Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States
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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BibTeX
@misc{justen2026deep,
title = {{Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States}},
author = {Lennart J. Justen and Clayton Rushford and Olivia S. Hershey and Róisín Floyd-O’Sullivan and Simon L. Grimm and William J. Bradshaw and Harmon Bhasin and Daniel P. Rice and Katherine Stansifer and Jo D. Faraguna and Michael R. McLaren and Alessandro Zulli and Alejandro Tovar-Mendez and Emma E. Copen and Kristen K. Shelton and Ayaaz Amirali and Sherin Kannoly and Sofia Pesantez and Aiden Stanciu and Iñigo Caballero Quiroga and Leopolda Silvera and Nicole Greenwood and Barbra Bongiovi and Austin Walkins and Ryan Love and Scott Lening and Kaylyn Patterson and Theresa Johnston and Sandra Hernandez and Aymara Benitez and Billie Jo McCarley and Samantha Engelage and Suguna Pillay and Cindy Calender and Brent Herring and Carey Robinson and Monett Wastewater Treatment Plant and Columbia Missouri Wastewater Treatment Plant and Daniel Cunningham-Bryant and Gordon Adams and Jillian Paull and Jamie Devlin and Vamsi Thiriveedhi and Sarah E. Turbett and Jacob E. Lemieux and Rose S. Kantor and David H. O’Connor and John J. Dennehy and Rachel Poretsky and Jason A. Rothman and Helena M. Solo-Gabriele and Jason R. Vogel and Pardis C. Sabeti and Jeff Kaufman and Marc C. Johnson},
howpublished = {medRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.03.05.26345726},
url = {https://doi.org/10.64898/2026.03.05.26345726},
note = {CC0},
}
RIS
TY - UNPB
TI - Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States
AU - Lennart J. Justen
AU - Clayton Rushford
AU - Olivia S. Hershey
AU - Róisín Floyd-O’Sullivan
AU - Simon L. Grimm
AU - William J. Bradshaw
AU - Harmon Bhasin
AU - Daniel P. Rice
AU - Katherine Stansifer
AU - Jo D. Faraguna
AU - Michael R. McLaren
AU - Alessandro Zulli
AU - Alejandro Tovar-Mendez
AU - Emma E. Copen
AU - Kristen K. Shelton
AU - Ayaaz Amirali
AU - Sherin Kannoly
AU - Sofia Pesantez
AU - Aiden Stanciu
AU - Iñigo Caballero Quiroga
AU - Leopolda Silvera
AU - Nicole Greenwood
AU - Barbra Bongiovi
AU - Austin Walkins
AU - Ryan Love
AU - Scott Lening
AU - Kaylyn Patterson
AU - Theresa Johnston
AU - Sandra Hernandez
AU - Aymara Benitez
AU - Billie Jo McCarley
AU - Samantha Engelage
AU - Suguna Pillay
AU - Cindy Calender
AU - Brent Herring
AU - Carey Robinson
AU - Monett Wastewater Treatment Plant
AU - Columbia Missouri Wastewater Treatment Plant
AU - Daniel Cunningham-Bryant
AU - Gordon Adams
AU - Jillian Paull
AU - Jamie Devlin
AU - Vamsi Thiriveedhi
AU - Sarah E. Turbett
AU - Jacob E. Lemieux
AU - Rose S. Kantor
AU - David H. O’Connor
AU - John J. Dennehy
AU - Rachel Poretsky
AU - Jason A. Rothman
AU - Helena M. Solo-Gabriele
AU - Jason R. Vogel
AU - Pardis C. Sabeti
AU - Jeff Kaufman
AU - Marc C. Johnson
PY - 2026
DA - 2026/10/19
PB - medRxiv
DO - 10.64898/2026.03.05.26345726
UR - https://doi.org/10.64898/2026.03.05.26345726
AB - 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.
ER -