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Fig. 5 | Retrovirology

Fig. 5

From: Molecular clock of HIV-1 envelope genes under early immune selection

Fig. 5

Virus pair diversity comparisons. Diversity of wild–wild virus pairs (white bars), wild-mutant pairs (light grey bars), virus pairs from different mutant lineages (dark grey bars), and virus pairs from a single mutant lineage (black bars). The sequence data from subject CH077, SUMA0874, and WEAU0575 were obtained from Ref. [30] and the sequence data from subject CH164 were obtained from Ref. [32]. The sample time point is 14, 56, 30, and 15 days after the first sample at Fiebig stage I/II for subject CH077, CH164, SUMA, and WEAU, respectively. Table 2 lists wild and mutant epitope sequences of each subject at a given time point. For example, subject CH077’s sample 14 days after the first sample had one wild type lineage with the epitope QFRNKTIVF and two mutant lineages with either the epitope QFKNKTIVF or QFRNKAIVF. Here, the wild-type lineage was designated in reference to the consensus sequence of the first time point sequences of each individual. The full envelope gene sequence diversity of mutant-type pairs from distinct lineages was comparable to that of the wild-type lineage. As predicted by our model, the diversity within each mutant lineage was considerably smaller than that of wild–wild pairs, wild-mutant pairs, and virus pairs from different mutant lineages (Wilcoxon–Mann–Whitney test, p = 0.067 for CH077, p = 0.067 for CH164, p = 0.067 for SUMA0874, and p = 0.00073 for WEAU0575)

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