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Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, The Institute of Technology.
Karolinska Institutet, Stockholm.
Karolinska Institutet, Stockholm.
Karolinska Institutet, Stockholm.
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2012 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 7, no 2Article in journal (Refereed) Published
Abstract [en]

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
National Category
Bioinformatics and Systems Biology
URN: urn:nbn:se:liu:diva-77340DOI: 10.1371/journal.pone.0030875ISI: 000302741300031OAI: diva2:526315

Funding Agencies|Swedish Research Council|2010-3754|

Available from: 2012-05-11 Created: 2012-05-11 Last updated: 2012-12-10
In thesis
1. Bioinformatic methods for characterization of viral pathogens in metagenomic samples
Open this publication in new window or tab >>Bioinformatic methods for characterization of viral pathogens in metagenomic samples
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Virus infections impose a huge disease burden on humanity and new viruses are continuously found. As most studies of viral disease are limited to theinvestigation of known viruses, it is important to characterize all circulating viruses. Thus, a broad and unselective exploration of the virus flora would be the most productive development of modern virology. Fueled by the reduction in sequencing costs and the unbiased nature of shotgun sequencing, viral metagenomics has rapidly become the strategy of choice for this exploration.

This thesis mainly focuses on improving key methods used in viral metagenomics as well as the complete viral characterization of two sets of samples using these methods. The major methods developed are an efficient automated analysis pipeline for metagenomics data and two novel, more accurate, alignment algorithms for 454 sequencing data. The automated pipeline facilitates rapid, complete and effortless analysis of metagenomics samples, which in turn enables detection of potential pathogens, for instance in patient samples. The two new alignment algorithms developed cover comparisons both against nucleotide and  protein databases, while retaining the underlying 454 data representation. Furthermore, a simulator for 454 data was developed in order to evaluate these methods. This simulator is currently the fastest and most complete simulator of 454 data, which enables further development of algorithms and methods. Finally, we have successfully used these methods to fully characterize a multitude of samples, including samples collected from children suffering from severe lower respiratory tract infections as well as patients diagnosed with chronic fatigue syndrome, both of which presented in this thesis. In these studies, a complete viral characterization has revealed the presence of both expected and unexpected viral pathogens as well as many potential novel viruses.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2013. 65 p.
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1489
National Category
Natural Sciences
urn:nbn:se:liu:diva-86194 (URN)978-91-7519-745-6 (ISBN)
Public defence
2013-01-25, Planck, Fysikhuset, Campus Valla, Linköpings universitet, Linköping, 10:15 (English)
Available from: 2012-12-10 Created: 2012-12-10 Last updated: 2012-12-10Bibliographically approved

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