FIG. 2.

Within-group diversity among linked and unlinked Zambian transmission pairs and corresponding reference sequences. Subtype C reference sequences (n = 15) from the Los Alamos HIV/SIV Sequence Database (Table 1) were subjected to pairwise sequence comparisons in the region corresponding to the PCR-amplified gp41 fragment shown in Fig. 1. Pairwise sequence distances were also calculated for 66 subtype C transmission pairs classified as linked and 15 subtype C transmission pairs classified as unlinked in the same genomic region. The distribution of distance values for these three different groups is depicted as boxes, with the lower and upper limits of the box delineating the 25th and 75th percentiles and the bars indicating the 10th and 90th percentiles, respectively. The median distance of the linked viral group (median = 1.5) was significantly different from that of both the unlinked viral group (median distance = 8.8) and the reference sequence group (median distance = 8.2) (P < 0.0001, one-sided Mann-Whitney test [17]). In contrast, the median sequence distance of the unlinked viral group was not statistically different from that of the reference sequence group (P > 0.05, Mann-Whitney test).