Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting

Jordan P. Skittrall*, Michael Wilson, Anna A. Smielewska, Surendra Parmar, Mary D. Fortune, Dominic Sparkes, Martin Curran, Hongyi Zhang, Hamid Jalal

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)


Objectives: When the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is low, many positive test results are false positives. Confirmatory testing reduces overdiagnosis and nosocomial infection and enables real-world estimates of test specificity and positive predictive value. This study estimates these parameters to evaluate the impact of confirmatory testing and to improve clinical diagnosis, epidemiological estimation and interpretation of vaccine trials. Methods: Over 1 month we took all respiratory samples from our laboratory with a patient's first detection of SARS-CoV-2 RNA (Hologic Aptima SARS-CoV-2 assay or in-house RT-PCR platform), and repeated testing using two platforms. Samples were categorized by source, and by whether clinical details suggested COVID-19 or corroborative testing from another laboratory. We estimated specificity and positive predictive value using approaches based on maximum likelihood. Results: Of 19 597 samples, SARS-CoV-2 RNA was detected in 107; 52 corresponded to first-time detection (0.27% of tests on samples without previous detection). Further testing detected SARS-CoV-2 RNA once or more (‘confirmed’) in 29 samples (56%), and failed to detect SARS-CoV-2 RNA (‘not confirmed’) in 23 (44%). Depending upon assumed parameters, point estimates for specificity and positive predictive value were 99.91–99.98% and 61.8–89.8% respectively using the Hologic Aptima SARS-CoV-2 assay, and 97.4–99.1% and 20.1–73.8% respectively using an in-house assay. Conclusions: Nucleic acid amplification testing for SARS-CoV-2 is highly specific. Nevertheless, when prevalence is low a significant proportion of initially positive results fail to confirm, and confirmatory testing substantially reduces the detection of false positives. Omitting additional testing in samples with higher prior detection probabilities focuses testing where it is clinically impactful and minimizes delay.

Original languageEnglish
Pages (from-to)469.e9-469.e15
Number of pages7
JournalClinical Microbiology and Infection
Issue number3
Publication statusPublished - Mar 2021

Bibliographical note

Funding Information:
The authors declare that they have no conflicts of interest. JPS is funded by a fellowship from the Mason Medical Research Foundation . No other author has received external funding for this study.

Publisher Copyright:
© 2020 European Society of Clinical Microbiology and Infectious Diseases

Copyright 2021 Elsevier B.V., All rights reserved.


  • COVID-19 diagnostic testing
  • COVID-19 pandemic
  • Nucleic acid amplification techniques
  • SARS-CoV-2
  • Sensitivity and specificity


Dive into the research topics of 'Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting'. Together they form a unique fingerprint.

Cite this