Oral cavity samples as a non-invasive method for respiratory virus detection in Pediatric patients: A comparative study.

Publication date: May 26, 2026

Respiratory viruses are the leading cause of acute respiratory infections (ARIs) worldwide. Despite preventive measures, these infections remain a major cause of morbidity and mortality in children. In Colombia, the most common viral agents include respiratory syncytial virus (RSV), influenza (flu), rhinovirus (RV), adenovirus (AdV) and SARS-CoV-2. Although timely detection is crucial for effective treatment and monitoring, standard diagnostic sampling such as nasopharyngeal swabs (NPS) and aspirates (NPA), are invasive, uncomfortable and often poorly tolerated, particularly in pediatric populations. This has led to a growing interest in non-invasive alternatives, such as oral swabs and saliva samples, which are easier to collect and more cost-effective. To evaluate the usefulness of oral cavity (OC) samples as a non-invasive method for the detection of respiratory viruses. We conducted a paired, comparative study including 133 pediatric patients presenting with signs or symptoms of acute respiratory disease. For each patient, both NPA and OC samples were collected and analyzed using a multiplex RT-qPCR assay targeting five respiratory viruses. Concordance between sampling methods was assessed using Cohen’s kappa coefficient. The OC samples showed significant concordance with the NPA for the detection of FluA (_705 = 0. 755) and RSV (_705 = 0. 693), and weak agreement with AdV (_705 = 0. 404). No reliable agreement could be determined for FluB and SARS-CoV-2 due to the low number of positive samples. These findings support oral cavity sampling as a feasible non-invasive method for detecting selected respiratory viruses in children, while highlighting virus-dependent differences in performance.

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