Fig. 3: DNA virome over time in shedders and non-shedders.

A Samples grouped by DNA virome community cluster. Samples are shown as vertical bars colored by family relative abundance. Metadata is shown as rows of colored squares beneath the samples. ART antiretroviral therapy. B DNA virome alpha diversity (viral contig richness and Shannon index) by duration of ART. Shedder and non-shedder samples are plotted together. Purple lines indicate the linear regression lines, and 95% confidence bands are shown in gray. Statistical significance was assessed by LME, p = 7.7 × 10⁻¹⁰ for richness and p = 8.3 × 10⁻⁸ for Shannon index. C Viral Bray–Curtis dissimilarity (weighted) between pairs of samples from the same individual (within-individual comparisons; n = 116 pairwise comparisons for non-shedder samples and n = 49 pairwise comparisons for shedder samples) or from different individuals (between-individual comparisons; n = 3205 pairwise comparisons for non-shedder samples and n = 512 pairwise comparisons for shedder samples). In this and D 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. In this and D center lines show the median, box bounds show the interquartile range and whiskers show the minimum and maximum. D Viral Sorensen dissimilarity (unweighted) between pairs of samples from the same individual (within-individual comparisons; n = 116 pairwise comparisons for non-shedder samples and n = 49 pairwise comparisons for shedder samples) or from different individuals (between-individual comparisons; n = 3205 pairwise comparisons for non-shedder samples and n = 512 pairwise comparisons for shedder samples). E PCoA of shedder and non-shedder samples, using Bray–Curtis dissimilarity calculated from virus contig relative abundance. Samples are colored by duration of ART. Non-shedder samples are shown as circles, and shedder samples are shown as triangles. Statistical significance was determined by PERMANOVA, p = 0.001 for ART duration and p = 0.016 for shedder/non-shedder status. F Anelloviridae relative abundance (left) and Papillomaviridae relative abundance (right) by ART duration. Shedder and non-shedder samples are plotted together. Purple lines indicate the linear regression lines, and 95% confidence bands are shown in gray. Statistical significance was determined using MaAsLin2, adjusted two-sided p-value = 8.8 × 10⁻⁵ for Anelloviridae and adjusted p-value = 0.037 for Papillomaviridae.