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This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children\u2019s Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The<jats:italic>Influenza A<\/jats:italic>(InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of<jats:italic>Mycoplasma pneumoniae<\/jats:italic>,<jats:italic>Human adenovirus<\/jats:italic>, and<jats:italic>Human rhinovirus<\/jats:italic>also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of<jats:italic>Human respiratory syncytial virus<\/jats:italic>,<jats:italic>Human parainfluenza<\/jats:italic>virus, and<jats:italic>Human metapneumovirus<\/jats:italic>increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of<jats:italic>Human respiratory syncytial virus<\/jats:italic>,<jats:italic>Human parainfluenza<\/jats:italic>virus, and<jats:italic>Human metapneumovirus<\/jats:italic>increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12985-021-01669-y","type":"journal-article","created":{"date-parts":[[2021,10,10]],"date-time":"2021-10-10T20:16:05Z","timestamp":1633896965000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["Comparison of 11 respiratory pathogens among hospitalized children before and during the COVID-19 epidemic in Shenzhen, China"],"prefix":"10.1186","volume":"18","author":[{"given":"Li","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heping","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ailiang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongjun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Zhi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuejie","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanming","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunsheng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjian","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,9]]},"reference":[{"issue":"14","key":"1669_CR1","doi-asserted-by":"publisher","first-page":"2000326","DOI":"10.2807\/1560-7917.ES.2020.25.14.2000326","volume":"25","author":"PY Boelle","year":"2020","unstructured":"Boelle PY, Souty C, Launay T, Guerrisi C, Turbelin C, Behillil S, et al. 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