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Combined Assembly of Metagenomic Libraries from The Faecal Samples of IBD and PSC Patients Allowed The Identification of African Swine Fever Virus-like Sequences Open Access


Other title
Combined assembly
Next generation sequencing
Metagenomic libraries
Viral metagenomics
African swine fever virus-like sequences
Type of item
Degree grantor
University of Alberta
Author or creator
Reza, Md Salman
Supervisor and department
Wong, Gane (Medicine)
Mason, Andrew (Medicine)
Examining committee member and department
Montano-Loza, Aldo (Medicine)
Marchant, David (Medical Microbiology & Immunology)
McMurtry, Michael Sean (Medicine)
Department of Medicine
Experimental Medicine
Date accepted
Graduation date
Master of Science
Degree level
Metagenomics is an emerging discipline to explore microbial diversity in clinical samples, independent of the limitations of cell cultures. This method is widely accepted as a modern technique to detect novel viruses in clinical and environmental samples and has the potential to contribute to the identification of unknown etiological agents causing diseases. This thesis utilizes the combined assembly approach on deep sequencing data in search for novel viral populations in clinical samples of patients diagnosed with inflammatory bowel disease (IBD) and primary sclerosing cholangitis (PSC), which is an extraintestinal manifestation of IBD. In this study, twelve mammalian viral sequences and other plant, bird and insect viral sequences were found. Among the viral sequences, we have detected many sequences of African swine fever like virus (ASFLV) in the IBD and PSC patients after the combined assembly approach but not in the initial metagenomics data sets of the assembly from the individual patient. Interestingly, the ASFLV sequences showed similarity to thirty-nine genes along the ASFV genome, but only 38-62% identity at the amino acid level, suggesting that they are related by distinct sequences. Phylogenetic analyses positioned the ASFLV sequences in a clade different from those clustering ASFV and that was consistent for the topoisomerase, capsid and helicase genes. Furthermore, nested PCR confirmed the presence of ASFLV sequences in one ulcerative colitis and PSC patients for multiple loci including the capsid, helicase and origin binding proteins. Thus, we report for the first time the presence of ASFLV sequences in human clinical samples in North America. This study also investigates the suitability of several viral enrichment methods to isolate viruses from clinical samples before performing metagenomics. The detection of ASFLV sequences was possible only after adopting the combined assembly approach, which enabled the identification of a novel virus sequences and improved the overall identification of viruses in the metagenomic libraries.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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