Phylogeny of the gp120 V2 region in PLVs.

<p>The Phylogenetic tree (unrooted, left panel) was constructed based on whole genome nucleotide sequences, using a neighbor-joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069406#pone.0069406-Saitou1" target="_blank">[43]</a> and bootstrapping for 1000 steps. The associated gp120 V2 region sequence alignment was accomplished using the Clustal W program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069406#pone.0069406-Chenna1" target="_blank">[44]</a>. The twin-cysteine residues are colored red and marked with a red bar, and the conserved tyrosine (Y) in green. The residues are numbered based on the standard system, which uses HXBc2 as a reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069406#pone.0069406-Korber1" target="_blank">[45]</a>. The viral strains used for the phylogenetic tree construction are as follows respectively: HIV-1, AF033819; HIV-2, M30502; SIVcpzANT, U42720; SIVcpzTAN, EF394356; SIVsmm, AF4679.