Performance and characteristics of three digital PCR platforms for detection and quantification of viral targets in wastewater

Aims The wider implementation of wastewater-based surveillance (WBS) has increased the necessity for nucleic acid detection and quantification from complex samples. Here, we compared the performance and the characteristics of three digital PCR (dPCR) platforms. Methods and Results The dPCR platforms selected in this study included the QX200 AutoDG Droplet Digital PCR System from Bio-Rad, the QIAcuity One, 2plex Device from Qiagen, and the 3-color Naica System manufactured by Stilla Technologies. Platforms were compared and described based on their handling in the laboratory and performance quantifying two viral targets – SARS-CoV-2 and Norovirus GII – in wastewater samples. Our findings showed that no single platform consistently outperformed the others in terms of target quantification. Moreover, we observed similarities amongst the systems with respect to resilience to inhibition, but differences in laboratory handling including sample throughput and method of quantification. Conclusions This study suggests that all three selected dPCR platforms are similarly suitable for WBS, as quantitative performance of the systems for viral RNA targets extracted from wastewater is comparable. Decisions on platform selection can be driven by researcher preference on handling, throughput, and other differentiating characteristics.