Genetic investigations provide insights into Hepatitis E virus and other potential foodborne viral pathogens in Ireland (2016-2019)

Foodborne viruses, including Hepatitis A virus (HAV), Norovirus (NoV), Sapovirus (SaV), and Hepatitis E virus (HEV) are increasingly recognised as a threat to public health in Ireland. This study, carried out between 2016 and 2019, uses existing and novel molecular techniques to determine the prevalence and genetic characteristics of putative foodborne viruses in a symptomatic patient cohort in Ireland. The study also determines the prevalence of viral contaminants in high-risk food matrices and defines the genetic characteristics of HEV infection in Irish pig herds. The genetic relatedness of viruses derived from human, pig, and food matrices is explored using bespoke bioinformatic pipelines and comparative phylogenetic analysis. In symptomatic patients, NoV was the dominant gastroenteritis-causing pathogen (3,543 cases), followed by SaV (591 cases), while acute hepatitis was attributed to HEV (188 cases) and HAV (154 cases) in a small proportion of cases. Indications point towards foodborne transmission for several infections. For the first time, contamination with viral RNA was described in berries and pork products at the point of retail in Ireland. Of fresh and frozen berries sampled (n=240), 5.4% (HAV n=5, NoV n=3, HEV n=3, HAdV-F n=5) had detectable nucleic acid. A similar survey of pork products determined 4.8% (9/188) to contain HEV RNA. Genetic divergence in human NoV, SaV, HAV, and HEV infections in this cohort is high. Continuous transmission of NoV (GII.4) and HEV (3c) subtypes highlights the potential for type-specific vaccines. Sporadic emergent variants, including HEV 3m and NoV GII.4 Sydney, were identified in 2016 and 2018, influencing national prevalence. Increased HEV G3 divergence was observed in Irish patients, mainly with 3c, 3e, and 3f subtypes. However, pig-derived HEV G3 (n=27) and a small food sample set (n=2) were genetically more uniform, primarily showcasing subtype 3e. Strong genetic similarity between G3 variants in Irish patients and animals in the UK and Europe implies imported infection routes. The presence of similar 3e variants in Irish pigs and patients suggests local transmission is plausible. Moreover, identifying matching HEV 3e variants in pig-derived food at the retail level supports the theory of foodborne zoonotic transmission between pigs and humans. The novel WGS techniques developed in this study will facilitate further genetic surveillance to increase our understanding of the complex transmission pathways for HEV G3 in Ireland.