At 3 months of HIV-1 infection, we found that the hierarchy of Gag and Nef protein-specific T-cell responses was correlated with CD4 T-cell counts (R =  − 0.849, P = 0.016 and R = 0.777, P = 0.040, respectively), whereas none of the Gag, Pol, and Nef protein-specific T-cell response hierarchy was associated with VLs (P > 0.05) (Fig. 2a). Here, CD4 is linked to HIV-1 infection.