Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120

Abstract

Although the HVTN 505 DNA/recombinant adenovirus type 5 vector HIV-1 vaccine trial showed no overall efficacy, analysis of breakthrough HIV-1 sequences in participants can help determine whether vaccine-induced immune responses impacted viruses that caused infection. We analyzed 480 HIV-1 genomes sampled from 27 vaccine and 20 placebo recipients and found that intra-host HIV-1 diversity was significantly lower in vaccine recipients (P ≤ 0.04, Q-values ≤ 0.09) in Gag, Pol, Vif and envelope glycoprotein gp120 (Env-gp120). Furthermore, Env-gp120 sequences from vaccine recipients were significantly more distant from the subtype B vaccine insert than sequences from placebo recipients (P = 0.01, Q-value = 0.12). These vaccine effects were associated with signatures mapping to CD4 binding site and CD4-induced monoclonal antibody footprints. These results suggest either (i) no vaccine efficacy to block acquisition of any viral genotype but vaccine-accelerated Env evolution post-acquisition; or (ii) vaccine efficacy against HIV-1s with Env sequences closest to the vaccine insert combined with increased acquisition due to other factors, potentially including the vaccine vector.

Fig 1. Maximum likelihood phylogenetic tree including 774 envelope gp120 nucleotide sequences.

Sequences from HVTN 505 vaccine (in red) and placebo (in blue) recipients (n = 486) are depicted along with 288 HIV-1 subtype B sequences from the US and sampled since 2005. Sequences from two vaccine recipients who were each dually-infected (with two independent strains) are highlighted with orange and magenta shading. Subjects with multiple founder variants are highlighted with yellow shading.

Fig 2. Intra-host mean pairwise diversity among amino acid sequences.

Intra-host mean pairwise diversity values were calculated among all the sequences from a given participant separately for each protein corresponding to a vaccine insert, with vaccine recipients in red and placebo recipients in blue. The upper panel included all participants; the lower panel included only participants with single HIV-1 founder viruses. Two-sided Mann-Whitney p-values comparing the vaccine and placebo groups are shown above the panels.

Fig 3. Pairwise distances between breakthrough sequences and each Env vaccine sequence or Env Consensus B.

Participant-specific mean distances of breakthrough sequences to the subtype A, B, and C Env vaccine sequences and the Consensus B sequence (labeled VRC-A, VRC-B, VRC-C and Cons.B, respectively). Distances from breakthrough sequences from vaccine recipients are in red and placebo recipients in blue. Distances are based on Env-gp120 sequences with the hypervariable segments deleted (HXB2 positions from signal peptide 10–16; V1 loop 132–152; V2 loop 186–191; V3 loop 309–310; V4 loop 392–413; and V5 loop 460–464). Two-sided Mann-Whitney p-values comparing the vaccine and placebo groups are shown above the panels.

Fig 4. Overlap between HIV-1 Env-gp120 k-mer, AA site and mAb footprint signatures identified with different scanning methods.

Positive sieve effects, i.e., greater divergences of sequences from vaccine recipients than from placebo recipients from the vaccine strain, were detected for all 34 CD4bs, CD4i and V3 footprints (S15 Table). The figure represents signatures detected with a Q-value ≤ 0.2 across Env-gp120 (gray bands identify the HIV-1 features labeled at the top of the figure): six k-mer regions are shown as orange bands (labeled a-f as in Table 1); two individual sites, 133 and 429, are labeled in bold on the x-axis; and the 19 of 34 CD4bs, CD4i, and V3 mAb footprints with a Q-value ≤ 0.2 are indicated by dark blue points and labeled on the y-axis in bold font. The 15 mAb footprints that are not statistically significant signatures are indicated by light blue points and labeled on the y-axis in gray. Footprint site sets were grouped by mAb class (CD4bs, CD4i, and V3) and ranked within class by P-value. Footprint site sets for mAb classes where no significant effect was identified are not shown (Quarternary, Env-gp41, and Glycan; see S15 Table).

Fig 5. Distance-specific vaccine efficacy.

Boxplots of hamming distances of mindist sequences to the subtype B vaccine strain by treatment group for three sets of Env-gp120 sites: (A) all Env-gp120 sites that could be aligned with confidence (n = 432); (C) the 93 CD4bs antibody contact sites; and (E) 54 sites corresponding to the 4 k-mers overlapping the CD4bs where significant sieve effects were found (Table 1). The mid-line of the box denotes the median and the ends of the box denote the 25^th and 75^th percentiles. The whiskers that extend from the top and bottom of the box extend to the most extreme data points that are no more than 1.5 times the interquartile range or if no value meets this criterion, to the data extremes. (B, D, F) Distance-specific hazard ratio based on the corresponding distances shown in panels A, C, and E, respectively. The solid black lines show the estimated hazard ratio as a function of distance, and the dashed red lines represent a 95% point-wise confidence interval (CI) around that estimate. The ‘Sieve test’ 2-sided p-value reports the result of the test of [30] for whether the hazard ratio varies with distance.

Fig 6. Involvement of two signature k-mers within gp120 in the formation of the bridging sheet and exposure of the V3 loop.

(A) The pre-fusion closed state (structure 4TVP [45]) and (B) the CD4-bound state (structure 2B4C [46]). The V3 loops from two gp120 monomers are in orange and 4 spheres represent its tip (GPGQ/R residues 312–315). The two signature segments are shown in turquoise (AA192-207) and in yellow (AA425-437) labeled c and e, respectively, as in Table 1 and Fig 4. Segments c and e map to the bridging sheet corresponding to sites AA119-126, AA196-205, and AA422-436. In the CD4-bound state, the bridging sheet is formed and the V3 loop is released and becomes more accessible to V3 antibodies.