Diagnostic testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in symptomatic and asymptomatic children remains integral to care, particularly for supporting return to and attendance in schools. The concordance of SARS-CoV-2 detection in children using various specimen types has not been widely studied.


To compare three sample types for SARS-CoV-2 PCR testing in children collected and tested at a single facility


We prospectively recruited 142 symptomatic and asymptomatic children into a sample comparison study performed in a single healthcare system. Each child provided self-collected saliva, and a trained healthcare provider collected a mid-turbinate nasal swab and nasopharyngeal (NP) swab. Specimens were assayed within 24 hours of collection using reverse transcriptase-polymerase chain reaction (RT-PCR) to detect SARS-CoV-2 on a single testing platform.


Concurrently collected saliva and mid-turbinate swabs had >95% positive agreement with NP swabs when obtained within 10 days of symptom onset. Positive agreement of saliva and mid-turbinate samples collected from children with symptom onset >10 days prior, or without symptoms, was 82% compared to NP swab samples. Cycle threshold (Ct) values for mid-turbinate nasal samples more closely correlated with Ct values from NP samples than saliva sample Ct values.


These findings suggest that all three sample types from children are useful for SARS-CoV-2 diagnostic testing by RT-PCR, and that concordance is greatest when the child has symptoms of coronavirus disease 2019 (COVID-19) within the past 10 days. This study provides scientific justification for utilizing sample types other than the NP swab for SARS-CoV-2 testing in pediatric populations.

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Author notes

The authors have no relevant financial interest in the products or companies described in this article.

This work was supported by a grant from the National Institutes of Health for Rapid Acceleration oof Diagnostics (RADx).