Viral quasispecies inference from 454 pyrosequencing
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...
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th-mahidol.311432018-10-19T12:09:06Z Viral quasispecies inference from 454 pyrosequencing 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 Biochemistry, Genetics and Molecular Biology Computer Science Mathematics 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. 2018-10-19T04:33:41Z 2018-10-19T04:33:41Z 2013-12-05 Article BMC Bioinformatics. Vol.14, No.1 (2013) 10.1186/1471-2105-14-355 14712105 2-s2.0-84888988927 https://repository.li.mahidol.ac.th/handle/123456789/31143 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84888988927&origin=inward |
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Biochemistry, Genetics and Molecular Biology Computer Science Mathematics 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 Viral quasispecies inference from 454 pyrosequencing |
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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. |
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National University of Singapore |
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National University of Singapore 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 |
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Article |
author |
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 |
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Wan Ting Poh |
title |
Viral quasispecies inference from 454 pyrosequencing |
title_short |
Viral quasispecies inference from 454 pyrosequencing |
title_full |
Viral quasispecies inference from 454 pyrosequencing |
title_fullStr |
Viral quasispecies inference from 454 pyrosequencing |
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Viral quasispecies inference from 454 pyrosequencing |
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viral quasispecies inference from 454 pyrosequencing |
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2018 |
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https://repository.li.mahidol.ac.th/handle/123456789/31143 |
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1763490011264581632 |