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

Paper by Mustafa Karatas et al: “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…(More)”.