Four Methods for Monitoring SARS-CoV-2 and Influenza A Virus Activity in Schools

This cross-sectional study describes 4 parallel approaches used simultaneously to monitor influenza A virus and SARS-CoV-2 activity within a Wisconsin school district during the Fall 2022 semester and briefly following winter break.


Introduction
As community-based SARS-CoV-2 testing programs waned, alternatives for monitoring virus activity emerged.Kindergarten through 12th grade (K-12) schools provided excellent venues for surveillance given their role in respiratory virus amplification. 1 Methods recently evaluated in school settings include rapid antigen testing (RAT), pooled specimen testing by reverse transcription-polymerase chain reaction (RT-PCR), wastewater monitoring, 2 and screening with dogs. 3 In this study we describe 4 parallel approaches (home-based specimen collection using RT-PCR, cause-specific absenteeism monitoring, school-based RAT, and air sampling) used simultaneously to monitor influenza A virus (IAV) and SARS-CoV-2 activity within a south-central Wisconsin school district during the Fall 2022 semester and briefly following winter break.

Methods
The Oregon School District (OSD) serves 4114 K-12 students.We examined the concordance of 4 independent surveillance methods for IAV and SARS-CoV-2 in OSD schools, comparing the weekly results of each program in this cross-sectional study.See eMethods in Supplement 1 for detailed information.This study was approved by the University of Wisconsin Health Sciences institutional review board.ORCHARDS participants provided written informed consent; the other systems were exempted from informed consent by the institutional review board due to anonymity of composite data.We followed the STROBE reporting guideline.
The Oregon Child Absenteeism Due to Respiratory Disease Study (ORCHARDS) is a schoolbased respiratory virus surveillance study initiated in 2015; the methods have been described elsewhere. 1Specimens, collected with parental permission from students with acute respiratory infection, were tested for IAV, SARS-CoV-2, and other respiratory viruses using RT-PCR.Daily counts of cause-specific student absenteeism due to influenza-like illness (a-ILI) or COVID-19 (a-CoV) were collected from OSD as a component of ORCHARDS. 1 Research staff provided training and Sofia 2 Flu+SARS Antigen Fluorescent Immunoassay RAT supplies (Quidel) to OSD health offices in August of 2021; rapid testing of students and staff has been ongoing during the academic year since that time.
Air samplers (ThermoFisher AerosolSense) were placed in communal gathering spaces (eg, cafeterias) in all 7 OSD schools, and cartridges were analyzed twice weekly for the presence of IAV and SARS-CoV-2 using a workflow as previously described. 4IAV and SARS-CoV-2 genetic material captured in air samples were detected using previously developed quantitative RT-PCR assays targeting the IAV M gene, 5 SARS-CoV-2 N1 and N2, and RNaseP as an internal control. 6Two-sided

Discussion
Air sampling provided equivalent results to 3 parallel methods for SARS-CoV-2 and IAV monitoring using study participant sampling with RT-PCR, cause-specific absenteeism, and school-based rapid antigen detection over a 22-week period.Differing patterns between these 2 viruses emerged.While SARS-CoV-2 detections were stable (endemic), IAV demonstrated a substantial (epidemic) increase throughout November and December, receding after winter break.These contrasting activity patterns were reflected in each surveillance platform, except for RAT postwinter break, which did not detect SARS-CoV-2 activity.This study was limited by evaluating a single school district for only 22 weeks.Use of complementary surveillance tools in K-12 schools, including air sampling, may enhance detection of respiratory virus outbreaks.

Figure
Figure.Comparisons of In-School Disease Surveillance Methods