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Activity Number:
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7
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Type:
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Invited
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Date/Time:
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Sunday, August 11, 2002 : 2:00 PM to 3:50 PM
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Sponsor:
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WNAR
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| Abstract - #300386 |
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Title:
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Finding Recombination Breakpoints in HIV Molecular Sequences from an Individual
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Author(s):
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Jinko Graham*+ and Brad McNeney and Francoise Seillier-Moiseiwitsch
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Affiliation(s):
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Simon Fraser University and Simon Fraser University and University of Maryland, Baltimore County
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Address:
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8888 University Drive, Burnaby, British Columbia, V5A 1S6, CANADA
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Keywords:
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HIV-1 ; sequence alignment ; permutation test ; recombination ; genomic sequences
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Abstract:
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Retroviral recombination is an issue in studies of HIV-1 evolution within individuals who harbor a genetically diverse virus population. The nature of retroviral replication is such that recombinant HIV-1 genomes would be expected to be a complex mosaic of parental sequences. However, given the comparatively low levels of virus diversity within an individual, relatively few recombination breakpoints are expected to be detectable. Under these circumstances, a sequential search for breakpoints is expected to be effective. We consider a sequential procedure in which additional recombination breakpoints are simultaneously tested for and estimated, given the location of previously known breakpoints. The procedure can be used to assess the number and location of recombination breakpoints in a sequence alignment from an individual and is based on phylogenetic profiling. We investigate properties of the test and apply it to an alignment of HIV-1 env gene sequences sampled from a patient harbouring a heterogeneous population of subtype A virus.
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