Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV - Fig 2

(A) Maximum likelihood phylogenetic tree of Gag majority sequences confirms mother-to-child transmission (mother, M = closed diamond; child, C = open diamond) with no evidence of larger transmission networks within cohort (see S1B and S1C Fig for Pol and Nef). (B) Intra-individual genetic diversity of Gag quasispecies was significantly higher in the mother than the child (N = 26, p = 0.0001; paired t-test) with similar results obtained for Pol and Nef (see S1E and S1F Fig). Data are represented as mean ± SE. (C) Significant positive correlation across all proteins for nucleotide differences (%) between mother/child pairs and age at sampling (time since transmission) (N = 23, p = 0.007; mixed-effects linear regression model). There was a significant difference between the nucleotide differences (%) for the different proteins (N = 23, p<0.0001; linear regression). p<0.001 (***).