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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

2022; Nature Portfolio; Volume: 609; Issue: 7925 Linguagem: Inglês

10.1038/s41586-022-05049-6

1476-4687

Smruthi Karthikeyan, Joshua I. Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham, Kristen Jepsen, Sawyer Farmer, Helena M. Tubb, Tommy Valles, Caitlin 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 Eisner, Alma L. Lastrella, Elijah S. Lawrence, Clarisse 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 A. Brenner, Judith C. Bruner, Anne F. Buckley, M. Ellison, Jeffrey Gattas, Steven L. Gonias, Matt Hale, Faith Hawkins, Lydia Ikeda, Hemlata Jhaveri, Ted W. Johnson, Vince Kellen, Brendan Kremer, Gary Matthews, Ronald W. McLawhon, Pierre Ouillet, Daniel Park, Allorah Pradenas, Sharon L. Reed, Lindsay Riggs, Alison Sanders, Bradley Sollenberger, Angela Song, Benjamin L. 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 Ramesh, Refugio Robles‐Sikisaka, Madison A. Schwab, Emily Spencer, Shirlee Wohl, Laura Nicholson, Ian McHardy, David Dimmock, Charlotte A. Hobbs, Omid Bakhtar, Aaron Harding, Art Mendoza, Alexandre Bolze, David G. 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 A.M. Anderson, Natasha K. Martin, Robert T. Schooley, Brett Austin, Duncan MacCannell, Stephen F. Kingsmore, William Lee, Seema Shah, Eric McDonald, Alexander T. Yu, Mark Zeller, Kathleen M. Fisch, Chris Longhurst, Patty Maysent, David T. Pride, Pradeep K. Khosla, Louise C. Laurent, G Yeo, Kristian G. Andersen, Rob Knight,

Biosensors and Analytical Detection

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 biases 1–3 . SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing 4,5 . 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.