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

Am J Clin Pathol. 2021 Jan 4;155(1):69-78. doi: 10.1093/ajcp/aqaa181.


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.

Publication types

  • Comparative Study

MeSH terms

  • Adult
  • Aged
  • COVID-19 / diagnosis*
  • COVID-19 Nucleic Acid Testing / methods*
  • COVID-19 Nucleic Acid Testing / standards
  • Cohort Studies
  • False Negative Reactions
  • Female
  • Humans
  • Logistic Models
  • Male
  • Middle Aged
  • Sensitivity and Specificity