Association of clinical characteristics and vaccines with risk of persistently viral clearance in patients infected with SARS-CoV-2 Omicron variant in Shanghai, China

Importance: The global COVID-19 pandemic does not appear to end in the near future. Currently, limited data are available on the risk factors for delayed viral clearance in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection.Objective: This study aimed to investigate the association of clinical characteristics and vaccination with prolonged viral clearance. Methods: This retrospective cohort included 16,985 patients who had contracted the SARS-CoV-2 Omicron variant between April 5 and May 30, 2022, in Shanghai, China, and had mild or no symptoms. The patients were admitted to the quarantine venue at the Shanghai New International Expo Center.Results: Of the 16,985 participants, the occurrence of viral clearance was <= 8 and > 8 days in 11,009 (64.8 %) and 5976 (35.2 %) participants, respectively. Risk factors related to patients who remained persistently polymerase chain reaction (PCR)-positive were sex (Male, odds ratio [OR] 1.221, p < 0.001), older age (35-49, OR 1.389, p < 0.001; 50-64, OR 1.659, p < 0.001;>= 65, OR 2.139, p < 0.001), presence of symptoms (OR 1.093, p = 0.030), number of vaccinations (two doses, OR 0.753, p < 0.001; three doses, OR 0.797, p < 0.001; four doses, OR 0.543, p < 0.001), and cycle threshold (Ct) value for ORF1ab gene at diagnosis (25-35, OR 0.235, p < 0.001; >35, OR 0.079, p < 0.001). The lower rates of increase in Ct values were observed in the later viral shedding group than in the early viral shedding group for ORF1ab (beta =-0.791, p < 0.001) and N genes (beta =-0.825, p < 0.001).Conclusion: Prolonged SARS-CoV-2 RNA detection and higher viral concentrations were associated with factors such as male sex, older age, symptomatic status, and fewer doses of vaccination in patients admitted to Shanghai Makeshift Hospital between April 5 and May 30, 2022.