Fig. 5: Papillomavirus diversity over time in shedders and non-shedders.

A Papillomavirus E1–E2–L2–L1 nucleotide phylogeny. Colored tips (red, blue, and orange) represent sequences generated in this study. Reference sequences are shown in black. B Weighted papillomavirus UniFrac distance between pairs of samples from the same individual (within-individual comparisons; n = 108 pairwise comparisons for non-shedder samples and n = 49 pairwise comparisons for shedder samples) or from different individuals (between-individual comparisons; n = 2973 pairwise comparisons for non-shedder samples and n = 512 pairwise comparisons for shedder samples). Statistical significance was assessed using a two-sided, two-sample permutation test, and p-values were adjusted for multiple comparisons using the Benjamini–Hochberg method. The center lines show the median, box bounds show the interquartile range, and whiskers show the minimum and maximum. C PCoA of shedder and non-shedder samples, using weighted UniFrac distance calculated from papillomavirus phylogeny and relative abundance. Samples are colored by duration of ART (antiretroviral therapy). Non-shedder samples are shown as circles and shedder samples are shown as triangles. Statistical significance was determined by PERMANOVA, p = 0.33 for ART duration and p = 0.28 for shedder/non-shedder status.