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

Autor: Karthikeyan, Smruthi, Levy, Joshua I, De Hoff, Peter, Humphrey, Greg, Birmingham, Amanda, Jepsen, Kristen, Farmer, Sawyer, Tubb, Helena M, Valles, Tommy, Tribelhorn, Caitlin E, Tsai, Rebecca, Aigner, Stefan, Sathe, Shashank, Moshiri, Niema, Henson, Benjamin, Mark, Adam M, Hakim, Abbas, Baer, Nathan A, Barber, Tom, Belda-Ferre, Pedro, Chacón, Marisol, Cheung, Willi, Cresini, Evelyn S, Eisner, Emily R, Lastrella, Alma L, Lawrence, Elijah S, Marotz, Clarisse A, Ngo, Toan T, Ostrander, Tyler, Plascencia, Ashley, Salido, Rodolfo A, Seaver, Phoebe, Smoot, Elizabeth W, McDonald, Daniel, Neuhard, Robert M, Scioscia, Angela L, Satterlund, Alysson M, Simmons, Elizabeth H, Abelman, Dismas B, Brenner, David, Bruner, Judith C, Buckley, Anne, Ellison, Michael, Gattas, Jeffrey, Gonias, Steven L, Hale, Matt, Hawkins, Faith, Ikeda, Lydia, Jhaveri, Hemlata, Johnson, Ted, Kellen, Vince, Kremer, Brendan, Matthews, Gary, McLawhon, Ronald W, Ouillet, Pierre, Park, Daniel, Pradenas, Allorah, Reed, Sharon, Riggs, Lindsay, Sanders, Alison, Sollenberger, Bradley, Song, Angela, White, Benjamin, Winbush, Terri, Aceves, Christine M, Anderson, Catelyn, Gangavarapu, Karthik, Hufbauer, Emory, Kurzban, Ezra, Lee, Justin, Matteson, Nathaniel L, Parker, Edyth, Perkins, Sarah A, Ramesh, Karthik S, Robles-Sikisaka, Refugio, Schwab, Madison A, Spencer, Emily, Wohl, Shirlee, Nicholson, Laura, McHardy, Ian H, Dimmock, David P, Hobbs, Charlotte A, Bakhtar, Omid, Harding, Aaron, Mendoza, Art, Bolze, Alexandre, Becker, David, Cirulli, Elizabeth T, Isaksson, Magnus, Schiabor Barrett, Kelly M, Washington, Nicole L, Malone, John D, Schafer, Ashleigh Murphy, Gurfield, Nikos, Stous, Sarah, Fielding-Miller, Rebecca, Garfein, Richard S, Gaines, Tommi, Anderson, Cheryl, Martin, Natasha K

Publikováno v: Nature, vol 609, iss 7925

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, particip

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::d390ec1dd94d3357040b0a0c8ff3ebca
https://escholarship.org/uc/item/56w9r0w8

