Wastewater Surveillance Using ddPCR Reveals Highly Accurate Tracking of Omicron Variant Due to Altered N1 Probe Binding Efficiency

Wastewater Surveillance - State of the Science and Its Uses for Monitoring Public Health
Oral Presentation

Prepared by M. Schussman1, S. McLellan2, A. Schmoldt2, A. Roguet3, B. Dinan4
1 - Department of Civil and Envionmental Engineering, School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave, Milwaukee, WI, 53204, United States
2 - School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E Greenfield Ave, Milwaukee, WI, 53204, United States
3 - Wisconsin State Laboratory of Hygiene, 2601 Agriculture Dr, Madison, WI, 53718, United States
4 - School of Freshwater Sciences, University of Wisconsin-Milwaukee,, 600 E Greenfield Ave, Milwaukee, WI, 53204, United States


Contact Information: [email protected]; 414-303-9261

ABSTRACT

Wastewater surveillance for SARS-CoV-2 is being used worldwide to understand COVID-19 infection trends in a community. We found the emergence and rapid timeline for dominance of the Omicron variant was accurately reflected in wastewater when measured with droplet digital (dd)PCR. We were able to distinguish Omicron from the circulating Delta variant because Omicron has a mutation in the N1 probe binding region that diminished the fluorescent signal within individual droplets. The ddPCR platform may be advantageous for wastewater surveillance since analysis of the data can segregate fluorescent signals from different individual templates. In contrast, platforms such as qPCR that rely solely on the intensity of fluorescence for quantification would not distinguish a subset of variants with mutations affecting the reaction and could underestimate SARS-CoV-2 concentrations. Overall, the proportion of Omicron in wastewater was tightly correlated to clinical cases in five cities and provided a higher resolution timeline of appearance and dominance (>75%) than sequenced clinical samples, which were limited in less populated areas. Taken together, this work demonstrates wastewater is a reliable metric for tracking SARS-CoV-2 at a population level, however, PCR methods should be continually evaluated for any effects on quantification by emerging variants.