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. 2010 Jul 28;5(7):e11833. doi: 10.1371/journal.pone.0011833

Figure 3. Mosaic pattern of HIV-1 CRF_BF in Brazil.

Figure 3

Panel A depicts the recombination pattern of CRF_28BF isolates (12609, 12817 and 12313) and panel B depicts the recombination pattern of the CRF_29BF isolates (11948, 16704 and 99ufrj1). The x-axis shows the sequence length in base pairs (bp). The y-axis displays the bootstrap support based on 100 replicates. Red line corresponds to genome regions of CRF_BF related with the subtype B lineage and green line correspond to regions related with the subtype F lineage. Analyses were performed using a neighbor-joining method and the Kimura two-parameter model in 500-bp windows sliding along sequences in increments of 80 bp. The GenBank accession numbers of the non-recombinant sequences used as parental references are: subtype A (AF004885), subtype B (AY423387, M38432, and AY331295), subtype D (K03454, AY253311, and U88824), subtype G (AF084936 and AF061642), subtype J (AF082394), subtype K (AJ249235 and AJ249239), subtype C (U52953, AF067155, and AY772699), subtype H (AF005496) and subtype F (AF005494). The bootscan analysis was performed with Simplot v.2.5 (http://sray.med.som.jhmi.edu/RaySoft).