Epidemiological shifts in pediatric respiratory pathogens in Shenzhen, China: impacts of COVID-19 control measures and relaxation

This retrospective study analyzed epidemiological features of infections by 13 common respiratory pathogens among children in Shenzhen, China, from January 2020 to February 2025. A total of 73,886 throat swabs from pediatric patients with suspected respiratory infections were tested using multiplex fluorescence PCR-capillary electrophoresis. Human rhinovirus (HRV), respiratory syncytial virus (RSV), <i>Mycoplasma pneumoniae</i> (MP), and human parainfluenza virus (HPIV) were the most prevalent, with positive rates of 24.57%, 12.46%, 11.46%, and 6.86%, respectively. Pathogen positivity rates significantly differed between the coronavirus disease 2019 (COVID-19) pandemic (2020-2022) and post-relaxation period (2023-2025) (<i>P</i> < 0.0001). Seasonal patterns shifted: HPIV peaked in summer, HRV in autumn-winter, MP in summer-autumn, and RSV in spring. After control measures eased, positivity increased across all age groups. HPIV was highest in children aged 6 months to 1 year, HRV in 3-6 years, MP in >6 years, and RSV in 0-6 months. Age- and sex-related differences were significant (all <i>P</i> < 0.001). These findings indicate that evolving COVID-19 mitigation strategies have altered epidemiological patterns, highlighting the need for targeted prevention considering high-risk groups, co-infections, and seasonality.<b>IMPORTANCE</b>This large-scale pediatric study reveals how coronavirus disease 2019 control measures and their relaxation reshaped respiratory pathogen epidemiology in Southern China. We identified major shifts in seasonal peaks, age-specific susceptibility, and overall infection prevalence, particularly for human rhinovirus, respiratory syncytial virus, <i>Mycoplasma pneumoniae</i>, and human parainfluenza virus. The narrowing or shifting of epidemic windows implies altered transmission dynamics, likely driven by nonpharmaceutical interventions and subsequent immunity gaps. The significant post-relaxation surge across all age groups underscores the vulnerability of children to multiple pathogens once restrictions ease. These findings provide crucial evidence for optimizing pediatric respiratory infection surveillance and designing adaptive, season- and age-specific prevention strategies to mitigate future outbreaks.