Abstract: Background：The quantitative analysis focused on virus shedding duration of immunocompromised (IC) children infected with SARSCoV2 during the Omicron wave is rare. Objective：To investigate the differences in virus shedding duration between IC and nonIC patients infected with Omicron and to provide firstline information for public health policy making and precise epidemic prevention strategy. Design：Retrospective cohort study. Methods：The study population was Omicron infected inhospital pediatric patients. According to their immune condition, these patients were divided into IC and nonIC groups. The immunocompromised state was divided into complete immunocompromised condition, relative immunocompromised condition, and immunosuppressive therapy. The nonIC group was matched with gender, age, type of SARSCoV2 infection, and 1:3 ratio in the IC group. The SARSCoV2 genome PCR test detected nasal swab samples. Cycle threshold (Ct) value ≥35 was the endpoint. Main outcome measures：SARSCoV2 virus shedding time. Results：From April 12 to May 12, 2022, we enrolled 728 patients hospitalized in Renji Hospital, School of Medicine, Shanghai Jiao Tong University, the dedicated hospital in Shanghai. Among them, 33 patients were in the IC group, including 8 cases in complete immunocompromised state and 23 cases in a relative immunocompromised state. Two patients without complete or relative immunocompromised state received immunosuppressive therapy. Ninetynine patients were included in the nonIC group. No significant differences were detected in clinical phenotypes, treatment, and vaccination between the two groups. The virus shedding time between IC and nonIC groups had a significant difference (16.5±6.8 vs. 10.3±4.4 days). The virus shedding duration of mild type was (14.0±8.3) and (9.7±3.1) days, (18.3±4.9) and (11.2±5.9) days in moderate type. Significant differences were detected. The virus shedding duration of the two groups had significant differences during the 9th14th days (P=0.0050.039). The virus shedding duration of moderate type in two groups had significant differences during the 10th15th days. Three patients (9%) in the IC group had positive PCR test results again after two weeks. The disease type of these three patients were milder than the previous infection. All three patients were unvaccinated. Conclusion：Virus shedding duration of IC patients was significantly longer than that of nonIC patients in Omicron wave. The prolonged virus shedding duration in IC patients was mainly in the 9th14th days. The IC patients had a higher risk of recurrent positive PCR results, which indicated longer isolation time and a strict nucleic acid test strategy after negative PCR test results.

Key words: SARS-COV-2, Immune system phenomena, Nucleic acid amplification techniques, Virus shedding