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

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 COVID19 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-CoV2 detection, especially for the samples with extremely low viral load, such as recurrent COVID-19 patients.

Automated summary

Digital PCR (dPCR) is more sensitive than qPCR in detecting SARS-CoV-2, especially for samples with low viral load, while it has similar specificity to qPCR. It can effectively distinguish other human coronaviruses and influenza viruses, and is more sensitive than qPCR in detecting the virus in negative samples from recurrent COVID-19 patients.