Computer-Aided Medical Microbiology Monitoring Tool: A Strategy to Adapt to the SARS-CoV-2 Epidemic and That Highlights RT-PCR Consistency

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR, with up to 1,007 tests per day. To maintain a rapid turnaround time to support patient management and public health authorities' decisions, we moved from a case-by-case validation of RT-PCR to an automated validation and immediate transmission of the results to clinicians. To maintain high quality and to track possible aberrant results, we developed a quality-monitoring tool based on a homemade algorithm coded in R. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results corresponding to 30,198 patients. Patients tested several times led to 4,939 pairwise comparisons; 88% concordant and 12% discrepant. Among the 573 discrepancies, 428 were automatically solved by the algorithm. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to "Clinical evolution", 27.9% to "Preanalytical" problems, and 25.3% to "Stochastic". Finally, 11 discrepant results could not be explained, including 8 received from external partners for which clinical data were not available. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable TAT. This work highlighted the high RT-PCR consistency for the detection of SARS-CoV-2 and the importance of automated processes to handle a huge number of samples while preserving quality.