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

Front Cell Infect Microbiol. 2021 Sep 13:11:594577. doi: 10.3389/fcimb.2021.594577. eCollection 2021.


Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on 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. To maintain a rapid turnaround time, we moved from a case-by-case validation of RT-PCR results to an automated validation and immediate results transmission to clinicians. A quality-monitoring tool based on a homemade algorithm coded in R was developed, to preserve high quality and to track aberrant results. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results. Patients tested several times led to 4,939 pairwise comparisons: 88% concordant and 12% discrepant. The algorithm automatically solved 428 out of 573 discrepancies. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to the clinical evolution of the disease, 27.9% to preanalytical factors, and 25.3% to stochasticity of the assay. Finally, 11 discrepant results could not be explained, including 8 for which clinical data was not available. For patients repeatedly tested on the same day, the second result confirmed a first negative or positive result in 99.2% or 88.9% of cases, respectively. 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 turnaround time. This work highlights the high RT-PCR consistency for the detection of SARS-CoV-2 and the necessity for automated processes to handle a huge number of microbiological results while preserving quality.

Keywords: COVID-19; R-script, algorithm; RT-PCR; SARS-CoV-2; biomedical validation; delta checks; quality-monitoring.

MeSH terms

  • COVID-19*
  • Computers
  • Humans
  • Pandemics
  • Reverse Transcriptase Polymerase Chain Reaction
  • SARS-CoV-2*
  • Sensitivity and Specificity