Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools

Creators: Fielding-Miller, Rebecca; Karthikeyan, Smruthi; Gaines, Tommi; Garfein, Richard S.; Salido, Rodolfo A.; Kohn, Laura; Wynn, Adriane; Wijaya, Carrissa; Nguyen, Megan; Vo, Anh V.; Le, Tina; Tweeten, Samantha; Nasamran, Chanond A.; Moshiri, Niema; Fisch, Kathleen M.; Humphrey, Greg; Valles, Tommy; Morris, Justin; Kang, Jaeyoung; Khaleghi, Behnam; Young, Colin; Akel, Ameen D.; Eilert, Sean; Eno, Justin; Curewitz, Ken; Laurent, Louise C.; Rosing, Tajana; Knight, Rob; Baer, Nathan A.; Barber, Tom; Chacón, Marisol; Cheung, Willi; Crescini, Evelyn S.; Eisner, Emily R.; Franco Vargas, Lizbeth; Hakim, Abbas; Lastrella, Alma L.; Lawrence, Elijah S.; Matteson, Nathaniel L.; Gangavarapu, Karthik; Ngo, Toan T.; Seaver, Phoebe; Smoot, Elizabeth W.; Tsai, Rebecca; Xia, Bing; Aigner, Stefan; Sathe, Shashank; Andersen, Kristian G.; Kurzban, Ezra

Others:: Baer, Nathan A.; Barber, Tom; Castro-Martinez, Anelizze; Chacón, Marisol; Cheung, Willi; Crescini, Evelyn; Eisner, Emily R.; Franco, Vargas; Hakim, Abbas; Hobbs, Charlotte; Lastrella, Alma L.; Lawrence, Elijah S.; Matteson, Nathaniel L.; Gangavarapu, Karthik; Ngo, Toan T.; Seaver, Phoebe; Smoot, Elizabeth W.; Tsai, Rebecca; Xia, Bing; Aigner, Stefan; Anderson, Catelyn; Belda-Ferre, Pedro; Sathe, Shashank; Zeller, Mark; Andersen, Kristian; Yeo, Gene W.; Kurzban, Ezra

Abstract

Background. Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods. The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. Findings. In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%–98%); 67% were associated with a positive wastewater sample (95% CI: 57%–77%), and 40% were associated with a positive surface sample (95% CI: 29%–52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation. Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy.

Additional Information

Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). We are deeply grateful to the leadership, staff, students, and families at our partner school districts and school sites across San Diego County. This project would not have been possible without their enthusiasm and generosity. We thank our colleagues at the County of San Diego, Health and Human Services Agency for their vision and support, particularly John Malone, Sarah Stous, and Rorick Luepton. At UCSD, Isabella Cuturrofo, Jeanessa Mendoza, Kristine Ngo, Jessica Ni, and Elizabeth Frost all provided vital support with project implementation. Austin Dahl provided extensive support with data management and visualization. RFM thanks Ms. Esther J. Krohne for inspiring the project. The opinions and assertions expressed herein are those of the authors and do not necessarily reflect the official policy or position of the County of San Diego Health and Human Services Agency. Funding: County of San Diego, Health and Human Services Agency (R.F.-M.). National Institutes of Health Grant K01MH112436 (R.F.-M.). National Institute of Health Grant UL1TR001442. National Institute of Health Grant S10OD026929 (Jepsen). NSF Grants Numbers 1730518, 1826967, 1659104, 2100237, 2112167, 2052809, 2028040 (Rosing). Centers for Disease Control BAA Contract 75D30120C09795 (Andersen). This work was supported in part by CRISP, one of six centers in JUMP, an SRC program sponsored by DARPA (Rosing). Contributors. All authors have read the final version of the manuscript and meet the International Committee for Medical Journal Ethics (ICMJE) criteria for authorship. Dr. Fielding-Miller takes full responsibility for the study. Specific contributions are listed below according to the CRediT roles taxonomy. R.F.-M.: Conceptualization; Methodology; Formal Analysis; Investigation; Writing - original draft; Visualization; Supervision; Funding Acquisition. S.K.: Methodology; Formal Analysis; Investigation; Data curation; Writing - original draft; Visualization. T.G.: Methodology; Formal Analysis; Writing - original draft. R.S.G.: Methodology; Data curation; Writing - original draft; Visualization; Supervision. R.A.S.: Methodology; Formal Analysis; Investigation; Writing - original draft. V.J.C.: Methodology; Formal Analysis; Investigation; Data curation; Writing - original draft. L.K.: Conceptualization; Methodology; Investigation; Data curation; Writing - original draft; Supervision; Project administration; Funding Acquisition. N.K.M.: Methodology; Writing - original draft. A.W.: Methodology; Data curation; Formal Analysis; Writing – revised draft. C.W.: Supervision; Project administration. M.F.: Investigation; Data curation. V.O.: Investigation; Data curation. A.M.: Investigation; Data curation. P.G.-Z.: Investigation; Supervision. M.N.: Investigation; Data curation. A.V.V.: Investigation; Data curation; Visualization. T.L.: Investigation. D.D.: Investigation. A.H.: Investigation. S.T.: Resources; Supervision; Project administration. K.J.: Methodology; Investigation; Resources. B.H.: Methodology; Investigation. A.H.: Methodology; Investigation. A.B.: Methodology; Investigation. A.M.M.: Methodology; Investigation. C.A.N.: Methodology; Investigation. S.B.R.: Methodology; Investigation. N.M.: Methodology; Investigation. K.M.F.: Methodology; Investigation. G.H.: Investigation; Data curation. S.F.: Investigation; Data curation. H.M.T.: Investigation; Data curation. T.V.: Investigation; Data curation. J.M.: Investigation; Data curation. J.K.: Investigation; Data curation. B.K.: Investigation; Data curation. C.Y.: Investigation; Data curation. A.D.A.: Investigation; Data curation. S.E.: Investigation; Data curation. J.E.: Investigation; Data curation. K.C.: Investigation; Data curation. L.C.L.: Resources. T.R.: Investigation; Data curation. R.K.: Conceptualization; Methodology; Resources; Writing - original draft; Supervision. Data sharing statement. School level environmental, diagnostic, and consent data have been archived in the Dataverse repository and are available at https://doi.org/10.7910/DVN/HD62J4. All wastewater and nasal-swab sequencing data have been deposited to GISAID and their accession details provided in Supplemental File Data S1.

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