Fig 2. Phylogenetic analysis of HIV-1 BF and BC recombinants inferred with 1038 bp corresponding to the protease region and part of the reverse transcriptase, obtained in the state of Maranhão (Northeast Brazil).

Phylogenetic inference included reference sequences of various subtypes and the major BF and BC recombinants found in Brazil. Clusters of recombinant sequences were assigned by colors: green (9 sequences), red (14 sequences) and blue (three sequences). The mosaic pattern of BF and BC is shown in the figure (gray area). The diagram colors indicate the genome regions of protease composed by distinct parental subtypes and the arrows indicate the location (numbers correspond to the nucleotide position of the reference HIV-1 strain HXB2) of breakpoints. More detailed features of recombinant strains of this study were included in the S1 Material.