Phylogenetic analysis of gp40/15 sequences. All gp40/15 nucleotide sequences in the study and representative sequences deposited in GenBank were subjected to phylogenetic analysis by the maximum likelihood method using default settings in the Phylogeny.fr server http://www.phylogeny.fr/ (12). These included multiple sequence alignment using MUSCLE (13), alignment curation using G blocks (7), phylogeny using PhyML 3.0 (15), and tree rendering using TreeDyn (10). The numbers at nodes indicate branch support values assessed using the approximate likelihood ratio test (3). Samples from the study are indicated by the letter “n” followed by the sample number. Representative sequences from GenBank are indicated by the accession number. The subtype for each sequence is indicated following the sample number (n) or GenBank accession number.