Sensitivity and efficiency of RNA sample pooling for real-time quantitative polymerase chain reaction testing for SARS-CoV-2

ABSTRACT

Background: In spite of the worth of pool testing in public health, data on the sensitivity and efficiency of real-time quantitative polymerase chain reaction (RT-qPCR) pool testing for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in middle and low-income countries are limited. Methods: We mixed single specimens of extracted RNA positive for the SARS-CoV-2 envelope (E) gene by RT-qPCR with negative specimens, in pools of 4 (n=89), 8 (n=92), 16 (n=102), and 32 (n=105) specimens each. We estimated the average change in cycle threshold (Ct) for each pool size and added it to the Ct values of the first 1,350 tests in our lab, to obtain dilution-corrected Ct values. We estimated pool sensitivity as the proportion of samples with dilution-corrected Ct >40, and used it in simulations of the efficiency (tests used/true case detected) of binary split pool testing. Results: We tested 388 pools. Average Ct changes were 2.21, 2.51, 3.27, and 3.94 cycles, for pools of 4, 8, 16, and 32 specimens, respectively. Corresponding pool tests sensitivities were 91.1%, 89.6%, 85.8% and 82.5%. Pool testing was substantially more efficient than individual testing. For prevalence of 0.5% to 2.0%, the efficiency of pools of ≥8 specimens was 30% to 280% higher, and the number of people tested was 4.4 to 13.9 times higher than those of individual testing. Conclusions: Binary split pool testing substantially increases the number of people tested and the number of true cases detected per test used. This strategy is key to curtail the transmission of SARS-CoV-2, by increasing efficiency in the identification and isolation of symptomatic and asymptomatic infected individuals. © 2022 Journal of Innovation Management. All rights reserved.