Comparison of Throat and Nasopharyngeal Swabs for the Molecular Detection of Enterovirus in Pediatric Patients

Background: Enterovirus infections frequently occur in children worldwide. Molecular assays are widely used to detect enterovirus. Nasopharyngeal swabs (NPS) and throat swabs (TS) are common specimen types used in clinical practice. Here, the reliability of TS for detecting enterovirus in pediatric patients was compared with that of NPS using real-time reverse transcription polymerase chain reaction (RT-rPCR). Methods: Results obtained using the Allplex Respiratory Panel 2 (Seegene, Korea) for NPS (NPS-RP) and AccuPower EV Real-time RT-PCR (Bioneer, Korea) for TS (TS-EV), which were performed simultaneously between September 2017 to March 2020, were initially compared. Cross examination (Allplex Respiratory Panel 2 assay using TS and AccuPower EV assay with NPS) was performed for specimens collected between July 2019 to March 2020 to evaluate the performance of the enterovirus assays based on each specimen type. Results: Among the 742 case results of initial tests, 597 cases (80.5%) tested negative in both assays, and 91 cases (12.6%) tested positive in both assays. Fifty-four discrepant results were observed: 39 cases (5.3%) tested positive in TS-EV and negative in NPS-RP, and 15 cases (2.0%) tested positive in NPS-RP and negative in TS-EV. The overall percent agreement was 92.7%. In the 99 cases cross examined, overall percent agreements were 98.0%, 94.9%, 92.9%, and 89.9% for TS-EV vs. TS-RP, NPS-RP vs. NPS-EV, TS-EV vs. NPS-EV, and NPS-RP vs. TS-RP, respectively. Conclusions: TS yields a high agreement rate with NPS in detecting enterovirus, regardless of single-plex or multiplex RT-rPCR assays. Thus, TS could be a good alternative specimen in pediatric patients who are reluctant to NPS sampling.