Evaluation of specimen pooling for SARS-CoV-2 testing by real time RT-PCR in Khon Kaen province

Abstract

       The objective of this study was to determine the optimal pool size and evaluate the SARS-CoV-2 (Corona virus 2019) testing by a real time RT-PCR with pooled samples compared to a single sample. The results showed that the pool of 5 samples could be used to detect the SARS-CoV-2 with real time RT-PCR. A total number of 310 nasopharyngeal swab and throat swab samples (17 positives and 293 negatives) were tested in 62 pools samples compared to 310 single samples. The detection and non-detection rate of the pooled samples were 100% comparing to a single sample. With Cohen’s kappa analysis results indicated the perfect agreement of these two methods (K = 1). The Ct of pool sample testing was greater than a single sample from 0.78 to 3.55 and 1.01 to 3.05 for ORF-1ab and N gene, respectively. The Bland-Altman plots showed that the Ct differences of 17 positive samples between the two methods were inside the limit of agreement, and their mean Ct differences were 2.06 and 2.28 for ORF-1ab and N genes, respectively. This study shows that a range of pool sizes from 2 to 5 samples per pool can be used to detect the presence of SARS CoV-2 by a real time RT-PCR.  As the COVID-19 pandemic, the pool sample testing can increase the test capacity of the laboratory, reducing the turnaround time of the result and save the reagent, which limited and expensive. Lastly, it can relieve the workload of the laboratory. Nevertheless, the limitation of pool sample testing is that samples with low viral load or the Ct ≥ 38 could appear as a false-negative result.