Validation and Implementation of Pooled Testing Protocol for SARS-CoV-2 RTPCR: a strategy to counter delays in COVID-19 diagnosis

Abstract

Abstract BACKGROUND Indian Council of Medical Research (ICMR) laid guidelines for pooled testing of SARS-CoV-2 in areas with low prevalence (< 5%) due to high cost and turn-around time of PCR test. This study evaluated sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of pooled testing guidelines laid out by ICMR and performed the cost benefit analysis of the strategy. METHODS Study was divided in two phases. In first phase of study, 1000 samples were tested by pool and de-convoluted method to validate the pooling strategy advised by ICMR. A single pool was prepared from 5 VTMs of individual patients. RTPCR for E, ORF and RdRp genes was performed. In second phase, pooled testing strategy was applied to approximately 11,000 patient samples during low prevalence phase of Covid-19 pandemic, for cost benefit analysis. RESULTS Overall, sensitivity and specificity was >/= 95%. Negative predictive value was 99%; essential for mass screening. The average difference in CT values between pool and individual samples of E, ORF, and RdRp genes was 2.49, 2.62, and 2.28, respectively. Cost saved in second phase of study was INR 8,917,000/- . CONCLUSION The pooling strategy can be successfully applied for accurately and rapidly testing a large number samples. The cost saved was significant considering India is resource limited country with a large population.