BACKGROUND: Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription PCR (RT-PCR) method has limitations for clinical diagnosis and treatment. METHODS: A total of 323 samples from 76 COVID-19 confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based two target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging. RESULTS: In 95 samples tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy numbed of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). 4 (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral load ranging from 11.1 to 123.2 copies/test. Then the viral load of respiratory samples was compared and the average viral load in sputum (17429 +/- 6920 copies/test) was found to be significantly higher than in throat swabs (2552 +/- 1965 copies/test, p < 0.001) and nasal swabs (651 +/- 501 copies/test, p < 0.001). Furthermore, the viral load in the early and progressive stages were significantly higher than that in the recovery stage (46800 +/- 17272 vs 1252 +/- 1027, p < 0.001) analyzed by sputum samples. CONCLUSIONS: Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.
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