Development and evaluation of three automated media pooling and molecular diagnostic systems for the detection of SARS-CoV-2

Abstract

Pooled testing combined with molecular diagnostics for the detection of SARS-CoV-2 is a promising method that can increase testing capacities and save costs. However, pooled testing is also associated with the risks of decreased test sensitivity and specificity. To perform reliable pooled testing, we developed and validated three automated media pooling and molecular diagnostic systems. These pooling systems (geneLEAD-PS, Panther-PS, and Biomek-PS) comprised existing automated molecular detection platforms, corresponding automated media pooling devices, and laboratory information management systems. Analytical sensitivity analysis and mock sample evaluation were performed, and the obtained data were used to determine the sizes of the pool for the validation study. In the validation study, a total of 2,448, 3,228, and 6,420 upper respiratory samples were used for geneLEAD-PS, Panther-PS, and Biomek-PS, respectively, and the diagnostic performances were compared with the reference RT‒PCR assay. A pool size of 6 for geneLEAD-PS and a pool size of 4 for Panther-PS and Biomek-PS were selected for the validation studies. All three systems showed high positive percent agreement values of ≥90.5% and negative percent agreement values of ≥99.8% for any specimen type. Pooled testing resulted in a 65%-71% reduction in cost per sample. The testing capacities of geneLEAD-PS, Panther-PS, and Biomek-PS were 144 samples in 3 hours, 384 samples in 5.5 hours, and 376 samples in 4 hours, respectively. The developed pooling systems showed robust diagnostic performances and will increase the testing capacities of molecular diagnostic tests while saving costs and may contribute to infection control of COVID-19.IMPORTANCEDuring the COVID-19 pandemic, there have been surges in demand for accurate molecular diagnostic testing and laboratory supply shortages. Pooled testing combined with highly sensitive molecular testing, which entails mixing multiple samples as a single sample, is a promising approach to increase testing capacities while reducing the use of consumables. However, pooled testing is associated with risks that compromise diagnostic performance, such as false negatives due to dilution of positive samples or false positives due to cross-contamination. To perform reliable pooled testing, three different pooling systems (an automated pooling device, an automated molecular detection platform, and a laboratory information management system) were developed to accurately interpret pooled testing results. These three systems were validated using multiple clinical samples and showed high concordance with individual testing. The developed pooling systems will contribute to increasing reliable molecular testing capacities while using fewer consumables and saving costs.

Keywords: COVID-19; SARS-CoV-2; automation; liquid handling instrument; pooling.

Fig 1

Three pooling systems were developed in this study. The geneLEAD pooling system (geneLEAD-PS) comprised Pooling Mini Station (Precision System Science, Chiba, Japan), geneLEAD VIII (Precision System Science), and PSS LIS (Precision System Science). The Panther pooling system (Panther-PS) comprised Biomek 4000 (Beckman Coulter, Tokyo, Japan), Panther system (Hologic Japan, Tokyo, Japan), and SimpPCR (Nippon Control System, Yokohama, Japan). The Biomek pooling system (Biomek-PS) comprised JANUS G3 Primary Sample Reformatter (Revvity Japan, Yokohama, Japan), Biomek i5 (Beckman Coulter), and SimpPCR (Nippon Control System). Each pooling device included a liquid handler and a barcode reader. LIS, laboratory information management system.