FIG. 4.

(A) Intrapatient recombination. Open reading frames of the HIV-1 genome relative to the WC10C-12 sequence. Genital tract-like regions are depicted in blue, plasma-like sequences in red. (B) Simplot comparison of clone WC10C-12 with contemporaneous clones derived from CVL and plasma samples from the same patient. Each curve is a comparison of recombinant genome WC10C-12, derived from CVL, to nonrecombinant reference sequences derived from the plasma (red) and genital tract (blue) of the same patient. Similarity plots comparing WC10C-12 to strain HXB2 (black) and itself (green) are included for reference. Recombination breakpoints confirmed by informative-site analysis are indicated with black arrows. (C) Open reading frames of the HIV-1 genome relative to the WC10C-8 sequence. (D) Simplot comparison of clone WC10C-8 with clones derived from the genital tract and plasma of the same patient. Similarity plots comparing WC10C-8 to strain HXB2 and itself are also included.