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Activity Number:
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466
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Type:
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Topic Contributed
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Date/Time:
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Wednesday, August 1, 2007 : 2:00 PM to 3:50 PM
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Sponsor:
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WNAR
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| Abstract - #309872 |
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Title:
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Survey of Recombination in the HIV Genome: Hot Spots and Cold Spots
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Author(s):
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Karin Dorman*+ and Misha L. Rajaram and Marc A. Suchard and Vladimir N. Minin
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Companies:
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Iowa State University and Iowa State University and University of California, Los Angeles and University of California, Los Angeles
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Address:
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Department of Statistics, Ames, IA, 50011,
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Keywords:
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Bayesian phylogenetics ; Markov chain Monte Carlo ; change point model
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Abstract:
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Coinfection of a single cell with two or more HIV strains may produce recombinant viruses upon template switching by the replication machinery. We used a Bayesian multiple change point model to infer inter-subtype recombination occurring during the worldwide epidemic of HIV as recorded in Genbank. We examined 4074 sequences identified as recombinant in a preliminary screen and confirmed 2360 with strong evidence of recombination. These recombinants conservatively contained 1701 unique crossover points, but there is evidence that some co-located crossover points probably descended from distinct recombination events. Per-site recombination rate estimates confirmed the presence of a known hotspot in the envelope gene and a previously hypothesized hotspot in the gag gene. In contrast to previous findings, recombination rate was positively correlated with fast-evolving genomic regions.
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