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

TLDR

COVID‑19 is a global public‑health emergency, yet the standard RT‑PCR test has diagnostic and therapeutic limitations. The study analyzed 323 specimens from 76 confirmed patients using droplet digital PCR and RT‑PCR targeting ORF1ab and N genes, collecting nasal, throat, sputum, blood, and urine samples along with clinical imaging for staging. ddPCR copy numbers correlated strongly with RT‑PCR cycle thresholds, detected additional positives missed by RT‑PCR, revealed higher viral loads in sputum than throat or nasal swabs, and showed that early and progressive stages had markedly higher loads than recovery, indicating that quantitative lower‑respiratory‑tract viral monitoring can assess disease progression, especially when viral loads are low.

Abstract

Abstract Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription–polymerase chain reaction (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 2 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 that tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy number of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). Four (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral loads ranging from 11.1 to 123.2 copies/test. The viral load of respiratory samples was then compared and the average viral load in sputum (17 429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, P < .001) and nasal swabs (651 ± 501 copies/test, P < .001). Furthermore, the viral loads in the early and progressive stages were significantly higher than that in the recovery stage (46 800 ± 17 272 vs 1252 ± 1027, P < .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.