Increasing SARS-CoV-2 testing capacity through specimen pooling: An acute care center experience.

Innovation in laboratory testing algorithms to address seemingly uncontrollable global supply chain shortages in plastics and other consumables during emergencies such as the current COVID-19 pandemic have been urgently needed. We report our experience with specimen pooling on SARS-CoV-2 testing in an acute care hospital microbiology laboratory during a high testing demand period that exceeded available processing capacity. A fully automated four-in-one pooling algorithm was designed and validated. Correlation and agreement were calculated. A custom Microsoft Excel tool was designed for use by the technologists to aid interpretation, verification and result entry. Cost-per-test impact for pooling was measured in reference to the consumable cost and was denoted as the percentage reduction of cost versus the baseline cost-per-test of testing specimens individually. Validation showed a strong correlation between the signals observed when testing specimens individually versus those that were pooled. Average crossing point difference was 1.352 cycles (95% confidence interval of -0.235 and 2.940). Overall agreement observed between individually and pooled tested specimens was 96.8%. Stratified agreement showed an expected decreased performance of pooling for weakly positive specimens dropping below 60% after a crossing point of 35. Post-implementation data showed the consumable cost-savings achieved through this algorithm was 85.5% after 8 months, creating both testing and resource capacity. Pooling is an effective method to be used for SARS-CoV-2 testing during the current pandemic to address resource shortages and provide quick turnaround times for high test volumes without compromising performance.

Validation of the Cepheid Xpert® Xpress SARS-CoV-2 using upper and lower respiratory tract specimens.

This study validated the performance of the reverse transcriptase-polymerase chain reaction (rRT-PCR) based Cepheid Xpert® Xpress SARS-CoV-2 assay against the TIB MOLBIOL E-gene/EAV, a standard laboratory rRT-PCR SARS-CoV-2 assay. Upper and lower respiratory tract samples (nasopharyngeal and nasal swabs, bronchoalveolar lavage, and tracheal aspirate) were obtained from patients suspected to have contracted COVID-19. Results from the Xpert® Xpress and standard rRT-PCR assays were compared for positive and negative agreement and analyzed for precision, reproducibility, 95% confidence intervals, and coefficients of variation. The Xpert® Xpress assay demonstrated 100% agreement with the standard lab rRT-PCR for both upper and lower respiratory tract samples. Both the Xpert® Xpress and lab rRT-CPR identified weakly positive (Ct values 35-39) sample replicates with 100% reproducibility and showed 100% precision in identifying triplicates of upper respiratory tract samples. The single-cartridge Xpert® Xpress system has a short turnaround time and can be employed to improve patient management and hospital bed allocation. Further verification of the system is required before implementation and consideration must be paid to its higher cost and impracticality for high-throughput use.