The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale

Rouchka, Eric Christian; Chariker, Julia H.; Saurabh, Kumar; Waigel, Sabine; Zacharias, Wolfgang; Zhang, Mei; Talley, Daymond; Santisteban, Ian; Puccio, Madeline; Moyer, Sarah; Holm, Rochelle; Yeager, Ray; Sokoloski, Kevin J; Fuqua, Joshua; Bhatnagar, Aruni; Smith, Ted; Rouchka, Eric C.; Holm, Rochelle H.; Yeager, Ray A.; Sokoloski, Kevin J.

Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest / concern through next-generation sequencing have enhanced the understanding of the SARS-CoV-2 outbreak. In this report we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Our data indicates that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored. Importantly, these efforts confirm that regional emergence and spread of variants of interest / concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds.