ddPCR: a more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens

Suo, Tao; Liu, Xinjin; Feng, Jiangpeng; Guo, Ming; Hu, Wenjia; Guo, Dong; Ullah, Hafiz; Yang, Yang; Zhang, Qiuhan; Wang, Xin; Sajid, Muhanmmad; Huang, Zhixiang; Deng, Liping; Chen, Tielong; Liu, Fang; Xu, Ke; Liu, Yuan; Zhang, Qi; Liu, Yingle; Xiong, Yong; Chen, Guozhong; Lan, Ke; Chen, Yu

BackgroundReal-Time PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load in patient throat and the limitation of RT-PCR, significant numbers of false negative reports are inevitable, which should not be ignored. MethodsWe explored the feasibility of droplet digital PCR (ddPCR) to detect SARS-CoV-2 from 57 clinical pharyngeal swab samples and compared with RT-PCR in terms of the sensitivity and accuracy. Among 57 samples, all of which were reported as negative nucleic acid by officially approved clinical RT-PCR detection, 43 samples were collected from suspected patients with fever in clinic, and 14 were from supposed convalescents who were about to discharge after treatment. The experiment was double-blind. ResultsThe lower limit of detection of the optimized ddPCR is at least 500 times lower than that of RT-PCR. The overall accuracy of ddPCR for clinical detection is 94.3 %. 33 out of 35 negative pharyngeal swab samples checked by RT-PCR were correctly judged by ddPCR based on the follow-up investigation. In addition, 9 out of 14 (64.2 %) supposed convalescents with negative nucleic acid test twice by RT-PCR were positive by ddPCR detection. ConclusionsddPCR shows superiority for clinical detection of SARS-CoV-2 to reduce the false negatives, which could be a powerful complement to the current standard RT-PCR. Before the ddPCR to be approved for diagnosis, the current clinical practice that the convalescent continues to be quarantined for 2 weeks is reasonable and necessary.