Estimating the false positive rate of highly automated SARS-CoV-2 nucleic acid amplification testing
AbstractMolecular testing for infectious diseases is generally both very sensitive and specific. Well-designed PCR primers rarely cross-react with other analytes, and specificities seen during test validation are often 100%. However, analytical specificities measured during validation may not reflect real-world performance across the entire testing process. Here, we use the unique environment of SARS-CoV-2 screening among otherwise well individuals to examine the false positivity rate of high throughput so-called “sample-to-answer” nucleic acid amplification testing (NAAT) on three commercial assays: the Hologic Panther Fusion®, Hologic Aptima® transcription mediated amplification (TMA), and Roche cobas® 6800. We used repetitive sampling of the same person as the gold standard to determine test specificity rather than retesting of the same sample. We examined 451 people repetitively sampled over 7 months via nasal swab, comprising 7,242 results. During the study period there were twelve positive tests (0.17%) from 9 people. Eight positive tests (0.11%, five individuals) were considered bona fide true positives based on repeat positives or outside testing and epidemiological data. One positive test had no follow-up testing or metadata and could not be adjudicated. Three positive tests (three individuals) did not repeat as positive on a subsequent collection, nor did the original positive specimen test positive on an orthogonal platform. We consider these three tests false positives and estimate the overall false positive rate of high-throughput automated, sample-to-answer NAAT testing to be approximately 0.041% (3/7242). These data help laboratorians, epidemiologists, and regulators understand specificity and positive predictive value associated with high-throughput NAAT testing.