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Different methods for monitoring influenza A and SARS-CoV-2 in schools


In 43 of 154 school weeks, air samples were positive for influenza A virus (IAV) while SARS-CoV-2 was positive in air samples in 101 of 154 school weeks.

Different methods for monitoring influenza A and SARS-CoV-2 in schools | Image Credit: © Rawpixel.com - © Rawpixel.com - stock.adobe.com.

Different methods for monitoring influenza A and SARS-CoV-2 in schools | Image Credit: © Rawpixel.com - © Rawpixel.com - stock.adobe.com.


  • K-12 schools are considered excellent for respiratory virus surveillance, providing insights into SARS-CoV-2 and influenza A virus (IAV) activity.
  • Four parallel approaches were used in a Wisconsin school district to monitor IAV and SARS-CoV-2 during the 2022 Fall semester.
  • Surveillance tools included home-based specimen collection, cause-specific absenteeism monitoring, school-based rapid antigen testing, and air sampling.
  • Air sampling in communal spaces provided equivalent results to other methods and revealed different patterns between IAV and SARS-CoV-2.

Given their respective roles in respiratory virus amplification, kindergarten through 12th grade schools were “excellent” venues for virus surveillance, and to test multiple methods, according to a study published in JAMA Network Open.

When community-based SARS-CoV-2 testing programs faded, different options to monitor virus activity emerged, including rapid antigen testing (RAT), wastewater monitoring, screening with dogs, and pooled specimen testing by reverse transcription-polymerase chain reaction (RT-PCR).

According to investigators, 4 parallel approaches were used to simultaneously monitor influenza A virus (IAV) and SARS-CoV-2 activity in a Wisconsin school district amid the 2022 Fall semester, briefly after winter break.

The cross-sectional Oregon Child Absenteeism Due to Respiratory Disease Study (ORCHARDS) used home-based specimen collection using RT-PCR, cause-specific absenteeism monitoring, school-based RAT, and air sampling approaches to monitor virus activity in Oregon (Wisconsin) School District (OSD) schools and compared the weekly results of each program.

Specimens were collected with parental permission from students with acute respiratory infection and tested for IAV, SARS-CoV-2, and other viruses using RT-PCR.

As a component of ORCHARDS, daily counts of cause-specific absenteeism due to influenza-like illness (a-ILI) or COVID-19 (a-CoV) were collected from OSD. All 7 OSD schools featured air samplers in communal gathering spaces, with cartridges analyzed twice weekly.

Statistical analysis was performed from September 1, 2022, through January 28, 2023. Two-sided P < .05 was considered statistically significant.

During the statistical analysis period, 334 K-12 children participated in ORCHARDS. In this time period, 114 (34.1%) IAV detections and 32 (9.6%) SARS-CoV-2 RT-PCR detections were observed. There were 1425 a-ILI days and 883 a-CoV days recorded by student absenteeism monitoring.

In 43 of 154 school weeks, air samples tested positive for IAV while SARS-CoV-2 was present in air samples in 101 of 154 school weeks.

In all 4 surveillance platforms from December 11 to December 24, 2022, influenza activity exhibited a peak before dropping after winter break. In at least 2 schools each week during the study period, SARS-CoV-2 was detected by air surveillance.

According to the study, SARS-CoV-2 was detected continuously (moderate to low levels) in each ORCHARDS-based RT-PCR and school-based RAT. Cross-correlations among the platforms were significant, “and without lags for IAV,” the study authors wrote.

Over a 22-week period, 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,” the study authors stated.

Results revealed different patterns between IAV and SARS-CoV-2, as IAV demonstrated a substantial increase in November and December while SARS-CoV-2 detections were stable.

The authors concluded that the use of complementary surveillance tools in K-12 schools could enhance detection of respiratory virus outbreaks.


Temte J, Goss M, Barlow S, et al. Four methods for monitoring SARS-CoV-2 and influenza A virus activity in schools. JAMA Netw Open. 2023;6(12):e2346329. doi:10.1001/jamanetworkopen.2023.46329

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