Frontline Screening for SARS-CoV-2 Infection at Emergency Department Admission by Third Generation Rapid Antigen Test: Can We Spare RT-qPCR?

Abstract

To complement RT-qPCR testing for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, many countries have introduced the use of rapid antigen tests. As they generally display lower real-life performances than expected, their correct positioning as frontline screening is still controversial. Despite the lack of data from daily clinical use, third generation microfluidic assays (such as the LumiraDx SARS-CoV-2 Ag test) have recently been suggested to have similar performances to RT-qPCR and have been proposed as alternative diagnostic tools. By analyzing 960 nasopharyngeal swabs from 960 subjects at the emergency department admissions of a tertiary COVID-19 hospital, LumiraDx assay demonstrated a specificity of 97% (95% CI: 96-98), and a sensitivity of 85% (95% CI: 82-89) in comparison with RT-qPCR, which increases to 91% (95% CI: 86-95) for samples with a cycle threshold ≤ 29. Fifty false-negative LumiraDx-results were confirmed by direct quantification of genomic SARS-CoV-2 RNA through droplet-digital PCR (median (IQR) load = 5880 (1657-41,440) copies/mL). Subgenomic N and E RNAs were detected in 52% (n = 26) and 56% (n = 28) of them, respectively, supporting the presence of active viral replication. Overall, the LumiraDx test complies with the minimum performance requirements of the WHO. Yet, the risk of a misrecognition of patients with active COVID-19 persists, and the need for confirmatory RT-qPCR should not be amended.

Keywords: SARS-CoV-2; antigenic test; infectivity; rapid diagnostic test; subgenomic RNA; viral load.

Figure 1

SARS-CoV-2 RT-qPCR cycle thresholds against concordance results between RT-qPCR and LumiraDx SARS-CoV-2 Ag test. One-sided p-values comparing Ct of concordant samples (+/+) and Ct of discordant samples (+/−) were calculated by a Mann–Whitney U test. p-values < 0.05 were considered statistically significant. Ct = Cycle threshold; ORF1ab = open reading frame 1ab; S = spike.

Figure 2

SARS-CoV-2 genomic and subgenomic RNA load in antigenic false-negative samples. Gnm = genomic; sgm = subgenomic; E = envelope; N = nucleocapsid.