Pilot program for test-based SARS-CoV-2 screening and environmental monitoring in an urban public school district

Importance. Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in K-12 settings. Objectives. To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for K-12 in-person learning. Design, Setting, and Participants. The pilot program engaged three schools for weekly saliva PCR testing of staff and students participating in in-person learning over a 5-week period. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to determine surrogacy for case detection and interrogate transmission risk of in-building activities. Main Outcomes and Measures. SARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection. Results. 2,885 supervised self-collected saliva samples were tested from 773 asymptomatic staff and students during November and December, 2020. 46 cases (22 students, 24 staff) were detected, representing a 5.8- and 2.5-fold increase in case detection rates among students and staff, respectively, compared to conventional reporting mechanisms. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools, as well as in air samples collected from two choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with one school. Geographic analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools. Conclusions and Relevance. Weekly screening of asymptomatic staff and students by saliva PCR testing dramatically increased SARS-CoV-2 case detection in an urban public-school setting, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographic analyses suggest a dynamic interplay of school-based and community-derived transmission risk. Environmental testing for SARS-CoV-2 RNA in air and surface samples enabled real-time risk assessment of in-school activities and allowed for interventions in choir classes. Wastewater testing demonstrated the utility of school building-level SARS-CoV-2 surveillance. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the K-12 educational setting.