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

Smruthi Karthikeyan(University of California San Diego), Joshua I. Levy(Scripps Research Institute), Peter De Hoff(California Department of Public Health), Greg Humphrey(University of California San Diego), Amanda Birmingham(University of California San Diego), Kristen Jepsen(University of California San Diego), Sawyer Farmer(University of California San Diego), Helena M. Tubb(University of California San Diego), Tommy Valles(University of California San Diego), Caitlin Tribelhorn(University of California San Diego), Rebecca Tsai(University of California San Diego), Stefan Aigner(University of California San Diego), Shashank Sathe(University of California San Diego), Niema Moshiri(University of California San Diego), Benjamin Henson(University of California San Diego), Adam M. Mark(University of California San Diego), Abbas Hakim(California Department of Public Health), Nathan A. Baer(University of California San Diego), Tom Barber(University of California San Diego), Pedro Belda‐Ferre(University of California San Diego), Marisol Chacón(University of California San Diego), Willi Cheung(California Department of Public Health), Evelyn S. Cresini(University of California San Diego), Emily Eisner(University of California San Diego), Alma L. Lastrella(University of California San Diego), Elijah S. Lawrence(University of California San Diego), Clarisse Marotz(University of California San Diego), Toan T. Ngo(University of California San Diego), Tyler Ostrander(University of California San Diego), Ashley Plascencia(University of California San Diego), Rodolfo A. Salido(University of California San Diego), Phoebe Seaver(University of California San Diego), Elizabeth W. Smoot(University of California San Diego), Daniel McDonald(University of California San Diego), Robert M. Neuhard(University of California San Diego), Angela L. Scioscia(University of California San Diego), Alysson M. Satterlund(University of California San Diego), Elizabeth H. Simmons(University of California San Diego), Dismas B. Abelman(University of California San Diego), David A. Brenner(University of California San Diego), Judith C. Bruner(University of California San Diego), Anne F. Buckley(University of California San Diego), M. Ellison(University of California San Diego), Jeffrey Gattas(University of California San Diego), Steven L. Gonias(University of California San Diego), Matt Hale(University of California San Diego), Faith Hawkins(University of California San Diego), Lydia Ikeda(University of California San Diego), Hemlata Jhaveri(University of California San Diego), Ted W. Johnson(University of California San Diego), Vince Kellen(University of California San Diego), Brendan Kremer(University of California San Diego), Gary Matthews(University of California San Diego), Ronald W. McLawhon(University of California San Diego), Pierre Ouillet(University of California San Diego), Daniel Park(University of California San Diego), Allorah Pradenas(University of California San Diego), Sharon L. Reed(University of California San Diego), Lindsay Riggs(University of California San Diego), Alison Sanders(University of California San Diego), Bradley Sollenberger(University of California San Diego), Angela Song(University of California San Diego), Benjamin L. White(University of California San Diego), Terri Winbush(University of California San Diego), Christine M. Aceves(Scripps Research Institute), Catelyn Anderson(Scripps Research Institute), Karthik Gangavarapu(Scripps Research Institute), Emory Hufbauer(Scripps Research Institute), Ezra Kurzban(Scripps Research Institute), Justin Lee(Scripps Research Institute), Nathaniel L. Matteson(Scripps Research Institute), Edyth Parker(Scripps Research Institute), Sarah A. Perkins(Scripps Research Institute), Karthik Ramesh(Scripps Research Institute), Refugio Robles‐Sikisaka(Scripps Research Institute), Madison Schwab(Scripps Research Institute), Emily Spencer(Scripps Research Institute), Shirlee Wohl(Scripps Research Institute), Laura Nicholson(Scripps Health), Ian McHardy(Scripps Health), David Dimmock(Children’s Institute), Charlotte A. Hobbs(Children’s Institute), Omid Bakhtar(Sharp HealthCare Foundation), Aaron Harding(Sharp HealthCare Foundation), Art Mendoza(Sharp HealthCare Foundation), Alexandre Bolze(Helix (United States)), David G. Becker(Helix (United States)), Elizabeth T. Cirulli(Helix (United States)), Magnus Isaksson(Helix (United States)), Kelly M. Schiabor Barrett(Helix (United States)), Nicole Washington(Helix (United States)), John D. Malone(Health and Human Services Agency), Ashleigh Murphy Schafer(Health and Human Services Agency), Nikos Gurfield(Health and Human Services Agency), Sarah Stous(Health and Human Services Agency), Rebecca Fielding‐Miller(University of California San Diego), Richard S. Garfein(University of California San Diego), Tommi Gaines(University of California San Diego), Cheryl A.M. Anderson(Scripps Research Institute), Natasha K. Martin(University of California San Diego), Robert T. Schooley(University of California San Diego), Brett Austin(Sharp HealthCare Foundation), Duncan MacCannell(Centers for Disease Control and Prevention), Stephen F. Kingsmore(Children’s Institute), William Lee(Helix (United States)), Seema Shah(Health and Human Services Agency), Eric McDonald(Health and Human Services Agency), Alexander T. Yu(California Department of Public Health), Mark Zeller(Scripps Research Institute), Kathleen M. Fisch(University of California San Diego), Chris Longhurst(University of California San Diego), Patty Maysent(UC San Diego Health System), David T. Pride(University of California San Diego), Pradeep K. Khosla(University of California San Diego), Louise C. Laurent(University of California San Diego), G Yeo(University of California San Diego), Kristian G. Andersen(Scripps Research Institute), Rob Knight(University of California San Diego)
Nature
July 7, 2022
10.1038/s41586-022-05049-6
Cited by 517Open Access
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Abstract

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.

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