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. 2023 Nov 6;14:7137. doi: 10.1038/s41467-023-42906-y

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a Cohort overview with age and sex distributions. Single dots in age distributions represent individuals, bar graphs and error bars depict mean cohort age ± SD. One individual (HIV-1) reported neither sex nor age. b V gene segment usage distributions for heavy, kappa, and lambda chains, ordered by descending frequencies according to the uninfected control (CTRL) group (n = 57 for CTRL, n = 34 for HIV-1, and n = 12 for HCV). c Mean CDR3 length distributions for heavy, kappa, and lambda chains in amino acids (aa). Left panel shows the mean CDR3 length distributions across individuals for each cohort (n = 57 for CTRL, n = 34 for HIV-1, and n = 12 for HCV) as solid lines and standard deviations as shaded areas. Right panel shows mean CDR3 amino acid length as dots for each individual and cohort statistics as box-plots. d Mean V gene nucleotide mutation (mut.) frequencies for heavy, kappa, and lambda chains. Representation of mean distributions (left panel) and individual means (right panel) as in c for all three cohorts (n = 57 for CTRL, n = 34 for HIV-1, and n = 12 for HCV). One-way ANOVA with a two-sided Tukey-HSD post-hoc test was performed on the means in c and d. e Representative examples of clone trees for the cohorts based on heavy chain sequences. f The weights (i.e., the number of leaves deriving from a given node) were determined for the common ancestor of each clone (ω_anc.) and its immediate descendants (ω_D). Distributions of their ratios (ω_D/ω_anc.) were plotted (left panel) to illustrate the clone tree skewness (dashed line = neutral, see methods for details). The right panel shows the mean terminal/mean branch length distribution for clone trees. g Clone size distribution for the cohorts. h Clone diversity determined by Gini-Simpson index and entropy (n = 57 for CTRL, n = 34 for HIV-1, and n = 12 for HCV). Data is presented as mean values ± SD. Box-plots in panels b–d depict 25% and 75% percentiles with medians as average lines and minimum/maximum values as whiskers. Source data are provided as a Source Data file.