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

Autor: Karthikeyan S; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Levy JI; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., De Hoff P; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., Humphrey G; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Birmingham A; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA., Jepsen K; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA., Farmer S; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Tubb HM; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Valles T; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Tribelhorn CE; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Tsai R; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Aigner S; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Sathe S; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Moshiri N; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Henson B; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA., Mark AM; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA., Hakim A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., Baer NA; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Barber T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Belda-Ferre P; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Chacón M; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Cheung W; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., Cresini ES; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Eisner ER; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Lastrella AL; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Lawrence ES; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Marotz CA; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Ngo TT; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Ostrander T; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Plascencia A; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Salido RA; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Seaver P; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Smoot EW; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., McDonald D; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Neuhard RM; Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.; Return to Learn, University of California San Diego, La Jolla, CA, USA., Scioscia AL; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.; Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA., Satterlund AM; Student Affairs, University of California San Diego, La Jolla, CA, USA., Simmons EH; Academic Affairs, University of California San Diego, La Jolla, CA, USA., Abelman DB; Return to Learn, University of California San Diego, La Jolla, CA, USA., Brenner D; Return to Learn, University of California San Diego, La Jolla, CA, USA., Bruner JC; Return to Learn, University of California San Diego, La Jolla, CA, USA., Buckley A; Return to Learn, University of California San Diego, La Jolla, CA, USA., Ellison M; Return to Learn, University of California San Diego, La Jolla, CA, USA., Gattas J; Return to Learn, University of California San Diego, La Jolla, CA, USA., Gonias SL; Department of Pathology, University of California San Diego, La Jolla, CA, USA., Hale M; Return to Learn, University of California San Diego, La Jolla, CA, USA., Hawkins F; Return to Learn, University of California San Diego, La Jolla, CA, USA., Ikeda L; Return to Learn, University of California San Diego, La Jolla, CA, USA., Jhaveri H; Return to Learn, University of California San Diego, La Jolla, CA, USA., Johnson T; Return to Learn, University of California San Diego, La Jolla, CA, USA., Kellen V; Return to Learn, University of California San Diego, La Jolla, CA, USA., Kremer B; Return to Learn, University of California San Diego, La Jolla, CA, USA., Matthews G; Return to Learn, University of California San Diego, La Jolla, CA, USA., McLawhon RW; Return to Learn, University of California San Diego, La Jolla, CA, USA., Ouillet P; Return to Learn, University of California San Diego, La Jolla, CA, USA., Park D; Return to Learn, University of California San Diego, La Jolla, CA, USA., Pradenas A; Return to Learn, University of California San Diego, La Jolla, CA, USA., Reed S; Return to Learn, University of California San Diego, La Jolla, CA, USA., Riggs L; Return to Learn, University of California San Diego, La Jolla, CA, USA., Sanders A; Return to Learn, University of California San Diego, La Jolla, CA, USA., Sollenberger B; Return to Learn, University of California San Diego, La Jolla, CA, USA., Song A; Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.; Return to Learn, University of California San Diego, La Jolla, CA, USA., White B; Return to Learn, University of California San Diego, La Jolla, CA, USA., Winbush T; Return to Learn, University of California San Diego, La Jolla, CA, USA., Aceves CM; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Anderson C; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Gangavarapu K; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Hufbauer E; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Kurzban E; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Lee J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Matteson NL; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Parker E; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Perkins SA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Ramesh KS; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Robles-Sikisaka R; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Schwab MA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Spencer E; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Wohl S; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Nicholson L; Scripps Health, San Diego, La Jolla, CA, USA., McHardy IH; Scripps Health, San Diego, La Jolla, CA, USA., Dimmock DP; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA., Hobbs CA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA., Bakhtar O; Sharp Healthcare, San Diego, CA, USA., Harding A; Sharp Healthcare, San Diego, CA, USA., Mendoza A; Sharp Healthcare, San Diego, CA, USA., Bolze A; Helix, San Mateo, CA, USA., Becker D; Helix, San Mateo, CA, USA., Cirulli ET; Helix, San Mateo, CA, USA., Isaksson M; Helix, San Mateo, CA, USA., Schiabor Barrett KM; Helix, San Mateo, CA, USA., Washington NL; Helix, San Mateo, CA, USA., Malone JD; County of San Diego Health and Human Services Agency, San Diego, CA, USA., Schafer AM; County of San Diego Health and Human Services Agency, San Diego, CA, USA., Gurfield N; County of San Diego Health and Human Services Agency, San Diego, CA, USA., Stous S; County of San Diego Health and Human Services Agency, San Diego, CA, USA., Fielding-Miller R; Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.; Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA., Garfein RS; Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA., Gaines T; Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA., Anderson C; Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA., Martin NK; Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA., Schooley R; Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA., Austin B; Sharp Healthcare, San Diego, CA, USA., MacCannell DR; Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA., Kingsmore SF; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA., Lee W; Helix, San Mateo, CA, USA., Shah S; County of San Diego Health and Human Services Agency, San Diego, CA, USA., McDonald E; County of San Diego Health and Human Services Agency, San Diego, CA, USA., Yu AT; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA., Zeller M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Fisch KM; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA., Longhurst C; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA., Maysent P; Office of the UC San Diego Health CEO, University of California San Diego, La Jolla, CA, USA., Pride D; Department of Pathology, University of California San Diego, La Jolla, CA, USA.; Department of Medicine, University of California San Diego, La Jolla, CA, USA., Khosla PK; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Laurent LC; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA., Yeo GW; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA., Andersen KG; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Knight R; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.

Publikováno v: Nature [Nature] 2022 Sep; Vol. 609 (7925), pp. 101-108. Date of Electronic Publication: 2022 Jul 07.