Background:  Human lymphocyte antigen (HLA) -restricted CD8⁺ cytotoxic T lymphocytes (CTL) target and kill HIV-infected cells expressing cognate viral epitopes. This response selects for escape mutations within CTL epitopes that can diminish viral replication fitness. Here, we assess the fitness impact of escape mutations emerging in 7 CTL epitopes in the gp120 Env and p24 Gag coding regions of a subject (PIC1362) followed longitudinally from the time of acute HIV-1 infection.

Methods:  All 14 epitopic mutations observed in Gag p24 and Env gp120 coding regions of PIC1362 were individually introduced into the autologous, consensus clone from acute infection and then cloned into an NL4-3 backbone via the yeast-based recombination system (VIRUPRO). All viruses containing CTL escape mutations were then competed against the parental consensus clone in peripheral blood mononuclear cells (PBMC). Dual infection was tracked using a synonymous vif tag sequence that does not affect fitness.

Results:  When competed against virus harboring the parental protein, fitness loss was observed with only 1 of the 9 CTL escape mutations in gp120 whereas 4 had no effect and 3 conferred a slight increase in fitness. In contrast, both mutations conferring CTL escape in the p24 epitopes significantly decreased viral fitness and were observed later than the gp120 CTL escape mutations. In each of the 3 epitopes whose escape resulted in a fitness loss, we observed a complex pattern of evolution, leading to substantial recovery of viral fitness while maintaining or enhancing immunologic escape.

Conclusions:  We are the first to describe the replicative fitness costs from the full array of CTL escape mutations emerging in p24 and gp120 following acute infection. In general, fitness costs were associated with CTL escape mutations that emerge late in infection and with conserved sequence elements. Furthermore, cell-mediated immune response invokes a dynamic evolutionary process requiring a balance between CTL escape and maintenance of replicative fitness.