Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Feb;23(2):159-163.
doi: 10.1016/j.jmoldx.2020.11.008. Epub 2020 Dec 5.

Performance Characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 RT-PCR Tests in a Single Health System: Analysis of >10,000 Results from Three Different Assays

Travis K Price  1 , Brian C Bowland  1 , Sukantha Chandrasekaran  1 , Omai B Garner  1 , Shangxin Yang  2
Affiliations

Performance Characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 RT-PCR Tests in a Single Health System: Analysis of >10,000 Results from Three Different Assays

Travis K Price et al. J Mol Diagn. 2021 Feb.

Abstract

The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the approval of numerous molecular diagnostic assays with various performance and technical capacities. There are limited data comparing performance among assays. We conducted a retrospective analysis of >10,000 test results among three widely used RT-PCR assays for coronavirus disease 2019 (CDC, Simplexa Direct, and TaqPath) to assess performance characteristics. We also retested remnant weakly positive specimens to assess analytical sensitivity. All assays had strong linear correlation and little bias among CT values for PCR targets. In patients with first-test negative results (n = 811), most (795, 98.0%) remained negative for all subsequent testing. Retesting of weakly positive specimens (CT > 30) showed sensitivities as follows: TaqPath (97.8%), CDC (91%), Simplexa (75.3%). Our analysis showed no performance difference among PCR targets within the same assay, suggesting a single target is sufficient for SARS-CoV-2 detection. Lower respiratory tract specimens had a higher negative predictive value (100%) than upper respiratory tract specimens (98%), highlighting the utility of testing lower respiratory tract specimens when clinically indicated. Negative predictive value did not increase on further repeated testing, providing strong evidence for discouraging unnecessary repeated testing for SARS-CoV-2.

PubMed Disclaimer

Figures

Supplemental Figure S1
Supplemental Figure S1
Correlation and bias between CT values of the CDC COVID-19 RT-PCR assay for the N1 and N2 regions of the SARS-CoV-2 N gene. CT values for positive specimens are shown for the N1 and N2 targets. Specimen type is shown by color: blue (nasopharyngeal swab), yellow (bronchoalveolar lavage), green (expectorated sputum), and pink (other). A: Linear regression line (dotted line) was deduced from the CT values; the equation is shown. Correlation coefficient is R = 0.9814 (95% CI, 1.047–1.098; P < 0.001). B: Bland-Altman plot shows difference between N1 and N2 CT values versus the mean of the two measurements. The mean bias is −0.1 (red line), and the SD is 1.2 (two times SD is solid black lines). n = 132 positive specimens (A and B).
Supplemental Figure S2
Supplemental Figure S2
Correlation and bias between CT values of the Simplexa COVID-19 Direct assay for the SARS-CoV-2 S gene and ORF1ab. CT values for positive (both targets detected) specimens are shown for the S gene and ORF1ab targets. Specimen type is shown by color: blue (nasopharyngeal swab). A: Linear regression line (dotted line) was deduced from the CT values; the equation is shown. Correlation coefficient is R = 0.9594 (95% CI, 0.913–0.996; P < 0.001). B: Bland-Altman plot shows difference between S and ORF1ab CT values versus the mean of the two measurements. The mean bias is −1.0 (red line), and the SD is 1.3 (two times SD is solid black lines). n = 338 positive specimens (A and B).
Supplemental Figure S3
Supplemental Figure S3
Correlations among CT values of the TaqPath COVID-19 RT-PCR assay for the SARS-CoV-2 N gene, S gene, and ORF1ab. A–F: CT values for positive (all three targets detected) specimens are shown for the N and ORF1ab targets (A and B), S and ORF1ab targets (C and D), and S and N targets (E and F). Specimen type is shown by color: blue (nasopharyngeal swab) and yellow (bronchoalveolar lavage). A, C, and E: Linear regression lines (dotted lines) were deduced from the CT values; equations are shown. A: Correlation coefficient is R = 0.9605 (95% CI, 0.877–0.942; P < 0.001). C: Correlation coefficient is R = 0.9770 (95% CI, 0.942–0.994; P < 0.001). E: Correlation coefficient is R = 0.9508 (95% CI, 0.988–1.070; P < 0.001). B, D, and F: Bland-Altman plots show difference between pairs of CT values versus the mean of the two measurements. B: Difference between N and ORF1ab; mean bias is −0.1 (red line), and the SD is 1.4 (two times SD is solid black lines). D: Difference between S and ORF1ab; mean bias is 0.0 (red line), and the SD is 1.1 (two times SD is solid black lines). F: Difference between S and N; mean bias is 0.2 (red line), and the SD is 1.5 (two times SD is solid black lines). n = 131 positive specimens (A–F).
See this image and copyright information in PMC

References

    1. Zhu N., Zhang D., Wang W., Li X., Yang B., Song J., Zhao X., Huang B., Shi W., Lu R., Niu P., Zhan F., Ma X., Wang D., Xu W., Guizhen W., Gao G., Tan W. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727–733. - PMC - PubMed
    1. Chan J.F., Yuan S., Kok K.H., To K.K., Chu H., Yang J., Xing F., Liu J., Yip C.C., Poon R.W., Tsoi H.W., Lo S.K., Chan K.H., Poon V.K., Chan W.M., Ip J.D., Cai J.P., Cheng V.C., Chen H., Hui C.K., Yuen K.Y. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020;395:514–523. - PMC - PubMed
    1. Coronaviridae Study Group of the International Committee on Taxonomy of Viruses The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020;5:536–544. - PMC - PubMed
    1. Holshue M.L., DeBolt C., Lindquist S., Lofy K.H., Wiesman J., Bruce H., Spitters C., Ericson K., Wilkerson S., Tural A., Diaz G., Cohn A., Fox L., Patel A., Gerber S.I., Kim L., Tong S., Lu X., Lindstrom S., Pallansch M.A., Weldon W.C., Biggs H.M., Uyeki T.M., Pillai S.K. First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020;382:929–936. - PMC - PubMed
    1. Corman V.M., Landt O., Kaiser M., Molenkamp R., Meijer A., Chu D.K., Bleicker T., Brünink S., Schneider J., Schmidt M.L., Mulders D.G., Haagmans B.L., van der Veer B., van den Brink S., Wijsman L., Goderski G., Romette J.L., Joanna Ellis J., Zambon M., Peiris M., Goossens H., Reusken C., Koopmans M.P. Drosten CDetection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25:2000045. - PMC - PubMed