Schematic representation of recombinant viruses detected in 12 subjects showing recombination breakpoints.

<p>Localization of breakpoints between HIV-1 subtypes was done by SimPlot analysis and identified breakpoints were visually inspected in BioEdit. The numbers in each bar indicate breakpoints and were given HXB2 numbering. The first bar represents the protease and reverse transcriptase genes. The dashed lines indicate the positions where protease gene starts, 2, 253 (HXB2 numbering), and ends, 2,549 (HXB2 numbering). The genome segments are colored according to HIV-1 subtypes. Red, orange, yellow, blue, green, and light blue represent sequences from HIV-1 subtypes A1, A2, C, D, CRF10_CD and CRF35_AD, respectively. The black bar represents the unclassified (U) regions. Confirmation of recombination was conducted by constructing phylogenetic trees of the putative recombinant regions against reference HIV-1 subtypes.