HIV-1 adapts to HLA class II-associated selection pressure exerted by CD4⁺ and CD8⁺ T cells

Developing an effective HIV-1 vaccine is a global health priority, but HIV-1 mutational escape from T cells poses a challenge. While escape from human leukocyte antigen class I (HLA-I)-restricted CD8⁺ T cells is well characterized, less is known about HLA-II-restricted T cell escape. We used computational methods to identify 149 sites across the HIV-1 clade B genome under HLA-II-associated selection. Functional assays, including activation-induced intracellular cytokine staining and enzyme-linked immunospot for interferon-γ, revealed diverse mechanisms of HIV-1 adaptation to HLA-II-associated immune pressure, ranging from loss to sustained antigen recognition. T cell receptor and RNA sequencing demonstrated variable clonotype overlap of T cell clones to recognize adapted versus non-adapted peptides, with cells targeting adapted peptides exhibiting a dysfunctional transcriptomic state. Moreover, incorporating HLA-II-associated adaptation strengthened the correlation between Gag-specific viral adaptation and poor disease outcomes. Last, we mapped viral regions prone to HLA-II-associated adaptation and found that these adaptations can increase in frequency within populations.