

“…Both the ORF 1 and ORF2 regions are used for molecular typing of HEV for Sanger sequencing and NGS, and different subtypes can be determined [ 130 , 225 , 226 , 227 ]. HEV-3 subtypes c, e and f have been shown to be the most prevalent subtypes in Europe [ 4 ].…”

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

“…[11,12] Recent investigations showed that the viral isolates identified in Switzerland are genetically very close, belonging to a specific cluster within genotype 3h, designated here as 3h_s. [4,13,14] This homogeneity reduces the possible impact of viral diversity on clinical phenotype.…”