Abstract: Background: It is unknown whether the pathogen spectrum of acute respiratory infection (ARTI) have changed significantly since the outbreak of COVID-19. Objective: To analyze the etiological characteristics of hospitalized children with ARTI before and after COVID-19 epidemic in Shenzhen, in order to provide reference for the clinical diagnosis, treatment and prevention of ARTI. Design: Cross-sectional survey. Methods: Pharyngeal swab samples submitted for the first time excluding those of neonates after hospitalization for clinical diagnosis of ARTI in Shenzhen Children's Hospital from September 2, 2019 to February 28, 2021 were included. Multiple PCR and capillary electrophoresis were used to detect 13 kinds of common pathogens in nasopharyngeal secretion samples. Based on the data from March 2020 to February 2021, the pathogen profiles of ARTI in different seasons were compared, from March to May in spring, from June to August in summer, from September to November in autumn, and from December to February of the next year in winter. Data from September 2,2019 to January 24,2020 were used as pre-COVID-19 data and from September 2, 2020 to January 24, 2021 as post-COVID-19 data for comparison. Main outcome measures: Mycoplasma, chlamydia and common virus spectrum of ARTI. Results: Among 12,022 cases of nasopharyngeal secretion, pathogens were detected in 7,589 cases with the detection rate of 63.13%. The highest detection rate was for human rhinovirus (HRV,24.83%), followed by respiratory syncytial virus (RSV,14.12%), human parainfluenza virus (HPIV,8.33%), human metapneumovirus (HMPV,7.01%), and mycoplasma pneumoniae (MP,5.37%).There were 1,329 cases of mixed infection with two or more pathogens was detected simultaneously, accounting for 11.05% (1,329/12,022). HRV and MP were the most common combination. The highest detection rate was 66.99% (1,924/2,874) in autumn, with RSV ranked first in the list (25.89%), followed by HRV (24.01%).The lowest detection rate was 16.20% (132/815) in spring, with HRV ranked first in the list (5.03%), followed by MP (3.80%).The detection rate of pathogens in children aged 6 months to 6 years was higher than the overall average.With the increase of age, the detection rate of RSV and HPIV decreased significantly, while the detection rate of MP increased. There was no significant difference in the detection rate between male and female patients (P>0.05). Before COVID-19 epidemic, the detection rate of pathogens was 78.57%（2,592/3,299）, with HRV(36.37%), MP (15.40%), RSV(10.03%), adenovirus (9.03%) as the main pathogens. A total of 764 mixed infection cases were found (23.16%). After COVID-19 epidemic, the detection rate of pathogens during the same period was 65.89%（3,500/5,312）, with HRV (23.78%), RSV (14.74%), HMPV(12.65%) and HPIV (12.12%) as the main pathogens, and there were 459 cases (8.64%) of mixed infections. Conclusion: The pathogen spectrum of ARTI had changed significantly after the outbreak of COVID-19. The detection rate of HMPV,HPIV,RSV,Bocavirus had increased significantly. However, the detection rate of MP, chlamydia, influenza A,H1N1, H3N2, influenza B, HRV, adenovirus, mixed infections decreased significantly.

Key words: Acute respiratory infection, Children, Pathogens, COVID-19, Shenzhen