Based on metagenomic shotgun sequencing, the viral community structure, potential hosts, and specific functional genes in key monitoring sites of a typical drinking water supply system were explored. The result revealed the presence of massive unclassified viral species, with the dominance of double-stranded DNA viruses occupying 94%–100% of viral abundance. The phages Siphoviridae and Myoviridae were identified as the major known taxa. Conventional and advanced treatment processes reduced viral richness, diversity, and replication potentials, while the richness and diversity slightly increased after passing water supply pipe network. Both treatment processes restrained the roles of viruses in mediating the exchange of auxiliary metabolic genes (AMGs). Viral genomes in source water possessed various AMGs involved in energy metabolism and biosynthesis of carbohydrates, amino acids, and cofactors, which could contribute to bacterial host metabolization. However, after conventional treatment, they mainly encoded penicillin-binding proteins. Notably, in the water sample with a long-term exposure to hospital clinic settings, the abundance of viruses (35%) carrying antibiotic resistance genes (ARGs) was much higher than those (≤ 2.6%) of other samples. This study highlighted the significant impacts of drinking water treatment processes, transport pipe networks, and environmental risk exposure on viral guilds and functions, and provided a theoretical basis for optimizing operation and management of water supply systems. 

water supply system, viral community, potential hosts, auxiliary metabolic genes (AMGs), antibiotic resistance genes (ARGs), metagenomics