1. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
- Author
-
Smruthi Karthikeyan, Joshua I. Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham, Kristen Jepsen, Sawyer Farmer, Helena M. Tubb, Tommy Valles, Caitlin E. Tribelhorn, Rebecca Tsai, Stefan Aigner, Shashank Sathe, Niema Moshiri, Benjamin Henson, Adam M. Mark, Abbas Hakim, Nathan A. Baer, Tom Barber, Pedro Belda-Ferre, Marisol Chacón, Willi Cheung, Evelyn S. Cresini, Emily R. Eisner, Alma L. Lastrella, Elijah S. Lawrence, Clarisse A. Marotz, Toan T. Ngo, Tyler Ostrander, Ashley Plascencia, Rodolfo A. Salido, Phoebe Seaver, Elizabeth W. Smoot, Daniel McDonald, Robert M. Neuhard, Angela L. Scioscia, Alysson M. Satterlund, Elizabeth H. Simmons, Dismas B. Abelman, David Brenner, Judith C. Bruner, Anne Buckley, Michael Ellison, Jeffrey Gattas, Steven L. Gonias, Matt Hale, Faith Hawkins, Lydia Ikeda, Hemlata Jhaveri, Ted Johnson, Vince Kellen, Brendan Kremer, Gary Matthews, Ronald W. McLawhon, Pierre Ouillet, Daniel Park, Allorah Pradenas, Sharon Reed, Lindsay Riggs, Alison Sanders, Bradley Sollenberger, Angela Song, Benjamin White, Terri Winbush, Christine M. Aceves, Catelyn Anderson, Karthik Gangavarapu, Emory Hufbauer, Ezra Kurzban, Justin Lee, Nathaniel L. Matteson, Edyth Parker, Sarah A. Perkins, Karthik S. Ramesh, Refugio Robles-Sikisaka, Madison A. Schwab, Emily Spencer, Shirlee Wohl, Laura Nicholson, Ian H. McHardy, David P. Dimmock, Charlotte A. Hobbs, Omid Bakhtar, Aaron Harding, Art Mendoza, Alexandre Bolze, David Becker, Elizabeth T. Cirulli, Magnus Isaksson, Kelly M. Schiabor Barrett, Nicole L. Washington, John D. Malone, Ashleigh Murphy Schafer, Nikos Gurfield, Sarah Stous, Rebecca Fielding-Miller, Richard S. Garfein, Tommi Gaines, Cheryl Anderson, Natasha K. Martin, Robert Schooley, Brett Austin, Duncan R. MacCannell, Stephen F. Kingsmore, William Lee, Seema Shah, Eric McDonald, Alexander T. Yu, Mark Zeller, Kathleen M. Fisch, Christopher Longhurst, Patty Maysent, David Pride, Pradeep K. Khosla, Louise C. Laurent, Gene W. Yeo, Kristian G. Andersen, and Rob Knight
- Subjects
Wastewater-Based Epidemiological Monitoring ,Multidisciplinary ,SARS-CoV-2 ,Sequence Analysis, RNA ,COVID-19 ,Humans ,RNA, Viral ,Wastewater - Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
- Published
- 2022