Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

Abstract

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. 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. 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. Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.