Figure 3

(A) Phylogenetic trees (time-annotated MCMC) of the serial sequences and (B) HIV-1 viral loads and lymphocyte CD4 counts from four patients failing raltegravir (RAL) treatment. Maximum likelihood tree with bootstrap values for 1000 replicates drawn at the tree branches. Integrase resistance mutations are marked at the tip nodes; branches with developed drug resistance are marked red. Time points in which InI drug resistance mutations were noted are indicated with red arrows, while initiation of the raltegravir containing antiretroviral treatment is indicated with green arrow. TDF – tenofovir, MVC- maraviroc, FTC – emticitabine, DRV/r – ritonavir boosted darunavir, SQV – saquinavir.