Anatomical Site, Viral Ribonucleic Acid Abundance, and Time of Sampling Correlate With Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2 During Infection

Abstract

Background: Nasopharyngeal (NP) swabs are the standard for SARS-CoV-2 diagnosis. If less invasive alternatives to NP swabs (eg, oropharyngeal [OP] or nasal swabs [NS]) are comparably sensitive, the use of these techniques may be preferable in terms of comfort, convenience, and safety.

Methods: This study compared the detection of SARS-CoV-2 in swab samples collected on the same day among participants with at least one positive PCR test.

Results: Overall, 755 participants had at least one set of paired swabs. Concordance between NP and other swab types was 75% (NS), 72% (OP), 54% (rectal swabs [RS]), and 78% (NS/OP combined). Kappa values were moderate for the NS, OP, and NS/OP comparisons (0.50, 0.45, and 0.54, respectively). Highest sensitivity relative to NP (0.87) was observed with a combination of NS/OP tests (positive if either NS or OP was positive). Sensitivity of the non-NP swab types was highest in the first week postsymptom onset and decreased thereafter. Similarly, virus RNA quantity was highest in the NP swabs as compared with NS, OP, and RS within two weeks postsymptom onset. OP and NS performance decreased as virus RNA quantity decreased. No differences were noted between NS specimens collected at home or in clinic.

Conclusions: NP swabs detected more SARS-CoV-2 cases than non-NP swabs, and the sensitivity of the non-NP swabs decreased with time postsymptom onset. While other swabs may be simpler to collect, NP swabs present the best chance of detecting SARS-CoV-2 RNA, which is essential for clinical care as well as genomic surveillance.

Keywords: COVID-19; SARS-CoV-2; nasal swabs; nasopharyngeal; oropharyngeal.

Figure 1.

Sensitivity of alternative swab types compared with nasopharyngeal (NP) swabs collected on the same day in the Epidemiology, Immunology, and Clinical Characteristics of Emerging Infectious Diseases with Pandemic Potential (EPICC) study, categorized by days postsymptom onset (DPSO). d, days; NS, nasal swab; OP, oropharyngeal swab; RS, rectal swab.

Figure 2.

Severe acute respiratory syndrome coronavirus 2 log₁₀ N1 quantity (genome equivalents [GE]/reaction), log₁₀ N2 quantity (GE/reaction), and RNAse P gene (RP) cycle threshold (Ct) values, by swab type. Paired t tests were used to compare sample types. NP, nasopharyngeal swab; NS, nasal swab; OP, oropharyngeal swab; RS, rectal swab.