Hepatitis E virus in the virome of water and animals

This thesis was aimed to investigate viruses in different animals and water to get some understanding of viruses that disseminate into the environment. Next generation sequencing (NGS) was used to explore the virome from raw to treated water at two Swedish drinking water treatment plants (DWTP) and in tap water. The amount of viruses was lowered with 3-4 log10 after the treatments. The viral diversity was reduced from 26 different virus families in raw water to 12 in tap water. Hepatitis E virus (HEV), subtypes HEV3c/i and HEV3a, were identified in most water samples, with 10-130 International Units of HEV RNA/mL tap water. The viral diversity was also investigated in incoming and treated wastewater at two Swedish wastewater treatment plants (WWTP) in Knivsta, Stockholm, and Gryaab in Gothenburg. Ozone treatment was used after conventional treatment before the release of the treated wastewater from Knivsta WWTP. At least 327 virus species, belonging to 25 known virus families were detected in the raw wastewater. The virus concentration was reduced by 1-6 log10 for 21 human related viruses, with lowest removal efficiency for adenovirus. At Gryaab WWTP, seasonal differences in presence and concentration of 13 human viruses in raw and treated wastewater were investigated during one year. Twelve of the viruses were detected throughout the year in influent and effluent wastewater by either qPCR or NGS. HEV was found in effluents when released into the Göta River. The concentrations of all viruses in influent were reduced by 3-4 log10 in the effluents. Since HEV was identified in most water samples, its prevalence among their major hosts, wild boars and pigs, was investigated. HEV in Spanish and Swedish wild boars were compared. HEV RNA was found in 20% in Spanish wild boars vs. 15% in Swedish wild boars, while anti-HEV was significantly higher among Spanish wild boars (59% vs. 8%). Most Swedish and some Spanish wild boars were infected by subtype HEV3f, while several Spanish wild boars were infected by divergent HEV3c/i strains, indicating regional differences in infecting HEV strains. The Swedish wild boar strains were similar to strains from infected Swedes and Swedish domestic pigs. These wild boars were also infected with at least 27 different viruses, identified by NGS on liver samples. HEV3 was identified in 22% of piglets from 77% of 30 investigated pig farms sampled twice with more than one year apart. Most piglets were infected with HEV3f or HEV3e. Each pig farm had a unique HEV strain, and several strains were similar to human HEV3 strains. These studies showed that viruses are disseminated into the environment both from raw water, treated wastewater and animals, and may be found in tap water. The HEV3 strains identified in drinking water were different from those isolated from Swedish pigs and wild boars, and similar to strains from humans with unknown source of infection, indicating waterborne transmission also for HEV3