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

The tests currently used for the identification of SARS-CoV-2 include specimens taken from the upper and lower respiratory tract. Although recommendations from the World Health Organization prioritise the usage of a nasopharyngeal swab (NS), nasopharyngeal aspirates (NPA) are thought to be superior in identifying SARS-CoV-2 in children. To our knowledge, however, no paediatric study has been published on the subject. The aim of this study is to evaluate the diagnostic performances of NS referred to NPA for SARS-CoV-2 in children. We calculated the sensitivity and specificity of the NS referred to the NPA of the whole sample and considered both age and collection period as covariates in different analyses. We collected 300 paired samples. The NS had a specificity of 97.7% and a sensitivity of 58.1%. We found similar results for the group of subjects ≥ 6 years old, while for subjects < 6 years old, the sensitivity was 66.7% and the specificity 97.8%. Considering period as a covariate, the sensitivity and specificity for patients hospitalised in March (31 patients, 52 records) were 70.0% and 97.6%, while for patients involved in the follow-up (16 patients, 57 records), they were 57.2% and 89.7%. The NS has a low sensitivity in detecting SARS-CoV-2 in children when referred to the NPA, whereas its specificity is high. Our results suggest that in children under 6 years of age, NSs should be preferred whenever possible. Though statistically not significant, the sensitivity of the NS rises when performed before the NPA.