Comparison of qualitative and quantitative analyses of COVID-19 clinical samples

BACKGROUND: Qualitative and quantitative detection of nucleic acids of SARS-CoV-2, the pathogen that causes coronavirus disease 2019 (COVID-19), plays a significant role in COVID-19 diagnosis, surveillance, prevention, and control. METHODS: A total of 117 samples from 30 patients with confirmed COVID-19 and 61 patients without COVID-19 were collected. Reverse transcriptase quantitative PCR (RT-qPCR) and droplet digital PCR (ddPCR) were used for qualitative and quantitative analyses of these samples to evaluate the diagnostic performance and applicability of the two methods. RESULTS: The positive detection rates of RT-qPCR and ddPCR were 93.3% and 100%, respectively. Among the 117 samples, 6 samples were tested single-gene positive by RT-qPCR but positive by ddPCR, and 3 samples were tested negative by RT-qPCR but positive by ddPCR. The viral load of samples with inconsistent results were relatively low (3.1–20.5 copies/test). There were 17 samples (37%) with a viral load below 20 copies/test among the 46 positive samples, and only 9 of them were successfully detected by RT-qPCR. A severe patient was dynamically monitored. All 6 samples from this patient were tested negative by RT-qPCR, but 4 samples were tested positive by ddPCR with a low viral load. CONCLUSION: Qualitative analysis of COVID-19 samples can meet the needs of clinical screening and diagnosis, while quantitative analysis provides more information to the research community. Although both ddPCR and RT-qPCR can provide qualitative and quantitative results, ddPCR showed higher sensitivity and lower limit of detection than RT-qPCR, and it does not rely on the standard curve to quantify viral load. Therefore, ddPCR offers greater advantages than RT-qPCR.