Figure 4

Synonymous and non-synonymous amino acids variation along the HIV- 1 Env constant region 2 (C2), variable loop 3 (V3), constant region 3 (C3), and variable loop 4 (V4). Results are presented for maternal and infant samples collected at birth, as well as for infant samples collected from 6 to 67 months. Synonymous (green) and non-synonymous (red) changes per position for each sequence set were estimated in Datamonkey. The number and position of putative N-linked glycosylation sites (PNGS) (N × T/S) was estimated in N-GlycoSite http://hiv-web.lanl.gov/content/hiv-db/GLYCOSITE/glycosite.html. Within each set of contemporaneous sequences, constant PNGS are indicated in purple, and variable ones with blue (with their frequency in the blue outlined box). The overall rate of non-synonymous to synonymous substitutions (dN/dS) was estimated in PAML. N: number of sequences for each timepoint.