Water and surface surveillance can detect 93% of COVID-19 cases in schools

New study published on medRxiv* The prepress server examines the environmental monitoring of primary schools for severe acute respiratory syndrome, coronavirus 2 (SARS-CoV-2) by monitoring wastewater and surface samples. The researchers showed that 93% of COVID-19 cases in public primary schools could be identified using this method.

Study: Monitoring of wastewater and surfaces to detect COVID-19 in primary schools: The Safer School Early Warning Project.  Image credit: Maxbelchenko / Shutterstock


The coronavirus disease pandemic 2019 (COVID-19), caused by SARS-CoV-2, has closed institutions, jobs and businesses worldwide, in stages or in full, depending on government policy and direction. Based on mitigation and vaccination strategies for adults, the safe reopening of sites is determined by the spread of the disease in the country and the number of cases of infection.

The reopening of schools and their maintenance during the COVID-19 pandemic is a public health challenge. Schools need to be reopened for personal learning, which is essential for the social, physical and emotional well-being of children. Schools also allow the participation of the parent workforce by providing basic care for children. Job losses leading to poverty due to school closures can also be avoided.

However, unvaccinated children are at high risk of being exposed to SARS-CoV-2 at school because they spend long periods with each other in close proximity, usually indoors. As a result, functioning schools are becoming a potentially high-risk environment for virus transmission.

In addition to masking, improved ventilation, and symptom screening, strategies are needed to quickly identify cases of COVID-19 in low-vaccination and test communities to achieve health equity, reduce morbidity and mortality, and prevent the emergence of new options for concern.

Recently, the monitoring of wastewater by genome sequencing has attracted attention as a tool for passive monitoring of SARS-CoV-2 infections at the community level. In a previous report, large-scale wastewater monitoring allowed a significant residential university to identify cases in specific campus buildings and housing. This information has helped increase the acceptance of diagnostic tests among residents.

Similarly, this passive nature of wastewater sampling is promising for school monitoring of COVID-19 in communities where students, parents and staff work – who may face structural barriers to vaccination and diagnostic testing.

To monitor and detect cases of COVID-19 in environments such as primary schools and kindergartens, the present study uses wastewater and daily surface samples in a Safer School Early Warning Project (SASEA).

SASEA consists of four main components:

  1. Daily environmental sampling for SARS-CoV-2, using site-wide wastewater and surface swabs (usually in the center of the classroom floor) from individual classrooms;
  2. Notification of the results – quick reporting of the results to the administrators by e-mail (approximately 30 hours after taking the sample);
  3. Responsive testing: on-site diagnostic testing of students and staff upon detection of SARS-CoV-2 in wastewater or surface samples; and
  4. Reduce risk by changing the environment (eg relocating outdoor classrooms, increasing ventilation in classrooms with a potential case) and health communication (eg promoting double masking, recommending wider testing among household members).

The researchers undertook surface sampling and recovered traces of viral RNA in rooms occupied by infected individuals in hospital settings, suggesting that surface sampling may provide an additional approach to viral wastewater monitoring.

About the Study

The SASEA project was piloted in nine public elementary schools in San Diego County in the 2020-2021 school year. Researchers conducted daily monitoring of wastewater at each location and collected surface samples for testing from each classroom where children were present. In addition, to validate the environmental monitoring system, they also provided weekly diagnostic tests for all consenting students and staff on campus and used the results to correlate with data from wastewater or surface samples.

To collect the wastewater samples, the researchers used automatic samplers located above the ground when cleaning sewers and shafts. They were programmed to take samples every 10-15 minutes at seven-hour intervals.

During the 12-week study period, the researchers collected data on approximately 50 school days per site and detected SARS-CoV-2 in surface samples and wastewater samples. According to on-campus test results, the researchers reported that of the 89 SARS-CoV-2 positive cases identified on campus, 83 (93%) were associated with positive wastewater or a surface sample from the same room during the 7-day period. a window preceding the last day of the person on campus. The majority of them, 76%, are related to a positive wastewater sample.

Similarly, in a classroom, 40% of the cases correspond to a positive surface sample in the connected room. While 67% of cases are related only to a positive sample of wastewater.

The researchers observed that the absorption of tests in SASEA partner schools is higher than in nearby areas.

Importantly, in addition to tracking the spread of the virus in a community, sequencing the viral genome of positive wastewater samples can elucidate the geospatial distributions of the strain – thus identifying outbreak clusters and tracking predominant / emerging variants.

Sampling of wastewater and surfaces and 95% confidence interval throughout the 12-week pilot period and with consent at 70% or more (weeks 9-12)

Sampling of wastewater and surfaces and 95% confidence interval throughout the 12-week pilot period and with consent at 70% or more (weeks 9-12)

Sequencing of positive environmental samples gave results that confirmed the presence of variant Alpha (B.1.1.7) and variant Epsilon, which were also confirmed in diagnostic testing (nasal swabs).

One SARS-CoV-2 genome sequenced from a carpet floor surface was linked to a genome from a sample for clinical testing of SASEA by grouping in a phylogenetic tree. Researchers suggest that surface sampling provides a higher spatial resolution than wastewater sampling alone.

Limitations of passive monitoring of wastewater in school conditions

In non-residential environments, two significant concerns about the potential effectiveness of wastewater sampling are that 1) not all individuals have daily bowel movements in place to expel the virus, and 2) spatial resolution is limited to entire buildings or clusters of buildings as places to access the sewer.


The results of this study suggest that monitoring the environment by sampling wastewater and surfaces can be an effective passive screening tool that complements and potentially improves individual testing approaches.

Ninety-three percent of COVID-19 cases on campus in public elementary schools are related to either wastewater or a surface sample.

In addition, the study showed that 67% were associated with a positive wastewater sample and 40% were associated with a positive surface sample.

In particular, positive samples can be sequenced to observe variants of neighborhood-level concerns.

Researchers write that even in the absence of a diagnosed case, positive environmental samples serve as a behavioral signal to increase or re-apply risk reduction measures in the classroom or throughout the school.

*Important message

medRxiv publishes preliminary scientific reports that are not reviewed by partners and therefore should not be considered convincing, guiding clinical practice / health-related behavior, or treated as established information.

Reference journal:

  • Wastewater and Surface Surveillance Monitoring for COVID-19 in Primary Schools: The Safer School Early Warning Project, Rebecca Fielding-Miller, Smurty Cartikean, Tommy Gaines, Richard C. Garfein, Rodolfo Salido, Victor Cantou, Laura Conn , Natasha K Martin, Carissa Uijaya, Marlene Flores, Vinton Omaleki, Araz Majnunian, Patricia Gonzalez-Zuniga, Megan Nguyen, An Vi Vo, Tina Le, Dawn Duong, Ashkan Hasani, Austin Dahl, Samantha Twain, Kristen Jean Amanda Birmingham, Adam M. Mark, Chanond A Nasamran, Sarah Brin Rosenthal, Niema Moshiri, Kathleen M. Fish, Greg Humphrey, Sawyer Farmer, Helena M. Tub, Tommy Wales, Justin Morris, Jayong Kang, Benam Kalegi, Colin Young, Amin D Akel, Sean Eilert, Justin Eno, Ken Curewitz, Louise C Laurent, Tajana Rosing, SEARCH, Rob Knight, medRxiv 2021.10.19.21265226; doi: https://doi.org/10.1101/2021.10.19.21265226, https://www.medrxiv.org/content/10.1101/2021.10.19.21265226v1

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