FIG. 1.

SIVsmmFGb stock virus sequence grouping strategy for (A) Env V1, (B) Nef, and (C) Int. Viral RNA isolated from SIVsmmFGb stock virus was serially diluted and used to produce RT-PCR and PCR templates as described in Materials and Methods. Nested PCR for each gene was performed as described and at least 20 clones were analyzed from each reaction. Amino acid sequences of these clones were aligned via Clustal W and distance-based, neighbor-joining phylogenetic trees were produced. Clade consensus sequences from these first neighbor-joining trees were generated and realigned into a new neighbor-joining tree. Clade consensuses and, by extension, their composite sequences were broken into groups based on bootstrap support (1000 replicates) of clades in this second neighbor-joining tree. Bootstrap consensus of the second neighbor-joining tree for each gene is shown; group breakdown, and clades with greater than 50% bootstrap support, are indicated. Groups are indicated as follows: *group 1; **group 2; ***group 3; ****group 4.