Appendix Figure 3. Phylogenetic analysis of HIV-1 env C2-V5 sequences
from each of the nine participants. Sequences were aligned and visually
adjusted using GDE (4). The phylograms
were estimated by the method of neighbor-joining from a matrix of pairwise
maximum likelihood sequence distances (transition/transversion ratio =
1.4) using programs from version 3.5 of the PHYLIP package (1).
Trees were rooted to one of the sequences sampled at the first time point
using Treeview
(from R. Page). The legend for each phylogram shows the time of sampling
in months following seroconversion and is depicted in an arbitrary color
gradient. DNA sequences from PBMC are depicted as squares and plasma RNA
sequences as triangles. Sequence changes expected to confer an X4 phenotype
(SI phenotype on MT-2 cells and CXCR4 co-receptor specificity) based on
basic amino acid substitution at any of the three positions (#306, 319,
320 of gp120) are indicated by a red asterisk.