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

Abstract

Background: Real-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. Methods: We 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. Results: The 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. Conclusions: ddPCR 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. ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial This study does not contain a clinical trial. ### Funding Statement This study was supported by National Science and Technology Major Project (#2018ZX10733403 and #2018YFA0900801), China NSFC grants (#81672008) and Hubei Natural Science Foundation (#2018CFA035), Basic Scientific Research Foundation of Central Universities (#2042019gf0026), Ministry of Science and Technology of China, the National Mega Project on Major Infectious Disease Prevention (#2017ZX10103005) and National Key Research and Development Program of China (#2018YFE0204500). None of the funders had any role in the study design and the collection, analysis, and interpretation of data or in the writing of the article and the decision to submit it for publication. The researchers confirm their independence from funders and sponsors. ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The authors confirm that the data supporting the findings of this study are available within the article.

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Citation:

Suo Tao, Liu Xinjin, Guo Ming, Feng Jiangpeng, Hu Wenjia, Yang Yang, Zhang Qiuhan, Wang Xin, Sajid Muhanmmad, Guo Dong, Huang Zhixiang, Deng Liping, Chen Tielong, Liu Fang, Xu Ke, Liu Yuan, Zhang Qi, Liu Yingle, Xiong Yong, Guo Guozhong, Chen Yu, Lan Ke. (2020). ddPCR: a more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens. Cold Spring Harbor Laboratory Press