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

Clin Infect Dis. 2020 Mar 28;ciaa345. doi: 10.1093/cid/ciaa345. Online ahead of print.


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.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; Viral load; ddPCR.