HIV-1 blood and CSF populations early during infection can be equilibrated or compartmentalized.

<p>Neighbor-joining phylogenetic trees depicting sequence relationships from subjects with (A) equilibrated and (B) compartmentalized viral populations. <i>env s</i>equences from the CSF (blue circles) and blood plasma (red triangles) are shown. Bootstrap values ≥35 are included (*) at the appropriate nodes. Genetic distance is indicated at the bottom of each figure (0.001, number of nucleotide substitutions per site between <i>env</i> sequences). Compartmentalized CNS populations are designated by an open circle at the appropriate node and a solid blue bracket. Clonal amplification is indicated by a solid black bar.