Wastewater samples from ARA Werdhölzli were analyzed for the presence of SARS-CoV-2 RNA from December 2020 through March 2021 using digital PCR. The digital PCR assay was a drop-off assay using primers and probes covering the spike deletion 69-70 and the ORF1a deletion 3675-5677. The drop-off assay allows quantitative estimates of the proportion of the total SARS-CoV-2 RNA in the wastewater that contains the target deletion regions. The data was collected, analyzed, and reported within the following manuscript: Caduff L, Dreifuss D, Schindler T, Devaux AJ, Ganesanandamoorthy P, Kull A, Stachler E, Fernandez-Cassi X, Beerenwinkel N, Kohn T, Ort C, Julian TR. Inferring transmission fitness advantage of SARS-CoV-2 variants of concern in wastewater using digital PCR. In Preparation.