Regional Replacement of SARS-CoV-2 Variant Omicron BA.1 with BA.2 as Observed through Wastewater Surveillance

• Type of Material: Article
• Authors: Alexandria B Boehm, Stanford University; Bridgette Hughes, Verily Life Sciences; Marlene Wolfe, Emory University; Bradely J White, Verily Life Sciences; Dorothea Duong, Verily Life Sciences; Vikram Chan-Herur, Verily Life Sciences
• Language: English
• Date: 2022-06-14
• Publisher: AMER CHEMICAL SOC
• Publication Version: Final Published Version
• Copyright Statement: © 2022 The Authors. Published by American Chemical Society
• Final Published Version (URL): http://dx.doi.org/10.1021/acs.estlett.2c00266
• Title of Journal or Parent Work: ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
• Volume: 9
• Issue: 6
• Start Page: 575
• End Page: 580
• Grant/Funding Information: This work is supported by the CDC Foundation. Numerous people contributed to sample collection and case data acquisition, including Srividhya Ramamoorthy (Sac), Michael Cook (Sac), Ursula Bigler (Sac), James Noss (Sac), Lisa C. Thompson (Sac), Payak Sarkar (SJ), Noel Enoki (SJ), and Amy Wong (SJ), Lily Chan (Ocean), and the Oceanside plant operations personnel, Karin North (PA), Armando Guizar (PA), Saeid Vaziry (Gil), Chris Vasquez (Gil), Alo Kauravlla (Sun), Maria Gawat (SVCW), Tiffany Ishaya (SVCW), and Jeromy Miller (Dav).
• Keywords: SARS-CoV-2;   wastewater; Environmental Sciences; Life Sciences & Biomedicine; Technology; Engineering, Environmental; Engineering; Science & Technology; Omicron; Environmental Sciences & Ecology; wastewater-based epidemiology
• Research Categories: Environmental Sciences; Health Sciences, Public Health

Abstract

Greater knowledge of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro. We then applied these assays to daily wastewater solid samples from eight publicly owned treatment works in the greater Bay Area of California, United States, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data. This study highlights the utility of wastewater surveillance for real-time tracking of SARS-CoV-2 sublineage circulation. The results suggest that concerted efforts to design RT-PCR assays that target variant and variant sublineage characteristic mutations for wide-scale wastewater monitoring implementation will be informative for pandemic response.