Fig. 2

a Inter and intra-clade genetic relatedness of INSO-SA 2007 autologous HIV-1 clade C env (gp160) amino acids. Maximum likelihood phylogenetic tree was constructed with 50 bootstrapped replicates and inferred by using Jones–Taylor–Thornton (JTT) model [35]. Values next to the nodes of each branch indicate percentage of trees in which the associated taxa are clustered together. Branch length represents residues substitution per site. The scale shown at the bottom of the tree indicates 0.02 substitutions per amino acid residue. b Alignment of amino acid sequences of V1 loop of autologous envs. N-linked glycans are highlighted in red and their positions are highlighted. c Comparison of amino acid sequences between the V3 region of the autologous HIV-1 env clones. Amino acid sequences were aligned using ClustalW algorithm using Mega 5.2 program and the alignment file was further processed in Seqpublish tool which is available in www.hiv.lanl.gov. The N301 and N332 glycan residues including the core amino acid motif IGDIR important for PGT128 sensitivity are highlighted. Amino acid numbering was done relative to HXBc2 (http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/HXB2.html)