Comparison between Nasal and Nasopharyngeal Swabs for SARS-CoV-2 Rapid Antigen Detection in an Asymptomatic Population, and Direct Confirmation by RT-PCR from the Residual Buffer

Abstract

Containment measures employed during the COVID-19 pandemic included prompt recognition of cases, isolation, and contact tracing. Bilateral nasal (NA) swabs applied to a commercial antigen-based rapid diagnostic test (Ag-RDT) offer a simpler and more comfortable alternative to nasopharyngeal (NP) collection; however, little is known about the sensitivity of this method in an asymptomatic population. Participants in community-based asymptomatic testing sites were screened for SARS-CoV-2 using an Ag-RDT with NP sampling. Positive individuals returned for confirmatory molecular testing and consented to repeating the Ag-RDT using a bilateral NA swab for comparison. Residual test buffer (RTB) from Ag-RDTs was subjected to real-time reverse transcription-PCR (RT-PCR). Of 123,617 asymptomatic individuals, 197 NP Ag-RDT-positive participants were included, with 175 confirmed positive by RT-PCR. Of these cases, 154 were identified from the NA swab collection with Ag-RDT, with a sensitivity of 88.0% compared to the NP swab collection. Stratifying results by RT-PCR cycle threshold demonstrated that sensitivity of the nasal collection method varied based on the cycle threshold (C_T) value of the paired RT-PCR sample. RT-PCR testing on the RTB from the Ag-RDT using NP and NA swab collections resulted in 100.0% and 98.7% sensitivity, respectively. NA swabs provide an adequate alternative to NP swab collection for use with Ag-RDT, with the recognition that the test is most sensitive in specimens with high viral loads. With the high sensitivity of RT-PCR testing on RTB from Ag-RDT, a more streamlined approach to confirmatory testing is possible without recollection or use of paired collections strategies. IMPORTANCE Nasal swabbing for SARS-CoV-2 (COVID-19) comes with many benefits but is slightly less sensitive than traditional nasopharyngeal swabbing; however, confirmatory lab-based testing could be performed directly from the residual buffer from either sample type.

Keywords: COVID-19; SARS-CoV-2; antigen; nasal; nasopharyngeal; rapid.

FIG 1

Diagram illustrating the testing outcomes of samples tested by Ag-RDT and RT-PCR from asymptomatic community members used in analysis. Ag-RDT, antigen-based rapid diagnostic test; Ct, cycle threshold; NA, nasal; NP, nasopharyngeal; RTB, residual test buffer; NAAT, nucleic acid amplification test (NAAT); RT-PCR, reverse transcription-PCR.

FIG 2

Possible confirmation strategies for Ag-RDT results using a laboratory-based NAAT. Typically, confirmation of Ag-RDT results relies on (i) the recollection of an additional specimen (e.g., NP in VTM) for NAAT testing following a positive Ag-RDT result (orange arrows); or (ii) performing individual paired collections for Ag-RDT and RT-PCR and comparing results of the Ag-RDT and the laboratory-based NAAT (blue arrows). A third strategy was investigated to reduce the need for paired collection, or return for recollection, where NAAT testing is performed directly on RTB following a positive Ag-RDT (green arrows). Ag-RDT, antigen-based rapid diagnostic test; NA, nasal; NP, nasopharyngeal; NAAT, nucleic acid amplification test; RTB, residual test buffer; VTM, viral transport media.