Analytical comparisons of SARS-COV-2 detection by qRT-PCR and ddPCR with multiple primer/probe sets. Issue 1 (1st January 2020)

• Record Type: Journal Article
• Authors: Liu, Xinjin; Feng, Jiangpeng; Zhang, Qiuhan; Guo, Dong; Zhang, Lu; Suo, Tao; Hu, Wenjia; Guo, Ming; Wang, Xin; Huang, Zhixiang; Xiong, Yong; Chen, Guozhong; Chen, Yu; Lan, Ke
• Is Part Of: Emerging microbes & infections. Volume 9:Issue 1(2020)
• Page Start: 1175
• Page End: 1179
• Publication Date: 2020-01-01
• Subjects: SARS-CoV-2 -- diagnosis -- digital PCR -- real time PCR -- false positive -- false negative; Medical microbiology -- Periodicals; Communicable diseases -- Periodicals; Infection -- Periodicals; 616.9041
• DOI: 10.1080/22221751.2020.1772679
• Languages: English
• ISSNs: 2222-1751

Abstract

ABSTRACT: Different primers/probes sets have been developed all over the world for the nucleic acid detection of SARS-CoV-2 by quantitative real time polymerase chain reaction (qRT-PCR) as a standard method. In our recent study, we explored the feasibility of droplet digital PCR (ddPCR) for clinical SARS-CoV-2 nucleic acid detection compared with qRT-PCR using the same primer/probe sets issued by Chinese Center for Disease Control and Prevention (CDC) targeting viral ORF1ab or N gene, which showed that ddPCR could largely minimize the false negatives reports resulted by qRT-PCR [Suo T, Liu X, Feng J, et al. ddPCR: a more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens. medRxiv [Internet]. 2020;2020.02.29.20029439. Available from: https://medrxiv.org/content/early/2020/03/06/2020.02.29.20029439.abstract]. Here, we further stringently compared the performance of qRT-PCR and ddPCR for 8 primer/probe sets with the same clinical samples and conditions. Results showed that none of 8 primer/probe sets used in qRT-PCR could significantly distinguish true negatives and positives with low viral load (10 −4 dilution). Moreover, false positive reports of qRT-PCR with UCDC-N1, N2 and CCDC-N primers/probes sets were observed. In contrast, ddPCR showed significantly better performance in general for low viral load samples compared to qRT-PCR. Remarkably, the background readouts of ddPCR are relatively lower, which could efficiently reduce the production of false positive reports.