A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data
As clinical specimens are collected and analyzed less for SARS-CoV-2, variant detection in wastewater provides a readily accessible and rich source of information on SARS-CoV-2 evolution. The detection of pathogen targets in wastewater samples using PCR assays is a sensitive, cost-effective way to monitor the levels of infectious diseases, like SARS-CoV-2, in a community. Unfortunately, because PCR-based methods are typically not used to distinguish between viral variants, most wastewater testing labs must rely on more expensive, time-consuming, and resource-intensive sequencing methods for these results. Building upon recent developments for variant detection using quantitative PCR, we developed and assessed a novel, customizable digital PCR-based genotyping method for SARS-CoV-2 variant detection in wastewater, which is more rapid, cost-effective, and accessible than sequencing. We characterize the method and offer insights for improvement in future implementations.
Authors
- Stephanie M. Greenwald
- Christine L. Moe (ORCID: https://orcid.org/0000-0003-3628-1783)
- Chi-Yu Lin
- DAVID O. WHITE
- Robbie Barbero
- Lauren P. Saunders (ORCID: https://orcid.org/0009-0003-3498-6496)
- Elizabeth Donahue
- Anurag Patnaik
- Sarah A. Kane (ORCID: https://orcid.org/0000-0001-5417-9913)
- Sarah M. Owens (ORCID: https://orcid.org/0000-0002-9946-2787)
- Patrick Andersen (ORCID: https://orcid.org/0000-0003-4987-1643)
- Stephen Patrick Hilton (ORCID: https://orcid.org/0000-0002-0326-3231)
- Dagmara S. Antkiewicz (ORCID: https://orcid.org/0000-0003-1282-5483)
- Orlando Sablon
- Pengbo Liu (ORCID: https://orcid.org/0000-0002-5269-2497)
- Rachel Poretsky (ORCID: https://orcid.org/0000-0001-5401-449X)
- Olivia Swahn
- Andrew Jones (ORCID: https://orcid.org/0000-0002-3739-2322)
- Daniel Goldfarb (ORCID: https://orcid.org/0000-0001-6014-387X)
- Kayley H. Janssen (ORCID: https://orcid.org/0000-0001-9546-5799)
- Chamodya Ruhunusiri
- Adélaïde Roguet (ORCID: https://orcid.org/0000-0003-3688-4525)
- Tim Wesselman
- Ian Bradley (ORCID: https://orcid.org/0000-0001-5338-1167)
- Marlene K. Wolfe (ORCID: https://orcid.org/0000-0002-6476-0450)
- James Erickson (ORCID: https://orcid.org/0000-0002-6716-5454)
- Jean Lozach
- Stephanie M. Barksdale
- Patrick T. Acer (ORCID: https://orcid.org/0000-0002-4457-2604)
- Denton Munns
- Yinyin Ye (ORCID: https://orcid.org/0000-0003-0625-9657)
- Jeremy Davis‐Turak (ORCID: https://orcid.org/0000-0002-4462-5171)
- Ross Dunlap
- Tara Jones-Roe
- Michael Kilroy
- Modou Lamin Jarju
- Hien Thi Thu Le (ORCID: https://orcid.org/0000-0001-8847-6369)
- Yuke Wang (ORCID: https://orcid.org/0000-0002-9615-7859)
- Jim Huang
- Emily Milich
- Jared Obermeyer
- Ganit Pricer
- Marion T. Reven
- Kalpita Vengurlekar
- Aouda Patricia Flores-Baffi
- Siya Kashwala
- Erica Camarato
- Regan Wied
- Sophia Bellakbira
- Michael Secreto
- Dalton Bunde
- Mayumi E. Pascual
- Johannah Gillespie
- Benjamin Lepene
- Dolores Sanchez Gonzalez
- Dalaun Richardson
- Shreya Shrestha
- Sayed Mohammad R. Mosavi
- Ayan Mohamed
- Soumya Sibani Sahoo (ORCID: https://orcid.org/0009-0003-7213-7452)
- Sydney Gallo
- Rosemarie Wilton
- Aaron Stanz
Institutions
- Argonne National Laboratory (US)
- University of Wisconsin–Madison (US)
- Emory University (US)
- University of Illinois Chicago (US)
- Engineering Data Management (US)
- Rosalind Franklin Institute (GB)
- Ceres Nanosciences (US)
- Water Sanitation and Hygiene Institute (IN)
- University at Buffalo, State University of New York (US)
Publication Details
- Journal
- mSystems
- Published
- 2025-10-22
- DOI
- https://doi.org/10.1128/msystems.00229-25
- Primary Topic
- SARS-CoV-2 detection and testing
- Type
- article
- Field-Weighted Citation Impact
- 0.00