A Comparison of Five SARS-CoV-2 Molecular Assays With Clinical Correlations

Abstract

Objectives: Comparative assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular assays that have been operationalized through the US Food and Drug Administration's Emergency Use Authorization process are warranted to assess real-world performance. Characteristics such as sensitivity, specificity, and false-negative rate are important to inform clinical use.

Methods: We compared five SARS-CoV-2 assays using nasopharyngeal and nasal swab specimens submitted in transport media; we enriched this cohort for positive specimens, since we were particularly interested in the sensitivity and false-negative rate. Performance of each test was compared with a composite standard.

Results: The sensitivities and false-negative rates of the 239 specimens that met inclusion criteria were, respectively, as follows: Centers for Disease Control and Prevention 2019 nCoV Real-Time RT-PCR Diagnostic Panel, 100% and 0%; TIB MOLBIOL/Roche z 480 Assay, 96.5% and 3.5%; Xpert Xpress SARS-CoV-2 (Cepheid), 97.6% and 2.4%; Simplexa COVID-19 Direct Kit (DiaSorin), 88.1% and 11.9%; and ID Now COVID-19 (Abbott), 83.3% and 16.7%.

Conclusions: The assays that included a nucleic acid extraction followed by reverse transcription polymerase chain reaction were more sensitive than assays that lacked a full extraction. Most false negatives were seen in patients with low viral loads, as extrapolated from crossing threshold values.

Keywords: COVID-19; Coronavirus; Nucleic acid amplification tests; SARS-CoV-2.

Figure 1

Scatterplots of crossing threshold (Ct), as a surrogate for viral load, vs the days since onset of symptoms for the five molecular severe acute respiratory syndrome coronavirus 2 assays studied. A, Centers for Disease Control and Prevention assay. B, Cepheid assay. C, Roche assay. D, Abbott assay. E, DiaSorin assay. Performance characteristics (eg, TP, TN) are listed and color coded. The y-axis is on a reversed scale. FN, false negative; FP, false positive; Neg, negative; Pos, positive; TN, true negative; TP, true positive.