Feasibility of Pooled Testing in a Fully Automated High Throughput Platform for Effective Management of SARS-CoV-2 in India

Abstract

Introduction: Testing for extreme acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been hit tremendously worldwide, as the scarcity of test kits has now become a major bottleneck, with the need for testing throughput growing. The study assessed the feasibility of pooled testing in the high throughput machine of Roche Cobas 6800 rapidly increasing the testing number for containing the virus spread and management of cases.Methodology: ICMR-RMRC, Bhubaneswar receives samples from various district hospitals from different districts of Odisha. Pooled testing was conducted in 2 methods. Firstly, we adopted the simple two-stage testing algorithm known as Dorfman pooling with minor modification to avoid selection bias and secondly we evaluated the ability of COBAS for detection of a single positive sample within a pool of negative samples.Results: The Cobas 6800 was able to detect the SARS-COV virus in all the samples, however, the amplified RNA reached the threshold later as the number of negative samples increased in the pool. We demonstrated strategies for pooling, which improve test efficiency and while maintaining high sensitivity in a high-throughput system. The comparison of 1410 samples tested individually and in pools of five samples/pool showed that test results were not significantly affected. Implementing the five-sample Dorfman pooling to test 1410 samples, we identified 42 (2.9%) SARS-CoV-2 positive samples, achieving a 3-fold increase in throughput with one-third of the cost.Conclusion: To the best of our knowledge this study is 1st of its kind to assess the feasibility of pooled testing in high throughput machines. As ICMR has always stressed, aggressive timely testing is the standard protocol for containing the virus spread and management of cases, these high throughput machines installed in six states with a high prevalence of COVID-19, can effectively increase the testing capacity by 2-3 fold, adopting the pooled testing strategy for successful management of SARS-CoV-2.