Compartmentalized Replication of R5 T Cell-Tropic HIV-1 in the Central Nervous System Early in the Course of Infection
Fig 4
Compartmentalization can persist and evolve independently within the CSF over time.
Neighbor-joining phylogenetic trees showing how compartmentalization can: (A) be persistent with multiple clonal expansions allowing recombination; (B) consist of sequential transient clonal expansions; and (C) be established with a transmitted variant. env sequences from the CSF are labeled with circles (C, colors designated in figure) and env sequences from the blood plasma are labeled with triangles (P, colors designated in figure). Days p.i. are noted. Bootstrap values ≥ 50 are indicated (*) at the appropriate nodes to highlight the more significant branch points. Genetic distance is indicated at the top of each phylogenetic tree (0.001, number of nucleotide substitutions per site between env sequences.) Compartmentalized populations are indicated at the appropriate node by an open circle and emphasized using a blue bar. BEAST-generated TMRCAs of the entire viral population are noted adjacent to the subject ID, and the TMRCAs of the different compartmentalized linages (subject 9040 and 9021) and transmitted parental lineages (subject 7146) are also noted.