title: Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing.
abstract: The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.
authors.affiliation: IFM Bioinformatics and Swedish e-Science Research Centre (SeRC), Linköping University, Linköping, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Lysholm
authors.forename: Anna
authors.initials: A
authors.lastname: Wetterbom
authors.forename: Cecilia
authors.initials: C
authors.lastname: Lindau
authors.forename: Hamid
authors.initials: H
authors.lastname: Darban
authors.forename: Annelie
authors.initials: A
authors.lastname: Bjerkner
authors.forename: Kristina
authors.initials: K
authors.lastname: Fahlander
authors.forename: A Michael
authors.initials: AM
authors.lastname: Lindberg
authors.forename: Bengt
authors.initials: B
authors.lastname: Persson
authors.forename: Tobias
authors.initials: T
authors.lastname: Allander
authors.forename: Björn
authors.initials: B
authors.lastname: Andersson
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D006801:Humans; D009980:Influenza A virus / Q000235:genetics / Q000302:isolation & purification; D007251:Influenza, Human / Q000175:diagnosis / Q000235:genetics* / Q000821:virology; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics; D008875:Middle Aged; D009305:Nasopharynx / Q000821:virology; D010252:Paramyxoviridae / Q000235:genetics / Q000302:isolation & purification; D018184:Paramyxoviridae Infections / Q000175:diagnosis / Q000235:genetics* / Q000821:virology; D010802:Phylogeny; D010849:Picornaviridae / Q000235:genetics / Q000302:isolation & purification; D010850:Picornaviridae Infections / Q000175:diagnosis / Q000235:genetics* / Q000821:virology; D012141:Respiratory Tract Infections / Q000175:diagnosis / Q000235:genetics* / Q000821:virology; D055815:Young Adult