Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains |
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Authors: | Patricia Buendia Giri Narasimhan |
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Institution: | (1) Department of Biology and Center for Computational Science, University of Miami, Coral Gables, FL 33146, USA;(2) Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL 33199, USA |
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Abstract: | Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation,
among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method
1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special
focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with
a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal
sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral
population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with
charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary
relationships. |
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Keywords: | |
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