Maximum likelihood tree of HIV pol sequences generated using GTR model in PHYML with 100 bootstrap replicates. Sequences were trimmed to 986 bp with identified TDR mutation codons removed. 155 study cohort sequences are present in a background of 255 sequences further described in the methods. Orange box shows the D67N/K219Q cluster that was identified. For comparison purposes another cluster identified in the study cohort is identified in blue. ** Indicates the out-group N sequence N.CM.97.YBF106.