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

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

Posted 06 Mar 2020
medRxiv DOI: 10.1101/2020.02.29.20029439

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.

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