Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States

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Abstract
Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this capability by enabling broad, pathogen-agnostic detection of hundreds of viral taxa, including emerging threats. Here, we present data from CASPER (the Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs), a U.S.-based wastewater metagenomic sequencing network designed for deep, untargeted pathogen monitoring at national scale. This release includes 1,206 samples collected between December 2023 and December 2025 from 27 sites across nine states, covering 13 million people. Deep sequencing (∼1 billion read pairs per sample) generated 1.2 trillion read pairs (358 terabases), capturing diverse human, animal, and plant viruses including rare taxa. CASPER data tracks wastewater digital PCR and clinical abundance trends for SARS-CoV-2, influenza A, and respiratory syncytial virus, and recovers national-scale variant dynamics for SARS-CoV-2 and norovirus. As the largest publicly available untargeted wastewater sequencing dataset to date, CASPER provides a shared and growing resource for pathogen surveillance and microbial ecology.

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