Neighbor-joining phylogenetic analysis of the gp120 virus sequences. The Kimura-2 parameter and 100 replicates were used to calculate nucleotide distances and sequences from the Los Alamos HIV-1 database were used as reference strains. Circles indicate sequences from serum, diamonds from naïve CD4+ T cells, triangle from central memory and squares from effector memory cells. (A) Phylogeny of the strains isolated before initiation of therapy (B) Phylogeny of the strains isolated after therapy initiation. The black curved lines indicate strains from the effector memory population and the white curved lines indicate strains from serum. The dotted line indicates the two virus strains co-circulating in subject M12020.