Clearance of COVID-19 from the human body has not been established. Our study collected the laboratory test results from patients and analyzed the correlation between early changes in serum indices and the virus clearance by univariable and multivariable COX regression models, with an aim to explore the risk factors for prolonged viral clearance. The study included 61 patients with COVID-19 treated at the Fifth Medical Center of PLA General Hospital in Beijing from 20 January 2020 to 20 February 2020. We set the total observation of the disease course to 20 days and the patients were divided into two groups (prolonged group, > 20d vs. normal group, </= 20d). The 48 patients with COVID-19 included in this study, 13 remained positive for viral nucleic acid monitoring 20 days after onset. The median for virus clearance was 16 days (range, 6-35 days). The results showed that hypertension, a lactate dehydrogenase level > 211.5 U/L, an interleukin 6 (IL-6) level > 12.5 pg/ml, and a NK lymphocyte percentage > 0.5% were associated with prolonged viral clearance. Therefore, we showed that a history of hypertension, an elevated IL-6 level, and an elevated percentage of NK cells were risk factors for prolonged viral clearance.