Please use this identifier to cite or link to this item: https://doi.org/10.1186/1471-2105-14-355
Title: Viral quasispecies inference from 454 pyrosequencing
Authors: Poh, W.-T. 
Xia, E.
Chin-inmanu, K.
Wong, L.-P.
Cheng, A.Y.
Malasit, P.
Suriyaphol, P.
Teo, Y.-Y. 
Ong, R.T.H. 
Keywords: 454 pyrosequencing
Sequence alignment
Virus quasispecies
Issue Date: 5-Dec-2013
Citation: Poh, W.-T., Xia, E., Chin-inmanu, K., Wong, L.-P., Cheng, A.Y., Malasit, P., Suriyaphol, P., Teo, Y.-Y., Ong, R.T.H. (2013-12-05). Viral quasispecies inference from 454 pyrosequencing. BMC Bioinformatics 14 (1) : -. ScholarBank@NUS Repository. https://doi.org/10.1186/1471-2105-14-355
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.
Source Title: BMC Bioinformatics
URI: http://scholarbank.nus.edu.sg/handle/10635/109086
ISSN: 14712105
DOI: 10.1186/1471-2105-14-355
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
File Description SizeFormatAccess SettingsVersion 
2013-viral_quasispecies_inference_454_pyrosequencing-published.pdf1.54 MBAdobe PDF

OPEN

PublishedView/Download

SCOPUSTM   
Citations

4
checked on Jul 13, 2018

WEB OF SCIENCETM
Citations

6
checked on Jun 11, 2018

Page view(s)

54
checked on Jun 22, 2018

Download(s)

5
checked on Jun 22, 2018

Google ScholarTM

Check

Altmetric


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.