Work

Wastewater surveillance using ddPCR accurately tracked Omicron emergence due to altered N1 probe binding efficiency

Year: 2022

Type: article

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. 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.

Source: Environmental Science Water Research & Technology

DOI: 10.1039/d2ew00194b

Authors: Melissa K. Schussman, Adélaïde Roguet, Angela Schmoldt, Brooke Dinan, Sandra L. McLellan

Institutions: University of Wisconsin–Milwaukee, University of Wisconsin–Madison

Language: English

Topic: SARS-CoV-2 detection and testing

Subfield: Infectious Diseases

Field: Medicine

Domain: Health Sciences

SDGs: Good health and well-being, Clean water and sanitation

Open Access status: green

Funders: Milwaukee Metropolitan Sewerage District, Wisconsin Department of Health Services, Centers for Disease Control and Prevention