Objective To analyze the viral shedding time and its influencing factors in different site samples of patients infected with severe acute respiratory syndrome coronavirus 2 (SARA-CoV-2) omicron BA.2 variant. Methods Real-time fluorescence polymerase chain reaction was used to detect SARS-CoV-2 nucleic acid in nasopharyngeal swab, sputum and anal swab from 217 patients with coronavirus disease 2019 (COVID-19) who were infected with severe acute respiratory syndrome coronavirus 2 omicron BA.2 variant confirmed by gene sequencing in The First Affiliated Hospital of Naval Medical University (Second Military Medical University). The differences of viral shedding time of different site samples were compared. Stratified analysis and multiple linear regression analysis were used to explore the influencing factors of viral shedding time in different site samples. Results The age of the 217 COVID-19 patients was 32.0 (24.0, 50.5) years old, 59.0% of them were males (n=128), and 41.0% were females (n=89). Eight (3.7%) cases were diagnosed with asymptomatic infection, 184 (84.8%) cases were mild type, 21 (9.7%) cases were moderate type, 3 (1.4%) cases were severe type, and 1 (0.5%) case was critical type. A total of 70 (32.3%) patients were treated with molnupiravir. The viral shedding time of SARS-CoV-2 nucleic acid in nasopharyngeal swab, sputum and anal swab was 13.0 (11.0, 17.0) d, 16.5 (13.0, 21.0) d and 10.0 (5.3, 11.0) d, respectively, with the differences being significant between them (all P<0.001). Age ≥ 60 years old, underlying diseases (especially hypertension, coronary artery diseases, or neurological diseases), and clinical classification of moderate type were risk factors for prolonged viral shedding time in nasopharyngeal swab; male sex and underlying diseases were risk factors for prolonged viral shedding time in sputum; and male sex was a risk factor for prolonged viral shedding time in anal swab. Multiple linear regression analysis showed that critical type was an independent risk factor for prolonged viral shedding time in nasopharyngeal swab (P<0.05), and male sex and underlying diseases were independent risk factors for prolonged viral shedding time in sputum (both P<0.05). Conclusion Among patients infected with omicron BA.2 variant, the viral shedding time in sputum is the longest and that in anal swab is the shortest. Male patients and/or patients with underlying diseases have longer viral shedding time in sputum.