Performance Characteristics of SARS-CoV-2 PCR Tests in A Single Health System: Analysis of over 10,000 Results from Three Different Assays

Price, Travis K.; Bowland, Brian C.; Chandrasekaran, Sukantha; Garner, Omai B.; Yang, Shangxin

The current pandemic of 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 COVID-19 (CDC, Simplexa Direct, and TaqPath) to assess performance characteristics. We also re-tested remnant weakly positive specimens to assess analytical sensitivity. All assays had strong linear correlation and little bias among cycle threshold (Ct) values for PCR targets. In patients with first-test negative results (n=811), most (795, 98.0%) remained negative for all subsequent testing. Re-testing of weakly positive specimens (Ct>30) showed sensitivities as 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 (LRT) specimens had higher negative predictive value (NPV) (100%) than upper respiratory tract specimens (98%), highlighting the utility of testing LRT specimens when clinically indicated. NPV did not increase upon further repeat testing, providing strong evidence for discouraging unnecessary repeat testing for SARS-CoV-2.