Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing
2012 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 7, no 2Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
Public Library of Science , 2012. Vol. 7, no 2
Bioinformatics and Systems Biology
IdentifiersURN: urn:nbn:se:liu:diva-77340DOI: 10.1371/journal.pone.0030875ISI: 000302741300031OAI: oai:DiVA.org:liu-77340DiVA: diva2:526315
Funding Agencies|Swedish Research Council|2010-3754|2012-05-112012-05-112012-12-10