Background: Nasopharyngeal aspirate (NPA) is known as the best specimen for accurate diagnosis of viral respiratory infections in pediatric patients, but the procedure is very annoying. Recently introduced flocked swabs have been reported to be easy to obtain a good quality specimen and comfortable to patients. The purpose of this study was to compare the sensitivities between NPA and nasopharyngeal flocked swabs (NPFS) for detection of respiratory viruses in children.

Methods: For this study, 111 hospitalized children with acute respiratory tract infections were recruited. NPA and NPFS were performed in parallel from each patient. NPFS were always collected after NPA. Specimens were tested for six common respiratory viruses in triplicate using indirect immunofluorescence (IIF), viral cultures, and multiplex reverse transcription PCR (RT- PCR).

Results: The proportion of specimens inadequate for IIF was higher in NPA (23.4%) than NPFS (5.4%). According to the consensus positive, the positive rates of NPFS were higher than those of NPA when using IIF (45.7% and 30.6%, P=0.048) and culture (38.7% and 27.9%, P=0.004). However, the false-positive rates of NPFS were higher than those of NPA when using IIF (12.4% and 1.2%, P=0.004). The positive rates of NPFS and those of NPA were not different in multiplex RT-PCR (67.6% and 55.9%, P=0.055).

Conclusion: The higher sensitivity of IIF for NPFS specimens and of culture for respiratory viruses and the similar sensitivities in multiplex PCR could make them an alternative to NPA samples, especially in physician clinics or emergency rooms. (Ann Clin Microbiol 2015; 18:119-125)