Evolution of V1 and V3 regions. Clonal V1 and V3 amino acid sequences obtained over the course of infection from child 1 (panel A) and child 2 (panel B) were aligned against consensus sequences from the initial infecting isolate. Dots in the alignments indicate sequence identity to the consensus; dashes indicate deletions. Potential N-linked glycans (occurring at NXT/S) are represented in open boxes. Amino acids highlighted in light grey are involved in tropism change . Blue boxes in the consensus sequence represent published linear neutralizing epitopes in V1  and V3 ; red boxes in the consensus sequence represent a conformational epitope in V3 . Viral tropism is indicated at the right of the alignment as determined phenotypically or genotypically based on V3 loop sequence patterns. Black arrows signal fixed mutations.