Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

Abstract

We analyzed HIV-1 genome sequences from 68 newly infected volunteers in the STEP HIV-1 vaccine trial. To determine whether the vaccine exerted selective T cell pressure on breakthrough viruses, we identified potential T cell epitopes in the founder sequences and compared them to epitopes in the vaccine. We found greater distances to the vaccine sequence for sequences from vaccine recipients than from placebo recipients. The most significant signature site distinguishing vaccine from placebo recipients was Gag amino acid 84, a site encompassed by several epitopes contained in the vaccine and restricted by human leukocyte antigen (HLA) alleles common in the study cohort. Moreover, the extended divergence was confined to the vaccine components of the virus (HIV-1 Gag, Pol and Nef) and not found in other HIV-1 proteins. These results represent what is to our knowledge the first evidence of selective pressure from vaccine-induced T cell responses on HIV-1 infection in humans.

Fig. 1. Maximum-Likelihood phylogenetic tree of gag sequences

The tree comprises nucleotide sequences from each individual along with the MRKAd5, HXB2 and CON_B04 sequences, and is rooted with sequences from the only subject not infected with a subtype B virus (CRF02-AG). Sequences from placebo recipients are in blue, while sequences from vaccine recipients are in red. Sequences from individuals with two or more founder variants are highlighted in yellow. The sequences from related viruses found in two individuals are labeled with the two subjects’s identification numbers

Fig. 2. Epitope-specific protein distances between epitopes from founder sequences and the MRKAd5 HIV-1 vaccine sequence

Comparison of epitopic distances across treatment assignment based on NetMHC predictions using Gag, Pol and Nef epitopes combined (a), or separately (b-d).

Fig. 3. Protein distances between epitopes from founder sequences and HXB2 or HIV-1 CON_B04

Epitopic distances based on NetMHC predictions are compared across treatment groups, separately for epitopes derived from Gag, Pol and Nef (vaccine insert), and for epitopes derived from the six other HIV-1 proteins.

Fig. 4. Amino Acid Signature Sites

Ten AA signature sites distinguishing vaccine and placebo recipients are represented with bar graphs. Each bar represents the AA found in one individual: the upper/black bars represent the individuals with an AA matching the MRKAd5 HIV-1 insert at that position and the lower/red bars correspond to individuals with mismatched AA.

Fig. 5. Summary of sequence analyses and IFN-g ELISpot data from Gag (a,b), Nef (c,d) and Pol (e,f)

For each protein, the upper panel (a,c,e) represents the location of predicted epitopes based on NetMHC in vaccine and placebo groups (light and medium gray columns, respectively), amino acid signature sites (dashed lines), and signature k-mers (horizontal bars). The lower panel (b,d,f) corresponds to IFN-γ ELISpot responses detected in 21 vaccine recipients prior to infection. 15mer peptides overlapping by 11 amino acids were used to assess responses. The region covered by each responsive peptide is shown as the box width, whereas the number of subjects reacting with that peptide is given by the box height.