The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale
Eric C. Rouchka,
Julia H. Chariker,
Kumar Saurabh,
Sabine Waigel,
Wolfgang Zacharias,
Mei Zhang,
Daymond Talley,
Ian Santisteban,
Madeline Puccio,
Sarah Moyer,
Rochelle H. Holm,
Ray A. Yeager,
Kevin J. Sokoloski,
Joshua Fuqua,
Aruni Bhatnagar,
Ted Smith
Affiliations
Eric C. Rouchka
Department of Biochemistry and Molecular Genetics, University of Louisville, 323 E. Chestnut St., Louisville, KY 40202, USA
Julia H. Chariker
KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY 40202, USA
Kumar Saurabh
Brown Cancer Center, University of Louisville, 530 S. Jackson St., Louisville, KY 40202, USA
Sabine Waigel
Department of Medicine, University of Louisville, 530 S. Jackson St., Louisville, KY 40402, USA
Wolfgang Zacharias
Department of Medicine, University of Louisville, 530 S. Jackson St., Louisville, KY 40402, USA
Mei Zhang
Department of Neuroscience, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
Daymond Talley
Louisville/Jefferson County Metropolitan Sewer District, Morris Forman Water Quality Treatment Center, 4522 Algonquin Parkway, Louisville, KY 40211, USA
Ian Santisteban
Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
Madeline Puccio
Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
Sarah Moyer
Department of Health Management and System Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, USA
Rochelle H. Holm
Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
Ray A. Yeager
Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
Kevin J. Sokoloski
Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
Joshua Fuqua
Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
Aruni Bhatnagar
Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
Ted Smith
Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
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 has 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. Through the use of next-generation sequencing approaches the polymorphism signatures of Variants of Concern/Interest were evaluated to determine the likelihood of their prevalence within the community on the basis of their relative dominance within sequence datasets. Our data indicate 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, as our efforts detected the introduction and emergence of variants of concern in the city of Louisville. 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. Furthermore, the information gained from these efforts enabled targeted public health efforts including increased outreach to at-risk communities and the deployment of mobile or community-focused vaccination campaigns.
