Phylogenetic tree for subtype A1 and C.

<p>HIV-1 A1 (N = 94) and C (N = 8) <i>pol</i> sequences obtained from the Rwandan study participants were analyzed in connection to reference sequences from the Los Alamos database originating from Rwanda (N = 4) and the five surrounding countries collected between 1992 and 2009 (272 A1 and 212 C). The four subtype D (analysis 2, data not shown) and the 25 A1/C recombinant sequences were further examined in two separate analyses including 376 subtype D reference sequences and 6 A1/C reference sequences, respectively (analysis 3 data not shown). Country of origin of each sequence is color coded, with Rwanda in grey. The bootstrap values >85% are indicated in red. Related sequences found within subtype A1 (bootstrap value 100) are shown in detail in the three rectangular phylogenetic tree zoomed inserts.