Figure 2

Outline of all unique recombinant HIV-1 gag forms.

a. Ten women carried one predominant URF, whereas five women carried several distinct URFs (ML199, ML900, ML1765, ML1812, ML2033); in three cases these URFs incorporated sections from additional HIV-1 subtypes (ML900, ML1765, ML1812). Blue = HIV subtype A1 (HIV-A); cyan = HIV subtype A2 (HIV-A2); green = HIV subtype C (HIV-C); red = HIV subtype D (HIV-D); yellow = HIV subtype F (HIV-F); and white = gap. A unique breakpoint pattern was found in patients ML1700 and ML2033. b. Outline of the construction of sequence alignments. Subtype-specific alignments (labelled X and Y) were created by dividing the recombinant sequences into subtype-specific sections and using the longest shared subtype-section and matching sections of the HHS sequences from the rest of the women in the cohort and sequences from the HIV database. c,d. Outline of the subtype-specific Bayesian phylogenetic analysis based on the assumption that a URF will not recombine again to become an HHS. Any recombinant patient sequence on the tree whose parent node (yellow circle) has an HHS descendant likely is derived from an HHS, which means that the recombinant sequence is likely to be a URF (c). If the parent node only has recombinant descendants, then the patient is likely to be infected with a CRF (d). The branch on which the recombination event is suspected to have occurred is shown in red.