Comparison of nasopharyngeal samples for SARS-CoV-2 detection in a paediatric cohort

Aim The diagnosis of coronavirus disease 2019 (COVID-19) depends on accurate and rapid testing. Choosing an appropriate sample may impact diagnosis. Naso-oropharyngeal swabs (NOS) are most frequently used, despite several limitations. Since studies suggest nasopharyngeal aspirate (NPA) as a superior alternative in children, we hypothesised collecting both nasopharyngeal swab and aspirate would improve our diagnostic accuracy. Methods Observational, longitudinal, prospective study from 7 March to 7 May in a tertiary paediatric hospital in Lisbon. The objective was to compare the rate of detection of SARS-CoV-2 between NOS and NPA samples collected simultaneously. Results A total of 438 samples collected from 85 patients with confirmed COVID-19. There were 47.7% overall positive specimens - 32% (70/219) positive NOS and 63.5% (139/219) positive NPA. The tests were 67.6% concordant (k = 0.45). 50.3% had positive NPA with negative NOS, while 1.3% had positive NOS with negative NPA. NPA proved to be more sensitive (98.6% with 95% confidence interval 91.2-99.9% vs. 49.6% with 95% confidence interval 41.1-58.2%, P < 0.001). Additionally, the difference between NPA and NOS positive samples was statistically significant across all population groups (age, health condition, clinical presentation, contact with COVID-19 patients or need for hospitalisation), meaning NPA is more sensitive overall. Conclusions Nasopharyngeal aspirates had greater sensitivity than naso-oropharyngeal swabs in detecting SARS-CoV-2. Our results suggest paediatric patients would benefit from collecting nasopharyngeal aspirates in hospital settings, whenever feasible, to improve diagnosis of COVID-19.