HIV-1 prime-boost vaccination shapes distinct clonal trajectories and memory precursor states of Env- and Gag-specific T cells

Xu, G.; Yee, J. X.; Ilcisin, S. M.; Kaul, S. N.; Mayer-Blackwell, K.; Moelhman, E.; Glass, D. R.; Minervina, A. A.; Karuna, S. T.; Sobieszczyk, M. E.; Hart, M. R.; Thomas, P. G.; Skene, P. J.; De Rosa, S. C.; McElrath, M. J.; Fiore-Gartland, A.; Newell, E. W.

doi:10.64898/2026.09.23.752815

bioRxiv · 10.64898/2026.09.23.752815

HIV-1 prime-boost vaccination shapes distinct clonal trajectories and memory precursor states of Env- and Gag-specific T cells

Xu, G.·Yee, J. X.·Ilcisin, S. M.·Kaul, S. N.·Mayer-Blackwell, K.·Moelhman, E.·Glass, D. R.·Minervina, A. A.·Karuna, S. T.·Sobieszczyk, M. E.·Hart, M. R.·Thomas, P. G.·Skene, P. J.·De Rosa, S. C.·McElrath, M. J.·Fiore-Gartland, A.·Newell, E. W.

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Abstract

Despite decades of HIV-1 vaccine development, the clonal and cellular determinants of durable vaccine-induced T cell memory remain incompletely understood. Here, we combined antigen-specific T cell receptor (TCR) identification, longitudinal TCR sequencing, and single-cell multi-omics to characterize Env- and Gag-specific memory precursor T cells elicited by the HIV Vaccine Trials Network (HVTN) 505 DNA prime-recombinant adenovirus serotype 5 (rAd5) boost (DNA/rAd5) vaccine regimen. We developed a generalizable high-throughput approach to identify HIV-1 Env- and Gag-specific TCRs and found distinct patterns of clonal expansion, persistence, and contribution to memory between Env- and Gag-specific CD8 T cell responses. The DNA prime and rAd5 boost differentially shaped these repertoires, with rAd5-induced clones contributing proportionally more to the Gag-specific than to the Env-specific memory precursor compartment. Single-cell immune profiling further revealed distinct memory precursor states, with Env-specific responses enriched for GZMBPRF1 cytotoxic effector-memory (EM) CD8 T cells and Gag-specific responses containing a larger cycling/proliferative population. Together, these findings demonstrate that heterologous DNA/rAd5 vaccination generates antigen-specific CD8 T cell memory with distinct clonal trajectories and cellular programs, providing new insights into how vaccine platform and antigen-specificity shape the durability and functional properties of HIV-1 specific cellular immunity.

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Xu, G., Yee, J. X., Ilcisin, S. M., Kaul, S. N., Mayer-Blackwell, K., Moelhman, E., Glass, D. R., Minervina, A. A., Karuna, S. T., Sobieszczyk, M. E., Hart, M. R., Thomas, P. G., Skene, P. J., De Rosa, S. C., McElrath, M. J., Fiore-Gartland, A., Newell, E. W.. 2026-09-29. HIV-1 prime-boost vaccination shapes distinct clonal trajectories and memory precursor states of Env- and Gag-specific T cells. https://doi.org/10.64898/2026.09.23.752815

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