Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as the cause of a worldwide pandemic. Many commercial SARS-CoV-2 reverse transcription-PCR (RT-PCR) assays have received Emergency Use Authorization from the U.S. Food and Drug Administration. However, there are limited data describing their performance, in particular the performance of high-throughput SARS-CoV-2 RT-PCR systems. We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. The overall agreement between the platforms was 96.4% (375/389). Cohen's kappa analysis rated the strength of agreement between the two platforms as "almost perfect" (κ = 0.922; standard error, 0.051). Furthermore, there was no significant difference between corresponding cycle threshold values generated on the two systems (P value = 0.88; Student's t test). Taken together, these data imply that the two platforms can be considered comparable in terms of their clinical performance. We believe that this information will be useful for those who have already adopted these platforms or are seeking to implement high-throughput RT-PCR testing to stem the SARS-CoV-2 pandemic.

Keywords: coronavirus disease 19 (COVID-19); high throughput; platform; reverse transcription-PCR (RT-PCR); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); system.

FIG 1

Box-and-whisker plot of 127 positive specimens (retrospective, 94, and prospective, 33) that had C_T values for the same target (ORF1ab) detected by each assay. The points along the y axis are presented from 40 through 10, as the C_T value is inversely proportional to the viral burden, with a specimen exhibiting a C_T value of 10 having a higher viral burden than one with a C_T value of 40.