Increased Respiratory Pathogen Positivity and Diversity in Hospitalized Children Following the COVID-19 Pandemic in Malaysia

Background: Respiratory tract infections are a major cause of pediatric hospitalization. However, in the post-COVID-19 era, atypical surges and disrupted circulation patterns of respiratory pathogens have been observed globally. Methods: We retrospectively analyzed respiratory pathogen among hospitalized children aged 28 days to 18 years at the largest quaternary hospital in Malaysia, from January 2018 to May 2023. The study period was classified into pre-pandemic (2018–2019), pandemic (2020–2021), and post-pandemic (2022–2023) phases. Pathogens were identified using a multiplex nucleic acid assay (FilmArray BioFire® Respiratory Panel 2.1). Results: Among 20,556 hospitalized children, 7,707 (37.5%) underwent multiplex respiratory testing. Overall pathogen positivity remained similar during the pre-pandemic and pandemic periods (50.4% and 50.9%) and increased substantially in the post-pandemic period (86.2%). Single-pathogen infections increased from 46.4% pre-pandemic and 43.1% during the pandemic to 64.6% post-pandemic, while co-infections rose from 4.0% and 7.9% to 21.6%. Human rhinovirus/enterovirus and respiratory syncytial virus were consistently detected across all periods, whereas adenovirus and influenza viruses increased significantly post-pandemic. Influenza A and B showed low detection during the pandemic and re-emerged post-pandemic. Monthly positivity rates remained below 25% until late 2021, and increases through 2022–2023, with a peak in early 2023 with 94.4%. Despite increased pathogen detection, intensive care unit admissions remained low across all periods. Conclusion: Post-pandemic, higher respiratory pathogen positivity, co-infections, and pathogen diversity were observed in hospitalized children, despite stable severity. These findings demonstrate temporal shifts in pediatric respiratory pathogen detection following the COVID-19 pandemic in a tropical hospital setting, suggesting possible post-pandemic immune dysregulation.