Diagnosis of SARS-CoV-2 in children: accuracy of nasopharyngeal swab compared to nasopharyngeal aspirate

The tests currently used for the direct identification of SARS-CoV-2 include specimens taken from upper and lower respiratory tract; recommendations from Word Health Organization prioritise nasopharyngeal swab (NS). In literature there are not available paediatric studies about the identification of SARS-CoV-2 through nasopharyngeal aspirate (NPA), but the use of NPA is deemed to be better than NS to identify respiratory viruses in children. The aim of our study is to evaluate diagnostic performances of NS compared to NPA for the detection of SARS-CoV-2 in children. We collected 300 paired samples (NS and NPA) from children hospitalized and followed up in our paediatric unit. We calculated the sensitivity and specificity of NS referred to NPA of the whole sample and then, considering both the age (≥ and < 6 years old) and the period of collection (March vs follow up) as covariates in different analysis. The NS has a low sensitivity in detecting SARS-CoV-2 in children when referred to NPA; whereas its specificity results high. In children under 6 years of age, our results suggest to prefer the collection of NS, whenever possible. Though statistically not significant, the sensitivity of NS becomes higher if it is performed before NPA.