Figure. Genetic organization and recombination breakpoints in HIV-1 genomic sequences isolated from patients TV721 (A), TV725 (B), TV749 (C), and TV919 (D). Nucleotide sequences were submitted to GenBank (accession nos. HM215249–HM215252). Similarity plots were produced with Simplot version 3.5.1 (http://sray.med.som.jhmi.edu/SCRoftware/simplot) by using windows of 500 nt and increments of 50 nt to guide the choice of reference sequences used for bootscanning (8). Bootscan analyses were then performed according to the neighbor-joining method and Kimura 2-parameter distances. The size of the sliding window was set at 300 nt with 10-nt increments (9). Reference sequences used were subtype A1: A1.AU.03 (DQ676872), A1.KE.94 (AF004885), A1.RW.92 (AB253421); subtype A2: A2.CD.97 (AF286238), A2.CY.94 (AF286237); subtype D: D.CD.83.ELI (K03454), D.CM.01 (AY371157), D.TZ.01 (AY253311); subtype G: G.BE.96 (AF084936), G.KE.93 (AF061641), G.NG.92 (U88826); subtype J: J.CD.97 (EF614151), J.SE.93 (AF082394), J.SE.94 (AF082395); and CRF11_cpx: 11_cpx.CM.95 (AF492624). Phylogenetic reconstructions based on the neighbor-joining method and the Kimura 2-parameter distance model were computed by MEGA4 (10) and used to confirm the structures of the recombinants. Bootstrap values >80% (500 replicates) were considered significant. Vertical dashed lines indicate the position of recombination breakpoints. Numbering of residues is based on the sequence of HIV-1 HXB2 (GenBank accession no. K03455).