Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)
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Abstract
Using deep sequencing technologies such as Illumina’s platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw deep sequencing reads into Sequence Alignment Mapping (SAM) files. We propose that interpretation tools should process these SAM files, directly translating individual reads to amino acids in order to extract statistics of interest such as the proportion of different amino acid residues at specific sites. This preserves per-read linkage between nucleotide variants at different positions within a codon location. The samReporter is a subsystem of the GLUE software toolkit which follows this direct read translation approach in its processing of SAM files. We test samReporter on a deep sequencing dataset obtained from a cohort of 241 UK HCV patients for whom prior treatment with direct-acting antivirals has failed; deep sequencing and resistance testing have been suggested to be of clinical use in this context. We compared the polymorphism interpretation results of the samReporter against an approach that does not preserve per-read linkage. We found that the samReporter was able to properly interpret the sequence data at resistance-associated locations in nine patients where the alternative approach was equivocal. In three cases, the samReporter confirmed that resistance or an atypical substitution was present at NS5A position 30. In three further cases, it confirmed that the sofosbuvir-resistant NS5B substitution S282T was absent. This suggests the direct read translation approach implemented is of value for interpreting viral deep sequencing data.
| Item Type: | Articles |
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| Additional Information: | This work was funded by the Medical Research Council (MRC) of the United Kingdom, award number MC_UU_12014/12. JBS was also part funded by a MRC Confidence in Concept award to the University of Glasgow, MC_PC_16045. ECT was funded by theWellcome Trust (102789/Z/13/Z). EB is funded by the MRC, the Oxford National Institute for Health Research (NIHR) Biomedical Research Centre and is an NIHR Senior Investigator. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Aranday-Cortes, Dr Elihu and Robertson, Professor David and Singer, Dr Josh and Tong, Dr Lily and Da Silva Filipe, Dr Ana and Hughes, Dr Joseph and Gifford, Dr Robert and Thomson, Professor Emma and McLauchlan, Professor John |
| Authors: | Singer, J. B., Thomson, E. C., Hughes, J., Aranday-Cortes, E., McLauchlan, J., Da Silva Filipe, A., Tong, L., Manso, C. F., Gifford, R. J., Robertson, D. L., Barnes, E., Ansari, M. A., Mbisa, J. L., Bibby, D. F., Bradshaw, D., and Smith, D. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Viruses |
| Publisher: | MDPI |
| ISSN: | 1999-4915 |
| ISSN (Online): | 1999-4915 |
| Copyright Holders: | Copyright © 2019 The Authors |
| First Published: | First published in Viruses 11(4):323 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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