Wastewater viromics reveals host-structured viral signals and non-human pathogens

Abstract

Wastewater represents a powerful platform for human virus surveillance. However, the entry of animal- and plant-associated viruses into sewage is heterogeneous and incompletely understood, creating uncertainty about how reliably wastewater reflects non-human virus circulation. Here, we address this by analysing monthly wastewater metagenomic data from two distinct periods (2020–2021 and 2024–2025) across five major Finnish wastewater treatment plant catchments using a targeted hybrid-capture approach to characterise the composition, host range, and spatial distribution of the non-human wastewater virome. Nearly half of the detected viral accessions were non-human, indicating substantial diversity, despite human-associated viruses accounting for 83% of normalised viral reads. Rodent-, livestock-, and bird-associated viruses showed spatial structuring consistent with regional host populations. The wastewater viromics also detected four EU-regulated plant pathogens, including tomato brown rugose fruit virus, which was highly prevalent in wastewater two years before its first official detection in Finland. Together, these results show that wastewater contains structured, host-linked viral signals, supporting its use as an ecological proxy for non-human virus circulation.