Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: A prospective comparative clinical trial

Abstract

Background: Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs), saliva RT-PCR and nasopharyngeal (NP) RT-PCR have shown different performance characteristics to detect patients infected by SARS-CoV-2, according to the viral load (VL)-and thus transmissibility.

Methods: In October 2020, we conducted a prospective trial involving patients presenting at testing centres with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR, according to VL and symptoms duration.

Results: Out of 949 patients enrolled, 928 patients had all three tests performed. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) ≥106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively. Sensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients, 94.5% (91.5-96.7%) for those with VL≥105 and 96.5% (93.6-98.3%) for those with VL≥106. Sensitivity of STANDARD-Q®, Panbio™ and COVID-VIRO® Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL≥106, sensitivity was 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. No patient with VL<104 was detected by RDT. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%, 83.5-91.3%) and ≥4 days (85.7%, 75.9-92.6%) after symptoms onset (p = 0.6). Sensitivity of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR.

Conclusions: RDT results allow rapid identification of COVID cases with immediate isolation of most contagious individuals. RDT can thus be a game changer both in ambulatory care and community testing aimed at stopping transmission chains, and even more so in resource-constrained settings thanks to its very low price. When PCR is performed, saliva could replace NP swabbing.

Trial registration: ClinicalTrial.gov Identifier: NCT04613310 (03/11/2020).

Fig 1. Study patients’ flow.

Fig 2. Detection rates of COVID patients by RDT, nasopharyngeal PCR and saliva PCR.

A) all positive patients; B) positive patients with viral loads ≥10⁶ copies/ml by any PCR (supposedly significantly contagious).

Fig 3. Sensitivity of three brands of antigen RDT compared to nasopharyngeal PCR.

A) all positive patients; B) positive patients with viral loads ≥10⁶ copies/ml (supposedly significantly contagious).

Fig 4. Number of patients positive by RDT (in red) and nasopharyngeal PCR (in blue) and sensitivity of RDT according to viral load categories.

Fig 5. Log viral loads by NP PCR according to the RDT brand used.

Fig 6

Log viral loads by NP PCR and saliva PCR according to A) RDT result and B) intensity band of positive RDT.

Fig 7

Log viral loads according to symptoms duration by nasopharyngeal PCR (A) and sensitivity of antigen RDT (B).

Fig 8. Comparison between log viral loads by nasopharyngeal PCR and saliva PCR.

A) Log viral loads in RDT positive (black dots) and negative (white dots) patients. Dotted lines: Mean log viral loads; Black line: Considered threshold for presence of cultivable virus (nasopharyngeal PCR); B) Bland-Altman analysis showing the difference between nasopharyngeal and saliva log viral loads; SD = Standard deviation.

Fig 9. Log viral loads by saliva PCR saliva volume: Low volume corresponds to a gingivo-buccal swab only; high volume corresponds to a gingivo-buccal swab with <0.5 ml of saliva in addition.