Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples

• Type of Material: Article
• Authors: Marlene Wolfe, Emory University; Bridgette Hughes, Verily Life Sciences; Dorothea Duong, Verily Life Sciences; Vikram Chan-Herur, Verily Life Sciences; Krista R Wigginton, University of Michigan; Bradley J White, University of Michigan; Alexandria B Boehm, Stanford University
• Language: English
• Date: 2022-04-05
• Publisher: AMER SOC MICROBIOLOGY
• Publication Version: Final Published Version
• Copyright Statement: © 2022 Wolfe et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1128/aem.00045-22
• Title of Journal or Parent Work: APPLIED AND ENVIRONMENTAL MICROBIOLOGY
• Volume: 88
• Issue: 8
• Start Page: e0004522
• End Page: e0004522
• Grant/Funding Information: This work was funded by a gift from the CDC Foundation.
• Keywords: epidemiology; Omicron; Delta; COVID-19; Microbiology; wastewater; Biotechnology & Applied Microbiology; SARS-CoV-2; Life Sciences & Biomedicine; Science & Technology
• Research Categories: Engineering, Environmental; Engineering, Civil

Abstract

Changes in the circulation of SARS-CoV-2 variants of concern (VOCs) may require changes in the public health response to the COVID-19 pandemic, as they have the potential to evade vaccines and pharmaceutical interventions and may be more transmissive than other SARS-CoV-2 variants. As such, it is essential to track and prevent their spread in susceptible communities. We developed digital reverse transcription (RT)- PCR assays for mutations characteristic of VOCs and used them to quantify those mutations in samples of wastewater settled solids collected from a publicly owned treatment works (POTW) during different phases of the COVID-19 pandemic. Wastewater concentrations of single mutations characteristic of each VOC, normalized by the concentration of a conserved SARS-CoV-2 N gene, correlate with regional estimates of the proportion of clinical infections caused by each VOC. These results suggest that targeted RT-PCR assays can be used to detect variants circulating in communities and inform the public health response to the pandemic.