Diverse pathways of escape from all well-characterized VRC01-class broadly neutralizing HIV-1 antibodies
Fig 5
Alteration of Loop D residues is preferred to that of V5 residues for viral escape of CD4bs bNAbs.
(A) The frequency of mutation at each amino acid position in the Loop D and V5 regions of the VRC07 selected passage 5 virus swarm. The top 150 sequences determined by their copy numbers detected through deep sequencing, was analyzed. Soft-randomized residues are shown on X-axis, and bold “N” indicates a putative N-glycosylation site. ‘Control passage 15’ virus is the library virus passaged in the absence of an antibody but the same number of times as the VRC07-selected viruses. The residue alterations in the control virus likely represent those advantageous for replication in GHOST-R3/X4/R5 cells. Mutations in Loop D appear to be more frequently selected than those in V5, and loss of glycosylation is one of the most frequently selected changes in both regions. (B) Amino acid substitutions in the Loop D and V5 regions of VRC07 selected passage 5 viruses are shown in 2-dimensional heat maps. The relative frequency of the substitutions of a residue is represented by a color gradient. (C) Three Loop D (N276, D279 and A281) and two V5 (N461 and S465) residues found most frequently substituted in escape variants are indicated in orange in a space-filling model of an Env trimer (PDB 5V8M). In this structure, Env is derived from a clade A isolate, BG505, and its residue 279 is N, and both 461 and 465 are T. Residues involved in the association of VRC07 are derived from the VRC07-bound Env monomer structure (PDB 4OLU) and are indicated in blue. One monomer of gp120 is shown in light green, 2nd gp120 monomer in grey, and gp41 molecules in pink. N-glycans are represented as balls and sticks in dark green.