The Changing Landscape of Respiratory Viruses Contributing to Hospitalizations in Quebec, Canada: Results From an Active Hospital-Based Surveillance Study

Background: A comprehensive description of the combined effect of SARS-CoV-2 and respiratory viruses other thanSARS-CoV-2 (ORVs) on acute respiratory infection (ARI) hospitalizations is lacking. Objective: This study aimed to compare the viral etiology of ARI hospitalizations before the pandemic (8 prepandemic influenzaseasons, 2012-13 to 2019-20) and during 3 pandemic years (periods of increased SARS-CoV-2 and ORV circulation in 2020-21,2021-22, and 2022-23) from an active hospital-based surveillance network in Quebec, Canada. Methods: We compared the detection of ORVs and SARS-CoV-2 during 3 pandemic years to that in 8 prepandemic influenzaseasons among patients hospitalized with ARI who were tested systematically by the same multiplex polymerase chain reaction(PCR) assay during periods of intense respiratory virus (RV) circulation. The proportions of infections between prepandemic andpandemic years were compared by using appropriate statistical tests. Results: During prepandemic influenza seasons, overall RV detection was 92.7% (1384/1493) (respiratory syncytial virus[RSV]: 721/1493, 48.3%; coinfections: 456/1493, 30.5%) in children (<18 years) and 62.8% (2723/4339) (influenza: 1742/4339,40.1%; coinfections: 264/4339, 6.1%) in adults. Overall RV detection in children was lower during pandemic years but increasedfrom 58.6% (17/29) in 2020-21 (all ORVs; coinfections: 7/29, 24.1%) to 90.3% (308/341) in 2021-22 (ORVs: 278/341, 82%;SARS-CoV-2: 30/341, 8.8%; coinfections: 110/341, 32.3%) and 88.9% (361/406) in 2022-23 (ORVs: 339/406, 84%; SARS-CoV-2:22/406, 5.4%; coinfections: 128/406, 31.5%). In adults, overall RV detection was also lower during pandemic years but increasedfrom 43.7% (333/762) in 2020-21 (ORVs: 26/762, 3.4%; SARS-CoV-2: 307/762, 40.3%; coinfections: 7/762, 0.9%) to 57.8%(731/1265) in 2021-22 (ORVs: 179/1265, 14.2%; SARS-CoV-2: 552/1265, 43.6%; coinfections: 42/1265, 3.3%) and 50.1%(746/1488) in 2022-23 (ORVs: 409/1488, 27.5%; SARS-CoV-2: 337/1488, 22.6%; coinfections: 36/1488, 2.4%). No influenzaor RSV was detected in 2020-21; however, their detection increased in the 2 subsequent years but did not reach prepandemiclevels. Compared to the prepandemic period, the peaks of RSV hospitalization shifted in 2021-22 (16 weeks earlier) and 2022-23(15 weeks earlier). Moreover, the peaks of influenza hospitalization shifted in 2021-22 (17 weeks later) and 2022-23 (4 weeksearlier). Age distribution was different compared to the prepandemic period, especially during the first pandemic year. Conclusions: Significant shifts in viral etiology, seasonality, and age distribution of ARI hospitalizations occurred during the3 pandemic years. Changes in age distribution observed in our study may reflect modifications in the landscape of circulating RVs and their contribution to ARI hospitalizations. During the pandemic period, SARS-CoV-2 had a low contribution to pediatricARI hospitalizations, while it was the main contributor to adult ARI hospitalizations during the first 2 seasons and dropped belowORVs during the third pandemic season. Evolving RVs epidemiology underscores the need for increased scrutiny of ARIhospitalization etiology to inform tailored public health recommendations.