The Hologic Aptima SARS-CoV-2 assay enables high ratio pooling saving reagents and improving turnaround time.

BACKGROUND: The Hologic Aptima™ TMA SARS-CoV-2 assay was employed to test pooled nasopharyngeal (NP) samples to evaluate the performance of pooled sample testing and characterize variables influencing results. METHODS: Results on 1033 previously tested NP samples were retrieved to characterize the relative light units (RLU) of SARS-CoV-2-positive samples in the tested population. The pooling strategy of combining 10 SARS-CoV-2 samples into one pool (10/1) was used in this study. The results were compared with neat sample testing using the same Aptima™ TMA SARS-CoV-2 assay and also the CDC RT-PCR and the Cepheid SARS-CoV-2 assays. RESULTS: The Aptima assay compares favorably with both CDC RT-PCR and the Cepheid SARS-CoV-2 assays. Once samples are pooled 10 to 1 as in our experiments, the resulting signal strength of the assay suffers. A divide opens between pools assembled from strong-positive versus only weak-positive samples. Pools of the former can be reliably detected with positive percent agreement (PPA) of 95.2%, while pools of the latter are frequently misclassified as negative with PPA of 40%. When the weak-positive samples with kRLU value lower than 1012 constitute 3.4% of the total sample profile, the assay PPA approaches 93.4% suggesting that 10/1 pooled sample testing by the Aptima assay is an effective screening tool for SARS-CoV-2. CONCLUSION: Performing pooled testing, one should monitor the weak positives with kRLU lower than 1012 or quantification cycle (Cq) value higher than 35 on an ongoing basis and adjust pooling approaches to avoid reporting false negatives.

Pathology Informatics and Robotics Strategies for Improving Efficiency of COVID-19 Pooled Testing.

The global rise of the coronavirus disease 2019 pandemic resulted in an exponentially increasing demand for severe acute respiratory syndrome coronavirus 2 testing, which resulted in shortage of reagents worldwide. This shortage has been further worsened by screening of asymptomatic populations such as returning employees, students, and so on, as part of plans to reopen the economy. To optimize the utilization of testing reagents and human resources, pool testing of populations with low prevalence has emerged as a promising strategy. Although pooling is an effective solution to reduce the number of reagents used for testing, the process of pooling samples together and tracking them throughout the entire workflow is challenging. To be effective, samples must be tracked into each pool, pool-tested and reported individually. In this article, we address these challenges using robotics and informatics.

Optimizing COVID-19 testing capabilities and clinical management using pathology informatics.

Coronavirus disease 2019, first reported in China in late 2019, has quickly spread across the world. The outbreak was declared a pandemic by the World Health Organization on March 11, 2020. Here, we describe our initial efforts at the University of Florida Health for processing of large numbers of tests, streamlining data collection, and reporting data for optimizing testing capabilities and superior clinical management. Specifically, we discuss clinical and pathology informatics workflows and informatics instruments which we designed to meet the unique challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We hope these results benefit institutions preparing to implement SARS-CoV-2 testing.