Abstract
The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition. To explore this, we used viromic analysis of RNA and DNA virus-like particles to holistically track virus communities entering and leaving wastewater treatment plants and the connecting river catchment system and estuary. We reconstructed >40 000 partial viral genomes into 10 149 species-level groups, dominated by dsDNA and (+)ssRNA bacteriophages (Caudoviricetes and Leviviricetes) and a small number of genomes that could pose a risk to human health. We found substantial viral diversity and geographically distinct virus communities associated with different wastewater treatment plants. River and estuarine water bodies harboured more diverse viral communities in downstream locations, influenced by tidal movement and proximity to wastewater treatment plants. Shellfish and beach sand were enriched in viral communities when compared with the surrounding water, acting as entrapment matrices for virus particles. Extensive phylogenetic analyses of environmental-derived and reference sequences showed the presence of human-associated sapovirus GII in all sample types, multiple rotavirus A strains in wastewater and a diverse set of picorna-like viruses associated with shellfish. We conclude that wastewater-derived viral genetic material is commonly deposited in the environment and can be traced throughout the freshwater-marine continuum of the river catchment, where it is influenced by local geography, weather events and tidal effects. Our data illustrate the utility of viromic analyses for wastewater- and environment-based ecology and epidemiology, and we present a conceptual model for the circulation of all types of viruses in a freshwater catchment.
Highlights
The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition and is a potential hazard to human health
Previous research has demonstrated that wastewater contains a plethora of viruses, including humanpathogenic and zoonotic viruses, and that wastewater treatment processes do not remove human viruses with sufficient efficacy understood because of knowledge gaps in the ecology and connectivity of viromes across human populations and the freshwater-marine continuum
The surface river water samples showed a trend of increasing viral richness moving downstream, as further inputs of wastewater from treatment plants and other anthropogenic sources occurred (Fig. 1)
Summary
The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition and is a potential hazard to human health. We further investigated the differential patterns of abundance of each UViG in each library by mapping reads of all samples against the vOTU database and visualised the data with Anvi’o (Fig. 2), to identify 13 categories of viral species abundance and composition patterns (Table 1).
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