FIG. 3.

Evidence that a CXCR4-using Env clone in patient B arose as a result of recombination between CCR5-tropic and CXCR4-using variants. An outlying CXCR4-using Env clone from day 433 was compared to CCR5-tropic (red) and CXCR4-using (blue) variants from the same patient using the RIP tool (Los Alamos HIV Sequence Database: http://www.hiv.lanl.gov/content/hiv-db/mainpage.html). The graph indicates the similarity between the outlying Env clone and the CCR5- and CXCR4-using variants (y axis) at each position along the entire gp160 sequence (x axis), using a window length of 200 bp. The thickness of each line indicates the confidence in the best match, with a thick line representing >95% confidence. The green arrow shows the point of likely recombination at approximately 1,050 bp.