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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.
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.
  • 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.
  • Humphrey G; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Birmingham A; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA.
  • Jepsen K; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Farmer S; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA.
  • Tubb HM; Institute for Genomic Medicine, 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; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Sathe S; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Moshiri N; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Henson B; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Mark AM; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
  • Hakim A; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
  • Baer NA; Center for Computational Biology and Bioinformatics, 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; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Chacón M; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA.
  • Cheung W; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, 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; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Ngo TT; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, 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; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Neuhard RM; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Scioscia AL; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Satterlund AM; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Simmons EH; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Abelman DB; Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Brenner D; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
  • Bruner JC; Operational Strategic Initiatives, 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; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
  • Gattas J; Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA.
  • Gonias SL; Student Affairs, University of California San Diego, La Jolla, CA, USA.
  • Hale M; Academic Affairs, 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.
Nature ; 609(7925): 101-108, 2022 09.
Article in English | MEDLINE | ID: covidwho-1921636
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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Waste Water / Wastewater-Based Epidemiological Monitoring / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Nature Year: 2022 Document Type: Article Affiliation country: S41586-022-05049-6

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Waste Water / Wastewater-Based Epidemiological Monitoring / SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Nature Year: 2022 Document Type: Article Affiliation country: S41586-022-05049-6