Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

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dc.contributor.authorLemey, Philippeen_ZA
dc.contributor.authorLott, Martinen_ZA
dc.contributor.authorMartin, Darrenen_ZA
dc.contributor.authorMoulton, Vincenten_ZA
dc.date.accessioned2015-10-30T09:30:53Z
dc.date.available2015-10-30T09:30:53Z
dc.date.issued2009en_ZA
dc.description.abstractBACKGROUND:Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. RESULTS: Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. CONCLUSION: Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package http://www.cmp.uea.ac.uk/~vlm/visrd.en_ZA
dc.identifier.apacitationLemey, P., Lott, M., Martin, D., & Moulton, V. (2009). Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. <i>BMC Bioinformatics</i>, http://hdl.handle.net/11427/14514en_ZA
dc.identifier.chicagocitationLemey, Philippe, Martin Lott, Darren Martin, and Vincent Moulton "Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning." <i>BMC Bioinformatics</i> (2009) http://hdl.handle.net/11427/14514en_ZA
dc.identifier.citationLemey, P., Lott, M., Martin, D. P., & Moulton, V. (2009). Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC bioinformatics, 10(1), 126.en_ZA
dc.identifier.ris TY - Journal Article AU - Lemey, Philippe AU - Lott, Martin AU - Martin, Darren AU - Moulton, Vincent AB - BACKGROUND:Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. RESULTS: Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. CONCLUSION: Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package http://www.cmp.uea.ac.uk/~vlm/visrd. DA - 2009 DB - OpenUCT DO - 10.1186/1471-2105-10-126 DP - University of Cape Town J1 - BMC Bioinformatics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2009 T1 - Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning TI - Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning UR - http://hdl.handle.net/11427/14514 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/14514
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-10-126
dc.identifier.vancouvercitationLemey P, Lott M, Martin D, Moulton V. Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics. 2009; http://hdl.handle.net/11427/14514.en_ZA
dc.language.isoengen_ZA
dc.publisherBioMed Central Ltden_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Licenseen_ZA
dc.rights.holder2009 Lemey et al; licensee BioMed Central Ltd.en_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_ZA
dc.sourceBMC Bioinformaticsen_ZA
dc.source.urihttp://www.biomedcentral.com/bmcbioinformatics/en_ZA
dc.subject.otherComputational Biologyen_ZA
dc.subject.otherEvolution, Molecularen_ZA
dc.subject.otherHIV Infectionsen_ZA
dc.subject.otherRecombination, Geneticen_ZA
dc.titleIdentifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanningen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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