Interpreting viral deep sequencing data with GLUE

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
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:Gifford, Dr Robert and Aranday-Cortes, Dr Elihu and Robertson, Professor David and Da Silva Filipe, Dr Ana and Singer, Dr Joshua and Thomson, Dr Emma and Hughes, Dr Joseph and Tong, Dr Lily 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 > Institute of Infection Immunity and Inflammation
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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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
3007420Accelerating Precision Diagnostics - Bridging the GapAnna DominiczakMedical Research Council (MRC)MC_PC_16045CAMS - Cardiovascular Science
645101T-cell mediated evolution of hepatitis C virus during acute infectionEmma ThomsonWellcome Trust (WELLCOTR)102789/Z/13/ZMVLS III - CENTRE FOR VIRUS RESEARCH