Prediction of genomic recombination in CRF22_01A1. Genomic regions are indicated at the top of the plot with the segment numbers and breakpoints (HBX2 numbering). In the center, the genomic recombinants of cluster HIV-1 subtypes are plotted for the 02CMLT72 genome based on jpHMM output. At the bottom, each of the resulting six genomes was analyzed by jpHMM separately; recombinant structures of 02CMLT72, 02CM1867LE, 02CM1917LE, 02CM3097MN, 01CM001BBY, and 01CM53122 were determined and listed. Open bar, subsubtype A1; gray, CRF01_AE. (Color image can be found at www.liebertonline.com).