Nasal Swab Performance by Collection Timing, Procedure, and Method of Transport for Patients with SARS-CoV-2

Abstract

The urgent need for large-scale diagnostic testing for SARS-CoV-2 has prompted interest in sample collection methods of sufficient sensitivity to replace nasopharynx (NP) sampling. Nasal swab samples are an attractive alternative; however, previous studies have disagreed over how nasal sampling performs relative to NP sampling. Here, we compared nasal versus NP specimens collected by health care workers in a cohort of individuals clinically suspected of COVID-19 as well as SARS-CoV-2 reverse transcription (RT)-PCR-positive outpatients undergoing follow-up. We compared subjects being seen for initial evaluation versus follow-up, two different nasal swab collection protocols, and three different transport conditions, including traditional viral transport media (VTM) and dry swabs, on 307 total study participants. We compared categorical results and viral loads to those from standard NP swabs collected at the same time from the same patients. All testing was performed by RT-PCR on the Abbott SARS-CoV-2 RealTime emergency use authorization (EUA) (limit of detection [LoD], 100 copies viral genomic RNA/ml transport medium). We found low concordance overall, with Cohen's kappa (κ) of 0.49, with high concordance only for subjects with very high viral loads. We found medium concordance for testing at initial presentation (κ = 0.68) and very low concordance for follow-up testing (κ = 0.27). Finally, we show that previous reports of high concordance may have resulted from measurement using assays with sensitivity of ≥1,000 copies/ml. These findings suggest nasal-swab testing be used for situations in which viral load is expected to be high, as we demonstrate that nasal swab testing is likely to miss patients with low viral loads.

Keywords: COVID-19; NP swab; SARS-CoV-2; limit of detection; nasal swab.

FIG 1

Viral loads for NP (x axes) versus nasal swab (y axes) for (a) initial versus (b) follow-up testing, (c) shallow/short versus (d) deep/long collection procedures, collection (e) in GITC versus (f) dry versus (g) in VTM, and (h) for all data, with 2 × 2 tables and concordance values measured by Cohen’s kappa, κ. In each plot, the diagonal is a 1:1 line. Dots along the bottom and left axes are negatives.

FIG 2

Concordance (measured by Cohen’s kappa [κ]) plotted against assay LoD for all data (thick line), only initial-testing data (thin solid line), and only follow-up-testing data (dotted line). With its LoD of 100 copies/ml (solid arrowhead), the Abbott assay detects false negatives in nasal-swab samples, resulting in low overall concordance (κ = 0.49); even lower concordance for follow-up testing (κ = 0.27), likely because viral loads in this population are lower than they are overall; and still-low concordance for initial testing (κ = 0.71), despite viral loads being higher for initial tests than overall. In contrast, an assay with an LoD of 1,000 copies/ml (open arrowhead) would have missed these false negatives, which would have yielded substantially higher observed concordances regardless of subset.