Clinical Testing for COVID-19, Influenza, and RSV in Hospitalized Youths, 2016-2024

Studies of COVID-19, influenza, and respiratory syncytial virus (RSV) disease clinical epidemiology, disease burden, and vaccine effectiveness often rely on clinical testing to identify cases, particularly with increasing use of electronic health record data. However, few data are available describing clinical testing practices to inform interpretation of these studies. To characterize clinical testing frequency for SARS-CoV-2, influenza, and RSV among children and adolescents hospitalized with acute respiratory illness during the 2016 to 2024 respiratory illness seasons by age, intensive care unit admission, and time period (2016-2020 and each season in 2020-2024); estimate the case fraction missed by clinical testing alone; and identify patient characteristics associated with clinical testing. This cross-sectional study analyzed data collected through prospective surveillance with systematic molecular testing (surveillance testing) for SARS-CoV-2, influenza viruses, and RSV among children and adolescents younger than 18 years hospitalized with acute respiratory illness at 6 US medical centers during the winter respiratory illness seasons of 2016 to 2024. In-hospital clinical molecular testing data were abstracted from the medical record. The proportion of children and adolescents with clinical molecular testing for SARS-CoV-2, influenza viruses, and RSV. During 2016 to 2024, a total of 26 073 hospitalized youths were enrolled (14 459 aged <2 years 55.5%; 14 833 male 56.9%), including 12 090 youths during 2016 to 2020 combined. Overall, 10 450 youths (40.1%) had an underlying medical condition. The proportion of youths with clinical testing decreased for SARS-CoV-2 from 3965 of 4388 youths (90.4%) during 2020 to 2021 to 2802 of 3685 youths (76.0%) during 2023 to 2024 (P < .001). In contrast, clinical testing increased from the 2016 to 2020 seasons to the 2023 to 2024 season for influenza viruses (5384 of 12 090 youths 44.5% to 2740 of 3685 youths 74.4%; P < .001) and RSV (5072 youths 42.0% to 2638 youths 71.6%; P < .001). During the 2023 to 2024 season, the proportion of youths identified as positive for each virus by surveillance testing alone (ie, without clinical testing) was 23 of 112 youths (20.5%) for SARS-CoV-2, 78 of 286 youths (27.3%) for influenza, and 290 of 979 youths (29.6%) for RSV; youths were more likely to receive clinical testing if they were admitted to the intensive care unit (eg, SARS-CoV-2: adjusted odds ratio aOR, 2.62; 95% CI, 2.06-3.33) or had underlying conditions (eg, any vs no underlying condition for SARS-CoV-2: aOR, 1.56; 95% CI, 1.33-1.84). In this study, SARS-CoV-2 clinical testing decreased between 2020 to 2021 and 2023 to 2024 seasons, whereas influenza and RSV testing increased significantly between 2016 to 2020 and 2023 to 2024 seasons; approximately three-quarters of children and adolescents were tested for the 3 viruses in 2023 to 2024.