title: Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique.
abstract: Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples. Human rhinovirus C was the virus most frequently detected and was identified in seven samples. Human measles virus, adenovirus B 55 and coxsackievirus A10 were also identified. Metagenomic sequencing also provided virus genomic sequences, which enabled genotype characterization and phylogenetic analysis. For cases of multiple infection, metagenomic sequencing afforded information regarding the quantity of each virus in the sample, which could be used to evaluate each viruses' role in the disease. Our study highlights the potential of metagenomic sequencing for pathogen identification in UP cases.
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Zou
authors.affiliation: Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
authors.forename: Guangpeng
authors.initials: G
authors.lastname: Tang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Huang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Lei
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Wenbing
authors.initials: W
authors.lastname: Chen
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Wenfei
authors.initials: W
authors.lastname: Zhu
authors.affiliation: Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhuang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Yang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Zhaomin
authors.initials: Z
authors.lastname: Feng
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
authors.forename: Dayan
authors.initials: D
authors.lastname: Wang
authors.affiliation: Guizhou Provincial Center for Disease Control and Prevention, Guiyang, 550004, China. cfswdm@gzscdc.org.
authors.forename: Dingming
authors.initials: D
authors.lastname: Wang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China. yshu@cnic.org.cn.
authors.forename: Yuelong
authors.initials: Y
authors.lastname: Shu
mesh_terms: D000256:Adenoviridae / Q000302:isolation & purification; D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D019295:Computational Biology; D004770:Enterovirus / Q000302:isolation & purification; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D008459:Measles virus / Q000302:isolation & purification; D056186:Metagenomics; D008875:Middle Aged; D010802:Phylogeny; D011024:Pneumonia, Viral / Q000175:diagnosis* / Q000821:virology; D012229:Rhinovirus / Q000302:isolation & purification; D014780:Viruses / Q000145:classification / Q000302:isolation & purification*; D055815:Young Adult
keywords: metagenomics; next-generation sequencing; unexplained pneumonia