A 1-year Study on SARS-CoV-2 Variant Shifts in Wastewater Using dPCR: Comparison with Clinical and GISAID Data
- Caryn Tyler
- Nov 12
- 2 min read
Wastewater testing can be used to monitor SARS-CoV-2 infections in communities. Data from PCR-based wastewater testing are usually available to public health authorities within 5–7 days after excreta and other body fluids enter the sewer. While PCR-based methods can accurately detect and quantify SARS-CoV-2, sequencing-based methods are usually required to distinguish between variants, delaying the results and adding cost to the process. We developed and assessed a novel, customizable digital PCR (dPCR)-based genotyping method for SARS-CoV-2 variant detection in wastewater, which is more cost-effective, faster, and more accessible than sequencing. This approach was applied to more than 1,400 wastewater samples collected from six states between April 2023 and May 2024, with results displayed on a public dashboard alongside clinical data from the same period. The wastewater dPCR-based method effectively detected emerging variants, mirroring trends observed in clinical settings and in data on the Global Initiative on Sharing All Influenza Data (GISAID) platform; this method also provided early warning signals, as variants like EG.5 and FL were identified in wastewater before clinical detection. A subset of the wastewater samples was analyzed using both dPCR genotyping and sequencing, with good agreement between the two methods. The range of concordance for four different variants was between 62% and 98%. The successful development and implementation of this dPCR-based genotyping for wastewater samples demonstrates its cost-effectiveness and scalability. With the decline in clinical testing, wastewater surveillance becomes increasingly vital for monitoring SARS-CoV-2 variants and supplementing clinical surveillance efforts.
ARTICLE: SKU 44XXX
Mosavi SMR, Acer P, Andersen P, Barbero R, Barksdale S, Bellakbira S, Bunde D, Dunlap R, Erickson J, Goldfarb D, Jones-Roe T, Kilroy M, Le H, Lepene B, Milich E, Mohamed A, Munns D, Obermeyer J, Patnaik A, Pricer G, Reven MT, Richardson D, Ruhunusiri C, Sahoo SK, Saunders LP, Swahn O, Vengurlekar K, White D, Davis-Turak J, Stanz A, Flores-Baffi AP, Lozach J, Wesselman T, Hilton S, Kashwala S, Liu P, Moe CL, Sablon O, Wang Y, Wolfe M, Antkiewicz D, Camarato E, Janssen K, Roguet A, Shrestha S, Wied R, Gillespie J, Huang J, Jones A, Kane S, Gonzalez DS, Jarju ML, Lin C, Pascual ME, Poretsky R, Secreto M, Bradley I, Gallo S, Ye Y, Donahue E, Greenwald SM, Owens S, Wilton R. 0. A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data. mSystems 0:e00229-25.
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