Performance of anterior nares and tongue swabs for nucleic acid, Nucleocapsid, and Spike antigen testing for detecting SARS-CoV-2 against nasopharyngeal PCR and viral culture

Abstract

Objectives: This study assesses and compares the performance of different swab types and specimen collection sites for SARS-CoV-2 testing, to reference standard real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and viral culture.

Methods: Symptomatic adults with COVID-19 who visited routine COVID-19 testing sites used spun polyester and FLOQSwabs to self-collect specimens from the anterior nares and tongue. We evaluated the self-collected specimen from anterior nares and tongue swabs for the nucleocapsid (N) or spike (S) antigen of SARS-CoV-2 by RT-PCR and then compared these results with results from RT-PCR and viral cultures from nurse-collected nasopharyngeal swabs.

Results: Diagnostic sensitivity was highest for RT-PCR testing conducted using specimens from the anterior nares collected on FLOQSwabs (84%; 95% CI 68-94%) and spun polyester swabs (82%; 95% CI 66-92%), compared to RT-PCR tests conducted using specimens from nasopharyngeal swabs. Relative to viral culture from nasopharyngeal swabs, diagnostic sensitivities were higher for RT-PCR and antigen testing of anterior nares swabs (91-100%) than that of tongue swabs (18-81%). Antigen testing of anterior nares swabs had higher sensitivities against viral culture (91%) than against nasopharyngeal RT-PCR (38-70%). All investigational tests had high specificity compared with nasopharyngeal RT-PCR. Spun polyester swabs are equally effective as FLOQSwabs for anterior nasal RT-PCR testing.

Conclusions: We found that anterior nares specimens were more sensitive than tongue swab specimens or antigen testing for detecting SARS-CoV-2 by RT-PCR. Thus, self-collected anterior nares specimens may represent an alternative method for diagnostic SARS-CoV-2 testing in some settings.

Keywords: COVID-19; SARS-CoV-2; antigen detection; diagnostic performance.

Figure 1

NP RT-PCR Ct value versus days since symptom onset for symptomatic participants with an NP RT-PCR result (n=249). Abbreviations: NP = nasopharyngeal; PCR = polymerase chain reaction.

Figure 2

NP swab Ct value versus qualitative intervention test result. Ct values and qualitative intervention test result of all samples that were positive by NP RT-PCR. Plots are organized by sample site (anterior nares vs tongue), and intervention test (N antigen, S antigen, FLOQSwab PCR, spun polyester PCR). Black lines indicate median Ct values. To improve visibility of plots, randomized jitter of 0.15 was added in the direction of the x-axis. Abbreviations: Ct = cycle threshold; N = nucleocapsid; NP = nasopharyngeal; PCR = polymerase chain reaction; RT-PCR = reverse transcriptase-polymerase chain reaction; S = spike.