Digital PCR assay for the effective detection of COVID-19 patients with SARS-CoV-2 low viral load

Yong Sun; Chengchao Ding; Qingqing Chen; Jiajia Xie; Junling Yu; Yonglin Shi; Chengcheng Jiang; Zhuhui Zhang; Hongliang He; Yinglu Ge; Wenting Li; Jun He; Yong Gao

doi:10.1016/j.jviromet.2021.114185

Digital PCR assay for the effective detection of COVID-19 patients with SARS-CoV-2 low viral load

J Virol Methods. 2021 Sep:295:114185. doi: 10.1016/j.jviromet.2021.114185. Epub 2021 May 26.

Authors

Yong Sun¹, Chengchao Ding², Qingqing Chen¹, Jiajia Xie², Junling Yu¹, Yonglin Shi¹, Chengcheng Jiang², Zhuhui Zhang¹, Hongliang He², Yinglu Ge¹, Wenting Li², Jun He³, Yong Gao⁴

Affiliations

¹ Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China.
² First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
³ Anhui Center for Disease Control and Prevention, Hefei, Anhui, 230601, China; Key Laboratory for Medical and Health of the 13th Five-Year Plan, 12560, Fanhua Avenue, Hefei, Anhui, China. Electronic address: heliosking@sina.com.
⁴ First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China. Electronic address: ygao387@ustc.edu.cn.

Abstract

Objective: Viral nucleic acid detection by real-time reverse transcription polymerase chain reaction (qPCR) is the current standard method for diagnosis of SARS-CoV-2 infection. However, due to low viral load in some COVID-19 patients, false negative results from this method have been repeatedly reported.

Method: In this study, we compared the sensitivity and specificity of digital PCR (dPCR) in simulated samples and clinical samples with qPCR assay through a series of vigorous tests.

Results: The results showed that dPCR was more sensitive than qPCR especially for samples with low viral load (≤3 copies). In addition, dPCR had similar specificity as qPCR and could effectively distinguish other human coronaviruses and influenza virus from SARS-CoV-2. More importantly, dPCR was more sensitive than qPCR in detecting the virus in the "negative" samples from recurrent COVID-19 patients.

Conclusions: In summary, dPCR could serve as a powerful complement to the current qPCR method for SARS-CoV-2 detection, especially for the samples with extremely low viral load, such as recurrent COVID-19 patients.

Keywords: Digital PCR (dPCR); Recurrent COVID-19 patient; SARS-CoV-2; Sensitivity; Specificity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 / diagnosis*
COVID-19 / virology
COVID-19 Nucleic Acid Testing / methods*
Humans
RNA, Viral / genetics
Real-Time Polymerase Chain Reaction / methods*
Recurrence
SARS-CoV-2 / genetics
SARS-CoV-2 / isolation & purification*
Sensitivity and Specificity
Viral Load*

Substances

RNA, Viral