MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

Graham R. Wood; Eugene V. Ryabov; Jessica M. Fannon; Jonathan D. Moore; David J. Evans; Nigel Burroughs

doi:10.1093/nar/gku524

MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

Graham R. Wood^*, Eugene V. Ryabov, Jessica M. Fannon, Jonathan D. Moore, David J. Evans, Nigel Burroughs

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.

Original language	English
Article number	e123
Number of pages	14
Journal	Nucleic Acids Research
Volume	42
Issue number	16
DOIs	https://doi.org/10.1093/nar/gku524
Publication status	Published - 15 Sept 2014

Keywords

Deformed-wing-virus
Apis-mellifera l.
Mite varroa-destructor
RNA viruses
Honey-bee

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10.1093/nar/gku524

Nucl. Acids Res.-2014-Wood-e123
Copyright The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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Cite this

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title = "MosaicSolver: a tool for determining recombinants of viral genomes from pileup data",

abstract = "Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.",

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AU - Wood, Graham R.

AU - Ryabov, Eugene V.

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AU - Moore, Jonathan D.

AU - Evans, David J.

AU - Burroughs, Nigel

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MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

Abstract

Keywords

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