The potential application of digital PCR in detecting different SARS-CoV-2 viral loads

Rapid, effective, and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial. It is essential to control the spread of the virus and ensure accurate treatment for the disease. In the study, a total of 170 clinical specimens from 164 patients were collected and analyzed through digital PCR (dPCR) and real time quantitative reverse transcription PCR (RT-qPCR). The results showed an 86.41 % agreement between dPCR and RT-qPCR, with differences primarily noted in suspected cases. RT-qPCR exhibited a sensitivity of 84.78 %, specificity of 95.83 %, and accuracy of 86.42 %, which were comparatively lower than the 100 % accuracy of dPCR. Subsequently, we explored the potential correlation between these two methodologies based on Ct value groups. A strong negative correlation was observed between RT-qPCR and dPCR techniques in the Ct value group between 25 and 35, while the correlation was weakest in the Ct > 35 group. Moreover, the concordance rate for detecting the ORF1 (142/162) gene by RT-qPCR was lower compared to that of the N gene (149/162). Additionally, nucleic acid concentrations for ORF1 gene detection were lower than those for N gene detection in dPCR. In conclusion, this study shows that dPCR provides more reliable detection than RT-qPCR, especially for samples with low viral loads. Furthermore, dPCR effectively tracked changes in viral load during hospitalization, facilitating the diagnosis and treatment of COVID-19.