Fig. 1: Intra-host diversity of SARS-CoV-2 spike sequences in PWH and PWOH.

a Maximum-likelihood phylogenetic analysis of spike gene haplotypes detected in each participant. Trees were generated separately for each participant and then joined for visualization with Wuhan-Hu-1 (Hu-1). The maximum frequency of each haplotype during each two-week period is shown via the dot plot. Trees from hospitalized and outpatient cohorts are separated to reflect differences in infecting Pango lineages. Color coding of PWOH and PWH subgroups applies to all figures. b Comparison of spike genetic diversity among PWOH and subgroups of PWH. Individual samples from longitudinal sample sets in each person are represented by separate datapoints (sample size: n = 96 in CD4 < 200, n = 10 in CD4 ≥ 200, n = 14 in CD4 unknown, n = 59 in PWOH). Statistical significance was assessed by one-way ANOVA with multiple comparisons (Kruskal-Wallis test and Dunn’s multiple comparisons test); p values < 0.05 are shown. c Genetic divergence (number of mutations, y-axis) from ancestral Wuhan-Hu-1 in SARS-CoV-2 spike sequences from PWH subgroups, PWOH, and matched public data. Numbers of sequences (x-axis) indicate total numbers of single-genome sequences (SGS) for all participants combined in PWOH and PWH subgroups, or total numbers of single-person consensus sequences obtained from the NCBI Virus database. Statistical significance was assessed by one-way ANOVA with multiple comparisons (Friedman test and Dunn’s multiple comparisons test); statistically significant p values were detected for the following comparisons: CD4 < 200 vs. NCBI (p = 0.005), CD4 < 200 vs. CD4 ≥ 200 (p = 0.002), and CD4 < 200 vs. PWOH (p = 0.006). d Analysis of secondary intra-host Pango lineages. Distinct lineages are indicated as columns; individual participants are indicated as rows. Dots represent relative frequencies of individual lineages among all SGS from each participant. Source data are provided as a Source Data file.