Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method

The increased complexity of HIV-1 genetic heterogeneity raises the issue for reliable classification and analysis of these sequences. Until now, bootscanning analysis has been the main method used for the analysis of potential HIV-1 intersubtype recombinants. We show evidence that in some cases of complex recombinants, where three or more segments with discordant phylogenetic signal may exist in protease (PR) and partial reverse transcriptase (RT) region, Bayesian scanning provides a clearer picture than bootscanning plots about the boundaries of potential recombination. Thus, a recently developed Bayesian scanning tool can facilitate the analysis and classification of HIV-1 mosaic sequences.