Adaptation dynamics following transmission affected by bottleneck event, immune selection pressure, replicative cost and drift.

(A) The % of quasispecies for all adapted amino acids in Gag, Pol, and Nef in the mother/child pairs (N = 633) were plotted on the x-axis for the mother, and the y-axis for the child. Points are superimposed on each other and the color range reflects number of superimposed points with red (maximum, max) and blue (minimum, min). ‘Maintained’ adaptations are present in the top right corner (≥90% in the child), ‘reverted’ in the bottom right corner (<10% in the child), and ‘de novo’ adaptations along the y-axis (<10% in the mother), with respect to the child. (B) Adaptations that are potentially under immune selection pressure in both the mother and child (shared maternal HLA; N = 249; scenarios 1–3 in the child from Fig 1). (C) Adaptations that are in a non-selective immune environment in the mother, but potential selective environment in the child (paternal HLA; N = 181; scenarios 4–5 for the mother and 1–3 for the child from Fig 1). (D) Adaptations that are potentially under a selective environment in the mother, but a non-selective immune environment in the child (mother-only HLA; N = 203; scenarios 1–3 for the mother and 4–5 for the child from Fig 1). In all panels, percentages denote adaptations that are present in that quadrant for that grouping. Panels B-D also indicate the likely influence of selection on, and replicative cost of (theoretical), adaptations along the axes.