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Title: Viral quasispecies inference from 454 pyrosequencing
Authors: Wan Ting Poh
Eryu Xia
Kwanrutai Chin-inmanu
Lai Ping Wong
Anthony Y. Cheng
Prida Malasit
Prapat Suriyaphol
Yik Ying Teo
Rick Twee Hee Ong
National University of Singapore
Mahidol University
Thailand National Center for Genetic Engineering and Biotechnology
Genome Institute of Singapore
Keywords: Biochemistry, Genetics and Molecular Biology;Computer Science;Mathematics
Issue Date: 5-Dec-2013
Citation: BMC Bioinformatics. Vol.14, No.1 (2013)
Abstract: Background: Many potentially life-threatening infectious viruses are highly mutable in nature. Characterizing the fittest variants within a quasispecies from infected patients is expected to allow unprecedented opportunities to investigate the relationship between quasispecies diversity and disease epidemiology. The advent of next-generation sequencing technologies has allowed the study of virus diversity with high-throughput sequencing, although these methods come with higher rates of errors which can artificially increase diversity.Results: Here we introduce a novel computational approach that incorporates base quality scores from next-generation sequencers for reconstructing viral genome sequences that simultaneously infers the number of variants within a quasispecies that are present. Comparisons on simulated and clinical data on dengue virus suggest that the novel approach provides a more accurate inference of the underlying number of variants within the quasispecies, which is vital for clinical efforts in mapping the within-host viral diversity. Sequence alignments generated by our approach are also found to exhibit lower rates of error.Conclusions: The ability to infer the viral quasispecies colony that is present within a human host provides the potential for a more accurate classification of the viral phenotype. Understanding the genomics of viruses will be relevant not just to studying how to control or even eradicate these viral infectious diseases, but also in learning about the innate protection in the human host against the viruses. © 2013 Poh et al.; licensee BioMed Central Ltd.
ISSN: 14712105
Appears in Collections:Scopus 2011-2015

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