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.