FIG. 4.

Evidence of immune selection in two subjects sampled at later Fiebig stages. (A) Highlighter analysis of SGA-derived env sequences (left panel) from subject ZM180M (Fiebig stage VI), and corresponding nucleotide (middle panel) and amino acid (right panel) sequence alignments from the overlapping rev gene. Boxes indicate mutations that cluster within a 27-nt region that corresponds to a 9-mer in the Rev protein sequence. (B) Highlighter analysis of SGA-derived env sequences (left panel) from subject ZM206F (Fiebig stage VI), and corresponding nucleotide (middle panel) and amino acid (right panel) sequence alignments of the V1 region. Boxes indicate mutations that cluster within a 27-nt region that corresponds to a 9-mer of the V1 loop. In Highlighter analyses, nucleotide substitutions and gaps are color coded. The consensus sequence is at the top of each alignment; lowercase letters show residues where mutations occurred. Dashes in the alignments indicate sequence identity to the consensus; dots indicate deletions.