{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T05:56:13Z","timestamp":1791870973917,"version":"4.3.4"},"reference-count":48,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T00:00:00Z","timestamp":1723161600000},"content-version":"vor","delay-in-days":8,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81902037"],"award-info":[{"award-number":["81902037"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Influenza Resp Viruses"],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We employed de novo assembly and combined homology\u2010 and feature\u2010based methods to characterize the respiratory virome in whole\u2010genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia\u2010reduced vOTUs for infecting <jats:italic>Prevotella<\/jats:italic>, <jats:italic>Neisseria<\/jats:italic>, and <jats:italic>Veillonella<\/jats:italic>, whereas pneumonia\u2010enriched vOTUs included polyomavirus, human adenovirus, and phages targeting <jats:italic>Staphylococcus<\/jats:italic>, <jats:italic>Streptococcus<\/jats:italic>, <jats:italic>Granulicatella<\/jats:italic>, and <jats:italic>Actinomyces<\/jats:italic>. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia\u2010enriched OP vOTUs in NP and BALF samples compared to pneumonia\u2010reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)\u2010based testing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.<\/jats:p><\/jats:sec>","DOI":"10.1111\/irv.13362","type":"journal-article","created":{"date-parts":[[2024,8,9]],"date-time":"2024-08-09T08:45:46Z","timestamp":1723193146000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Next\u2010Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia"],"prefix":"10.1111","volume":"18","author":[{"given":"Song","family":"Cui","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, College of Basic Sciences Dalian Medical University  Dalian China"},{"name":"Department of Critical Care Medicine Dalian Municipal Central Hospital  Dalian China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruochun","family":"Guo","sequence":"additional","affiliation":[{"name":"Puensum Genetech Institute  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changming","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Rheumatology and Immunology The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine  Guiyang China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Zhang","sequence":"additional","affiliation":[{"name":"Puensum Genetech Institute  Wuhan 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Genetech Institute  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2697-4562","authenticated-orcid":false,"given":"Qiulong","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Basic Sciences Dalian Medical University  Dalian China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufang","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, College of Basic Sciences Dalian Medical University  Dalian China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,8,9]]},"reference":[{"key":"e_1_2_10_2_1","unstructured":"B.Dadonaite andM.Roser \u201cPneumonia \u201d (2019) 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