The impact of the COVID-19 pandemic on respiratory virus activity in children has been studied globally, but no published study in the Philippines has provided viral profiling and epidemiological data on children during and after the pandemic’s peak.

To identify respiratory pathogens detected using a multiplex RT-PCR assay (BioFire® Respiratory 2.1 Panel) among pediatric patients with respiratory symptoms admitted to St. Luke’s Medical Center–Global City during (March 2020–February 2022) and after (March 2022–March 2023) the peak of the COVID-19 pandemic; to compare the prevalence of these pathogens between the two periods; and to assess the clinico-demographic characteristics, diagnostic test results, and clinical outcomes of patients with single-pathogen infections versus co-infections.

A single-center, cross-sectional study was conducted through a retrospective chart review of pediatric patients with respiratory symptoms tested using a multiplex RT-PCR assay (BioFire® Respiratory 2.1 Panel) at St. Luke’s Medical Center–Global City from March 2020 to March 2023.

Of 739 children, 92.02% were positive for at least one respiratory pathogen, mostly viruses. Rhinovirus/enterovirus (50.59%), RSV (19.71%), and COVID-19 (12.50%) were the most common. COVID-19 and Influenza A were more prevalent during the peak, while rhinovirus/enterovirus and adenovirus were higher post-peak. Most patients were male, aged 1–5 years, and cough (89.99%) was the most common symptom. Normal leukocyte, CRP, and procalcitonin levels were observed in 70.09%, 47.31%, and 68.25%, respectively. No significant differences were noted in diagnostic test results based on pathogen detection. Antibiotics were given to 53.31% of patients, and 99.86% were discharged. The average length of stay was 3.69 days

The prevalence of respiratory pathogens among children admitted to our institution during and after the peak of the COVID-19 pandemic predominantly consisted of viruses, showing statistically significant differences. Rhinovirus/enterovirus and RSV were the leading respiratory pathogens in both periods. The peak group showed a higher prevalence of COVID-19 and Influenza A whereas the post-peak group exhibited a higher prevalence of rhinovirus/enterovirus and adenovirus. Single viral infections were more prevalent compared to co-infections