Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth
Figure 2
Amino acid alignment of longitudinal R880F Envs.
Longitudinal Env amino acid sequences from 20 R880F contemporaneous plasma escape variants were aligned and examined using Sequencher v5.0 and Geneious v5.0.3 software, with particular emphasis on the three mutational hot spots–C2, the alpha2 helix in C3, and V5–that developed during early infection, as compared to the transmitted/founder Env (0-A6/B24). Dashes represent conserved positions. Subject-specific amino acid numbering labels the demarcated regions at their points of origination. Five residues including 295, 335, 338, 341, and 456 (HXB2 residues 293, 334, 337, 340, and 460) were specifically interrogated to define their contributions to nAb evasion and have been highlighted in black in 0-A6/B24 for easy identification. Colored sequences (2-A9/2-A13 in magenta, 2-B31 in red, 2-B12 in cyan, and 5-B52 in green) indicate Envs that succumbed to neutralization, in varying combinations, by the isolated R880F mAbs. Note that additional differences from the transmitted/founder Env, which occurred over time in these sequences but are not diagrammed here, may be viewed in Figure S1.