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

Journal name:
Nature Medicine
Year published:
Published online


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.

At a glance


  1. Maximum-likelihood phylogenetic tree of gag sequences.
    Figure 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, whereas 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' identification numbers. The scale bar at the bottom refers to the degree of the sequence mismatch.

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

    (ad) Comparison of epitopic distances across treatment assignment based on NetMHC predictions using Gag, Pol and Nef epitopes combined (a), or separately (b–d), respectively. Mean distance values are indicated.

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

    (ad) Epitopic distances based on NetMHC predictions are compared across treatment groups, separately for epitopes derived from Gag, Pol and Nef (vaccine insert) (a,c) and for epitopes derived from the six other HIV-1 proteins (b,d). a and b are compared to HXB2; c and d are compared to CON_B04. Mean distance values are indicated.

  4. Amino acid signature sites.
    Figure 4: Amino acid signature sites.

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

  5. Summary of sequence analyses and IFN-[gamma] ELISPOT data.
    Figure 5: Summary of sequence analyses and IFN-γ ELISPOT data.

    (af) Data from Gag (a,b), Nef (c,d) and Pol (e,f). For each protein, the top graph (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 bottom graph (b,d,f) corresponds to IFN-γ ELISPOT responses detected in 21 vaccine recipients before infection. Fifteen–amino-acid 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.

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Referenced accessions



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Author information

  1. These authors contributed equally to this work.

    • Morgane Rolland,
    • Sodsai Tovanabutra,
    • Allan C deCamp &
    • Nicole Frahm


  1. Department of Microbiology, University of Washington, Seattle, Washington, USA.

    • Morgane Rolland,
    • Laura Heath,
    • Kim Wong,
    • Hong Zhao,
    • Dana N Raugi,
    • Stephanie Sorensen,
    • Julia N Stoddard,
    • Brandon S Maust,
    • Wenjie Deng &
    • James I Mullins
  2. US Military HIV Research Program, Rockville, Maryland, USA.

    • Sodsai Tovanabutra,
    • Eric Sanders-Buell,
    • Meera Bose,
    • Andrea Bradfield,
    • Annemarie O'Sullivan,
    • Jacqueline Crossler,
    • Teresa Jones,
    • Marty Nau,
    • Nelson L Michael,
    • Jerome Kim &
    • Francine E McCutchan
  3. Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

    • Allan C deCamp,
    • Nicole Frahm,
    • Peter B Gilbert,
    • Craig A Magaret,
    • John Hural,
    • Lawrence Corey,
    • Fusheng Li,
    • Steve G Self,
    • Ann Duerr &
    • M Juliana McElrath
  4. Merck Research Laboratories, West Point, Pennsylvania, USA.

    • Sheri Dubey,
    • John Shiver,
    • Danilo R Casimiro &
    • Michael N Robertson
  5. San Francisco Department of Health, San Francisco, California, USA.

    • Susan Buchbinder
  6. Present address: Bill and Melinda Gates Foundation, Seattle, Washington, USA.

    • Francine E McCutchan


M.R., A.C.D., P.B.G., and J.I.M. designed the sequence analysis. M.R., A.C.D., P.B.G., C.A.M., L.H., B.S.M., W.D., F.L. and J.I.M. conducted the analyses. M.R., A.C.D., N.F., P.B.G. and J.I.M. analyzed the data. M.R., A.C.D., N.F., P.B.G. and J.I.M. wrote the manuscript. J.I.M., F.E.M., S.T., E.S.-B. and N.F. designed lab experiments. M.B., A.B., A.O., J.C., T.J., M.N., K.W., H.Z., D.N.R., S.S., J.N.S. and N.F. performed lab experiments. J.H., L.C., S.B., D.R.C., M.N.R., A.D., M.J.M., S.G.S., S.D., N.L.M., J.K. and J.S. conducted the STEP trial, provided material and oversaw laboratories.

Competing financial interests

M.N.R. and D.R.C. are paid employees of Merck, own Merck stock and have Merck stock options.

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    Supplementary Methods, Supplementary Results, Supplementary Tables 1 and 2 and Supplementary Figures 1–5

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