Hybrid-capture-enabled longitudinal metagenomics allows strain-resolved human-associated virus surveillance in wastewater

Abstract

Hybrid-capture wastewater sequencing has shown promise for episodic viral epidemiology, but its value for multi-year, multi-pathogen, strain-resolved surveillance benchmarked against clinical data remains unclear. Here we applied hybrid-capture viral metagenomics to 127 weekly 24-h composite influent samples from a single sentinel wastewater treatment plant in Leuven, Belgium, collected over 31 months, and linked wastewater time series to national clinical indicators of multiple pathogens. Our approach recovered a genome-resolved target-enriched virome spanning 339 viral species and 715 strains, captured seasonal community turnover and showed that rotavirus A in wastewater typically preceded clinical surveillance by ~1 week. It also identified signals beyond routine wastewater programmes, notably a parvovirus B19 surge starting in April 2023, about 1 year before the national public health alert. Overall, here we show that longitudinal hybrid-capture metagenomics can extend wastewater surveillance from detection to strain-resolved, multi-virus epidemiology and can provide early circulation signals for clinically relevant viruses. Using hybrid-capture metagenomics, an analysis of 31 months of wastewater samples detected 339 viral species and 715 strains, retrospectively tracked seasonal trends and provided early warnings of clinically relevant outbreaks, including rotavirus A and parvovirus B19.