Back to Search Start Over

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

Authors :
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
Rob Knight
Source :
Nature. 609:101-108
Publication Year :
2022
Publisher :
Springer Science and Business Media LLC, 2022.

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.

Details

ISSN :
14764687 and 00280836
Volume :
609
Database :
OpenAIRE
Journal :
Nature
Accession number :
edsair.doi.dedup.....bc578e5c58cb6a0cf1c43406a685a849