Abstract
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.
Highlights
The rapid spread of the COVID-19 pandemic caused unprecedented challenges for diagnostic microbiology laboratories
Since the implementation of SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) assays and for a period of four months, 30,198 patients were tested by Interestingly, 7 of the discrepancies observed in the 1-3 days interval were explainable by nosocomial (n=6) or community (n=1) acquired infections based on health records, which explained the quick negative to positive transition
Over 10 day, the clinical evolution of the disease was the main explanation (72.1%, n=220/305) for discrepancies, as it was the default explanation retained by our automatic pipeline for discrepant results from samples collected more than 10 days apart in absence of any other explanation
Summary
The rapid spread of the COVID-19 pandemic caused unprecedented challenges for diagnostic microbiology laboratories. Rapid and high throughput SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) developed early during the crisis became the cornerstone of patient diagnosis as well as hospital and public health management (Caruana et al, 2020; Corman et al, 2020; Tadini et al, 2020). Microbiology laboratories were reorganized to respond to the high demand for SARS-CoV-2 testing (Posteraro et al, 2020). This situation required (i) the rapid adaptation of infrastructures, (ii) quick validation and implementation of new RT-PCR assays, (iii) working hour extension and new workforce employment. The quality of results provided by clinical microbiology laboratories, SARSCoV-2 testing and routine analyzes, had to be maintained throughout the crisis. To maintain a minimal TAT, results were released to the clinicians after technical validation based on the FastFinder software (UgenTec NV, Hasselt, Belgium) that automatically analyzes RT-PCR amplification curves
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