Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project
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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 – 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.
Funding
County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control
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SciScore for 10.1101/2021.10.19.21265226: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: All wastewater and nasal-swab sequencing data have been deposited to GISAID and their accession details provided in Supplemental File Data S1 Methods Data S1: Wastewater and nasal-swab sequencing data GISAID accession details Human Subjects and IRB: All study procedures were reviewed and approved by the University of California, San Diego Institutional Review Board (IRB), which determined the human subjects portion of the study to be minimal risk and therefore exempt from oversight (protocol 201627).
Consent: All participants provided informed consent (if 18 or above) or assent plus parental consent (if under the age of 18).Sex as a biological variable Among students, 37.6% were female, … SciScore for 10.1101/2021.10.19.21265226: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: All wastewater and nasal-swab sequencing data have been deposited to GISAID and their accession details provided in Supplemental File Data S1 Methods Data S1: Wastewater and nasal-swab sequencing data GISAID accession details Human Subjects and IRB: All study procedures were reviewed and approved by the University of California, San Diego Institutional Review Board (IRB), which determined the human subjects portion of the study to be minimal risk and therefore exempt from oversight (protocol 201627).
Consent: All participants provided informed consent (if 18 or above) or assent plus parental consent (if under the age of 18).Sex as a biological variable Among students, 37.6% were female, 39.8% were male, and 22.6% of parents declined to provide information related to gender. Randomization We computed 95% confidence intervals for the retrospective and prospective outcomes by randomly sampling 10,000 times from independent normal distributions for the two proportions. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Analysis was limited to sites that participated in the SASEA program throughout the validation phase and whose diagnostic test could be linked back to a classroom (for assessing concordance between diagnostic test and surface samples). SASEAsuggested: NoneAll analysis were conducted in STATA version 16 (STATA Corp, College Station, Texas). STATAsuggested: (Stata, RRID:SCR_012763)Consensus sequences are then called with iVar consensus(1), and a multiple sequence alignment is inferred using ViralMSA(7) wrapping around Minimap2(4). iVarsuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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