Effectiveness of a Sample Pooling Strategy to Detect SARS-CoV-2, Thimphu, Bhutan, January–February 2021

This retrospective study aimed to evaluate the effectiveness of a pooling strategy to detect SARS-CoV-2 by comparing cycle threshold (Ct) values of pooled samples and deconvoluted samples, and its cost savings. We evaluated 2,687 pools of 5 samples (n=13,435) and 5,444 pools of 10 samples (n=54,440). Of these, 51 and 40 pools were positive from the 5- and 10-sample pools, respectively. We analyzed the Ct values of positive samples obtained through pooled testing and compared them to the Ct values of their corresponding individual positive samples. We observed a decrease in the mean Ct value by 2.0 for the 5-sample pools and by 3.6 for the 10-sample pools when the pooled samples were deconvoluted and individually tested. The drop in the mean Ct value was more pronounced in samples with a low viral load. Where the known positive COVID-19 prevalence rate was 0.13%, the pooling strategy resulted in significant savings of 89.26% for pools of 10 samples and 78.10% for pools of 5 samples when compared to individual testing. Employing this pooling approach led to substantial savings in resources and time when conducting mass screening.